Phenoscape curation
PI(s): | Wasila Dahdul (University of South Dakota) |
Start Date: | 1-Sep-2008 |
Keywords: |
What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach this question due to a lack of computational tools that allow researchers to integrate developmental genetic and comparative morphological/anatomical data. We are addressing this by developing a database of evolutionarily variable morphological characters for a large clade of fishes (the Ostariophysi) and connecting this database to the large collection of mutant phenotypes in the ZFIN database, the central database of the zebrafish model organism community. The evolutionary and mutant phenotypes are being described using common ontologies. The database with its web-interface, called EQSYTE (Entity-Quality System for Trait Evolution), together with the extended ontologies and data curation tools, will allow researchers to ask novel questions about the genetic and developmental regulation of evolutionary morphological transitions. Tool and database development are being guided by use cases, or driving research questions, defined by the devo-evo community. These tools are being developed under an open-source, open-development model, and in such a way that they can be used for additional biological systems in the future.
This project is a unique collaboration between evolutionary and model organism biologists including two national centers (NESCent and NCBO), the ZFIN model organism database, the Cypriniformes Tree of Life project, the DeepFin Research Coordination Network, and the morphological image databases used by the evolutionary biology community (Morphbank, MorphoBank, DigiMorph, Digital Fish Library).
For further information about this project please visit http://www.phenoscape.org
Related products
Publications- Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize and Aaron 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, volume 4, issue 1, pp. 31
- A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia J. P. Balhoff, I. Miko, M. J. Yoder, P. L. Mullins and A. R. Deans. 2013. A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia, Systematic Biology, volume 62, issue 5, pp. 639-659
- A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation Patricia Mullins, Ricardo Kawada, James Balhoff and Andrew Deans. 2012, A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation, ZooKeys, volume 223, issue 0, pp. 1-38
- A Unified Anatomy Ontology of the Vertebrate Skeletal System Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield, Paula M. Mabee and Marc Robinson-Rechavi. 2012. A Unified Anatomy Ontology of the Vertebrate Skeletal System, PLoS ONE, volume 7, issue 12, pp. e51070
- Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment M. A. Bertone, I. Miko, 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, volume 2013, issue 0, pp. bas057-bas057
- Minard, A. 2009. Yard-long Megapiranha Fossil Found. National Geographic News. http://news.nationalgeographic.com/news/2009/06/photogalleries/giant-piranha-pictures-evolution/
- Flam, Faye. 2009. Unearthing the megapiranha. Philadelphia Inquirer. http://www.philly.com/inquirer/magazine/20090706_Unearthing_the_megapiranha.html
- Fields, H. 2009. ScienceNOW Daily News: How the Piranha Got Its Teeth. Science. http://sciencenow.sciencemag.org/cgi/content/full/2009/629/1
- 2009. Toothy 3-foot piranha fossil found: Remains bridge evolutionary gap between flesh eaters and plant eaters. MSNBC News. http://www.msnbc.msn.com/id/31553901/ns/technology_and_science-science/
- 2009. Huge 'Megapiranha' fossil found in South America. Fox News. http://www.foxnews.com/story/0,2933,529195,00.html