Annotation - Ontology terms tagged to free-text such as a character description or a taxon name
Character - Feature specified in a morphological phylogenetic matrix
Entity - An organismal feature, such as an anatomical part, function, or behavior. In Phenoscape, anatomical entities are represented by terms from the Uberon anatomy ontology
Inference - A statement (in our case, a phenotype statement) that is a logical consequence from an asserted fact or facts. For example, the presence of a pectoral fin can be inferred from the presence of pectoral fin rays because the term ‘pectoral fin ray’ in the anatomy ontology has a part_of relationship to ‘pectoral fin’.
Quality - A term that describes how an entity varies in its features (e.g., shape, size, color…). Phenotypic qualities are represented by terms from the PATO ontology
Ontology - Ontologies are knowledge graphs that represent the knowledge for a particular domain (e.g., anatomy, taxonomy, environment), with terms (concepts) linked by well-defined relationships.
OntoTrace - A KB tool that automatically generates synthetic presence/absence supermatrices from phenotypes in the KB. For any anatomical entity and taxon, OntoTrace produces a matrix containing both author-asserted and inferred presence/absence characters.
Phenotype - An annotation of a phenotypic description with terms from an anatomy ontology and quality ontology.
Taxon annotations - Phenotypes that are linked to taxa. In Phenoscape, taxa are represented by terms from the Vertebrate Taxonomy Ontology
Trait - An observable feature of an organism.