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Bradley Marshall bradmars at yahoo.com
Mon Jul 1 10:37:51 PDT 2002


--- Ruteja Barve <ruteja at yahoo.com> wrote:
> 
> I had a couple of questions about the GO XML files
> (in
> RDF format).
> 1: In the GO terms, there is a  'is a' link gives
> only
> the immediate parent for that node. Is there an
> efficient  way of getting all the parents/childern
> for
> each node from the XML file?

There's no way to do this without writing a perl
script or loading the XML into a database or into an
RDF object model like redland.  (Well, you can do it
with text searching in any text editor, but this gets
tedious.)  The reason for this is that the fact that
the GO is a graph rather than a tree (terms can have
multiple parents).  Because of this it is not possible
to nest the terms in XML tags.  Each term needs to
stand on its own with a reference to its parents.


> 2: What is the difference between "is a" and "part
> of"
> links? 

These are two fundamentally different concepts.  An
orange "is a" fruit and an orange peel is "part of" an
orange.

> Both seem to give the parent node.

I'm not sure what you mean by that.  The following
three terms say that cell communication "is a"
biological process which is "part of" the gene
ontology.

        <go:term focus="yes"
rdf:about="http://www.geneontology.org/go#GO:0003673"
n_associations="31411">
            <go:accession>GO:0003673</go:accession>
            <go:name>Gene_Ontology</go:name>
        </go:term>

   
        <go:term focus="yes"
rdf:about="http://www.geneontology.org/go#GO:0008150"
n_associations="23834">
            <go:accession>GO:0008150</go:accession>
            <go:name>biological_process</go:name>
            <go:definition>A phenomenon marked by
changes that lead to a particular result, mediated by
one or more gene products.</go:definition>
            <go:part-of
rdf:resource="http://www.geneontology.org/go#GO:0003673"
/>
        </go:term>

        <go:term
rdf:about="http://www.geneontology.org/go#GO:0007154"
n_associations="4746">
            <go:accession>GO:0007154</go:accession>
            <go:name>cell communication</go:name>
            <go:definition>Any process that mediates
interactions between a cell and its surroundings.
Encompasses interactions such as signaling or
attachment between one cell and another cell, between
a cell and an extracellular matrix, or between a cell
and any other aspect of its
environment.</go:definition>
            <go:isa
rdf:resource="http://www.geneontology.org/go#GO:0008150"
/>
        </go:term>


Brad

> 
> Thanks!
> -Ruteja
> 
> 
> 
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