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About the Phenoscape Knowledgebase

The Phenoscape Knowledgebase is an expert system that enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms.

Rationale

Decades of comparative anatomical studies have resulted in a rich body of "free-text" data. As these data grow, they are increasingly hard to align and synthesize across taxonomic groups, and synthetic questions concerning the developmental and genetic basis of evolutionary changes in morphology cannot be easily or efficiently addressed. To analyze this volume of comparative anatomical data in a developmental genetic context, it must first be rendered computable. This can be achieved using ontologies, constrained structured vocabularies with logical relationships among terms.

Data

With the broader ichthyological community, we have developed two ontologies, the Teleost Anatomy Ontology and the Teleost Taxonomy Ontology that were used along with several other ontologies to represent systematic characters. To date, over 4,500 characters from a comprehensive set of phylogenetic papers for Ostariophysi (a monophyletic group of ~8,300 teleost fishes) were represented using combinations of ontology terms and software for data curation (Phenex).

PhenoscapeKB combines these evolutionary phenotypes with information about genetically characterized phenotypes from ZFIN, the zebrafish community database. Through ontology-based reasoning over expert knowledge in taxonomy, comparative anatomy and developmental genetics, PhenoscapeKB can be used to address a host of questions spanning the domains of genetics, development and evolutionary biology, such as the nature of the genetic changes underlying phenotypic variation among taxa in nature.

Data availability

The Phenoscape Knowledgebase is intended to enhance knowledge and progress in the scientific community. For this reason, the contents are made available according to the terms of a Creative Commons Attribution 3.0 Unported license. This license allows any party to distribute, reuse, and derive works from the data for commercial or non-commercial uses provided that appropriate attribution is given. Any contents to which this license does not apply (such a copyrighted images provided by third parties) are specifically marked as such. Contributions to Phenoscape are predominantly based on data reported in the published literature; the copyright to the original publication remains with the original owner, and contributors to the database are individually acknowledged. Users are requested to cite the original paper (or, in some cases, unpublished manuscript) from which the data were derived, as well as a citation of the following form:

PhenoscapeKB, [U.S. National Evolutionary Synthesis Center], http://kb.phenoscape.org; [Date on which data was retrieved].

Data downloads and query API

Data in the Knowledgebase can be queried and downloaded in bulk via our documented web service API. Data can be returned in either JSON or spreadsheet (tab-delimited) formats. Source data files can be downloaded directly from our Subversion repository.

More Information

For further information about the Phenoscape project and project partners, please see our project wiki.

Technology

Database and web services

Web application

Source Code

Publications

Contact

For questions about the database or interface, please contact Phenoscape help at the National Evolutionary Synthesis Center: Email us

For questions about the Phenoscape project, contact one of the lead PIs, Paula Mabee or Todd Vision