[Biojava-l] GO web service

Brian Gilman gilmanb@genome.wi.mit.edu
Fri, 30 Aug 2002 10:57:16 -0400

On 8/30/02 9:50 AM, "Patrick McConnell" <MCCon012@mc.duke.edu> wrote:

Hello all,

    I'm just wondering if anyone has a design document or a sketch of how
the web service package of biojava?? I'd like to know exactly what I'd be
writing to/with? 

    Have there been design discussions about all these services on another
list?? Have people thought about security, reliability, scalability, object
persistence, round trip reduction etc??


> I am thinking of developing a Gene Ontology web service for the web
> services module for BioJava.  I believe this is a good candidate for a
> 'domain-specific' web service because a well developed and tested SQL
> schema exists.
> Does anyone have any thoughts on this?  Specifically, what sort of methods
> should be included?
> For the GO web service we built on site here, I included methods such as:
>     String getTerm(int goAcc)
>     String[][] getPathsToRoot(int goAcc)
>     boolean isAncestor(int goAcc, int ancestorGoAcc)
>     String getDescription(int goAcc)
>     int getRoot()
>     int[] getChildren(int goAcc)
>     int[] getParents(int goAcc)
> and so on...
> And, the most useful part:
>     int[] getGoAccsByLocus(String locusLinkId)
> but, that brings in non-standard data from NCBI.
> We have also integrated Tigr's data:
>     int getGoAccsByTigrId(String tigrId)
> but again, who knows how this data is set up in other peoples systems.  So,
> we will not be able to integrate that.
> Does this seem like a useful tool?  Does anyone have any suggestions on
> what web services should be used for the webservices module?  So far, I am
> planning on blast and go to show the utility of a tool-oriented web service
> and a data-oriented web service.
> Thanks for any input,
> -Patrick
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Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902