[Biojava-l] GO web service

Patrick McConnell MCCon012@mc.duke.edu
Fri, 30 Aug 2002 09:50:00 -0400

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,