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GO-KEGG API

Chris Mungall cjm at fruitfly.org
Fri Sep 9 10:53:10 PDT 2005


There are a number of APIs for retrieving data from GO and other
ontologies.

There is the go-db-perl API, developed by the GO consortium - this is the
API driving AmiGO. Currently there is no SOAP layer, so you have to access
it using perl. This requires a MySQL database backend. This API may be too
heavyweight for simply retrieving ontology data, as many of the methods
are for retrieving annotations. The GO database is already populated with
mapping between GO IDs and IDs in other ontologies and controlled
vocabularies, but not KEGG, but these can easily be populated if you have
the data.

There are numerous other APIs for retrieving information from an ontology,
many of which have SOAP layers. However, for you purposes, it sounds like
you are after some kind of ID-mapping database with SOAP API. I think
Descriptron may be exactly what you are after; see Daniel McGoldrick's
pages:

http://compbio.uchsc.edu/Hunter_lab/McGoldrick

I've redirected this response to gofriends, as others may have suggestions
too.

Cheers
Chris

On Fri, 9 Sep 2005, Maurice Ling wrote:

> Dear GO Experts,
>
> I am Maurice, a PhD candidate in University of Melbourne.
>
> Part of my work requires programmatic accessing of GO, EC etc etc, and
> to answer questions like "what are the corresponding ID numbers in EC,
> UniGene etc etc for a particular gene ontology ID?" The reverse question
> is also important, i.e., What  are the GO ID associated with a certain
> UniGene ID?
>
> At the same time, my work also requires a mapping between Gene Ontology
> IDs and KEGG Ontology IDs.
>
> I wish to seek your advice on the availability of such an API. My
> current plan  is to establish a database to contain such information and
> write a simple SOAP API for it. My idea is also to publish the database
> and API so that site installation can be achieved. Can I have your
> advice on this as well?
>
> Thank you for your time.
>
> Cheers
> Maurice
>
> --
> Maurice Han Tong LING, BSc(Hons)(Biochem), AdvDipComp, CPT, SSN, FIFA,
> MASBMB, MAMBIS, MACM
> Doctor of Philosophy (Science) Candidate, The University of Melbourne
> mobile: +61 4 22781753, +65 96669233
> mailing address: Department of Zoology, The University of Melbourne
> 		 Royal Parade, Parkville, Victoria 3010, Australia
> residence: 9/41 Dover Street, Flemington, Victoria 3031, Australia
> resume: http://maurice.vodien.com/maurice_resume.pdf
> www: http://www.geocities.com/beldin79/
>
>



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