Glossary of Terms

This glossary contains a list of commonly used ontology-related terms, particularly those you might encounter in Phenoscape KB or related resources. Some terms are copied from the glossary in Vogt et al (2022), and a larger list of terms can be found in that document.

• Annotation - Ontology terms tagged to free-text such as a character description or a taxon name

• API - An application programming interface (API) is a computing interface that allows two applications to talk to each other. It functions like a messenger that delivers a particular request to the provider (e.g., asking a database for a specific type of data content) and then delivers the response of the provider. In other words, an API is a set of instructions and standards for accessing a (Web-based) software application. An API is released to the public so that other software developers can create products that utilize the services of this application.

• Assertional statement - Relationships created by an authority and not inferred (E.g., humerus is comprised of bone tissue ). Statements about particulars. In Description Logic, they are referred to as ABox expressions.

• Character - Feature specified in a morphological phylogenetic matrix

• Class - A grouping concept for defining a general group. A class is always defined intensectionally by a predicate (i.e. connotative definition). Class definitions are universal or contingent statements that carry semantic conceptual content. All instances of a class possess the predicate that defines the class.

• Description logics (DL) - DL are a family of formal knowledge representation languages and as such provide the logical formalism for ontologies and the Semantic Web. OWL is based on DL. DLs are usually more expressive than propositional logic but less expressive than first-order logic. In DL, TBox expressions are distinguished from ABox expressions, with the former carrying universal statements and the latter assertional statements.

• 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’.

• Instance - A particular that instantiates a class. As an example, if the class is “dorsal fin”, an instance of that class would be an observation of a dorsal fin on a specimen

• Mutual exclusivity or compatibility of phenotypes - Phenotype annotations in the KB and their source character data can be used to provide evidence for the mutual exclusivity or compatibility of phenotypes, and this information is used as the basis for clustering phenotype annotations into synthetic characters and states for a phylogenetic analysis. For example:

  • Two phenotypes linked to the same character state at least once have strong evidence for mutual compatibility, and thus indicate that the phenotypes can be clustered into the same character state.

  • Two phenotypes linked to the same character at least once, but not to the same character state, have strong evidence for mutual exclusivity, and thus may represent different character states of the same character. See RPhenoscape documentation for a full description of the mutual exclusivity functions.

• 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 Phenoscape 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.

• OWL - The Web Ontology Language (OWL) is a set of knowledge representation languages for authoring semantic graphs. They are characterized by formal semantics and build upon RDF. OWL provides three increasingly expressive sub-languages, i.e. OWL Lite, OWL DL, and OWL Full, that support reasoning based on description logics to varying degrees.

• Phenoscape KB- Phenoscape Knowledgebase is a datastore of computable phenotypes for studies of evolution and genetics.

• Phenotype annotation- An annotation of a phenotypic description with terms from an anatomy ontology and quality ontology.

• 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

• Resource Description Framework (RDF) - A standard for describing web resources and their relationships. This is formatted as subject-predicate-object, e.g., zebrafish (NCBITaxon:7955) has a (NCIT:C82846) dorsal fin (ZFA:0001173). The Resource Description Framework (RDF) is a set of specifications of the World Wide Web Consortium (W3C) and is commonly used as a general method for modeling information using web resources. It provides a variety of syntax notations and data serialization formats and follows the general syntax of a triple statement. RDF plays an important role in knowledge management, ontologies, and the Semantic Web

• 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.