xu-hong/rphenoscape: Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase

Provides convenient access to the data, ontologies, and semantics-based analytics offered by the Phenoscape Knowledgebase (KB) API. The KB integrates morphological trait data curated from phylogenetic systematics studies with morphological phenotypes of model organism gene knock-outs, all linked to the same shared ontologies in the Entity-Quality (EQ) formalism. The available capabilities include finding ontology terms; finding studies by taxon and anatomical concepts, and obtaining their trait matrices; finding ontological phenotype expressions; generating synthetic presence-absence trait matrices; obtaining anatomical presence-absence dependency matrices; and computing semantic similarity metrics between traits.

install.packages("remotes")
remotes::install_github("xu-hong/rphenoscape")