== Using Ontologies to Categorize Pathways ==
We want to provide ontology-based terms to label pathways in a standardized way. 
Ontology-based labels or tags will not only provide information about the pathway
(i.e., relevant biological or experimental context) but also provide a means to
organize the pathways.  These terms will allow us to organize pathways relative to
each other (i.e., those that share terms) and relative to the source ontologies (i.e.,
parent-child relationships transfered from ontology to pathways). 

Ideally, we can also make use of the ontology terms associated with the component 
genes and proteins in a given pathway. For example, we might be able to auto-recommend
an ontology term for the pathway based on the predominate gene-level term or based on
the profile of terms at the gene level.

Futhermore, ontologies can help provide links into WikiPathways.  The Ontrez project
is a resource for browsing biomedical ontologies and provides links to other resources
that have material tags with any given term. For example, someone browsing "Molecular
Function" would find links to all of the pathways at WikiPathways tagged with that
Gene Ontology term.  Pretty neat!

== Implementation Steps ==

==== Pick an ontology service ====
I initially stumbled across the Stanford resource (SMD) and the associated Ontology Widget.
The developer of the widget recently moved on to another group and the SMD apparently
will not be around (i.e., updated) in a year or so. As an alternative, Nigam Shah (whom
I met at the BioPAX meeting) is actively developing BioPortal and Ontrez resources as part
of a big NCBO grant (one of 7 centers funded by NIH to support other bioinformatics tools, 
like ours!). They are not only keeping up to date with all biomedical ontologies, they are 
also integrating across ontologies to establish meaningful cross-links.

==== Develop an interface for add ontologies ====
The Ontology Widget may be an easy start, but it is likely a dead end. We could:
 1. Adapt it ourselves to use the BioPortal resource
 2. Make our own interface from scratch to access BioPortal (GSoC project?!)

BioPortal API - comming soon...

==== Populate ontology terms on pathways ====
We'll have to catch up and add a bunch of terms ourselves.  It will be critical to instruct
users on adding these terms themselves to help out and keep up with new content.
Some of this may be able to be automated?

==== Link back from Ontrez ====
This is done!  The flatfile output format should allow Ontrez to link back to WikiPathways
and stay up-to-date as we add ontology labels and add new ontology sources.

==== Inference from gene-level ontology terms ====
Reference to cross-ontology mappings = comming soon...