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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.)
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