Edit this page on GitHub
Publications and Posters
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
2024
- Girón Duque, J.C., Balk, M., Dahdul, W., Lapp, H., Mikó, I., Alhajjar,
E., Wynd, B., Tarasov, S., Lawrence, C., Khakurel, B., Porto, A., Yan,
L., E Fluck, I., Porto, D., Keating, J., Borokini, I., Seltmann, K.,
Montanaro, G., Mabee, P. (2024) Meeting Report for the Phenoscape
TraitFest 2023 with Comments on Organising Interdisciplinary Meetings.
Biodiversity Information Science and Standards 8: e115232.
https://doi.org/10.3897/biss.8.115232
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
- 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.
- Peter Midford, 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
2009 International Conference on Biomedical
Ontology in Buffalo, NY, July 25, 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.
- Paula Mabee, Wasila Dahdul, John Lundberg, Peter Midford, Todd
Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Monte
Westerfield (2009)
“PHENOSCAPE:
Curation of evolutionary phenotypes using the MOD model”. Poster
at the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009.
- Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Todd
Vision, Hilmar Lapp, Jim Balhoff, Cartik Kothari, Melissa Haendel,
Monte Westerfield (2009)
“Developing
a Multi-species Anatomy Ontology for Teleost Fishes”. Poster at
the 2009 Biocurator Conference in Berlin, Germany. April 18, 2009
2008
- 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: International Workshop Enhancing
Freshwater Fish Biodiversity Research in
Africa Grahamstown, South
Africa, Nov. 17, 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
- 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 at
the Evolution 2008 Conference, Minneapolis, MN, July 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
- Paula Mabee, J.P. Balhoff, W. Dahdul, H. Lapp, J. Lundberg, P.
Midford, T.J. Vision, M. Westerfield (2007)
Linking
Evolution to Genomics Using Phenotype Ontologies. Poster at the
2nd Int. BioCurator
Meeting, San
Jose, California, Oct 2007.
