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- “Phenex: Ontological Annotation of Phenotypic Diversity” will be published in PLoS ONE on Wednesday, May 5th
- “Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature” will be published in PLoS ONE on Thursday, May 20th (at that time see: http://dx.plos.org/10.1371/journal.pone.0010708)
- We recently held a Skeletal Anatomy Jamboree on April 9-10, 2010 at NESCent, where we re-evaluated the high-level skeletal system ontology hierarchy for fishes, and initiated a skeletal anatomy ontology for vertebrates.
- Our paper describing the development of the Teleost Anatomy Ontology was just published in Systematic Biology
- In March we held a workshop at the Field Museum of Natural History
- Check out the Beta version of the Phenoscape Knowledgebase!
- Phenex 1.0, our free and open-source software for ontology-based curation of phenotypic character matrices, was publicly released in November 2009.
- Check out the Phenoscape blog!
Contents
Linking Evolution to Genomics Using Phenotype Ontologies
About this project
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, 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).
The Role of Ontologies
Background
Ontologies are constrained, structured vocabularies with well defined relationships among terms. Ontologies represent the knowledge of a particular discipline and provide not only a mechanism for consistent annotation of data, but also greater interoperability among people and machines. The most widely used biological ontology is the Gene Ontology, which is utilized to annotate molecular function, biological processes and subcellular localization to gene products from different organisms.
Phenotype ontologies
Approximately 500 mutant zebrafish lines (alleles) with over 660 annotated phenotypic characters from the jaw or gill arches (n=250), fins (n=210), axial skeleton (n=190) and other features (n=10) of the skeleton have been described. Curators in the Zebrafish Information Network (ZFIN) are annotating mutant phenotypes using the zebrafish anatomy ontology and the Phenotype And Trait Ontology (PATO). PATO is a “universal” ontology of terms describing qualities (e.g. shape, color, size) that may be applied to any organism.
Anatomical ontologies
We have initiated a multi-species ontology for ostariophysan fishes, the Teleost Anatomy Ontology (TAO), which was initialized with the terms in the zebrafish anatomical ontology. The development of the TAO is currently focused on the skeletal system because it varies significantly across the Ostariophysi, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology.
This multi-species anatomy ontology is being used in combination with the PATO ontology (see EQ format) to describe the comparative morphological characters. We have also developed a separate catalog of homology statements for entities within the TAO, so that individual investigators may select particular relationships based on evidence.
Taxonomic ontology
Together with taxonomic experts, we have developed a taxonomic ontology (based on the Catalog of Fishes) to relate species with particular characters and states. The taxonomic ontology will include nodes ancestral to the Ostariophysi as far back as the Vertebrata in order to associate certain anatomical terms with more inclusive clades than the Ostariophysi.
Fish Morphology
Although the comparative anatomy of fishes has been documented in the literature for several hundred years, it is not available in a computable format. With the help of taxon experts for ostariophysan fishes, we have prioritized 76 papers for immediate curation. They are ranked as “A” papers on our publicly available Google spreadsheet. Our goal is to input approximately 4,000 morphological features in an “EQ” format (Mabee et al. 2007a) using a combination of ontologies.
Contact
Paula Mabee (University of South Dakota) is the Principal Investigator. Co-principal investigators are Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon, ZFIN), and Hilmar Lapp (NESCent) (see their contact addresses).
Acknowledgments
| This project is funded by NSF grant BDI-0641025, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0423641. This project arose from a NESCent Working Group led by Paula Mabee and Monte Westerfield, "Towards an Integrated Database for Fish Evolution." Goals and summaries of the group are archived on this wiki. |
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