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The Phenoscape Knowledgebase (KB) is Phenoscape's flagship online resource. It contains evolutionary phenotype data from more than 150 comparative morphology studies, currently with a focus on the vertebrate fin-to-limb transition and comparative fish morphology. The KB offers programmable (API) access to natural language phenotype descriptions annotated with formal ontologies so that machines can understand and compute with the semantics of descriptions at scale. Using shared ontologies for morphological, spatial, and other requisite domain knowledge, the KB links these data to phenotypes reported in genetic perturbation studies for pertinent model organisms (zebrafish and mouse), and to human genetic disease phenotypes.

For query answering the KB uses machine reasoning to match data by its semantics. The API also gives access to other machine reasoning-based algorithms. These include synthesizing characters and states that are implied by but not expressly asserted in the original studies; and finding evolutionary phenotype transitions semantically similar to gene phenotypes.

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