Fig. 2. Examples of bio-ontologies. An ontology captures relationships among terms and their definitions in a structured way. A structure used in many of the current ontologies is a `directed acyclic graph' that differs from a tree or outline in that one term can connect to many terms but the connection is oriented (shown by arrows rather than by lines) and no cycles are allowed. Commonly used relationships are `Is a' and `Part of': term A is an example of term B; structure A is part of structure B (see www.geneontology.org or www.bioontology.org for more information). (A) Phenotype ontology. Reproductive system development defects include vulval developmental abnormalities, which include more-specific phenotypes, such as vulvaless and abnormal cell-fate specification. (B) Anatomy ontology. The intestine is part of the `digestive tract' and `alimentary system' and is an `organ'. The intestine comprises intestinal cells, intestinal lumen and intestinal muscle. (A and B from WormBase WS180.) (C) Biological processes in the Gene Ontology (GO). `Spinal cord development' is a case of `anatomical structure development' and is part of `central nervous system (CNS) development'. Spinal cord development comprises the development of sub-structures and includes both cell differentiation and patterning. (From GO Biological Process.)