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GO Usage Question

Midori Harris midori at ebi.ac.uk
Wed Aug 1 04:38:22 PDT 2001


Hi,

This list is fine; the GO-database list covers database schema,
programming, etc.

When there's more than one path from a "leaf" term back to the root, every
path must be true. In the chitin biosynthesis example (which happens to be
one we often use to illustrate the principle!), when you annotate a gene
product to "cell wall chitin biosynthesis" you're saying that the gene
product is involved in cell organization and biogenesis, carbohydrate
metabolism, AND macromolecule biosynthesis. And indeed that's true--chitin
is a carbohydrate and a macromolecule.

It is one of our biggest challenges to organize the GO vocabularies so
that all paths are true. If someone does find a case where one path but
not another applies to a gene product, that means we have to modify the
relationships between GO terms. Do let us know if you find any!

Also let me know if you have any other questions.

Regards,
Midori

============================
Midori A. Harris
GO Editor
EMBL - EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at ebi.ac.uk

On Mon, 30 Jul 2001 smith.ts.2 at pg.com wrote:

> 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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