[Bioperl-l] Types of relationships

[Chris Mungall]

what kinds of relationships do you have in mind?

I'm imagining different ontologies here:

Sequence Ontology (for relationships between exons, transcripts, genes,
translations,..)

Interaction Ontology (binds-to, inhibitis, etc)

Comparative Ontology ??? not sure what would go in here other than
orth/par/hom ologous?

Mutation Ontology (between variation feature and gene feature -
characterises type of mutation)

mutation & sequence ontologies already exist in GOBO
see geneontology.org

i'll take a crack at this after bosc - i want to discuss getting some of
the go parsers into bioperl with anyone who wants to listen to me about
event based parsing frameworks

On Mon, 15 Jul 2002, David Block wrote:

> Following the discussion about IdentifiableI etc., and talking to Mark
> on my recent trip home, this sounds like a good time to throw into the
> ring the need for ...
> drumroll...
> yet another ontology!
>
> This would be an ontology, or at least a controlled vocab, that
> describes different types of relationships between two entities.
> Not everything is just 'homologous'.  DbXRefs can point to synonyms,
> homologs, orthologs, translations (DNA/RNA/AA),
> parents/children/siblings in trees, etc.
>
> So it needs to be done somewhere, and then once someone does it, we'll
> wrap it up and put it in BioSQL and use it.
>
> I'm *not* volunteering right now, but I'm hoping someone does. :-)
>
> Shalom,
> --
> David Block                                  dblock@gnf.org
> GNF - San Diego, CA             http://www.gnf.org
> Genome Informatics / Enterprise Programming
> Weblog:      http://radio.weblogs.com/0104507/
>
>
> --
> David Block                                  dblock@gnf.org
> GNF - San Diego, CA             http://www.gnf.org
> Genome Informatics / Enterprise Programming
> Weblog:      http://radio.weblogs.com/0104507/
>
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