Publications and Posters

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Publications

  • 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
  • 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
  • Washington, N.L., C.J. Mungall, M.Gibson, J.P. Balhoff, J. Day-Richter, and S. Lewis. Phenote: A biological data annotation editor using ontologies. Submitted
  • 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. doi:10.1093/sysbio/syq013
  • 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.
  • Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007 Jul; 22(7) 345-50. doi:10.1016/j.tree.2007.03.013
  • Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol 2007 Jun 28. doi:10.1002/jez.b.21181

Posters & Presentations

2009

Todd Vision (2009) Ontologies in Phenoscape: Morphology, Taxa and Evolution, Presentation at the iPlant Tree of Life Data Assembly Meeting, Phoenix, AZ, Nov 22, 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) Ontologies for large multi-species phenotype datasets. Poster at the 2009 International Conference on Biomedical Ontology in Buffalo, NY, July 25, 2009.

Hilmar Lapp, Jim Balhoff, Cartik Kothari, Todd Vision, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "Informatics obstacles for integrating evolutionary phenotype diversity with model organism data". Poster at the 2009 ISMB conference in Stockholm, Sweden.

Todd Vision, Jim Balhoff, Cartik Kothari, Hilmar Lapp, Wasila Dahdul, Paula Mabee, John Lundberg, Peter Midford, Monte Westerfield (2009) "Phenoscape: Linking phenotypic biodiversity to model organism genetics using ontologies". Poster at the e-Biosphere09 conference in London, UK.

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

Jim Balhoff, Cartik Kothari, Hilmar Lapp, Todd Vision (2009) "Software and database resources for curation and management of evolutionary phenotypes". Presentation (by T. Vision) at the 2nd Evolutionary Biology and Ontologies workshop in conjunction with the Annual Meeting of the Society for Integrative and Comparative Biology (SICB). Boston, MA, January 5, 2009.

Wasila Dahdul (2009) "Challenges of developing multi-species anatomy ontologies". Presentation at the 2nd Evolutionary Biology and Ontologies workshop in conjunction with the Annual Meeting of the Society for Integrative and Comparative Biology (SICB). Boston, MA, January 5, 2009.

Paula Mabee (2009) "Phenoscape: Extending model organism ontologies for devo-evo studies of evolutionary phenotypes". Presentation at the 2nd Evolutionary Biology and Ontologies workshop in conjunction with the Annual Meeting of the Society for Integrative and Comparative Biology (SICB). Boston, MA, January 5, 2009.

2008

Paula Mabee (2008) “Phenoscape: Bridging systematics and genetics with ontologies”. Panel presentation at “Establishing Fish Collections and Other Biodiversity Research Resources in Africa Countries” as part of International Workshop Enhancing Freshwater Fish Biodiversity Research in Africa Grahamstown, South Africa, Nov. 18, 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

Peter Midford (2008) Taxonomic ontologies: Bridging phylogenetic and taxonomic history. Presentation at the 2008 TDWG Conference, Fremantle, Western Australia, 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

Todd Vision and Hilmar Lapp (2008) Prospects for enabling phylogenetically informed comparative biology on the web. e-Science Institute PhyloInformatics Workshop, Edinburgh, UK, October 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.

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