Difference between revisions of "Publications and Posters"

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* 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).  
 
* 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).  
 
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)
 
* Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)
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* 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)  
+
* 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)
−
* 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)
+
* Data modeling, reasoning & ontologies: Mabee et al. (2020),  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)
  
 
== Publications by date ==
 
== Publications by date ==
 +
===2023===
 +
*Porto, D.S., Tarasov, S., Charpentier, C., Lapp, H., Balhoff, J.P., Vision, T.J., Dahdul W.M., Mabee, P.M., and Uyeda, J. (2023) rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits. Methods in Ecology and Evolution 14:2531-2540 doi: https://doi.org/10.1111/2041-210X.14210
 +
 +
===2022===
 +
*Porto, D.S., Dahdul, W.M., Lapp, H., Balhoff, J.P., Vision, T.J., Mabee, P.M., and Uyeda, J. (2022) Assessing bayesian phylogenetic information content of morphological data using knowledge from anatomy ontologies. Systematic Biology. https://doi.org/10.1093/sysbio/syac022
 +
 +
*Tarasov, S., and Uyeda, J.. (2022) Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution. bioRxiv 2022.07.04.498736; doi: https://doi.org/10.1101/2022.07.04.498736
 +
 +
===2021===
 +
* Fernando, P.C., Mabee, P.M., Zeng, E. (2021) Gene network module changes associated with the vertebrate fin to limb transition. bioRxiv 2021.01.28.428646; doi: https://doi.org/10.1101/2021.01.28.428646
 +
 +
===2020===
 +
*Fernando, P.C., Mabee, P.M. and E. Zeng. (2020) Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. BMC Bioinformatics 21, 442. https://doi.org/10.1186/s12859-020-03773-2
 +
*Porto, D.S., Alameida, E.A., and M.W. Pennell. (2020) Investigating morphological complexes using informational dissonance and Bayes Factors: A case study in corbiculate bees. Systematic Biology 70(2):295–306, https://doi.org/10.1093/sysbio/syaa059
 +
*Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., and T.J. Vision. (2020) A logical model of homology for comparative biology. Systematic Biology. 69(2):345–362, https://doi.org/10.1093/sysbio/syz067
 +
 +
===2019===
 +
*  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.
 +
 
===2018===
 
===2018===
−
*  Manda P, Vision T (2018) An analysis and comparison of the statistical sensitivity of semantic similarity metrics. bioRxiv https://doi.org/10.1101/327833
+
* 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
−
*  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
+
*  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)
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* 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
+
*  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
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* 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.
+
* 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
−
* 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.
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* 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
 +
* 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.
  
 
===2017===
 
===2017===
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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]
 
*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]
  
−
*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]
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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]
  
 
*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]
 
*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]
  
 +
===2013===
 
*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].
 
*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].
  
−
===2013===
 
 
*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]
 
*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]
  
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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]
 
*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]
 +
 +
*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]
  
 
===2012===
 
===2012===
−
*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]
 
−
 
 
*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]
 
*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]
  
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== Posters & Presentations ==
 
== Posters & Presentations ==
 +
===2022===
 +
* Porto, D.S., Tarasov, D., Charpentier, C., Dahdul, W., Lapp, H., Balhoff, J., Vision, T., Mabee, P., & Uyeda, J. rphenoscate: An R package for semantic-aware comparative analyses of organismal phenotypes. Annual Meeting of the Willi Hennig Society; 2022 July 24-28; Helsinki, Finland.
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* Lapp, H., Bradley, J., Xu, H., Rathee, A., Balhoff, J., and Dahdul, W. (2022). RPhenoscape: Semantic computing with morphological traits and ontologies. Bioinformatics Open Source Conference 2022, as part of ISMB 2022; 2022 July 14; Madison, WI
 +
* Lovill, K., Porto, D.S., Wasila, D., and Uyeda, J. (2022). Exploring Ontological Knowledge to Study Miniaturization in Ostariophysi Fish. Poster presented at: Dennis Dean Undergraduate Research and Creative Scholarship Conference; 2022 April 29; Blacksburg, VA.
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 +
===2021===
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* Porto, D (presenter), W Dahdul, H Lapp, J Balhoff, T Vision, P Mabee, J Uyeda. (2021) Assessing Phylogenetic information content of anatomy ontologies. Evolution 2021, virtual, June 22, 2021.
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=== 2019 ===
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* Uyeda, J. (2019) The Measurement of Macroevolutionary Causes. Emerging Leader Invited Plenary Talk, SouthEastern Population Ecology and Evolutionary Genetics Conference, Clemson, SC.
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* Tarasov S, Miko I, Yoder M, and Uyeda J. (2019) Exploring and reconstructing ancestral anatomies using ontology-informed approaches. In session: Exploring Biodiversity Knowledge by Ontologies, Biodiversity Next meeting, Leiden, Netherlands, October 22, 2019. https://doi.org/10.3897/biss.3.37038
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* Mabee, P. (2019) Answering research questions requires semantic traits. In session: Operationalizing Trait-Based Biodiversity, Biodiversity Next meeting, Leiden, Netherlands, October 24, 2019. https://doi.org/10.3897/biss.3.37567
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* Uyeda J, Tarasov, S (2019) Extracting meaning from phylogenetic comparative methods: The necessity of considering process. Evolution 2019, Providence RI, June 25, 2019.
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* 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
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* 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.
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* 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.
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* Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Center for Biodiversity Analysis, Australian National University, Canberra, Australia. April 1, 2019.
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* 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.
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* Mabee, P. (2019) Trait ontologies: logical links across biodiversity. Plant Traits Workshop. Royal Botanic Garden, Sydney, Australia. March 27, 2019.
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* 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.
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* 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.
 +
 
=== 2018 ===
 
=== 2018 ===
 +
* 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.
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* Uyeda, J.C. (presenter, poster) (2018). On the need for phylogenetic natural history. Evolution 2018, Montpellier, France. August 21, 2018.
 +
* 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
 +
* 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
 +
* 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.
 
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.
 
* Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.
 +
* 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.
 +
* 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.
 +
* 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.
 +
* 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.
  
−
* 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.
+
=== 2017 ===
  
−
* 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.
+
* 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.
−
 
 
−
=== 2017 ===
 
  
−
* 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.
+
* 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.
  
 
* 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.
 
* 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.

Revision as of 22:42, 17 November 2023

Publications by category

  • 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)
  • 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).
  • Software: Balhoff (2016), Balhoff et al. (2014), Balhoff et al (2010)
  • 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)
  • Data modeling, reasoning & ontologies: Mabee et al. (2020), 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)

Publications by date

2023

  • Porto, D.S., Tarasov, S., Charpentier, C., Lapp, H., Balhoff, J.P., Vision, T.J., Dahdul W.M., Mabee, P.M., and Uyeda, J. (2023) rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits. Methods in Ecology and Evolution 14:2531-2540 doi: https://doi.org/10.1111/2041-210X.14210

2022

  • Porto, D.S., Dahdul, W.M., Lapp, H., Balhoff, J.P., Vision, T.J., Mabee, P.M., and Uyeda, J. (2022) Assessing bayesian phylogenetic information content of morphological data using knowledge from anatomy ontologies. Systematic Biology. https://doi.org/10.1093/sysbio/syac022
  • Tarasov, S., and Uyeda, J.. (2022) Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution. bioRxiv 2022.07.04.498736; doi: https://doi.org/10.1101/2022.07.04.498736

2021

2020

  • Fernando, P.C., Mabee, P.M. and E. Zeng. (2020) Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. BMC Bioinformatics 21, 442. https://doi.org/10.1186/s12859-020-03773-2
  • Porto, D.S., Alameida, E.A., and M.W. Pennell. (2020) Investigating morphological complexes using informational dissonance and Bayes Factors: A case study in corbiculate bees. Systematic Biology 70(2):295–306, https://doi.org/10.1093/sysbio/syaa059
  • Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., and T.J. Vision. (2020) A logical model of homology for comparative biology. Systematic Biology. 69(2):345–362, https://doi.org/10.1093/sysbio/syz067

2019

  • 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.

2018

  • 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
  • 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)
  • 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
  • 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
  • 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
  • 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.

2017

2016

  • Balhoff, J.P. 2016. Scowl: a Scala DSL for programming with the OWL API. The Journal of Open Source Software. doi:10.21105/joss.00023
  • 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. doi:10.1371/journal.pone.0155680
  • 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. doi:10.1093/molbev/msv223
  • 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. doi:10.1371/journal.pone.0149102
  • 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 doi:10.1186/s13326-016-0088-7

2015

  • Balhoff JP, Manda P, Lapp H, Mabee P, Vision TJ 2015 Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Bio-ontologies SIG at ISMB 2015
  • 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. PDF
  • 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:10.1093/database/bav040
  • 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
  • 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. doi:10.1093/sysbio/syv031
  • 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://dx.doi.org/10.1002/dvg.22878
  • 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
  • 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

2014

  • 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
  • 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
  • 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
  • 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. doi:10.1126/science.1258750

2013

  • 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.
  • 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
  • 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.
  • 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
  • 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

2012

  • 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
  • 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
  • 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
  • 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

2011

  • 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 PDF

2010

  • 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. doi:10.1371/journal.pone.0010500
  • 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. doi:10.1371/journal.pone.0010708
  • 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. doi:10.1093/sysbio/syq013

2008

  • Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. 2008. 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.

2007

  • 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.  doi:10.1002/jez.b.21181
  • 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. doi:10.1016/j.tree.2007.03.013

Posters & Presentations

2022

  • Porto, D.S., Tarasov, D., Charpentier, C., Dahdul, W., Lapp, H., Balhoff, J., Vision, T., Mabee, P., & Uyeda, J. rphenoscate: An R package for semantic-aware comparative analyses of organismal phenotypes. Annual Meeting of the Willi Hennig Society; 2022 July 24-28; Helsinki, Finland.
  • Lapp, H., Bradley, J., Xu, H., Rathee, A., Balhoff, J., and Dahdul, W. (2022). RPhenoscape: Semantic computing with morphological traits and ontologies. Bioinformatics Open Source Conference 2022, as part of ISMB 2022; 2022 July 14; Madison, WI
  • Lovill, K., Porto, D.S., Wasila, D., and Uyeda, J. (2022). Exploring Ontological Knowledge to Study Miniaturization in Ostariophysi Fish. Poster presented at: Dennis Dean Undergraduate Research and Creative Scholarship Conference; 2022 April 29; Blacksburg, VA.

2021

  • Porto, D (presenter), W Dahdul, H Lapp, J Balhoff, T Vision, P Mabee, J Uyeda. (2021) Assessing Phylogenetic information content of anatomy ontologies. Evolution 2021, virtual, June 22, 2021.

2019

  • Uyeda, J. (2019) The Measurement of Macroevolutionary Causes. Emerging Leader Invited Plenary Talk, SouthEastern Population Ecology and Evolutionary Genetics Conference, Clemson, SC.
  • Tarasov S, Miko I, Yoder M, and Uyeda J. (2019) Exploring and reconstructing ancestral anatomies using ontology-informed approaches. In session: Exploring Biodiversity Knowledge by Ontologies, Biodiversity Next meeting, Leiden, Netherlands, October 22, 2019. https://doi.org/10.3897/biss.3.37038
  • Mabee, P. (2019) Answering research questions requires semantic traits. In session: Operationalizing Trait-Based Biodiversity, Biodiversity Next meeting, Leiden, Netherlands, October 24, 2019. https://doi.org/10.3897/biss.3.37567
  • Uyeda J, Tarasov, S (2019) Extracting meaning from phylogenetic comparative methods: The necessity of considering process. Evolution 2019, Providence RI, June 25, 2019.
  • 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
  • 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.
  • 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.
  • Mabee, P. (2019) Integrating traits across genes and trees: a semantic approach. Center for Biodiversity Analysis, Australian National University, Canberra, Australia. April 1, 2019.
  • 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.
  • Mabee, P. (2019) Trait ontologies: logical links across biodiversity. Plant Traits Workshop. Royal Botanic Garden, Sydney, Australia. March 27, 2019.
  • 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.
  • 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.

2018

  • 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.
  • Uyeda, J.C. (presenter, poster) (2018). On the need for phylogenetic natural history. Evolution 2018, Montpellier, France. August 21, 2018.
  • 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
  • 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
  • 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.
  • Mabee, P.M. (2018). Phenotyped. Second Annual Digital Data in Biodiversity Research Conference, UC Berkeley Campus, June 4, 2018.
  • 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.
  • 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.
  • 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.
  • 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.

2017

  • 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.
  • 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.
  • 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.
  • 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. doi:10.6084/m9.figshare.5262868.v1
  • 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.
  • 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.
  • 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) doi: 10.7490/f1000research.1114056.1
  • 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.
  • 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. doi:10.7490/f1000research.1113878.1
  • 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. doi:10.7490/f1000research.1113805.1
  • Mabee, PM. (2017). Ontology-enabled reasoning across phenotypes from evolution and model organisms. George Washington University. Washington, D.C. March 3, 2017.
  • 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.

2016

  • 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.
  • 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.
  • Mabee, P. (presenter) (2016) Phenotypes, Databases and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.
  • Balhoff, J. (presenter) (2016) Reasoning with Phenotypes and Ontologies, The Loci of Evolution Meta-Analysis Workshop, Paris, September 5, 2016.
  • 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.
  • Mabee, P. (presenter) (2016) Inference Expands Morphological Data: Filling in the “Unknown Knowns”. 2016 Evolution Meetings, Austin, TX. June 2016.
  • 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.
  • 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.
  • Dahdul, W. (presenter) (2016) Integration challenges: integrating phylogenetic and phenotypic data. Fifth Annual Summit Meeting of the Phenotype RCN, Tucson, AZ. February 27, 2016.
  • 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.
  • 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.
  • Dahdul, W (presenter) (2016) Phenoscape: computable phenotypes for comparative biology. FuturePhy Workshop, University of Florida, Gainesville, FL; February 2016.
  • 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.
  • 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.

2015

  • 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.
  • 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.
  • 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.
  • 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.

2014

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Mabee, P. M. Anatomy in the genomics age. Seminar to Department of Biology, Salisbury University, MD. 27 February 2014.

2013

  • 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).
  • 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).
  • 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).
  • Balhoff, J.P. Introduction to OWL. INCF Cross-Program Meeting, Karolinska Institute, Stockholm, Sweden (August 30, 2013).
  • 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).
  • 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.
  • 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.
  • Vision, T. Prospects for computational assistance of phenotype curation in Phenoscape, Third annual summit meeting, Phenotype RCN. 25 March 2013, NESCent, NC.
  • Cui, H., et al. 2013. CharaParser and associated software. Pro-ibiosphere workshop. Leiden, the Netherlands, Feb 2013.

2012

  • Balhoff, J.P. "Linking phenotypes using ontologies." Invited seminar, California Academy of Sciences, March 28, 2012.
  • Vision T. "Phenotypes, descriptive data, and measuring similarity using structured vocabularies". Invited seminar, University of Gottingen, March 8, 2012.
  • 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.
  • 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).
  • 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]
  • 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.
  • 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).
  • 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).
  • 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.
  • 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.
  • 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.
  • Ibrahim, N. "Dinosaurs of the Sahara". Department of Biology, University of South Dakota, Vermillion (December 3, 2012).

2011

  • 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.
  • 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, Extended abstract from Proceedings.
  • 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
  • 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
  • J . Balhoff, W. Dahdul, H. Lapp, P. Mabee, P. Midford, T. Vision, M. Westerfield (2011) Phenoscape Knowledgebase, Data integration challenge entry presentation for iEvoBio Conference 2011.
  • James P. Balhoff and Hilmar Lapp (2011) Phenotype RCN Meeting, Boulder, CO, "The challenge of expressive reasoning over large knowledgebases", June 1, 2011.
  • 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.
  • Richard.C.Edmunds (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.
  • Monte Westerfield (2011) Phenotype Ontology Project Meeting, Berlin, "Update on Phenoscape", Germany, February 11-14, 2011.

2010

  • James P. Balhoff (2010) iEvoBio Conference, Portland, OR, "Phenex: Ontological Annotation of Phenotypic Diversity", June 29, 2010
  • Monte Westerfield (2010) Vertebrate Anatomy Workshop, Hinxton, UK, "Anatomy Representation in Phenoscape", June 25-29, 2010.
  • Richard.C.Edmunds (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.
  • Paula Mabee (2010) Hymenoptera Anatomy Ontology meeting, Raleigh, NC, "Phenoscape: Integration with ontologies" October 16, 2010.
  • Paula Mabee and Wasila Dahdul (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.
  • Paula Mabee (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.
  • Paula Mabee (2010), Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, NSF Collections Web RCN (http://www.collectionsweb.org), New Orleans, LA, "Phenoscape integration", March 26, 2010.
  • Paula Mabee (2010), Informatics tools for integrating morphological data, Encyclopedia of Life and Phenoscape (via NSF), Field Museum of Natural History, Chicago, IL, March 19, 2010.
  • Paula Mabee (2010), Phenotype and Trait Ontology Workshop, PATO (NIH funded), Rome, Italy, "Phenoscape and use of the PATO ontology", February 27, 2010.
  • Paula Mabee (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.

2009

  • Paula Mabee (2009) Introduction to Phenoscape and relation to AmphibAnat. Presentation at the AmphibAnat Meeting, Kansas City, KS Nov. 6, 2009.
  • 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.
  • Hilmar Lapp, 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.
  • Monte Westerfield. 2009. Linking animal models and human diseases. 'Ontologies for Ichthyology and Herpetology' symposium. Joint Meeting of Ichthyologists and Herpetologists, Portland, OR. July 25, 2009.
  • Paula Mabee, 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.
  • Wasila Dahdul. 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.

2008

  • Paula Mabee (2008). "Introduction to Phenoscape, annotation and ontologies". Presentation at AmphibAnat workshop St. Louis, MO, Nov. 7, 2008
  • 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 Society of Vertebrate Paleontology Annual Meeting, Cincinnati, OH, October 2008
  • Todd Vision, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield (2008) How to enable computable phenotypes? Assembling the Tree of Life Principal Investigators Meeting, Hilton St. Charles, New Orleans, LA, March 2008.
  • Paula Mabee. Keynote presentation at the NSF conference "Where to Next with the Tree of Life?" http://www.biology.uiowa.edu/ATOL/index.htm “Development of an Informatics System to bridge AToL and Evo-Devo”. April 4, 2008.

2007

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