Re: [Obo-discuss] Ontology_submission

[Alan R. <ala...@gm...>]

Hello,

I'm participating in the BioPAX effort so I thought that I would put =20
my 2 cents in, though it should be understood as my own views, rather =20=

than the group's.

I'm quite excited to see any pathway ontology put up, and I'll be =20
reviewing this one in more detail. Perhaps someone could elaborate on =20=

what it would mean for the this to be *the* pathway ontology. I would =20=

hope that it wouldn't imply any exclusion.

Again, speaking for myself, I think that there is much work to be =20
done in the area of pathway representation. Although BioPAX bills =20
itself as an exchange format, myself and a number of colleague think =20
that in order to be effective at that, we must be careful and =20
thoughtful about what we mean by terms and how they relate. I think =20
that this effort would put our work in the same field of endeavor as =20
the OBO effort, and I personally hope that we will be able to submit =20
our work for inclusion in OBO at the appropriate time, as well as =20
take advantage of appropriate OBO ontologies in our own effort.

Victoria is listed as one of the participants in the upcoming BioPAX =20
workshop. As one of the organizers of the workshop I will contact her =20=

about how we could spend some time at the workshop to advance our =20
shared goals.

For those who are interested in getting some more background on the =20
effort, let me direct you to http://biopaxwiki.org/ where you can get =20=

a flavor of the nature of our discussions. Let me also encourage you =20
to contribute your comments and criticisms, which would be greatly =20
appreciated.

Sincerely,
Alan

On Oct 19, 2005, at 11:33 AM, Petri, Victoria wrote:

> Hello,
>
>
>
> We would like to submit an obo controlled vocabulary that we have =20
> developed and which is dedicated to pathways. I talked to Chris and =20=

> after some back and forth discussions and some revisions, here was =20
> his last comment:
>
>
>
> One (final!) request - given that the ontology names should be =20
> unique, and there will undoubtedly be more than one pathway =20
> ontology (eg BioPAX), perhaps we should make the name more unique - =20=

> eg RDG_Pathway_Ontology (with the name reflecting the source rather =20=

> than any inherent species bias). The alternative is that we =20
> designate this *the* OBO pathway ontology, which may be fine, but =20
> we should have some initial discussion on the obo-discuss mailing list
>
>
>
> I subscribed to the mailing list but never heard anything. Here is =20
> the reply I sent to Chris:
>
>
>
> I have not seen anything on the obo-discussion regarding naming the =20=

> Pathway Ontology. Anyways, I believe it is correct to have it as =20
> the OBO file as it is the only pathway specific obo controlled =20
> vocabulary that I know of. BioPAX, as mentioned, is an environment =20
> for pathway data exchange - and is Prot=E9g=E9-Owl, not obo. There is =
a =20
> provision in BioPAX for the use of external controlled vocabularies =20=

> and I think that the use of PW (Pathway Ontology) would facilitate =20
> pathway data exchange by providing unique IDs for pathway terms - =20
> creating new ones as necessary, that can be used across the varied =20
> pathway resources that BioPAX seeks to integrate.
>
> I=92m providing the links to the ftp site and the full path to the =20
> ontology. Maybe if submitted there will be some discussions.
>
>
>
> The URL
>
>  ftp://rgd.mcw.edu/pub/data_release/
>
>
>
>
>
> full_path to the vocabulary file
>
> ftp://rgd.mcw.edu/pub/data_release/Pathway_Ontology.obo
>
>
>
> However, he is about to leave town:
>
> I'm just heading out to catch a plane to CSHL, sorry I forgot about =20=

> this. Feel free to post to the list yourself, or we can wait til =20
> next week..
>
> This is the email I got from him as I was sending mine =96 see above.
>
>
>
> The vocabulary is available from our site (see link above) and  =20
> from  the  knowledge zone  -
>
>  http://smi-protege.stanford.edu:8080/KnowledgeZone/
>
> We would like to have the ontology added to the list of ontologies =20
> currently posted at the Open Biomedical Ontologies site.
>
>
>
> Thank you,
>
>
>
> Victoria Petri
>
>
>
> Victoria Petri, Ph.D.
>
>  Scientific Curator for Gene Ontology
>  Rat Genome Database (http://www.rgd.mcw.edu)
>  Bioinformatics Research Center (http://www.brc.mcw.edu)
>
> Medical College of Wisconsin
>
> 8701 Watertown PlankRoad, Milwaukee, WI 53208
>
>  (414) 456-7507
>  (414) 456-6190 Fax
>  vp...@mc...
> vp...@ma...
>
>
>
>
>
>