INOH - pathway data and annotation ontologies
Ken-Ichiro Fukuda
(National Institute of Advanced Industrial Science and Technology, AIST)
INOH is a manually curated signal transduction pathway database.
Pathway is a series of interactions which biologists have found useful
to group together for biological importance.
The set of interactions typically form a network and
is decomposable into sub-sets representing smaller biological processes.
Conventional pathway data are highly structured and
we are working on a data exchange format as a member of the BioPAX working group.
However, many databases use open vocabularies to name pathway objects.
For example, terms such as "ranslocation", "transport", and "internalization"
are used to represent a translocation interaction of molecules.
And the definitions of these vocabularies and relations are typically not
recorded in databases. As this hampers data integrity, INOH uses a set of ontologies
for pathway data annotation. Every biological process is annotated
by the "Event Ontology" and physical entity is annotated by
the "MoleculeRole Ontology". For example, the MoleculeRole ontology captures
relations between generic molecule names, concrete molecule names,
sequence accession numbers and complexes and their subunits.
Consequently, INOH provides high-quality pathway data that
allow advanced ontological searches, thereby improving accuracy
by extending the search range using ontological trees.
The ontologies and pathway data are available at http://www.inoh.org.
The current INOH data includes 1379 interactions, 1619 biological events,
9008 physical-entities.