The Phenoscape Knowledgebase is currently in BETA testing - we would greatly value your feedback as we continue its development.The Phenoscape Knowledgebase is currently in BETA testing - we would greatly value your feedback as we continue its development.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.
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.
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 phenotype from zfin.org, 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.
We are working on making Knowledgebase data downloads available in NeXML and spreadsheet (tab-delimited) formats. Some background on the data repository can be found here. Source data files can be downloaded directly from our Subversion repository.
For further information about the Phenoscape project and project partners, please see our project wiki.
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 the PI, Paula Mabee, by email or phone: 605-677-6171