https://wiki.phenoscape.org/wg/phenoscape/api.php?action=feedcontributions&user=Todd+Vision&feedformat=atomphenoscape - User contributions [en]2024-03-29T05:03:10ZUser contributionsMediaWiki 1.31.10https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=12141Publications and Posters2020-01-07T14:52:17Z<p>Todd Vision: /* 2018 */</p>
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<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Dahdul et al. (2018), Dahdul et al. (2015), Cui et al. (2015), Arighi et al. (2013), Bertone et al. (2012), Dahdul et al. (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
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== Publications by date ==<br />
===2019===<br />
* Tarasov, S., Mikó, I., Yoder, M.J., Uyeda, J.C. (2019) PARAMO: A pipeline for reconstructing ancestral anatomies using ontologies and stochastic mapping. Insect Systematics and Diversity, Volume 3, Issue 6, https://doi.org/10.1093/isd/ixz009.<br />
* Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., Vision, T.J. (2019) A logical model of homology for comparative biology. Systematic Biology. https://doi.org/10.1093/sysbio/syz067<br />
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===2018===<br />
* Uyeda JC, Zenil-Ferguson R, Pennell MW (2018) Rethinking phylogenetic comparative methods, Systematic Biology, Volume 67, Issue 6, November 2018, Pages 1091–1109, https://doi.org/10.1093/sysbio/syy031<br />
* Manda P, Vision T (2018) On the statistical analysis of semantic similarity metrics. International Conference on Biological Ontology 2018. Oregon State University, Corvallis, OR, USA. http://ceur-ws.org/Vol-2285/ICBO_2018_paper_47.pdf (preprint: https://doi.org/10.1101/327833)<br />
* Dahdul W, Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. Database. 2018:bay110, https://doi.org/10.1093/database/bay110<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. (2018) Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Systematic Biology, 67(4):559–575, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. (2018) Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin. preprint https://peerj.com/preprints/26988<br />
* Braun I, Balhoff J, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ. (2018) Computable phenotypes enable comparative and predictive phenomics among plant species and across domains of life. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
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===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
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===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
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* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
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* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
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* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
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* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
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* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
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* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
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* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
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===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
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*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
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*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
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*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
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*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
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*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
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*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
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*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
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===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
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*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
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*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
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*Haendel, M.A., Balhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
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*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
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===2013===<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
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*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
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*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
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*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
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*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2013'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. Database 2013:bas056 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
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===2012===<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
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*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
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*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
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*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
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===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
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* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
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===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
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*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
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*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
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===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
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===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
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*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
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== Posters & Presentations ==<br />
=== 2019 ===<br />
* Mabee, P. (2019) Answering research questions requires semantic traits. In session: Operationalizing Trait-Based Biodiversity, Biodiversity Next meeting, Leiden, Netherlands, October 24, 2019. <br />
* Uyeda J, Tarasov, S (2019) Extracting meaning from phylogenetic comparative methods: The necessity of considering process. Evolution 2019, Providence RI, June 25, 2019. <br />
* Balhoff J, Dahdul W, Lapp H, Mabee P, Tarasov S, Uyeda J, Vision T (2019) Integrating ontologies in comparative analyses of trait evolution. Poster presented at Evolution 2019, Providence RI, June 22, 2019, https://doi.org/10.5281/zenodo.3252611<br />
* Balhoff, J.P. (2019) OWL reasoning in the Phenoscape Knowledgebase. Semantic Data Models in Anatomy workshop, Zoological Research Museum Alexander Koenig, Bonn, Germany, May 9, 2019.<br />
* Vision, T. (2019) Computing over descriptive phenotype data: Is Aristotle a help or hindrance? PIRS Minisymposium on Novel Candidate Gene Discovery by Computing on Phenotypes, Iowa State University, April 3, 2019.<br />
* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Center for Biodiversity Analysis, Australian National University, Canberra, Australia. April 1, 2019. <br />
* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Royal Botanic Gardens and Domain Trust Science Seminar Series. Royal Botanic Garden, Sydney, Australia. March 28, 2019. <br />
* Mabee, P. (2019) Trait ontologies: logical links across biodiversity. Plant Traits Workshop. Royal Botanic Garden, Sydney, Australia. March 27, 2019. <br />
* Balhoff, J.P. (2019) Using phenotype ontologies to incorporate domain knowledge into models of trait evolution. U.S. Semantic Technologies Symposium (US2TS 2019), Durham, NC, March 11, 2019.<br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, P. Mabee, S. Tarasov, J. Uyeda, T. Vision. (2019). Integrating ontologies in comparative analyses of trait evolution. Biocuration 2019. Cambridge UK. April 2019.<br />
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=== 2018 ===<br />
* Mabee, P.M. Anatomy ontologies supply the missing links for knowledge discovery and recovery. Invited talk for Biological Ontology Series, Iowa State University. Ames, Iowa, October 22, 2018.<br />
* Uyeda, J.C. (presenter, poster) (2018). On the need for phylogenetic natural history. Evolution 2018, Montpellier, France. August 21, 2018.<br />
* Collins M. (presenter), R. Tarvin, M. Kandziora, W. Dahdul, and D. Paul (2018) Phenomap - Challenges and successes in bringing together multiple data projects to build new visualizations of phenotypic information and specimen records. Biodiversity Information Science and Standards 2: e25698. https://doi.org/10.3897/biss.2.25698. Presented at Biodiversity Information Standards (TDWG), Dunedin, NZ, August 2018<br />
* Fernando, P. (presenter, poster), E. Zeng, P. Mabee. (2018) The integrative use of anatomy ontology and protein-protein interaction networks to study evolutionary phenotypic transitions. International Conference on Biological Ontology (2018), Corvallis, OR, August 7, 2018<br />
* Mabee, P., J. Balhoff, W. Dahdul (invited oral presentation), H. Lapp, C. Mungall, T. Vision. (2018). Reasoning over anatomical homology in the Phenoscape KB. Workshop: Data Standards and Knowledge Sharing in Biodiversity -Tools and Applications. International Conference on Biological Ontology (2018), Corvallis, OR, August 7, 2018.<br />
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, J. Uyeda, T. Vision, P. Mabee (2018). [https://www.idigbio.org/wiki/images/3/3d/Dahdul-iDigBio-poster.pdf Applications of ontology-based knowledge representation for comparative biology]. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Vision, TJ (2018) Skeletons, mutants and ontologies: What can we learn from linking phenotypes and genetics on a large scale? University of Southern California, Computational Biology Seminar, March 29, 2018.<br />
* Mabee, P.M. (2018) Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
* Mabee, P.M. (2018) Phenoscape: use case, tools, and outcomes. Explorer of Taxon Concepts and Authors Projects Joint Workshop: Enabling authors to produce computable phenotypic data. University of Arizona Biosphere. January 12, 2018.<br />
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=== 2017 ===<br />
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* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee (2017). A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Kansas City, MO. November 14-16, 2017.<br />
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* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Computational Biology Seminar, Oct 23, 2017.<br />
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* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
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* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
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* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
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* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
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* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=ComparativeAnalysis&diff=12133ComparativeAnalysis2019-12-13T20:33:51Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
* For more background on the SCATE project and its predecessors, see [[here|Main Page]].<br />
}}<br />
<br />
== Phylogenetic Comparative Analyses using Ontologies ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. <br />
<br />
=== Structured Markov Models ===<br />
<br />
Ontologies provide knowledge of dependencies among traits. For example, the ''humerus'' is a bone that is ''part of'' the ''forelimb''. Thus, the presence of a ''humerus'' depends on the presence of a ''forelimb''. Treating these as independent characters can result in, for example, ancestral reconstructions in which an organism has a humerus, but lacks a forelimb. Such dependencies can be built into how we model traits by making use of structured markov models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. By structuring the dependencies among traits (as described by [https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018]), we can reconstruct not only individual traits, but entire ancestral anatomies in a logically consistent framework. We have developed a stochastic mapping pipeline called ''PARAMO'' [https://academic.oup.com/isd/article/3/6/1/5584145 (Tarasov et al. 2019)] that allows users to reconstruct ancestral anatomies, seamlessly moving between levels of anatomical hierarchy to query the phenome and ask questions about evolutionary rates, ancestral states, and character evolution.<br />
<br />
=== Hidden State Models & Gene Regulatory Networks === <br />
<br />
In addition to modeling the dependencies of characters on each other, proper modeling of dependent phenotypic characters requires inclusion of ''hidden states'' ([https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018], [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz050/5541792 2019]), that is a character state in which the observable phenotype corresponds to different genetic states. Hidden states add the possibility of incorporating more knowledge regarding the evo-devo of traits and account for evolution of novel phenotypic traits. <br />
<br />
=== Character Construction ===<br />
<br />
Character construction is the first step of any comparative analysis, and involves categorizing different free-text semantic descriptions (e.g. ''pectoral fin curved'', ''pectoral fin round'', ''pectoral fin absent'', ''pectoral fin elongate'', ''pectoral fin circular''). Some of these phenotypes may be different ways of describing the same phenotypic state, while others may represent mutually exclusive states. This step of character construction has traditionally relied on expert opinion and reasoning. However, with phenotypic ontologies, such information can be automated to allow machine-reasoning to accomplish similar ends, while improving reproducibility. Furthermore, the distinction between character and character state disappears when using properly structured and hidden state models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. We are exploring how this principle can be leveraged in character construction together with semantic similarity (see below) to construct "well-behaved" character codings in phylogenetic analysis.<br />
<br />
=== Evolutionary Enrichment Analyses ===<br />
<br />
Phylogenetic analysis allows researchers to estimate the evolutionary history of phenotypic evolution. As with gene ontologies, we can ask question such as which branches and at which time periods in evolutionary history has there been a particularly rapid rate of change. Ontologies allow to not only ask which characters are enriched on a given branch, but also which concepts are enriched. For example, are features associated with the fin-to-limb developmental transition particularly evolvable during the Devonian? Does a suite of traits related to a specific gene regulatory network demonstrate concerted evolution across the phylogeny? <br />
<br />
=== Semantic Similarity ===<br />
<br />
Semantic similarity metrics measure concept similarity. We are working to integrate semantic similarity metrics into phylogenetic comparative models, as these contain information that allows users to partition, cluster and amalgamate different characters and character states to make sense of evolutionary patterns.</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=ComparativeAnalysis&diff=12132ComparativeAnalysis2019-12-13T20:33:35Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
* For more background on the SCATE project and its predecessors, see [[here|Main Page]].<br />
}}<br />
<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
== Phylogenetic Comparative Analyses using Ontologies ==<br />
<br />
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. <br />
<br />
=== Structured Markov Models ===<br />
<br />
Ontologies provide knowledge of dependencies among traits. For example, the ''humerus'' is a bone that is ''part of'' the ''forelimb''. Thus, the presence of a ''humerus'' depends on the presence of a ''forelimb''. Treating these as independent characters can result in, for example, ancestral reconstructions in which an organism has a humerus, but lacks a forelimb. Such dependencies can be built into how we model traits by making use of structured markov models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. By structuring the dependencies among traits (as described by [https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018]), we can reconstruct not only individual traits, but entire ancestral anatomies in a logically consistent framework. We have developed a stochastic mapping pipeline called ''PARAMO'' [https://academic.oup.com/isd/article/3/6/1/5584145 (Tarasov et al. 2019)] that allows users to reconstruct ancestral anatomies, seamlessly moving between levels of anatomical hierarchy to query the phenome and ask questions about evolutionary rates, ancestral states, and character evolution.<br />
<br />
=== Hidden State Models & Gene Regulatory Networks === <br />
<br />
In addition to modeling the dependencies of characters on each other, proper modeling of dependent phenotypic characters requires inclusion of ''hidden states'' ([https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018], [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz050/5541792 2019]), that is a character state in which the observable phenotype corresponds to different genetic states. Hidden states add the possibility of incorporating more knowledge regarding the evo-devo of traits and account for evolution of novel phenotypic traits. <br />
<br />
=== Character Construction ===<br />
<br />
Character construction is the first step of any comparative analysis, and involves categorizing different free-text semantic descriptions (e.g. ''pectoral fin curved'', ''pectoral fin round'', ''pectoral fin absent'', ''pectoral fin elongate'', ''pectoral fin circular''). Some of these phenotypes may be different ways of describing the same phenotypic state, while others may represent mutually exclusive states. This step of character construction has traditionally relied on expert opinion and reasoning. However, with phenotypic ontologies, such information can be automated to allow machine-reasoning to accomplish similar ends, while improving reproducibility. Furthermore, the distinction between character and character state disappears when using properly structured and hidden state models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. We are exploring how this principle can be leveraged in character construction together with semantic similarity (see below) to construct "well-behaved" character codings in phylogenetic analysis.<br />
<br />
=== Evolutionary Enrichment Analyses ===<br />
<br />
Phylogenetic analysis allows researchers to estimate the evolutionary history of phenotypic evolution. As with gene ontologies, we can ask question such as which branches and at which time periods in evolutionary history has there been a particularly rapid rate of change. Ontologies allow to not only ask which characters are enriched on a given branch, but also which concepts are enriched. For example, are features associated with the fin-to-limb developmental transition particularly evolvable during the Devonian? Does a suite of traits related to a specific gene regulatory network demonstrate concerted evolution across the phylogeny? <br />
<br />
=== Semantic Similarity ===<br />
<br />
Semantic similarity metrics measure concept similarity. We are working to integrate semantic similarity metrics into phylogenetic comparative models, as these contain information that allows users to partition, cluster and amalgamate different characters and character states to make sense of evolutionary patterns.</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=ComparativeAnalysis&diff=12131ComparativeAnalysis2019-12-13T20:33:15Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
* For more background on the SCATE project and its predecessors, see [[here|Main Page]].<br />
}}<br />
<br />
== Phylogenetic Comparative Analyses using Ontologies ==<br />
<br />
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. <br />
<br />
=== Structured Markov Models ===<br />
<br />
Ontologies provide knowledge of dependencies among traits. For example, the ''humerus'' is a bone that is ''part of'' the ''forelimb''. Thus, the presence of a ''humerus'' depends on the presence of a ''forelimb''. Treating these as independent characters can result in, for example, ancestral reconstructions in which an organism has a humerus, but lacks a forelimb. Such dependencies can be built into how we model traits by making use of structured markov models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. By structuring the dependencies among traits (as described by [https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018]), we can reconstruct not only individual traits, but entire ancestral anatomies in a logically consistent framework. We have developed a stochastic mapping pipeline called ''PARAMO'' [https://academic.oup.com/isd/article/3/6/1/5584145 (Tarasov et al. 2019)] that allows users to reconstruct ancestral anatomies, seamlessly moving between levels of anatomical hierarchy to query the phenome and ask questions about evolutionary rates, ancestral states, and character evolution.<br />
<br />
=== Hidden State Models & Gene Regulatory Networks === <br />
<br />
In addition to modeling the dependencies of characters on each other, proper modeling of dependent phenotypic characters requires inclusion of ''hidden states'' ([https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018], [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz050/5541792 2019]), that is a character state in which the observable phenotype corresponds to different genetic states. Hidden states add the possibility of incorporating more knowledge regarding the evo-devo of traits and account for evolution of novel phenotypic traits. <br />
<br />
=== Character Construction ===<br />
<br />
Character construction is the first step of any comparative analysis, and involves categorizing different free-text semantic descriptions (e.g. ''pectoral fin curved'', ''pectoral fin round'', ''pectoral fin absent'', ''pectoral fin elongate'', ''pectoral fin circular''). Some of these phenotypes may be different ways of describing the same phenotypic state, while others may represent mutually exclusive states. This step of character construction has traditionally relied on expert opinion and reasoning. However, with phenotypic ontologies, such information can be automated to allow machine-reasoning to accomplish similar ends, while improving reproducibility. Furthermore, the distinction between character and character state disappears when using properly structured and hidden state models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. We are exploring how this principle can be leveraged in character construction together with semantic similarity (see below) to construct "well-behaved" character codings in phylogenetic analysis.<br />
<br />
=== Evolutionary Enrichment Analyses ===<br />
<br />
Phylogenetic analysis allows researchers to estimate the evolutionary history of phenotypic evolution. As with gene ontologies, we can ask question such as which branches and at which time periods in evolutionary history has there been a particularly rapid rate of change. Ontologies allow to not only ask which characters are enriched on a given branch, but also which concepts are enriched. For example, are features associated with the fin-to-limb developmental transition particularly evolvable during the Devonian? Does a suite of traits related to a specific gene regulatory network demonstrate concerted evolution across the phylogeny? <br />
<br />
=== Semantic Similarity ===<br />
<br />
Semantic similarity metrics measure concept similarity. We are working to integrate semantic similarity metrics into phylogenetic comparative models, as these contain information that allows users to partition, cluster and amalgamate different characters and character states to make sense of evolutionary patterns.</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=ComparativeAnalysis&diff=12130ComparativeAnalysis2019-12-13T20:29:41Z<p>Todd Vision: </p>
<hr />
<div>== Phylogenetic Comparative Analyses using Ontologies ==<br />
<br />
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. <br />
<br />
=== Structured Markov Models ===<br />
<br />
Ontologies provide knowledge of dependencies among traits. For example, the ''humerus'' is a bone that is ''part of'' the ''forelimb''. Thus, the presence of a ''humerus'' depends on the presence of a ''forelimb''. Treating these as independent characters can result in, for example, ancestral reconstructions in which an organism has a humerus, but lacks a forelimb. Such dependencies can be built into how we model traits by making use of structured markov models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. By structuring the dependencies among traits (as described by [https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018]), we can reconstruct not only individual traits, but entire ancestral anatomies in a logically consistent framework. We have developed a stochastic mapping pipeline called ''PARAMO'' [https://academic.oup.com/isd/article/3/6/1/5584145 (Tarasov et al. 2019)] that allows users to reconstruct ancestral anatomies, seamlessly moving between levels of anatomical hierarchy to query the phenome and ask questions about evolutionary rates, ancestral states, and character evolution.<br />
<br />
=== Hidden State Models & Gene Regulatory Networks === <br />
<br />
In addition to modeling the dependencies of characters on each other, proper modeling of dependent phenotypic characters requires inclusion of ''hidden states'' ([https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018], [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz050/5541792 2019]), that is a character state in which the observable phenotype corresponds to different genetic states. Hidden states add the possibility of incorporating more knowledge regarding the evo-devo of traits and account for evolution of novel phenotypic traits. <br />
<br />
=== Character Construction ===<br />
<br />
Character construction is the first step of any comparative analysis, and involves categorizing different free-text semantic descriptions (e.g. ''pectoral fin curved'', ''pectoral fin round'', ''pectoral fin absent'', ''pectoral fin elongate'', ''pectoral fin circular''). Some of these phenotypes may be different ways of describing the same phenotypic state, while others may represent mutually exclusive states. This step of character construction has traditionally relied on expert opinion and reasoning. However, with phenotypic ontologies, such information can be automated to allow machine-reasoning to accomplish similar ends, while improving reproducibility. Furthermore, the distinction between character and character state disappears when using properly structured and hidden state models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. We are exploring how this principle can be leveraged in character construction together with semantic similarity (see below) to construct "well-behaved" character codings in phylogenetic analysis.<br />
<br />
=== Evolutionary Enrichment Analyses ===<br />
<br />
Phylogenetic analysis allows researchers to estimate the evolutionary history of phenotypic evolution. As with gene ontologies, we can ask question such as which branches and at which time periods in evolutionary history has there been a particularly rapid rate of change. Ontologies allow to not only ask which characters are enriched on a given branch, but also which concepts are enriched. For example, are features associated with the fin-to-limb developmental transition particularly evolvable during the Devonian? Does a suite of traits related to a specific gene regulatory network demonstrate concerted evolution across the phylogeny? <br />
<br />
=== Semantic Similarity ===<br />
<br />
Semantic similarity metrics measure concept similarity. We are working to integrate semantic similarity metrics into phylogenetic comparative models, as these contain information that allows users to partition, cluster and amalgamate different characters and character states to make sense of evolutionary patterns.<br />
<br />
== More Information ==<br />
For more background on the SCATE project and its predecessors, see [[Main Page]].</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=ComparativeAnalysis&diff=12129ComparativeAnalysis2019-12-13T20:29:17Z<p>Todd Vision: </p>
<hr />
<div>== Phylogenetic Comparative Analyses using Ontologies ==<br />
<br />
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. <br />
<br />
=== Structured Markov Models ===<br />
<br />
Ontologies provide knowledge of dependencies among traits. For example, the ''humerus'' is a bone that is ''part of'' the ''forelimb''. Thus, the presence of a ''humerus'' depends on the presence of a ''forelimb''. Treating these as independent characters can result in, for example, ancestral reconstructions in which an organism has a humerus, but lacks a forelimb. Such dependencies can be built into how we model traits by making use of structured markov models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. By structuring the dependencies among traits (as described by [https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018]), we can reconstruct not only individual traits, but entire ancestral anatomies in a logically consistent framework. We have developed a stochastic mapping pipeline called ''PARAMO'' [https://academic.oup.com/isd/article/3/6/1/5584145 (Tarasov et al. 2019)] that allows users to reconstruct ancestral anatomies, seamlessly moving between levels of anatomical hierarchy to query the phenome and ask questions about evolutionary rates, ancestral states, and character evolution.<br />
<br />
=== Hidden State Models & Gene Regulatory Networks === <br />
<br />
In addition to modeling the dependencies of characters on each other, proper modeling of dependent phenotypic characters requires inclusion of ''hidden states'' ([https://academic.oup.com/sysbio/article/68/5/698/5298740 Tarasov, 2018], [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz050/5541792 2019]), that is a character state in which the observable phenotype corresponds to different genetic states. Hidden states add the possibility of incorporating more knowledge regarding the evo-devo of traits and account for evolution of novel phenotypic traits. <br />
<br />
=== Character Construction ===<br />
<br />
Character construction is the first step of any comparative analysis, and involves categorizing different free-text semantic descriptions (e.g. ''pectoral fin curved'', ''pectoral fin round'', ''pectoral fin absent'', ''pectoral fin elongate'', ''pectoral fin circular''). Some of these phenotypes may be different ways of describing the same phenotypic state, while others may represent mutually exclusive states. This step of character construction has traditionally relied on expert opinion and reasoning. However, with phenotypic ontologies, such information can be automated to allow machine-reasoning to accomplish similar ends, while improving reproducibility. Furthermore, the distinction between character and character state disappears when using properly structured and hidden state models [https://academic.oup.com/sysbio/article/68/5/698/5298740 (Tarasov, 2018)]. We are exploring how this principle can be leveraged in character construction together with semantic similarity (see below) to construct "well-behaved" character codings in phylogenetic analysis.<br />
<br />
=== Evolutionary Enrichment Analyses ===<br />
<br />
Phylogenetic analysis allows researchers to estimate the evolutionary history of phenotypic evolution. As with gene ontologies, we can ask question such as which branches and at which time periods in evolutionary history has there been a particularly rapid rate of change. Ontologies allow to not only ask which characters are enriched on a given branch, but also which concepts are enriched. For example, are features associated with the fin-to-limb developmental transition particularly evolvable during the Devonian? Does a suite of traits related to a specific gene regulatory network demonstrate concerted evolution across the phylogeny? <br />
<br />
=== Semantic Similarity ===<br />
<br />
Semantic similarity metrics measure concept similarity. We are working to integrate semantic similarity metrics into phylogenetic comparative models, as these contain information that allows users to partition, cluster and amalgamate different characters and character states to make sense of evolutionary patterns.<br />
<br />
For more background on the SCATE project and its predecessors, see [[Main Page]].</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12128Main Page2019-12-13T20:27:09Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] for more information. For a little more background on the how and why of incorporating ontologies into comparative analysis, see [[ComparativeAnalysis]].<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12127Main Page2019-12-13T20:25:53Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] for more information. For a little more background on the how and why of incorporating ontologies into comparative analysis, go [[here|ComparativeAnalysis]].<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12126Main Page2019-12-13T20:25:06Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] for more information. For more background on the how and why of incorporating ontologies into comparative analysis, see [[here|Comparative Analysis]].<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12125Main Page2019-12-13T20:24:53Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] for more information. For more background on the how and why of incorporating ontologies into comparative analysis, see [[here|ComparativeAnalysis]].<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12124Main Page2019-12-13T20:24:15Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] for more information. For more background on the how and why of incorporating ontologies into comparative analysis, see and [[ComparativeAnalysis]].<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12123Main Page2019-12-13T20:22:33Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] and [[ComparativeAnalysis]] for more information.<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Ontology-enabled_reasoning_across_phenotypes_from_evolution_and_model_organisms&diff=12121Ontology-enabled reasoning across phenotypes from evolution and model organisms2019-12-13T20:11:32Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* '''This is the homepage of the now-concluded Phenoscape II project (funded by NSF grants DBI-1062404 and DBI-1062542 from August 2011 through June 2018'''). <br />
* For current projects, see the [[Main Page]]<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Follow us on Twitter at [https://twitter.com/_phenoscape @_phenoscape]<br />
}}<br />
<br />
== Ontology-enabled reasoning across phenotypes from evolution and model organisms ==<br />
<br />
=== About this project ===<br />
<br />
Our overall objective is to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions. In other words, we are trying to make descriptive observations amenable to large-scale computation so that they can be subjected to computational data integration and knowledge discovery techniques in ways similarly powerful as the techniques we are used to for numeric, quantitative observations.<br />
<br />
Our approach to accomplish this centers on transforming descriptive observations from the natural language text form in which they are typically reported, to fully computable logic expressions that utilize terms from shared ontologies. [[Guide to Character Annotation| We create these expressions]] (which we also call "annotations") for evolutionary phenotypes reported in the systematics literature, typically in the form of character state matrices. We use the [[EQ for character matrices| Entity-Quality (EQ) formalism]] to compose these expressions, which was initially conceived for making biomedical and mutant model organism phenotype observations interoperable.<br />
<br />
We combine the EQ annotations we create for evolutionary phenotypes with the EQ annotations created for the myriad of phenotypes observed for mutant model organisms in an [http://kb.phenoscape.org integrated knowledgebase] (essentially a triple-store). We then apply [[:Category:Reasoning| Description Logic-reasoning]] to evaluate which evolutionary phenotype transitions can be inferred as semantically similar to which mutant model organism phenotypes, and vice versa. Since the genetic cause of a mutant phenotype is usually known, the links between evolutionary and mutant phenotypes identified in this way can be used to construct testable hypotheses about the genetic correlates or causes of evolutionary transitions.<br />
<br />
[[Image:Phenoscape II tree view.jpg|right|380px]] In a previous project, titled [[Linking Evolution to Genomics Using Phenotype Ontologies]], we developed a working prototype as a successful proof-of-concept, using [[Phenoscape 1 Curated Publications| teleost fishes for evolutionary phenotypes]] and the [http://zfin.org zebrafish model organism] as a source of mutant phenotypes. Here, we aim to make the components of the prototype, including tools and workflows, sufficiently scalable so that they are adequate for the much more extensive volume and more diverse nature of skeletal phenotypes across all vertebrates, fossil and modern. Specifically, our aims encompass the following:<br />
# Develop a fast semantic similarity engine so that the integrated knowledgebase can be searched on-the-fly for biological taxa or genotypes bearing a profile of phenotypes that is similar, but not necessarily identical, to a query profile.<br />
# Develop an [[Reasoning over homology statements| ontological framework for reasoning over homology]] that can be scaled to a large number of anatomically diverse evolutionary lineages.<br />
# Reduce the time and cost of obtaining EQ statements from the literature, while at the same time improving the quality and consistency of those statements, by incorporating natural language processing tools and by improving curation software to allow for on-demand augmentation of community ontologies. [[Image:Phenoscape II architecture.png|right|450px]]<br />
# Build umbrella [[Ontologies#Vertebrate Taxonomy Ontology| taxonomic]] and [[Ontologies| anatomical ontologies]] for the vertebrates, the latter to be supplemented by explicit homology relations among anatomical structures.<br />
# Create a knowledgebase that integrates evolutionary phenotypes for vertebrate fin and limb characters with genetic and phenotype data from three vertebrate model organisms: [http://zfin.org zebrafish] (''Danio rerio''), [http://xenbase.org frog] (''Xenopus laevis''), and [http://www.informatics.jax.org/ mouse] (''Mus musculus'').<br />
# As a capstone, we will assess the results of our work by how well we can apply machine reasoning to retrieve candidate genes for the well-studied vertebrate fin-limb transition and other major events in skeletal evolution of vertebrates.<br />
In addition to a web-based interface, we will make all data, including the integrated knowledgebase, available in the Web Ontology Language (OWL), so that other researchers can reuse the data in as many ways as possible.<br />
<br />
=== The vertebrate fin/limb transition: the test system ===<br />
The evolution of limbs from fins is arguably one of the most well studied transitions in vertebrate history. The genes involved in positioning, growth, and patterning of the fin and limb at various stages are well-known and documented in the vertebrate model organism databases [http://zfin.org ZFIN], [http://xenbase.org Xenbase], and [http://www.informatics.jax.org/ MGI]; changes in skeletal morphology and corresponding assertions of homology are well-documented in the comparative morphological literature. Bringing together the genetic, developmental, morphological and evolutionary data in the Phenoscape Knowledgebase will provide an ideal test bed for judging the reliability of candidate gene predictions and the application of homology logic.<br />
<br />
=== Outreach===<br />
Outreach activities include:<br />
* Summer internships in bio-ontologies for undergraduate/graduate students, in partnership with the [http://www.deepfin.org/ DeepFin Research Coordination Network]<br />
* A "Junior Biocurator" program for advanced Chicago public high school students to be implemented by [http://www.projectexploration.org/ Project Exploration].<br />
* Undergraduate internship and community outreach to the Native American population through University of South Dakota programs.<br />
<br />
=== Contacts ===<br />
Paula Mabee (University of South Dakota) and Todd Vision (University of North Carolina Chapel Hill, National Evolutionary Synthesis Center) are the Principal Investigators of this project. Co-principal investigators are David Blackburn (California Academy of Sciences), Judith Blake (Mouse Genome Informatics, Jackson Laboratories), Hilmar Lapp (National Evolutionary Synthesis Center), Paul Sereno (University of Chicago), Monte Westerfield (ZFIN, University of Oregon), and Aaron Zorn (Xenbase, Cincinnati Children's Hospital Medical Center) (see their [[Contact| contact addresses]]).</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Main_Page&diff=12120Main Page2019-12-13T20:04:31Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
* Learn more in one of our upcoming [[training workshops]]<br />
}}<br />
<br />
== Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution ==<br />
<br />
The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). <br />
<br />
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. <br />
<br />
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.<br />
<br />
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. <br />
<br />
The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''.<br />
<br />
See the [http://scate.phenoscape.org project website] for more information.<br />
<br />
== Previous Phenoscape projects and Acknowledgements ==<br />
* Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]].<br />
* Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. <br />
* The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]."<br />
* These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]].<br />
<br />
https://www.nescent.org/about/images/nsf_logo.jpg</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Ontology-enabled_reasoning_across_phenotypes_from_evolution_and_model_organisms&diff=12119Ontology-enabled reasoning across phenotypes from evolution and model organisms2019-12-13T19:59:31Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* '''This is the homepage of the now-concluded Phenoscape II project (funded by NSF grants DBI-1062404 and DBI-1062542 from August 2011 through June 2018'''). <br />
* For current projects, see the [[Main Page]]<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
}}<br />
<br />
== Ontology-enabled reasoning across phenotypes from evolution and model organisms ==<br />
<br />
=== About this project ===<br />
<br />
Our overall objective is to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions. In other words, we are trying to make descriptive observations amenable to large-scale computation so that they can be subjected to computational data integration and knowledge discovery techniques in ways similarly powerful as the techniques we are used to for numeric, quantitative observations.<br />
<br />
Our approach to accomplish this centers on transforming descriptive observations from the natural language text form in which they are typically reported, to fully computable logic expressions that utilize terms from shared ontologies. [[Guide to Character Annotation| We create these expressions]] (which we also call "annotations") for evolutionary phenotypes reported in the systematics literature, typically in the form of character state matrices. We use the [[EQ for character matrices| Entity-Quality (EQ) formalism]] to compose these expressions, which was initially conceived for making biomedical and mutant model organism phenotype observations interoperable.<br />
<br />
We combine the EQ annotations we create for evolutionary phenotypes with the EQ annotations created for the myriad of phenotypes observed for mutant model organisms in an [http://kb.phenoscape.org integrated knowledgebase] (essentially a triple-store). We then apply [[:Category:Reasoning| Description Logic-reasoning]] to evaluate which evolutionary phenotype transitions can be inferred as semantically similar to which mutant model organism phenotypes, and vice versa. Since the genetic cause of a mutant phenotype is usually known, the links between evolutionary and mutant phenotypes identified in this way can be used to construct testable hypotheses about the genetic correlates or causes of evolutionary transitions.<br />
<br />
[[Image:Phenoscape II tree view.jpg|right|380px]] In a previous project, titled [[Linking Evolution to Genomics Using Phenotype Ontologies]], we developed a working prototype as a successful proof-of-concept, using [[Phenoscape 1 Curated Publications| teleost fishes for evolutionary phenotypes]] and the [http://zfin.org zebrafish model organism] as a source of mutant phenotypes. Here, we aim to make the components of the prototype, including tools and workflows, sufficiently scalable so that they are adequate for the much more extensive volume and more diverse nature of skeletal phenotypes across all vertebrates, fossil and modern. Specifically, our aims encompass the following:<br />
# Develop a fast semantic similarity engine so that the integrated knowledgebase can be searched on-the-fly for biological taxa or genotypes bearing a profile of phenotypes that is similar, but not necessarily identical, to a query profile.<br />
# Develop an [[Reasoning over homology statements| ontological framework for reasoning over homology]] that can be scaled to a large number of anatomically diverse evolutionary lineages.<br />
# Reduce the time and cost of obtaining EQ statements from the literature, while at the same time improving the quality and consistency of those statements, by incorporating natural language processing tools and by improving curation software to allow for on-demand augmentation of community ontologies. [[Image:Phenoscape II architecture.png|right|450px]]<br />
# Build umbrella [[Ontologies#Vertebrate Taxonomy Ontology| taxonomic]] and [[Ontologies| anatomical ontologies]] for the vertebrates, the latter to be supplemented by explicit homology relations among anatomical structures.<br />
# Create a knowledgebase that integrates evolutionary phenotypes for vertebrate fin and limb characters with genetic and phenotype data from three vertebrate model organisms: [http://zfin.org zebrafish] (''Danio rerio''), [http://xenbase.org frog] (''Xenopus laevis''), and [http://www.informatics.jax.org/ mouse] (''Mus musculus'').<br />
# As a capstone, we will assess the results of our work by how well we can apply machine reasoning to retrieve candidate genes for the well-studied vertebrate fin-limb transition and other major events in skeletal evolution of vertebrates.<br />
In addition to a web-based interface, we will make all data, including the integrated knowledgebase, available in the Web Ontology Language (OWL), so that other researchers can reuse the data in as many ways as possible.<br />
<br />
=== The vertebrate fin/limb transition: the test system ===<br />
The evolution of limbs from fins is arguably one of the most well studied transitions in vertebrate history. The genes involved in positioning, growth, and patterning of the fin and limb at various stages are well-known and documented in the vertebrate model organism databases [http://zfin.org ZFIN], [http://xenbase.org Xenbase], and [http://www.informatics.jax.org/ MGI]; changes in skeletal morphology and corresponding assertions of homology are well-documented in the comparative morphological literature. Bringing together the genetic, developmental, morphological and evolutionary data in the Phenoscape Knowledgebase will provide an ideal test bed for judging the reliability of candidate gene predictions and the application of homology logic.<br />
<br />
=== Outreach===<br />
Outreach activities include:<br />
* Summer internships in bio-ontologies for undergraduate/graduate students, in partnership with the [http://www.deepfin.org/ DeepFin Research Coordination Network]<br />
* A "Junior Biocurator" program for advanced Chicago public high school students to be implemented by [http://www.projectexploration.org/ Project Exploration].<br />
* Undergraduate internship and community outreach to the Native American population through University of South Dakota programs.<br />
<br />
=== Contacts ===<br />
Paula Mabee (University of South Dakota) and Todd Vision (University of North Carolina Chapel Hill, National Evolutionary Synthesis Center) are the Principal Investigators of this project. Co-principal investigators are David Blackburn (California Academy of Sciences), Judith Blake (Mouse Genome Informatics, Jackson Laboratories), Hilmar Lapp (National Evolutionary Synthesis Center), Paul Sereno (University of Chicago), Monte Westerfield (ZFIN, University of Oregon), and Aaron Zorn (Xenbase, Cincinnati Children's Hospital Medical Center) (see their [[Contact| contact addresses]]).</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Ontology-enabled_reasoning_across_phenotypes_from_evolution_and_model_organisms&diff=12118Ontology-enabled reasoning across phenotypes from evolution and model organisms2019-12-13T19:48:51Z<p>Todd Vision: </p>
<hr />
<div>{{EventBox1|<br />
* '''This is the homepage of the now-concluded Phenoscape II project (funded by NSF grants DBI-1062404 and DBI-1062542 from August 2011 through June 2018'''). <br />
* For current projects, see the [[Main Page]]<br />
* Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome!<br />
* Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog]<br />
}}<br />
<br />
== Ontology-enabled reasoning across phenotypes from evolution and model organisms ==<br />
<br />
=== About this project ===<br />
<br />
Our overall objective is to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions. In other words, we are trying to make descriptive observations amenable to large-scale computation so that they can be subjected to computational data integration and knowledge discovery techniques in ways similarly powerful as the techniques we are used to for numeric, quantitative observations.<br />
<br />
Our approach to accomplish this centers on transforming descriptive observations from the natural language text form in which they are typically reported, to fully computable logic expressions that utilize terms from shared ontologies. [[Guide to Character Annotation| We create these expressions]] (which we also call "annotations") for evolutionary phenotypes reported in the systematics literature, typically in the form of character state matrices. We use the [[EQ for character matrices| Entity-Quality (EQ) formalism]] to compose these expressions, which was initially conceived for making biomedical and mutant model organism phenotype observations interoperable.<br />
<br />
We combine the EQ annotations we create for evolutionary phenotypes with the EQ annotations created for the myriad of phenotypes observed for mutant model organisms in an [http://kb.phenoscape.org integrated knowledgebase] (essentially a triple-store). We then apply [[:Category:Reasoning| Description Logic-reasoning]] to evaluate which evolutionary phenotype transitions can be inferred as semantically similar to which mutant model organism phenotypes, and vice versa. Since the genetic cause of a mutant phenotype is usually known, the links between evolutionary and mutant phenotypes identified in this way can be used to construct testable hypotheses about the genetic correlates or causes of evolutionary transitions.<br />
<br />
[[Image:Phenoscape II tree view.jpg|right|380px]] In a previous project, titled [[Linking Evolution to Genomics Using Phenotype Ontologies]], we developed a working prototype as a successful proof-of-concept, using [[Phenoscape 1 Curated Publications| teleost fishes for evolutionary phenotypes]] and the [http://zfin.org zebrafish model organism] as a source of mutant phenotypes. Here, we aim to make the components of the prototype, including tools and workflows, sufficiently scalable so that they are adequate for the much more extensive volume and more diverse nature of skeletal phenotypes across all vertebrates, fossil and modern. Specifically, our aims encompass the following:<br />
# Develop a fast semantic similarity engine so that the integrated knowledgebase can be searched on-the-fly for biological taxa or genotypes bearing a profile of phenotypes that is similar, but not necessarily identical, to a query profile.<br />
# Develop an [[Reasoning over homology statements| ontological framework for reasoning over homology]] that can be scaled to a large number of anatomically diverse evolutionary lineages.<br />
# Reduce the time and cost of obtaining EQ statements from the literature, while at the same time improving the quality and consistency of those statements, by incorporating natural language processing tools and by improving curation software to allow for on-demand augmentation of community ontologies. [[Image:Phenoscape II architecture.png|right|450px]]<br />
# Build umbrella [[Ontologies#Vertebrate Taxonomy Ontology| taxonomic]] and [[Ontologies| anatomical ontologies]] for the vertebrates, the latter to be supplemented by explicit homology relations among anatomical structures.<br />
# Create a knowledgebase that integrates evolutionary phenotypes for vertebrate fin and limb characters with genetic and phenotype data from three vertebrate model organisms: [http://zfin.org zebrafish] (''Danio rerio''), [http://xenbase.org frog] (''Xenopus laevis''), and [http://www.informatics.jax.org/ mouse] (''Mus musculus'').<br />
# As a capstone, we will assess the results of our work by how well we can apply machine reasoning to retrieve candidate genes for the well-studied vertebrate fin-limb transition and other major events in skeletal evolution of vertebrates.<br />
In addition to a web-based interface, we will make all data, including the integrated knowledgebase, available in the Web Ontology Language (OWL), so that other researchers can reuse the data in as many ways as possible.<br />
<br />
=== The vertebrate fin/limb transition: the test system ===<br />
The evolution of limbs from fins is arguably one of the most well studied transitions in vertebrate history. The genes involved in positioning, growth, and patterning of the fin and limb at various stages are well-known and documented in the vertebrate model organism databases [http://zfin.org ZFIN], [http://xenbase.org Xenbase], and [http://www.informatics.jax.org/ MGI]; changes in skeletal morphology and corresponding assertions of homology are well-documented in the comparative morphological literature. Bringing together the genetic, developmental, morphological and evolutionary data in the Phenoscape Knowledgebase will provide an ideal test bed for judging the reliability of candidate gene predictions and the application of homology logic.<br />
<br />
=== Outreach===<br />
Outreach activities include:<br />
* Summer internships in bio-ontologies for undergraduate/graduate students, in partnership with the [http://www.deepfin.org/ DeepFin Research Coordination Network]<br />
* A "Junior Biocurator" program for advanced Chicago public high school students to be implemented by [http://www.projectexploration.org/ Project Exploration].<br />
* Undergraduate internship and community outreach to the Native American population through University of South Dakota programs.<br />
<br />
=== Contacts ===<br />
<br />
Paula Mabee (University of South Dakota) and Todd Vision (University of North Carolina Chapel Hill, National Evolutionary Synthesis Center) are the Principal Investigators of this project. Co-principal investigators are David Blackburn (California Academy of Sciences), Judith Blake (Mouse Genome Informatics, Jackson Laboratories), Hilmar Lapp (National Evolutionary Synthesis Center), Paul Sereno (University of Chicago), Monte Westerfield (ZFIN, University of Oregon), and Aaron Zorn (Xenbase, Cincinnati Children's Hospital Medical Center) (see their [[Contact| contact addresses]]).</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Ontology-enabled_reasoning_across_phenotypes_from_evolution_and_model_organisms&diff=12117Ontology-enabled reasoning across phenotypes from evolution and model organisms2019-12-13T19:46:52Z<p>Todd Vision: </p>
<hr />
<div>'''This is the homepage of the now-concluded Phenoscape II project (funded by NSF grants DBI-1062404 and DBI-1062542 from August 2011 through June 2018). For current projects, see the [[Main Page]].'''<br />
<br />
== Ontology-enabled reasoning across phenotypes from evolution and model organisms ==<br />
<br />
=== About this project ===<br />
<br />
Our overall objective is to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions. In other words, we are trying to make descriptive observations amenable to large-scale computation so that they can be subjected to computational data integration and knowledge discovery techniques in ways similarly powerful as the techniques we are used to for numeric, quantitative observations.<br />
<br />
Our approach to accomplish this centers on transforming descriptive observations from the natural language text form in which they are typically reported, to fully computable logic expressions that utilize terms from shared ontologies. [[Guide to Character Annotation| We create these expressions]] (which we also call "annotations") for evolutionary phenotypes reported in the systematics literature, typically in the form of character state matrices. We use the [[EQ for character matrices| Entity-Quality (EQ) formalism]] to compose these expressions, which was initially conceived for making biomedical and mutant model organism phenotype observations interoperable.<br />
<br />
We combine the EQ annotations we create for evolutionary phenotypes with the EQ annotations created for the myriad of phenotypes observed for mutant model organisms in an [http://kb.phenoscape.org integrated knowledgebase] (essentially a triple-store). We then apply [[:Category:Reasoning| Description Logic-reasoning]] to evaluate which evolutionary phenotype transitions can be inferred as semantically similar to which mutant model organism phenotypes, and vice versa. Since the genetic cause of a mutant phenotype is usually known, the links between evolutionary and mutant phenotypes identified in this way can be used to construct testable hypotheses about the genetic correlates or causes of evolutionary transitions.<br />
<br />
[[Image:Phenoscape II tree view.jpg|right|380px]] In a previous project, titled [[Linking Evolution to Genomics Using Phenotype Ontologies]], we developed a working prototype as a successful proof-of-concept, using [[Phenoscape 1 Curated Publications| teleost fishes for evolutionary phenotypes]] and the [http://zfin.org zebrafish model organism] as a source of mutant phenotypes. Here, we aim to make the components of the prototype, including tools and workflows, sufficiently scalable so that they are adequate for the much more extensive volume and more diverse nature of skeletal phenotypes across all vertebrates, fossil and modern. Specifically, our aims encompass the following:<br />
# Develop a fast semantic similarity engine so that the integrated knowledgebase can be searched on-the-fly for biological taxa or genotypes bearing a profile of phenotypes that is similar, but not necessarily identical, to a query profile.<br />
# Develop an [[Reasoning over homology statements| ontological framework for reasoning over homology]] that can be scaled to a large number of anatomically diverse evolutionary lineages.<br />
# Reduce the time and cost of obtaining EQ statements from the literature, while at the same time improving the quality and consistency of those statements, by incorporating natural language processing tools and by improving curation software to allow for on-demand augmentation of community ontologies. [[Image:Phenoscape II architecture.png|right|450px]]<br />
# Build umbrella [[Ontologies#Vertebrate Taxonomy Ontology| taxonomic]] and [[Ontologies| anatomical ontologies]] for the vertebrates, the latter to be supplemented by explicit homology relations among anatomical structures.<br />
# Create a knowledgebase that integrates evolutionary phenotypes for vertebrate fin and limb characters with genetic and phenotype data from three vertebrate model organisms: [http://zfin.org zebrafish] (''Danio rerio''), [http://xenbase.org frog] (''Xenopus laevis''), and [http://www.informatics.jax.org/ mouse] (''Mus musculus'').<br />
# As a capstone, we will assess the results of our work by how well we can apply machine reasoning to retrieve candidate genes for the well-studied vertebrate fin-limb transition and other major events in skeletal evolution of vertebrates.<br />
In addition to a web-based interface, we will make all data, including the integrated knowledgebase, available in the Web Ontology Language (OWL), so that other researchers can reuse the data in as many ways as possible.<br />
<br />
=== The vertebrate fin/limb transition: the test system ===<br />
The evolution of limbs from fins is arguably one of the most well studied transitions in vertebrate history. The genes involved in positioning, growth, and patterning of the fin and limb at various stages are well-known and documented in the vertebrate model organism databases [http://zfin.org ZFIN], [http://xenbase.org Xenbase], and [http://www.informatics.jax.org/ MGI]; changes in skeletal morphology and corresponding assertions of homology are well-documented in the comparative morphological literature. Bringing together the genetic, developmental, morphological and evolutionary data in the Phenoscape Knowledgebase will provide an ideal test bed for judging the reliability of candidate gene predictions and the application of homology logic.<br />
<br />
=== Outreach===<br />
Outreach activities include:<br />
* Summer internships in bio-ontologies for undergraduate/graduate students, in partnership with the [http://www.deepfin.org/ DeepFin Research Coordination Network]<br />
* A "Junior Biocurator" program for advanced Chicago public high school students to be implemented by [http://www.projectexploration.org/ Project Exploration].<br />
* Undergraduate internship and community outreach to the Native American population through University of South Dakota programs.<br />
<br />
=== Contacts ===<br />
<br />
Paula Mabee (University of South Dakota) and Todd Vision (University of North Carolina Chapel Hill, National Evolutionary Synthesis Center) are the Principal Investigators of this project. Co-principal investigators are David Blackburn (California Academy of Sciences), Judith Blake (Mouse Genome Informatics, Jackson Laboratories), Hilmar Lapp (National Evolutionary Synthesis Center), Paul Sereno (University of Chicago), Monte Westerfield (ZFIN, University of Oregon), and Aaron Zorn (Xenbase, Cincinnati Children's Hospital Medical Center) (see their [[Contact| contact addresses]]).</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=12070Publications and Posters2019-06-22T18:56:54Z<p>Todd Vision: /* 2019 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Dahdul et al. (2018), Dahdul et al. (2015), Cui et al. (2015), Arighi et al. (2013), Bertone et al. (2012), Dahdul et al. (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2019===<br />
* Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., Vision, T.J. (2019) A logical model of homology for comparative biology. Submitted for review 9 May 2019. Preprint available: bioRxiv https://doi.org/10.1101/588822<br />
<br />
===2018===<br />
* Manda P, Vision T (2018) On the statistical analysis of semantic similarity metrics. International Conference on Biological Ontology 2018. Oregon State University, Corvallis, OR, USA. Accepted. Preprint bioRxiv https://doi.org/10.1101/327833<br />
* Dahdul W, Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. Database. 2018:bay110, https://doi.org/10.1093/database/bay110<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. (2018) Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Systematic Biology, 67(4):559–575, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. (2018) Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin. preprint https://peerj.com/preprints/26988<br />
* Braun I, Balhoff J, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ. (2018) Computable phenotypes enable comparative and predictive phenomics among plant species and across domains of life. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Balhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
===2013===<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2013'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. Database 2013:bas056 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
===2012===<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2019 ===<br />
* Balhoff J, Dahdul W, Lapp H, Mabee P, Tarasov S, Uyeda J, Vision T (2019) Integrating ontologies in comparative analyses of trait evolution. Posster presented at Evolution 2019, Providence RI, June 22, 2019, https://doi.org/10.5281/zenodo.3252611<br />
* Vision, T. (2019) Computing over descriptive phenotype data: Is Aristotle a help or hindrance? PIRS Minisymposium on Novel Candidate Gene Discovery by Computing on Phenotypes, Iowa State University, April 3, 2019.<br />
* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Center for Biodiversity Analysis, Australian National University, Canberra, Australia. April 1, 2019. <br />
* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Royal Botanic Gardens and Domain Trust Science Seminar Series. Royal Botanic Garden, Sydney, Australia. March 28, 2019. <br />
* Mabee, P. (2019) Trait ontologies: logical links across biodiversity. Plant Traits Workshop. Royal Botanic Garden, Sydney, Australia. March 27, 2019. <br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, P. Mabee, S. Tarasov, J. Uyeda, T. Vision. (2019). Integrating ontologies in comparative analyses of trait evolution. Biocuration 2019. Cambridge UK. April 2019.<br />
<br />
=== 2018 ===<br />
* Mabee, P.M. Anatomy ontologies supply the missing links for knowledge discovery and recovery. Invited talk for Biological Ontology Series, Iowa State University. Ames, Iowa, October 22, 2018.<br />
* Uyeda, J.C. (presenter, poster) (2018). On the need for phylogenetic natural history. Evolution 2018, Montpellier, France. August 21, 2018.<br />
* Collins M. (presenter), R. Tarvin, M. Kandziora, W. Dahdul, and D. Paul (2018) Phenomap - Challenges and successes in bringing together multiple data projects to build new visualizations of phenotypic information and specimen records. Biodiversity Information Science and Standards 2: e25698. https://doi.org/10.3897/biss.2.25698. Presented at Biodiversity Information Standards (TDWG), Dunedin, NZ, August 2018<br />
* Fernando, P. (presenter, poster), E. Zeng, P. Mabee. (2018) The integrative use of anatomy ontology and protein-protein interaction networks to study evolutionary phenotypic transitions. International Conference on Biological Ontology (2018), Corvallis, OR, August 7, 2018<br />
* Mabee, P., J. Balhoff, W. Dahdul (invited oral presentation), H. Lapp, C. Mungall, T. Vision. (2018). Reasoning over anatomical homology in the Phenoscape KB. Workshop: Data Standards and Knowledge Sharing in Biodiversity -Tools and Applications. International Conference on Biological Ontology (2018), Corvallis, OR, August 7, 2018.<br />
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, J. Uyeda, T. Vision, P. Mabee (2018). [https://www.idigbio.org/wiki/images/3/3d/Dahdul-iDigBio-poster.pdf Applications of ontology-based knowledge representation for comparative biology]. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Vision, TJ (2018) Skeletons, mutants and ontologies: What can we learn from linking phenotypes and genetics on a large scale? University of Southern California, Computational Biology Seminar, March 29, 2018.<br />
* Mabee, P.M. (2018) Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
* Mabee, P.M. (2018) Phenoscape: use case, tools, and outcomes. Explorer of Taxon Concepts and Authors Projects Joint Workshop: Enabling authors to produce computable phenotypic data. University of Arizona Biosphere. January 12, 2018.<br />
<br />
=== 2017 ===<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee (2017). A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Kansas City, MO. November 14-16, 2017.<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=12069Publications and Posters2019-05-31T17:33:37Z<p>Todd Vision: /* 2019 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Dahdul et al. (2018), Dahdul et al. (2015), Cui et al. (2015), Arighi et al. (2013), Bertone et al. (2012), Dahdul et al. (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2019===<br />
* Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., Vision, T.J. (2019) A logical model of homology for comparative biology. Submitted for review 9 May 2019. Preprint available: bioRxiv https://doi.org/10.1101/588822<br />
<br />
===2018===<br />
* Manda P, Vision T (2018) On the statistical analysis of semantic similarity metrics. International Conference on Biological Ontology 2018. Oregon State University, Corvallis, OR, USA. Accepted. Preprint bioRxiv https://doi.org/10.1101/327833<br />
* Dahdul W, Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. Database. 2018:bay110, https://doi.org/10.1093/database/bay110<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. (2018) Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Systematic Biology, 67(4):559–575, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. (2018) Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin. preprint https://peerj.com/preprints/26988<br />
* Braun I, Balhoff J, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ. (2018) Computable phenotypes enable comparative and predictive phenomics among plant species and across domains of life. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Balhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
===2013===<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2013'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. Database 2013:bas056 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
===2012===<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2019 ===<br />
* Vision, T. (2019) Computing over descriptive phenotype data: Is Aristotle a help or hindrance? PIRS Minisymposium on Novel Candidate Gene Discovery by Computing on Phenotypes, Iowa State University, April 3, 2019.<br />
* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Center for Biodiversity Analysis, Australian National University, Canberra, Australia. April 1, 2019. <br />
* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Royal Botanic Gardens and Domain Trust Science Seminar Series. Royal Botanic Garden, Sydney, Australia. March 28, 2019. <br />
* Mabee, P. (2019) Trait ontologies: logical links across biodiversity. Plant Traits Workshop. Royal Botanic Garden, Sydney, Australia. March 27, 2019. <br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, P. Mabee, S. Tarasov, J. Uyeda, T. Vision. (2019). Integrating ontologies in comparative analyses of trait evolution. Biocuration 2019. Cambridge UK. April 2019.<br />
<br />
=== 2018 ===<br />
* Mabee, P.M. Anatomy ontologies supply the missing links for knowledge discovery and recovery. Invited talk for Biological Ontology Series, Iowa State University. Ames, Iowa, October 22, 2018.<br />
* Uyeda, J.C. (presenter, poster) (2018). On the need for phylogenetic natural history. Evolution 2018, Montpellier, France. August 21, 2018.<br />
* Collins M. (presenter), R. Tarvin, M. Kandziora, W. Dahdul, and D. Paul (2018) Phenomap - Challenges and successes in bringing together multiple data projects to build new visualizations of phenotypic information and specimen records. Biodiversity Information Science and Standards 2: e25698. https://doi.org/10.3897/biss.2.25698. Presented at Biodiversity Information Standards (TDWG), Dunedin, NZ, August 2018<br />
* Fernando, P. (presenter, poster), E. Zeng, P. Mabee. (2018) The integrative use of anatomy ontology and protein-protein interaction networks to study evolutionary phenotypic transitions. International Conference on Biological Ontology (2018), Corvallis, OR, August 7, 2018<br />
* Mabee, P., J. Balhoff, W. Dahdul (invited oral presentation), H. Lapp, C. Mungall, T. Vision. (2018). Reasoning over anatomical homology in the Phenoscape KB. Workshop: Data Standards and Knowledge Sharing in Biodiversity -Tools and Applications. International Conference on Biological Ontology (2018), Corvallis, OR, August 7, 2018.<br />
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, J. Uyeda, T. Vision, P. Mabee (2018). [https://www.idigbio.org/wiki/images/3/3d/Dahdul-iDigBio-poster.pdf Applications of ontology-based knowledge representation for comparative biology]. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Vision, TJ (2018) Skeletons, mutants and ontologies: What can we learn from linking phenotypes and genetics on a large scale? University of Southern California, Computational Biology Seminar, March 29, 2018.<br />
* Mabee, P.M. (2018) Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
* Mabee, P.M. (2018) Phenoscape: use case, tools, and outcomes. Explorer of Taxon Concepts and Authors Projects Joint Workshop: Enabling authors to produce computable phenotypic data. University of Arizona Biosphere. January 12, 2018.<br />
<br />
=== 2017 ===<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee (2017). A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Kansas City, MO. November 14-16, 2017.<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Journal_Club&diff=12010Journal Club2018-07-16T19:40:59Z<p>Todd Vision: /* 2018 */</p>
<hr />
<div><br />
= 2018 =<br />
1st and 3rd Fridays of month, 2:30-3:30 eastern<br />
<br />
Connection info:<br />
* Zoom: https://renci.zoom.us/j/929124809<br />
* US phone toll free: 877.853.5257, 855.880.1246<br />
* US phone not toll free: 669 900 6833, 646.558.8656<br />
* International #'s": https://renci.zoom.us/zoomconference?m=pZZ0jdZAKrL_L2SZsyjJ1rn04r0jrDVv<br />
* Meeting ID: 929 124 809<br />
<br />
Signup at [https://hackmd.io/FB8mQoBsSci5Aea1Y3KONw HackMD]<br />
<br />
Papers available on [https://paperpile.com/shared/30ynCr Paperpile]<br />
<br />
=2014=<br />
An older iteration of the journal club met once a month in the Grey building at NESCent. <br />
<br />
== 24-Sep-2014, 2-3pm==<br />
Oellrich et al (2014) The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics. 2014; 5(Suppl 1): S4.<br />
http://doi.org/10.1186/2041-1480-5-S1-S4<br />
<br />
==27-Aug-2014, 2-3pm==<br />
Despoina Magka, Markus Krötzsch and Ian Horrocks (2014) A rule-based ontological framework for the classification of molecules. http://dx.doi.org/10.1186/2041-1480-5-17<br />
<br />
== 30-Jul-2014, 2-3pm==<br />
Bada et al. (2014) Semantic Precision and Recall for Concept Annotation of Text, starting on p30 of the [https://docs.google.com/file/d/0B6AZUdKw1IVHQjI3MVFvWjFRWlE/edit Proceedings] from the most recent Bio-Ontologies SIG</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Journal_Club&diff=12009Journal Club2018-07-16T19:40:30Z<p>Todd Vision: </p>
<hr />
<div><br />
= 2018 =<br />
1st and 3rd Fridays of month, 2:30-3:30 eastern<br />
<br />
Connection info:<br />
* Zoom: https://renci.zoom.us/j/929124809<br />
* US phone toll free: 877.853.5257, 855.880.1246<br />
* US phone not toll free: 669 900 6833, 646.558.8656<br />
* International #'s": https://renci.zoom.us/zoomconference?m=pZZ0jdZAKrL_L2SZsyjJ1rn04r0jrDVv<br />
* Meeting ID: 929 124 809<br />
<br />
[https://hackmd.io/FB8mQoBsSci5Aea1Y3KONw Signup Sheet]<br />
<br />
Papers available on [https://paperpile.com/shared/30ynCr Paperpile]<br />
<br />
<br />
=2014=<br />
An older iteration of the journal club met once a month in the Grey building at NESCent. <br />
<br />
== 24-Sep-2014, 2-3pm==<br />
Oellrich et al (2014) The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics. 2014; 5(Suppl 1): S4.<br />
http://doi.org/10.1186/2041-1480-5-S1-S4<br />
<br />
==27-Aug-2014, 2-3pm==<br />
Despoina Magka, Markus Krötzsch and Ian Horrocks (2014) A rule-based ontological framework for the classification of molecules. http://dx.doi.org/10.1186/2041-1480-5-17<br />
<br />
== 30-Jul-2014, 2-3pm==<br />
Bada et al. (2014) Semantic Precision and Recall for Concept Annotation of Text, starting on p30 of the [https://docs.google.com/file/d/0B6AZUdKw1IVHQjI3MVFvWjFRWlE/edit Proceedings] from the most recent Bio-Ontologies SIG</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=12007Publications and Posters2018-06-08T19:02:34Z<p>Todd Vision: /* 2018 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Arighi et al. (2012), Bertone et al. (2012), Cui et al. (2015), Dahdul et al. (2010), Dahdul et al. (2015), Dahdul et al. (2018) <br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2018===<br />
* Manda P, Vision T (2018) An analysis and comparison of the statistical sensitivity of semantic similarity metrics. bioRxiv https://doi.org/10.1101/327833<br />
* Dahdul W, Manda P, Cui C, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. bioRxiv https://doi.org/10.1101/322156<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. 2018. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Systematic Biology, syx098, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. 2018 (in press). Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
* Braun I, Balhoff J, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ (in press) Computable phenotypes enable comparative and predictive phenomics among plant species and across domains of life. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2018 ===<br />
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
<br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, J. Uyeda, T. Vision, P. Mabee (2018). Applications of ontology-based knowledge representation for comparative biology. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
* Vision, TJ (2018) Skeletons, mutants and ontologies: What can we learn from linking phenotypes and genetics on a large scale? University of Southern California, Computational Biology Seminar, March 29, 2018.<br />
* Mabee, P.M. (2018) Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
<br />
=== 2017 ===<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=12006Publications and Posters2018-06-08T18:48:32Z<p>Todd Vision: /* Publications by date */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Arighi et al. (2012), Bertone et al. (2012), Cui et al. (2015), Dahdul et al. (2010), Dahdul et al. (2015), Dahdul et al. (2018) <br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2018===<br />
* Manda P, Vision T (2018) An analysis and comparison of the statistical sensitivity of semantic similarity metrics. bioRxiv https://doi.org/10.1101/327833<br />
* Dahdul W, Manda P, Cui C, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. bioRxiv https://doi.org/10.1101/322156<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. 2018. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Systematic Biology, syx098, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. 2018 (in press). Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
* Braun I, Balhoff J, Berardini TZ, Cooper L, Gkoutos G, Harper L, Huala E, Jaiswal P, Kazic T, Lapp H, Macklin JA, Specht CD, Vision T, Walls RL, Lawrence-Dill CJ (in press) Computable phenotypes enable comparative and predictive phenomics among plant species and across domains of life. In: Application of Semantic Technology in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2018 ===<br />
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
<br />
* Dahdul, W. (presenter, poster), J. Balhoff, H. Lapp, J. Uyeda, T. Vision, P. Mabee (2018). Applications of ontology-based knowledge representation for comparative biology. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.<br />
<br />
* Mabee, P.M. (2018). Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
<br />
=== 2017 ===<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11981Publications and Posters2018-05-16T14:42:09Z<p>Todd Vision: /* Publications by category */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Arighi et al. (2012), Bertone et al. (2012), Cui et al. (2015), Dahdul et al. (2010), Dahdul et al. (2015), Dahdul et al. (2018) <br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2018===<br />
* Dahdul W, Manda P, Cui C, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. bioRxiv https://doi.org/10.1101/322156<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. 2018. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Systematic Biology, syx098, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. 2018 (in press). Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technologies in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2018 ===<br />
<br />
* Mabee, P.M. (2018). Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
<br />
=== 2017 ===<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11980Publications and Posters2018-05-16T14:41:06Z<p>Todd Vision: /* 2018 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Mabee et al (2018), Thessen et al (2015), Manda et al (2015), Oellrich et al. (2015), Deans et al (2015), Mabee et al (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Jackson et al. (2018), Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Cui et al. (2015), Dahdul et al (2015), Arighi et al. (2012), Bertone et al (2012), Dahdul et al (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2018===<br />
* Dahdul W, Manda P, Cui C, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Vision T, Mabee, PM (2018) Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems. bioRxiv https://doi.org/10.1101/322156<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. 2018. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Systematic Biology, syx098, https://doi.org/10.1093/sysbio/syx098<br />
* Mabee P.M., Dahdul W., Balhoff J.P., Lapp, H., Manda, P., Uyeda, J., Vision, T.J., Westerfield, M. 2018 (in press). Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technologies in Biodiversity Science (A. Thessen, editor). IOS Press, Berlin.<br />
<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016: 132-143 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:34. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2018 ===<br />
<br />
* Mabee, P.M. (2018). Reasons to reason across disparate data types: linking species, phenotypes, genes, and more. Biodiversity Collections Network workshop: Addressing Legal Issues Involved in Digitized Collections: The Nagoya Protocol as a Test Case. Harvard University, March 27, 2018.<br />
<br />
=== 2017 ===<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11955Publications and Posters2017-11-01T14:48:15Z<p>Todd Vision: /* 2017 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Thessen AE et al. (2015), Manda P. et al. (2015), Oellrich et al. (2015), Deans et. al (2015), Mabee et al. (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Cui et al. (2015), Dahdul et al (2015), Arighi et al. (2012), Bertone et al (2012), Dahdul et al (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2017===<br />
* Manda P., Vision T.J. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
* Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., Mabee, P.M. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. (Accepted pending revision, Systematic Biology, April 2017)<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/071951 preprint doi:10.1101/071951]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:21. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2017 ===<br />
<br />
* Lapp H. (2017) Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution. Duke Duke Computational Biology Seminar, Oct 23, 2017.<br />
<br />
* Mabee, P (2017) Progress in comparative biology can be accelerated through semantic annotation. SSB workshop – Trees, traits and functions: semantics for comparative biology. Evolution Conference, Portland, OR, June 23, 2017.<br />
<br />
* Vision, T, J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp (presenter, poster), P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 23, 2017. [http://doi.org/10.6084/m9.figshare.5262868.v1 doi:10.6084/m9.figshare.5262868.v1]<br />
<br />
* Dahdul, W (presenter, poster), J Balhoff, H Lapp, T Vision, P Mabee. (2017). Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. 2017 RII Track-1 All Investigator Meeting. Oacoma, SD, May 2017.<br />
<br />
* Fernando, P (presenter, poster), L Jackson, J Balhoff, E Zeng, P Mabee. (2017) A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Great Lakes Bioinformatics Conference, Chicago, IL. F1000Research 2017, 6(ISCB Comm J):674 (poster) [http://doi.org/10.7490/f1000research.1114056.1 doi: 10.7490/f1000research.1114056.1]<br />
<br />
* Jackson LM (presenter, poster), FC Fernando, JP Balhoff, PM Mabee. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. University of South Dakota Ideafest. Vermillion, SD, April 5, 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 26, 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 27, 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
* Jackson LM (presenter), PC Fernando, JP Balhoff, PM Mabee. (2017). Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Annual Meeting of the Society for Integrative and Comparative Biology (SICB). New Orleans, LA, January 7, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. October 5, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Fernando, P (presenter, poster), P Mabee, E Zeng. “Investigating the Genomic Basis of Phenotypic Transitions Using a Novel Integrative Analysis of Anatomy Ontology and Protein-Protein Interaction Networks”Fifth Annual Summit Meeting of the Phenotype RCN, Biosphere2, Tucson, AZ, February 26-28, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11917Publications and Posters2017-05-30T19:24:57Z<p>Todd Vision: /* 2016 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Thessen AE et al. (2015), Manda P. et al. (2015), Oellrich et al. (2015), Deans et. al (2015), Mabee et al. (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Cui et al. (2015), Dahdul et al (2015), Arighi et al. (2012), Bertone et al (2012), Dahdul et al (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2017===<br />
* Manda P., Vision T.J.. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:21. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2017 ===<br />
<br />
* Vision, T (presenter, poster), J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp, P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 2017. <br />
<br />
* Dahdul, W (presenter, poster) (2017) Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. November 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11916Publications and Posters2017-05-30T19:23:02Z<p>Todd Vision: /* 2016 */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Thessen AE et al. (2015), Manda P. et al. (2015), Oellrich et al. (2015), Deans et. al (2015), Mabee et al. (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Cui et al. (2015), Dahdul et al (2015), Arighi et al. (2012), Bertone et al (2012), Dahdul et al (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2017===<br />
* Manda P., Vision T.J.. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [[http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. [http://doi.org/10.1142/9789814749411_0013 Proceedings of the Pacific Symposium on Biocomputing 2016 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:21. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2017 ===<br />
<br />
* Vision, T (presenter, poster), J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp, P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 2017. <br />
<br />
* Dahdul, W (presenter, poster) (2017) Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. November 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11915Publications and Posters2017-05-30T19:22:07Z<p>Todd Vision: /* Publications by date */</p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Thessen AE et al. (2015), Manda P. et al. (2015), Oellrich et al. (2015), Deans et. al (2015), Mabee et al. (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Cui et al. (2015), Dahdul et al (2015), Arighi et al. (2012), Bertone et al (2012), Dahdul et al (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2017===<br />
* Manda P., Vision T.J.. '''2017'''. Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [[http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Proceedings of the Pacific Symposium on Biocomputing 2016 [http://doi.org/10.1142/9789814749411_0013 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:21. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2017 ===<br />
<br />
* Vision, T (presenter, poster), J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp, P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 2017. <br />
<br />
* Dahdul, W (presenter, poster) (2017) Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. November 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
<br />
* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
<br />
* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
<br />
* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
<br />
* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
<br />
=== 2007 ===<br />
<br />
* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
<br />
* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
<br />
[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Publications_and_Posters&diff=11914Publications and Posters2017-05-30T19:21:37Z<p>Todd Vision: </p>
<hr />
<div>== Publications by category ==<br />
* Perspectives and reviews: Thessen AE et al. (2015), Manda P. et al. (2015), Oellrich et al. (2015), Deans et. al (2015), Mabee et al. (2012), Deans et al (2011), Vision et al. (2011), Mabee et al (2007)<br />
* Biological knowledge discovery: Edmunds et al (2016), Dececci et al (2015), Ibrahim et al (2014), Manda and Vision (2017), Mullins et al (2012), Mabee et al (2007). <br />
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)<br />
* Data curation: Cui et al. (2015), Dahdul et al (2015), Arighi et al. (2012), Bertone et al (2012), Dahdul et al (2010)<br />
* Data modeling, reasoning & ontologies: Manda et al. (2016), Balhoff et al. (2015), Balhoff et al (2013), Haendel et al (2014), Dahdul e al (2014), Midford et al (2013), Druzinsky et al (2013), Segerdell et al (2013), Balhoff et al (2013), Dahdul et al (2012), Haendel et al (2008)<br />
<br />
== Publications by date ==<br />
===2017===<br />
* Manda P., Vision T.J.. "2017". Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature. [http://doi.org/10.1145/3066911.3066919 Proceedings of The International Workshop on Semantic Big Data (SBD ’17)] (preprint [http://doi.org/10.7287/peerj.preprints.2747v1 doi:10.7287/peerj.preprints.2747v1]).<br />
<br />
===2016===<br />
* Manda P, Balhoff J, Vision TJ. '''2016'''. Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles. [[http://ceur-ws.org/Vol-1747/ Proceedings of the International Conference on Biological Ontology 2016] ([https://doi.org/10.1101/086306 preprint doi:10.1101/086306]).<br />
<br />
* Balhoff, J.P. '''2016'''. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. [http://dx.doi.org/10.21105/joss.00023 doi:10.21105/joss.00023]<br />
<br />
* Dececchi, T.A., Mabee, P.M., Blackburn, D. '''2016'''. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. [http://dx.doi.org/10.1371/journal.pone.0155680 doi:10.1371/journal.pone.0155680]<br />
<br />
* Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. '''2016'''. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. [http://doi.org/10.1093/molbev/msv223 doi:10.1093/molbev/msv223]<br />
<br />
* Druzinsky, R. E., Balhoff, J. P., Crompton, A. W., Done, J., German, R. Z., Haendel, M. A., Herrel, A., Herring, S.W., Lapp, H. Mabee, P.M., Muller, H., Mungall, C.J., Sternberg, P.W., Auken, K.V., Vinyard, C.J. , Williams, S.H., Wall, C. E. '''2016'''. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PloS One, 11(2), e0149102. [http://doi.org/10.1371/journal.pone.0149102 doi:10.1371/journal.pone.0149102]<br />
<br />
* Manda P, Mungall C, Balhoff J, Lapp H, Vision TJ '''2016'''. Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Proceedings of the Pacific Symposium on Biocomputing 2016 [http://doi.org/10.1142/9789814749411_0013 doi:10.1142/9789814749411_0013]<br />
<br />
* Diehl, A.D. (and 14 coauthors including W. Dahdul). '''2016'''. The Cell Ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Biomedical Semantics 7:44 [http://www.jbiomedsem.com/content/7/1/44 doi:10.1186/s13326-016-0088-7]<br />
<br />
===2015===<br />
* Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ '''2015''' Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. [http://phenoday2015.bio-lark.org/pdf/9.pdf Bio-ontologies SIG at ISMB 2015]<br />
<br />
*Cui, H., Dahdul, W., Dececchi, T.A., Ibrahim, N., Mabee, P., Balhoff, J.P., Gopalakrishnan, H. '''2015'''. CharaParser+EQ: Performance Evaluation without Gold Standard. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T) vol. 51. [https://www.asist.org/files/meetings/am15/proceedings/submissions/papers/9paper.pdf PDF]<br />
<br />
*Dahdul, W., T.A. Dececchi, N. Ibrahim, H. Lapp, P.M. Mabee. '''2015'''. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy. Database 2015: bav040. [http://dx.doi.org/10.1093/database/bav040 http://dx.doi:10.1093/database/bav040]<br />
<br />
*Deans, A.R., et al., (including Balhoff, Blackburn, Cui, Dahdul, Dececchi, Haendel, Ibrahim, Lapp, Mungall, Westerfeld, Zorn, & Mabee). '''2015'''. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. [http://dx.doi.org/10.1371/journal.pbio.1002033 http://dx.doi.org/10.1371/journal.pbio.1002033]<br />
<br />
*Dececchi, T.A., J.P. Balhoff, H. Lapp, P.M. Mabee. '''2015'''. Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. [http://doi.org/10.1093/sysbio/syv031 doi:10.1093/sysbio/syv031]<br />
<br />
*Manda P., Balhoff J. P., Lapp H., Mabee P., Vision T.J. '''2015'''. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 53 (8):561–571. [http://doi.org./10.1002/dvg.22878 http://dx.doi.org/10.1002/dvg.22878]<br />
<br />
*Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. '''2015''' The digital revolution in phenotyping. Brief Bioinform. [http://doi.org/10.1093/bib/bbv083 http://doi.org/10.1093/bib/bbv083]<br />
<br />
*Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. '''2015'''. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 [https://doi.org/10.7717/peerj.1470 https://doi.org/10.7717/peerj.1470]<br />
<br />
===2014===<br />
*Balhoff, J.P., W.M. Dahdul, T.A. Dececchi, H. Lapp, P.M. Mabee, and T.J. Vision. '''2014'''. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.1186/2041-1480-5-45 http://dx.doi.org/10.1186/2041-1480-5-45]<br />
<br />
*Balhoff, J.P., Dececchi, T.A., Mabee, P.M., Lapp, H. '''2014'''. Presence-absence reasoning for evolutionary phenotypes. Peer-reviewed conference paper, Bio-ontologies SIG at ISMB 2014. [http://phenoday2014.bio-lark.org/pdf/11.pdf http://phenoday2014.bio-lark.org/pdf/11.pdf] and [http://arxiv.org/abs/1410.3862 http://arxiv.org/abs/1410.3862]<br />
<br />
*Dahdul, W.M., H. Cui, P.M. Mabee, C.J. Mungall, D. Osumi-Sutherland, R. Walls, and M. Haendel. '''2014'''. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics. 5:21. [http://dx.doi.org/10.1186/2041-1480-5-34 http://dx.doi.org/10.1186/2041-1480-5-34]<br />
<br />
*Haendel, M.A., Ballhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Comte, A., Dahdul, W.A., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C. J. '''2014'''. Uberon: Unification of multi-species vertebrate anatomy ontologies for comparative biology. Journal of Biomedical Semantics. 5:21 [http://dx.doi.org/10.1186/2041-1480-5-21 http://dx.doi.org/10.1186/2041-1480-5-21]<br />
<br />
*Ibrahim, N., P. C. Sereno, C. Dal Sasso, S. Maganuco, M. Fabbri, D. M. Martill, S. Zouhri, N. Myhrvold, and D. A. Iurino '''2016''' Semiaquatic adaptations in a giant predatory dinosaur. Science. [http://dx.doi.org/10.1126/science.1258750 doi:10.1126/science.1258750]<br />
<br />
*Midford, P.E., Dececchi, T.A., Balhoff, J.P., Dahdul, W.M., Ibrahim, N., Lapp, H., Lundberg, J.G., Mabee, P.M., Sereno, P.C., Westerfield, M., Vision, T.J. '''2013'''. The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics. 4:34. [http://dx.doi.org/10.1186/2041-1480-4-34 http://dx.doi.org/10.1186/2041-1480-4-34].<br />
<br />
===2013===<br />
*Balhoff, J.P, I. Mikó, M.J. Yoder, P.L. Mullins, & A.R. Deans. '''2013'''. A semantic model for species description, applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639-659. [http://dx.doi.org/10.1093/sysbio/syt028 http://dx.doi.org/10.1093/sysbio/syt028]<br />
<br />
*Druzinsky, R.E., Mungall, C.J., Haendel, M., Lapp, H., Mabee, P.M. '''2013'''. What is an anatomy ontology? The Anatomical Record 296:1797-1799. [http://dx.doi.org/10.1002/ar.22805 http://dx.doi.org/10.1002/ar.22805].<br />
<br />
*Segerdell, E., V.G. Ponferrada, C. James-Zorn, K.A. Burns, J.D. Fortriede, W.M. Dahdul, P.D. Vize and A.M. Zorn. '''2013'''. Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. Journal of Biomedical Semantics. 4:31. [http://dx.doi.org/10.1186/2041-1480-4-31 http://dx.doi.org/10.1186/2041-1480-4-31]<br />
<br />
===2012===<br />
*Arighi, C, et al. (including Dahdul, Mabee, Cui, Haendel, Balhoff) '''2012'''. An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. 2013 [http://dx.doi.org/10.1093/database/bas056 http://dx.doi.org/10.1093/database/bas056]<br />
<br />
*Bertone, M.A., I. Mikó, M.J. Yoder, K.C. Seltmann, J.P. Balhoff, and A.R. Deans. '''2012'''. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: Results from a manual alignment. Database [http://dx.doi.org/10.1093/database/bas057 http://dx.doi.org/10.1093/database/bas057]<br />
<br />
*Dahdul W.M., Balhoff J.P, Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. '''2012'''. A unified anatomy ontology of the vertebrate skeletal system. PLoS ONE 7(12): e51070 [http://dx.plos.org/10.1371/journal.pone.0051070 http://dx.plos.org/10.1371/journal.pone.0051070]<br />
<br />
*Mabee P.M., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J., Westerfield M. '''2012'''. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology. Journal of Applied Ichthyology 28(3):300-305. [http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x http://dx.doi.org/10.1111/j.1439-0426.2012.01985.x]<br />
<br />
*Mullins P., Kawada R., Balhoff J.P., Deans A. '''2012'''. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223:1-38 [http://dx.doi.org/10.3897/zookeys.223.3572 http://dx.doi.org/10.3897/zookeys.223.3572]<br />
<br />
===2011===<br />
*Deans, A.R., M.J. Yoder, J.P. Balhoff. '''2011'''. Time to change how we describe biodiversity. Trends in Ecology & Evolution 27 (2):78-84. [http://dx.doi.org/10.1016/j.tree.2011.11.007 http://dx.doi.org/10.1016/j.tree.2011.11.007]<br />
<br />
* Vision TJ, Blake JA, Lapp H, Mabee PM, Westerfield M '''2011''' Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. Proceedings of the First International Workshop on Linked Science [http://ceur-ws.org/Vol-783/paper8.pdf PDF]<br />
<br />
===2010===<br />
*Balhoff, J. P., W. M. Dahdul, C. R. Kothari, H. Lapp, J. G. Lundberg, P. M. Mabee, P. E. Midford, M. Westerfield, and T. J. Vision. '''2010'''. Phenex: Ontological annotation of phenotypic diversity. PLoS ONE 5(5):e10500. [http://dx.doi.org/10.1371/journal.pone.0010500 doi:10.1371/journal.pone.0010500]<br />
<br />
*Dahdul, W. M., J. P. Balhoff, J. Engeman, T. Grande, E. J. Hilton, C. R. Kothari, H. Lapp, J. G. Lundberg, P. E. Midford, T. J. Vision, M. Westerfield, and P. M. Mabee. '''2010'''. Evolutionary characters, phenotypes and ontologies:curating data from the systematic biology literature. PLoS ONE 5(5):e10708. [http://dx.doi.org/10.1371/journal.pone.0010708 doi:10.1371/journal.pone.0010708]<br />
<br />
*Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. '''2010'''. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59(4):369-383. [http://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]<br />
<br />
===2008===<br />
*Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. '''2008'''. [[:File:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.<br />
<br />
===2007===<br />
*Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. '''2007'''. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol.&nbsp; [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181]<br />
<br />
*Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. '''2007'''. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013]<br />
<br />
== Posters & Presentations ==<br />
=== 2017 ===<br />
<br />
* Vision, T (presenter, poster), J Balhoff, W Dahdul, A Dececchi, P Fernando, H Lapp, P Mabee, P Manda, K Mastick, M Westerfield, E Zeng (2017) Machine reasoning about phenotypes: enhancing expert knowledge about the genetics of a fossil transition. Evolution Conference, Portland, OR, June 2017. <br />
<br />
* Dahdul, W (presenter, poster) (2017) Incorporating the logic of anatomical homology in a gene-phenotype knowledgebase: Phenoscape KB. Evolution Conference, Portland, OR, June 2017.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Hanscom J, Balhoff J, and Mabee P. (2017). A computational framework using ontologies to integrate large-scale trees and traits: exploring diversity across the teleost tree of life. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113878.1 doi:10.7490/f1000research.1113878.1]<br />
<br />
* Dahdul W (presenter, poster), Manda P, Cui H, Balhoff J, Dececchi A, Ibrahim N, Lapp H, Mabee PM, Vision TJ. (2017). Gold standard evaluation of machine and human generated annotations of biodiverse phenotypes. Biocuration 2017, Stanford, CA, March 2017. [http://doi.org/10.7490/f1000research.1113805.1 doi:10.7490/f1000research.1113805.1]<br />
<br />
* Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.<br />
<br />
=== 2016 ===<br />
* Dahdul, W (presenter) (2016) Beetles, barnacles, and catfishes: talking across lineages to build the tree of life. Department Seminar, California State University, Fullerton. October 12, 2016.<br />
<br />
* Mabee, P. (presenter) (2016) What does it mean to bring computable phenotypes linked to genes, to phylogenetic systematics? Willi Hennig Society Meeting, Buenos Aires, Argentina. November 2016.<br />
<br />
* Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.<br />
<br />
* Balhoff, J (presenter, poster), W Dahdul, P Manda, L Jackson, C Mao, H Xu, L Zhang, H Lapp, P Mabee, T Vision (2016) The Phenoscape Knowledgeable: tools and APIs for computing across phenotypes from evolutionary diversity to model organisms. International Conference on Biological Ontology, Corvallis, OR. August 2016.<br />
<br />
* Lapp, H. (presenter) (2016) [http://www.slideshare.net/hlapp/rphenoscape-connecting-the-semantics-of-evolutionary-morphology-to-comparative-phylogenetics Rphenoscape: Connecting the semantics of evolutionary morphology to comparative phylogenetics]. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Lapp, H. (presenter) (2016) [https://docs.google.com/document/d/1mxthw6C0gZ6Ms3ULPz6eU0SfgYHlE75r5ozuhDwlDUs/edit?usp=sharing Evolutionary Morphology, computable: The Phenoscape KB]. Software Bazaar at 2016 iEvoBio Conference, Austin, TX. June 2016. <br />
<br />
* Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016. <br />
<br />
* Vision, T. (presenter) (2016) [http://doi.org/10.6084/m9.figshare.3380380 The reaggregation of primary research outputs: A case study from Phenoscape]. FORCE 2016, April 18, 2016. <br />
<br />
* Balhoff, J. (presenter) (2016) Data aggregation: Use of ontologies in phylogenetic matrix building. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 26, 2016.<br />
<br />
* Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Vision, T. (presenter) (2016) Data analysis: Semantic similarity of genes and taxa. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.<br />
<br />
* Jackson LM (presenter, poster), Fernando P, Balhoff JP, Mabee PM. (2016). Poster. Automated Integration of Morphological Data Sheds Light on Paired Fin Loss in Actinopterygian Fishes. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 2016.<br />
<br />
* Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Jackson, LM (presenter) (2016) Integration of Phenomics Data to Investigate Paired Fin Loss: OntoTrace Case Study for Teleost Fishes. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.<br />
<br />
* Manda, P. (presenter), Mungall C., Balhoff J., Lapp H. (2016) Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. Talk at the Pacific Symposium on Biocomputing, Hawaii. USA. January 5, 2016.<br />
<br />
=== 2015 ===<br />
* Mabee, P.M. (presenter) (2015). Progress in Comparative Morphology can be accelerated through Semantic Annotation. In: Symposium in memory of Donn E. Rosen: Assumptions that inhibit scientific progress in comparative biology. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Jackson, L (presenter, poster), Fernando, P., Balhoff, J, and P. Mabee. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 17, 2015.<br />
<br />
* Dahdul, W. (presenter) (2015). How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy? JMIH (Joint Meeting of Ichthyologists & Herpetologists). Reno, NV. USA. July 18, 2015.<br />
<br />
* Balhoff, J.P. (presenter, poster/talk), P. Manda, H. Lapp, P. Mabee, T.J. Vision. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG Phenotype Day at ISMB 2015. Dublin, Ireland. July 11, 2015.<br />
<br />
=== 2014 ===<br />
* Balhoff, J.P. (presenter), Dececchi, T.A., Mabee, P.M., Lapp, H. (2014). Presence-absence reasoning for evolutionary phenotypes. ISMB (Intelligent Systems for Molecular Biology). Boston. <br />
<br />
* Mabee, P. M., Dececchi, T.A. (presenter), and D. Blackburn. 2014. Matrix versus monograph: Comparison of phenotypic richness across data sources. Talk at 74th annual meeting of the Society of Vertebrate Paleontology. Berlin, Germany. November 8th 2014.<br />
<br />
* Mabee, P. M. Connecting evolutionary morphology and model organism genetics. Symposium "What should Bioinformatics do for Evodevo" (organized by G. Plickert, M. Blaxter, A. Burke, and P. Mabee) at EuroEvoDevo conference. Vienna, Austria. 24 July 2014.<br />
<br />
* Dahdul, W. M., T.A. Dececchi, N. Ibrahim, H. Lapp, P. Mabee. 2014. Moving the mountain: How to transform comparative anatomy into computable anatomy? Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Balhoff, J., T.A. Dececchi, H. Lapp, P. Mabee. [http://f1000.com/posters/browse/summary/1095873 Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data.] Poster at Evolution 2014, Raleigh, NC. June 23, 2014.<br />
<br />
* Mabee, P. M. Big Anatomy: The new views from integrated anatomy, development, and genes. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Dececchi, T. A.., Mabee P.M., and J. Balhoff. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences, American Association of Anatomists, Experimental Biology meetings, San Diego, CA. April 29, 2014.<br />
<br />
* Lapp H. [http://www.slideshare.net/hlapp/cshals-2014-keynote-31803361 Semantics of and for the diversity of life: Opportunities and perils of trying to reason on the frontier]. Keynote at the 2014 Conference on Semantics in Healthcare and Life Sciences (CSHALS). &nbsp;28 February 2014.<br />
<br />
* Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.<br />
<br />
=== 2013 ===<br />
* Balhoff, J., Dececchi, T.A., Mabee, P., Lapp, H. [http://www.slideshare.net/balhoff/semantic-tools-for-aggregation-of-morphological-characters-across-studies Semantic tools for aggregation of morphological characters across studies]. Annual conference of the Taxonomic Database Working Group. Florence, Italy (November 1 2013)<br />
<br />
* Sears, K.E., Marcot, J.D., Mabee, P.M., and T.A. Dececchi. Evolution and development of the limb: Evolution of appendage modularity during the fin to limb transition. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M., Dececchi, T.A., Ibrahim, N., Sereno, P., Balhoff, J.P. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Poster presentation. Society of Vertebrate Paleontology, Annual Meeting, Los Angeles, CA (October 31, 2013).<br />
<br />
* Mabee, P.M. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. Muséum national d'Histoire naturelle, Paris, France (October 24, 2013).<br />
<br />
* Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).<br />
<br />
* Mabee, P.M. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain (July 11, 2013).<br />
<br />
* Balhoff, J.P. [http://www.slideshare.net/balhoff/balhoff-i-evobio2013 Computing with phenotypic diversity using semantic descriptions]. iEvoBio Conference, 26 June 2013, Snowbird, Utah.<br />
<br />
* Mungall, C.J., Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte, Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzanna E Lewis, Paula Mabee, Anne Niknejad, Melissa A Haendel. A merger of multi‐species anatomy ontologies. Biocuration Conference, April 7-10, 2013, Cambridge, UK.<br />
<br />
* Vision, T. Towards an integrated system for computationally linking vertebrate skeletal evolution and development genetics. Department of Ecology and Evolution, University of Lausanne, 10 June 2013.<br />
<br />
* Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.<br />
<br />
* Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.<br />
<br />
=== 2012 ===<br />
<br />
* Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.<br />
<br />
* Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.<br />
<br />
* Dahdul, W., Balhoff, J., Blackburn, D., Diehl, A., Haendel, M., Hall, B., Lundberg, J., Mungall, C., Ringwald, M., Segerdell, E., Van Slyke, C., Vickaryous, M.K., Westerfield, M., Mabee, P. "VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Poster. Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012.<br />
<br />
* Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. Proceedings of the BioCreative workshop 2012 (pp.137-144).<br />
<br />
* Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative-2012 Workshop (April 4-5, 2012). Fifth International Biocuration Conference, Georgetown (Washington, D.C.). April 2-4, 2012. [poster and software demo]<br />
<br />
* Balhoff, J.P., Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012.<br />
<br />
* Catlett, J., Block, A., P. Mabee. Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Green, C., Block, A., P. Mabee. Development of the hindlimb and pelvic fin. Poster presentation. 2012 Science Festival- It’s All About Science, Sanford Research Center, July 28, 2012. Sioux Falls, SD. (also presented at the 2012 Sanford Summer Research Symposium, Sioux Falls, SD, August 2, 2012).<br />
<br />
* Mabee, P. M. "Synthesis of evolutionary and developmental data for fishes using new informatics tools' Oral presentation, World Congress of Herpetology, Vancouver, BC, August 8-14, 2012.<br />
<br />
* Sereno, P.C., Ibrahim, N., Mabee, P., Vision, T., Lapp, H. "Phenoscape: A New Anatomical Ontology of Vertebrates". Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Dececchi, T.A., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp., H., Midford, P., Sereno, P.C., Vision, T., Westerfield, M., Mabee, P., Blackburn., D. "Phenoscape: Bridging the gap between fossils and genes".Society of Vertebrate Paleontology, Annual Meeting, October 18, 2012.<br />
<br />
* Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).<br />
<br />
=== 2011 ===<br />
<br />
* Paula Mabee (2011) Presentation "Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology”, Muséum national d'Histoire naturelle, Paris, Nov. 8, 2011.<br />
<br />
* Todd Vision, Judith Blake, Hilmar Lapp, Paula Mabee, Monte Westerfield (2011) Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. First International Workshop on Linked Science, Bonn, October 24, 2011, [[Media:Vision.etal.LISC2011.pdf|Extended abstract]] from [http://www.ceur-ws.org/Vol-783/ Proceedings].<br />
<br />
* James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY, July 26-30, 2011<br />
<br />
* Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee; (2011) Presentation; "Phenoscape: use cases and anatomy ontology requirements for linking evolutionary and model organism phenotypes", ICBO workshop: From fins to limbs to leaves: Facilitating anatomy ontology interoperability; International Conference on Biomedical Ontology; University at Buffalo, NY; Poster, July 26-30, 2011<br />
<br />
* James P. Balhoff, Peter E. Midford, Hilmar Lapp (2011) International Conference on Biomedical Ontology, Buffalo, NY, [http://www.mendeley.com/download/public/2280031/4561422715/faae92a74742bc35ceca9b3f5862cb94a4cde61e/dl.pdf Integrating anatomy and phenotype ontologies with taxonomic hierarchies], July 2011.<br />
<br />
* J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) [http://www.slideshare.net/balhoff/the-phenoscape-knowledgebase Phenoscape Knowledgebase], Data integration challenge entry presentation for iEvoBio Conference 2011.<br />
<br />
* James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.<br />
<br />
* Paula Mabee (2011) Keynote talk for Fish Skeletal Meeting (Tavira, Portugal) "500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology." April 28, 2011.<br />
<br />
* <u>Hilmar Lapp</u> (2011) [[Media:UF_Seminar_Mar2011_HL.pdf|Reasoning over phenotype diversity, character change, and evolutionary descent]]. Invited seminar at University of Florida, March 1, 2011.<br />
<br />
* <u>James P. Balhoff</u> (2011) [http://www.iscb.org/cshals2011-program/cshals2011-full-agenda Conference on Semantics in Healthcare and Life Sciences], Cambridge, MA, "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies" February 24, 2011.<br />
<br />
* <u>Richard.C.Edmunds</u> (2011) Northwest Developmental Biology Meeting, Society for Developmental Biology, Friday Harbor, WA "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" March 17, 2011.<br />
<br />
* Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.<br />
<br />
=== 2010 ===<br />
<br />
* James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010<br />
<br />
* Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.<br />
<br />
* <u>Richard.C.Edmunds</u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "Using Phenoscape to Uncover the Genetic Basis of Evolutionary Phenotypes" July 10, 2010.<br />
<br />
* <u>Hilmar Lapp</u> (2010) [http://www.bioontology.org/phenoscape Bringing reason to phenotype diversity, character change, and common descent], Webex recording of NCBO Webinar, November 17, 2010.<br />
<br />
* <u>Paula Mabee </u> (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.<br />
<br />
* <u>Paula Mabee and Wasila Dahdul </u> (2010) Joint Meeting of Ichthyologists and Herpetologists, American Society of Ichthyology and Herpetology, Providence, RI, "New Tools for Study of Development and Evolution of the Fish Skeleton" July 11, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Sanford Health USD Biomedical Research Symposium, University of South Dakota, Vermillion, SD, "Linking phenotypes of species, mutants, and human diseases to genetics and evolution" May 14, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN ([http://www.collectionsweb.org http://www.collectionsweb.org]), New Orleans, LA, "Phenoscape integration", March 26, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.<br />
<br />
* <u>Paula Mabee</u> (2010), Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany, "Phenoscape: species phenotypes, genes, development...and environment", February 22, 2010.<br />
<br />
=== 2009 ===<br />
<br />
* <u>Todd Vision</u> (2009) [[Media:Iplant_ontologies_2009_11_22.pdf|Ontologies in Phenoscape: Morphology, Taxa and Evolution]], Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.<br />
<br />
* <u>Peter Midford</u>, Paula Mabee, Todd Vision, Hilmar Lapp, Jim Balhoff, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield (2009) [http://precedings.nature.com/documents/3594/version/1%7CPhenoscape: Ontologies for large multi-species phenotype datasets.] Poster at the [http://icbo.buffalo.edu/%7C 2009 International Conference on Biomedical Ontology] in Buffalo, NY, July 25, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Lapp_et_al_ISMB2009.pdf|Informatics obstacles for integrating evolutionary phenotype diversity with model organism data]]". Poster at the 2009 ISMB conference in Stockholm, Sweden.<br />
<br />
* <u>Todd Vision</u>, Jim Balhoff, Cartik Kothari, <u>Hilmar Lapp</u>, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "[[Media:Vision_et_al_eBiosphere09.pdf|Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies]]". Poster at the e-Biosphere09 conference in London, UK.<br />
<br />
* Mabee, P., J.P. Balhoff, W. Dahdul, C. Kothari, H. Lapp, J. Lundberg, P. Midford, T. Vision, M. Westerfield. Phenoscape: evolutionary morphology linked to genes using informatics. Poster at Joint Meeting of Ichthyologists and Herpetologists, Portland, OR, 2009.<br />
<br />
* <u>Hilmar Lapp</u>, Todd J. Vision. 2009. A gentle introduction to ontologies for biology. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Monte Westerfield</u>. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Paula Mabee</u>, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2009). 2009. Phenoscape: Using ontologies to link comparative morphology to genes. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.<br />
<br />
* <u>Wasila Dahdul</u>. 2009. The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes. Department of Biological Science seminar at California State University, Fullerton, CA. May 13, 2009.<br />
<br />
* <u>Paula Mabee</u>, Wasila Dahdul, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte Westerfield (2009) "[[Media:Mabee_et_al._Biocurator_09.pdf|PHENOSCAPE: Curation of evolutionary phenotypes using the MOD model]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.<br />
<br />
* <u>Wasila Dahdul</u>, Paula Mabee, John Lundberg, Peter Midford, Todd Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel, Monte Westerfield (2009) "[[Media:Dahdul_et_al._Biocurator_09.pdf|Developing a Multi-species Anatomy Ontology for Teleost Fishes]]". Poster at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009<br />
<br />
* <u>Jim Balhoff</u>, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "[[Media:EvoBioOnt_SICB09_Vision.pdf|Software and database resources for curation and management of evolutionary phenotypes]]". Presentation (by T. Vision) at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Wasila Dahdul</u> (2009) "[[Media:EvoBioOnt_SICB09_Dahdul.pdf|Challenges of developing multi-species anatomy ontologies]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
* <u>Paula Mabee</u> (2009) "[[Media:EvoBioOnt_SICB09_Mabee.pdf|Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes]]". Presentation at the [http://www.bioontology.org/wiki/index.php/Evolutionary_Biology_and_Ontologies_2009 2nd Evolutionary Biology and Ontologies workshop] in conjunction with the [http://www.sicb.org/meetings/2009/index.php3 Annual Meeting of the Society for Integrative and Comparative Biology (SICB)]. Boston, MA, January 5, 2009.<br />
<br />
=== 2008 ===<br />
<br />
* Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 18, 2008.<br />
<br />
* Paula Mabee, Jim Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008) “Phenoscape: Morphology linked to genes using ontologies” Poster presentation (by P. Mabee) at: [http://www.museum.tulane.edu/ctolafrica/ International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa] Grahamstown, South Africa, Nov. 17, 2008.<br />
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* Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at [http://174.133.140.86/ AmphibAnat workshop] St. Louis, MO, Nov. 7, 2008<br />
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* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). Linking evolutionary morphology to genomics using ontologies. Poster (presented by Wasila Dahdul) at the [http://www.vertpaleo.org/meetings/past.cfm Society of Vertebrate Paleontology Annual Meeting], Cincinnati, OH, October 2008<br />
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* Peter Midford (2008) [http://www.tdwg.org/fileadmin/2008conference/slides/Midford_06_02_TaxonomicOntologies.ppt Taxonomic ontologies: Bridging phylogenetic and taxonomic history.] Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, October 2008.<br />
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* Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield (2008). [[Media:Evolution2008-phenoscape.ppt|Linking evolutionary morphology to genomics using ontologies]]. Poster at the Evolution 2008 Conference, Minneapolis, MN, July 2008.<br />
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* Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) [[Media:Atol.march08.pdf|How to enable computable phenotypes?]] Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.<br />
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* Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" [http://www.biology.uiowa.edu/ATOL/index.htm http://www.biology.uiowa.edu/ATOL/index.htm] “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.<br />
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=== 2007 ===<br />
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* Todd Vision and Hilmar Lapp (2008) [http://www.nesc.ac.uk/esi/events/710/programme.cfm Prospects for enabling phylogenetically informed comparative biology on the web]. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 2007.<br />
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* Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P. Midford, T.J. Vision, M. Westerfield (2007) [[Media:Biocurator2007-phenoscape.ppt|Linking Evolution to Genomics Using Phenotype Ontologies]]. Poster at the [http://tesuque.stanford.edu/biocurator.org/Mtg2007/ 2nd Int. BioCurator Meeting], San Jose, California, Oct 2007.<br />
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[[Category:Curation]]<br />
[[Category:Community]]</div>Todd Visionhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Contact&diff=11872Contact2017-01-07T15:58:32Z<p>Todd Vision: /* Principal investigators */</p>
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<div>==Principal investigators==<br />
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* '''Paula Mabee''': Principal Investigator<br />
:University of South Dakota<br />
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* '''Todd Vision''': Principal Investigator<br />
:University of North Carolina<br />
:Email: [mailto:tjv%40bio%2eunc%2eedu tjv&#64;bio&#46;edu]<br />
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* '''David Blackburn''': Co-principal Investigator<br />
:University of Florida, Gainesville<br />
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* '''Judith Blake''': Co-principal Investigator<br />
:Mouse Genome Informatics - Jackson Laboratories<br />
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* '''[[User:Hlapp|Hilmar Lapp]]''': Co-principal Investigator<br />
:Duke University<br />
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* '''Paul Sereno''': Co-principal Investigator<br />
:University of Chicago<br />
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* '''Monte Westerfield''': Co-principal Investigator<br />
:University of Oregon Institute of Neuroscience<br />
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* '''Aaron Zorn''': Co-principal Investigator<br />
:Xenopus model organism database, Cincinnati's Children's Hospital Medical Center<br />
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==Mailing lists==<br />
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=== Public mailing lists ===<br />
<br />
The following mailing lists have publicly accessible archives (linked to from the URLs below) and all interested people can subscribe themselves at the given URLs.<br />
* Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress): http://lists.sourceforge.net/lists/listinfo/phenoscape-curators<br />
* Discussion of EQ formalism, phenotype description, PATO terms: [mailto:obo-phenotype%40lists%2e.sourceforge%2enet obo-phenotype@lists&#46;sourceforge&#46;net] - ''[https://lists.sourceforge.net/mailman/listinfo/obo-phenotype List subscription and archives]''<br />
* Anatomy ontology terms<br />
** General anatomy: [mailto:obo-anatomy%40lists%2e.sourceforge%2enet obo-anatomy&#64;lists&#46;sourceforge&#46;net] - ''[https://lists.sourceforge.net/mailman/listinfo/obo-anatomy List subscription and archives]''<br />
** RCN Vertebrate Working Group: [mailto:rcn-vertebrate-working-group%40googlegroups%2e.com rcn-vertebrate-working-group@googlegroups.com] - ''[https://groups.google.com/forum/?hl=en#!forum/rcn-vertebrate-working-group List subscription and archives]''<br />
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=== Project-only mailing lists ===<br />
<br />
The following mailing lists have private archives, and subscription is usually restricted to project personnel. However, anybody may send email to them; the email may be held for moderation, but legitimate (i.e., non-spam) postings will typically be released quickly.<br />
* Project-specific mailing list (reaches all PIs and coPIs, project team members, and those closely affiliated): [mailto:phenoscape%40nescent%2eorg phenoscape&#64;nescent&#46;org]<br />
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==Blog==<br />
<br />
* Phenoscape blog: http://blog.phenoscape.org/ You can subscribe to the blog so that you receive a notification each time a new post is published. Scroll down until you see the box titled "Subscribe via Email", enter your email address, and click "Subscribe".<br />
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[[Category:Community]]</div>Todd Vision