About the KB

The Phenoscape Knowledgebase (KB) is a centralized repository of phenotype annotations for vertebrates linked to model organism genetics data in a shared semantic framework. The KB contains natural language phenotype descriptions from more than 250 comparative morphology studies, with a current focus on the vertebrate fin-to-limb transition and comparative fish morphology, annotated with terms from formal ontologies (i.e., logical descriptions of phenotype concepts linked in a graph) so that machines can understand and compute on semantic (ontological) descriptions at scale. This enables discovery as the logic underlying ontologies can surface relationships between traits that were previously unknown using traditional methods.

The KB is built on the RDF and OWL semantic web standards and consists of a back-end datastore, web services which provide a query API allowing exploration of the KB, and accessory tools for loading data. The API also gives access to other machine reasoning-based algorithms, such as inferring characters and states that are implied but not necessarily asserted in original studies, facilitating finding evolutionary phenotype transitions semantically similar to gene phenotypes.

The current Phenoscape subproject, SCATE (Semantics for Comparative Analysis of Trait Evolution), is creating infrastructure that provides comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions.

Further details, including relevant publications, KB data model, and API documentation can be found at Learning about the KB.