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GO Usage Question

Corradi, John John.Corradi at astrazeneca.com
Wed Aug 1 06:45:11 PDT 2001


Hi Tim,

Since this came to the GO Friends list, I'll take a stab at your question.
There are two components to the GO: 1) the terms themselves and 2) the
relationships between terms.  The terms are defined so that you may annotate
a gene product to a particular term (as opposed to a particular path to the
term).  Construction of the GO itself is carried out by the consortium, and
it is their responsibility to ensure that the relationships between terms
are universally true and logically consistent.  This means that in
annotating your gene product to a term, you should be able to retrieve your
gene by querying on any of the ancestral terms in any path to that specific
term, and it should be biologically correct.  If you run across an instance
in which your annotation does not make sense within the context of all the
paths to a GO term, you should let the consortium know.

For your example, any gene that is involved in "cell wall chitin metabolism"
is involved in a type of "cell organization and biogenesis" or a type of
"carbohydrate metabolism".  It seems to me that you are looking at the DAG
from the bottom up.  It is a directed graph, and should be viewed from the
top (root) down.  In other words, querying on "cell wall chitin metabolism"
is more specific than querying on "cell organization and biogenesis".  Does
that help to answer your question?

Cheers,
John

-----Original Message-----
From: smith.ts.2 at pg.com [mailto:smith.ts.2 at pg.com]
Sent: Monday, July 30, 2001 7:03 PM
To: gofriends at geneontology.org
Subject: GO Usage Question


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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