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GO Usage Question

smith.ts.2 at pg.com smith.ts.2 at pg.com
Mon Jul 30 16:03:08 PDT 2001


Hi all,

I'm very new to GO and have a question.  Since GO is a DAG and I must provide
evidence for my association of a GO term to a gene product, it would seem that I
would want to keep track of not only the "leaf" term I assign but also the path
taken to reach the leaf since my evidence will likely only support a specific
path.  Here's an example:

Looking at cell wall chitin biosynthesis in the process ontology we see the
following DAG showing three ways of reaching cell wall chitin biosynthesis:

biological process
  cell growth and/or maintenance
    cell organization and biogenesis
      cell wall organization and biogenesis
        cell wall biosynthesis (sensu Fungi)
          cell wall chitin metabolism
            cell wall chitin biosynthesis

    metabolism
       carbohydrate metabolism
         chitin metabolism
            cell wall chitin metabolism
              cell wall chitin biosynthesis

      biosynthesis
        macromolecule biosynthesis
          cell wall chitin biosynthesis

Assuming I'm reading an article about Fungi, I would choose the first path and
assign cell wall chitin biosynthesis to my gene product.  However, in the
current database schema there does not seem to be a way of recording the fact
that I selected a specific path to cell wall chitin biosynthesis.  For general
queries such as "give me everything associated with cell wall chitin
biosynthesis" that's OK but for more specific queries like "give me everything
associated with cell wall chitin biosynthesis involved in cell organization and
biogenesis" it appears that I've lost some of the knowledge used to assign the
term.  Is this the case or am I interpreting GO incorrectly or trying to use it
improperly?


Thanks in advance,

Tim Smith

PS.  Please let me know if this question should have been asked on the
GO-Database list instead.



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