[Biojava-l] GO web service

[Patrick McConnell]

None of that has been discussed.  In fact, much of that is still up in the
air in the web services community.  For instance, there has yet to be a
standard security protocol adopted for web services technology.

Actually, much of what you you say can (should?) be handled by the web
services engine.  I think we should be interested in developing interfaces
and implementations that are not concerned with how the service is hosted.
If we accept this abstraction, we can develop classes that simple run
processes/access data, parse results, and return well structure objects.
The rest, we leave up to the service engine.

Is this reasonable, or do you think we need to address these issues?

-Patrick





Brian Gilman <gilmanb@genome.wi.mit.edu> on 08/30/2002 10:57:16 AM

To:    Patrick McConnell <MCCon012@mc.duke.edu>, <biojava-l@biojava.org>
cc:

Subject:    Re: [Biojava-l] GO web service


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??

                            Best,

                                    -B
>
> 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