Glossary

Ontology

A flexible concept loosely encompassing any collection of Ontology elements and statements or relationships connecting them

Ontology element

A discrete part of an Ontology, with a unique persistent identifier. The most important elements are :ref:`Term`s, but other elements can include various metadata artefacts like :ref:`Annotation Property`s or :ref:`Subset`s

Term

A core element in an ontology, typically a Class, but sometimes used to include instances or relationship types, depending on context.

Concept

See Term

CURIE

A CURIE is a compact URI. For example, CL:0000001.

URI

A Uniform Resource Indicator, a generalization of URL. Most people think of URLs as being solely for addresses for web pages (or APIs) but in semantic web technologies, URLs can serve as actual identifiers for entities like ontology terms. Data models like OWL and RDF use URIs as identifiers. In OAK, URIs are mapped to :term:`CURIE`s

Label

Usually refers to a human-readable label corresponding to the rdfs:label predicate. Labels are typically unique per ontology. In OBO Format and in the bio-ontology literature, labels are sometimes called Names. Sometimes in the machine learning literature, and in databases such as Neo4J, “label” actually refers to a Category.

Name

Usually synonymous with Label, but in the formal logic and OWL community, “Name” sometimes denotes an Identifier

Class

An Ontology element that formally represents something that can be instantiated. For example, the class “heart”

Annotation

This term is frequently ambiguous. It can refer to Text Annotation, OWL Annotation, or Association.

Text Annotation

The process of annotating spans of texts within a text document with references to ontology terms, or the result of this process. This is frequently done automatically. The Bioportal implementation provides text annotation services. More advanced annotation services will be available through AI plugins in OAK in the future.

Mapping

See SSSOM

SSSOM

Simple Standard for Sharing Ontological Mappings. SSSOM is the primary Datamodel in OAK for passing around :term:`Mapping`s.

Graph

Formally a graph is a data structure consisting of Nodes and Edges. There are different forms of graphs, but for the purposes of OAK, an ontology graph has all Term`s as nodes, and relationships connecting terms (is-a, part-of) as edges. Note the concept of an ontology graph and an :term:`RDF graph do not necessarily fully align - RDF graphs of OWL ontologies employ numerous blank nodes that obscure the ontology structure.

OWL

An ontology language that uses constructs from Description Logic. OWL is not itself an ontology format, it can be serialized through different formats such as Functional Syntax, and it can be mapped to RDF and serialized via an RDF format.

RDF

A datamodel consisting of simple Subject Predicate Object Triples organized into an RDF Graph

OBO Format

A serialization format for ontologies designed for easy viewing, direct editing, and readable diffs. It is popular in bioinformatics, but not widely used or known outside the genomics sphere. OBO is mapped to OWL, but only expresses a subset, and provides some OWL abstractions in a more easy to understand fashion.

KGCL

Knowledge Graph Change Language (KGCL) is a Datamodel for communicating desired changes to an ontology. It can also be used to communicate differences between two ontologies. See KGCL docs.

OWL Annotation

In the context of OWL, the term Annotation means a piece of metadata that does not have a strict logical interpretation. Annotations can be on entities, for example, Label annotations, or annotations can be on Axioms.

Pronto

An Ontology Library for parsing obo and owl files

Iterator

A programming language construct used frequently in OAK - it allows for passing of results from API calls without fetching everything in advance.

Interface

A programmatic abstraction that allows us to focus on what something should do rather than how it is done. See Interfaces. The how is managed by an Implementation

Implementation

See Implementations

Datamodel

See Datamodels

Named Individual

An Ontology element that represents an instance of a class. . For example, the instance “John” or “John’s heart”. Note that instances are not commonly represented in ontologies, and are not currently well supported in OAK.

Property

An Ontology element that represents an attribute or a characteristic of an element. In OWL, properties are divided into disjoint categories:

  • ObjectProperty

  • AnnotationProperty

  • DatatypeProperty

Edge

See Relationship

Triple

See Relationship

Relationship

A Relationship is a type connection between two ontology elements. The first element is called the subject, and the second one the object, with the type of connection being the Relationship Type. Sometimes Relationships are equated with Triples in RDF but this can be confusing, because some relationships map to multiple triples when following the OWL RDF serialization. An example is the relationship “finger part-of hand”, which in OWL is represented using a Existential Restriction that maps to 4 triples.

Relationship Type

See Predicate

Predicate

An Ontology element that represents the type of a Relationship. Typically corresponds to an ObjectProperty in OWL, but this is not always true; in particular, the is-a relationship type is a builtin construct SubClassOf in OWL Examples:

  • is-a

  • part-of (BFO:0000050)

Subset

An Ontology element that represents a named collection of elements, typically grouped for some purpose

Reasoner

An ontology tool that will perform inference over an ontology to yield new axioms (e.g. new Edges) or to determine if an ontology is logically Coherent.

Bioportal

An Ontology Repository that is a comprehensive collection of multiple biologically relevant ontologies. Bioportal exposes an API endpoint, that is utilized by the OAK Bioportal Endpoint.

OLS

Ontology Lookup Service. An Ontology Repository that is a curated collection of multiple biologically relevant ontologies, many from OBO. OLS exposes an API endpoint, that is utilized by the OAK OLS Implementation

Ubergraph

A:term:Triplestore and a Ontology Repository that allows for SPARQL querying of integrated OBO ontologies. Accessible via AK Ubergraph Implementation

Semantic SQL

Semantic SQL is a proposed standardized schema for representing any RDF/OWL ontology, plus a set of tools for building a database conforming to this schema from RDF/OWL files. See Semantic-SQL

Semantic Similarity

A means of measuring similarity between either pairs of ontology concepts, or between entities annotated using ontology concepts. There is a wide variety of different methods for calculating semantic similarity, for example Jaccard Similarity and Information Content based measures.

Information Content

A measure of how informative an ontology concept is; broader concepts are less informative as they encompass many things, whereas more specific concepts are more unique. This is usually measured as -log2(Pr(term)). The method of calculating the probability varies, depending on which predicates are taken into account (for many ontologies, it makes sense to use part-of as well as is-a), and whether the probability is the probability of observing a descendant term, or of an entity annotated using that term.