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Gene attributes that don't fit into process, component and fu nction ontologies?

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Fri Feb 16 02:31:06 PST 2001


Friends

I think that I was a bit brusque when I replied to Fritz's mail !
Richard's mail and that from WinHide show that Fritz has touched a chord.

1.  On the question of expression ontologies there is, of course,
a working party on this due to report at the MGED meeting in
March: see
http://www.cbil.upenn.edu/Ontology/MGED_ontology.html

2.  I am not quite sure what WinHide is trying to attain.  Unless I
have completely missed the point (not unknown, I am told) most
of his list is satisfied by a well formed GenBank/EMBL-Bank/DDBJ
FT statement for a mRNA, e.g.


 join(AC004277:5175..5676,AC004277:5821..6157,
 AC004277:6214..6918,AC004277:7020..7153,
 AC004277:7250..7401)

Win, cannot we compute most of what you want from that ? and then
represent it in text is you so wish ?

>The relative expression of each exon
 ... I am not sure what you mean here; do you mean expression of
each differently spliced protein isoform ?  Does it make sense
to talk about the expression of an exon independently of the mRNA
within which it is contained ?

3. With respect to Richard's email (which I take the liberty of
attaching as it was not sent to the list) I do agree that we must
extend the domains of cvo's. I also agree that the GO Consortium could
evolve into an umbrella group for related cvo's (at the very least
for their distribution, but also I would hope for uniformity of
syntax, semantics and tools for maintaining and querying).  With that
in mind I would certainly include the following:

anatomy
microarray experiments
phenotypic variation


But I do not think that we should attempt to duplicate work being done
by, eg, the Swiss-Prot team on proteins.

Best


Michael
-----------------------------------------------------------------------------
>From R.BRUSKIEWICH at cgiar.org Fri Feb 16 00:13:58 2001
Envelope-to: ma11 at gen.cam.ac.uk
Delivery-date: Fri, 16 Feb 2001 00:13:58 +0000
Date: Thu, 15 Feb 2001 15:55:31 -0800
From: "Bruskiewich, Richard" <R.BRUSKIEWICH at CGIAR.ORG>
Subject: RE: Gene attributes that don't fit into process,
 component and fu	nction ontologies?
To: "'ma11 at gen.cam.ac.uk'" <ma11 at gen.cam.ac.uk>, froth at hms.harvard.edu
MIME-version: 1.0
X-Mailer: Internet Mail Service (5.5.2653.19)

Hi Michael and Fritz,

I generally agree with you Michael, that we need to keep the current GO
project tractable by limiting the controlled vocabularies/ontologies (cvo)
to the three current themes. 

That said, I think we do need to start thinking along the lines Fritz has
indicated and chart out a broader map for the future. I'm already doing this
within the plant community by developing trait and mutant descriptive
ontologies, leveraging the protocols and tools of the GO consortium for
cvo's. There are also other efforts in biological ontology for example the
microarray groups, even the various XML driven annotation data exchange
protocols, all represent cvo's.  

Our recent Plant & Animal Genome workshop on cvo's was well received by
delegates. Based upon my discussions during a recent trip to Japan, our
japanese colleagues are also keen to participate.  I think many people are
recognizing the value of community level protocols for labeling database
data to facilitate tractable functional genomic computing and
interoperability of heterogeneous databases.

The basic question is: can we identify a consortium of consortia dealing
with cvo's in various targeted domains and encourage the development of
common protocols and tools, leaving content development to each specialist
group?

Cheers
Richard Bruskiewich
Bioinformatics Specialist

International Rice Research Institute (IRRI)    
http://www.cgiar.org/irri
Tel. +63 (2) 845-0563 Fax +63 (2) 845-0606   
Email: r.bruskiewich at cgiar.org
Mailing address:  MCPO Box 3127, 1271 Makati City, The Philippines
Shipping: Suite 1009, 6776 Ayala Ave, Makati City, The Philippines

 

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