Biology Reference
In-Depth Information
many complex descriptions in biology. Some ontologies do provide
homology relationships. PATIKA,
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a pathway ontology, includes a
“homology” relation; in practice, it is used to manage paralogy inside
gene families. Protein homology is defined as a “synonym” in the
MoleculeRole Ontology of the INOH Pathway Database. To our knowl-
edge, the most detailed implementation of the concept of homology is
found in the Sequence Ontology
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: it includes a “homologous_to” rela-
tion, which is the only child of “similar_to”; and has three children,
“orthologous_to”, “paralogous_to”, and “non_functional_homolog_to”.
The latter is an interesting formalization of the relation between a gene
and a pseudogene. The child relation to “similar_to” shows that a mor-
phological definition of homology was chosen, whereas the Cell
Ontology uses a definition of historical homology.
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However, in the Cell
Ontology, the relation is not implemented explicitly. Instead, homology
is the default for the same term in different species (e.g. “muscle_cell” in
human and fly); otherwise, several lineage-specific terms are created, as
in “pigment_cell_(sensu_Vertebrata)” and “pigment_cell (sensu_Nematoda_
and_Protostoma)”. A similar approach is used in the Plant Ontology.
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In several ontologies, homology is not defined as a type of relation, but
is discussed in the definitions. For example, good discussions of anatom-
ical homology, including serial homology and analogy, appear in defini-
tions of the ontologies of mosquito
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or corn.
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3.2. Modeling Homology Relationships
To conduct evo-devo studies computationally, we need to define homol-
ogy relationships between ontologies describing the anatomy and devel-
opment of different species. Designing such relationships consists in
finding correspondences (homology relationships) between the concepts
(organs) of these ontologies. This problem is a special case of “schema
matching” or “ontology alignment”. Ontology alignment
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is the process
of determining correspondences between ontology concepts. Usually,
this technique is used to find the common concepts present in two
ontologies. In the case of anatomical ontologies, the concepts to align are
not strictly common, but rather related: a homology relationship is not
an equivalence relationship. For this reason, classical ontology alignment
