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Integration of terms into SQL db

Chris Larsen clarsen at
Fri Apr 19 07:12:48 PDT 2002

Hello GO freinds,

We at Cognia are developing biological databases. After a long effort to make sure that the Java/SQL structure is up, stable in Windows NT, and can readily accept curated proteins, complexes, interactions, genes, and compounds live over the web from remote literature-reading curators, we have reached a point where the apparently difficult task of incorporating GO terms into our offerings has to be addressed. Previously I had tried to digest the terms from the huge list, by hand, and actually made good progress in producing 700 ubiquitin-specific terms. BUT,

This has its problems:
1    Does not address the terminology for the substrates of Ubiquitylation (80% of the cell?!)
2    List is static and does not evolve
3    List must be hard coded into a JSP page or as table values in SQL
4    Modifying the list is ridiculously cumbersome.


Does anyone have a strong method for incorporating terms? 

such that:
1    The evolution of GO is coupled to the database "live"
2    The huge number of terms is navigable to a curator when inputting data
3    Terms changes can be back corrected, after the curator has used a term that becomes known as antiquated (aliasing?)

We also might like to have, or know whether to generate if it hasnt been done, a live converter from EC to GO (to Cognia) numbers. (Biojava module?)
If theres any help to be had here, please let me know. If we could automate this fully, that would be great, but our solutions right now are not up to large scale curation standards.  I suspect the right answer will be painfully simple and elegant, and in fact that's probably the one we want.



Christopher Larsen, Ph.D.
Product Manager
Cognia Corporation
117 E 55th St.
New York, NY 10022
e: clarsen at
w: 212-331-7840
h:  718-777-6558 
c:  347-837-0727      
f:   801-459-8850
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