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FW: GO & SwissProt

Midori Harris midori at ebi.ac.uk
Fri Nov 9 08:28:48 PST 2001


Hello,

The SwissProt "function" field may contain several different types of
information, corresponding to both "molecular function" and "biological
process" GO categories as well as some things that fall outside the scope
of GO.

The GO documentation explains the distinction between molecular function
and biological process and indicates what GO does and does not include.
See:

  http://www.geneontology.org/GO.doc.html
  http://www.geneontology.org/GO.usage.html

In the second example, GO terms have not yot been assigned to the protein.

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 Thu, 8 Nov 2001 matthew-alan.roberts at rdls.nestle.com wrote:

> Thanks for your reply. I have listed below two examples where the SwissProt
> "function" doesn't match up or is in someway different than the functional
> indication by GO. Overall, we are implementing GO more and more in our data
> analysis, but the subtelties of applying it for interpretation of large
> datasets still eludes us. Thanks for your help.
> 
> Best Regards, Matthew A. Roberts- Project Leader Nutritional Genomics
> "Leave your drugs in the chemists pot if you can heal the patient with
> food!"
>                                              - HIPPOCRATES, the Father
> of Medicine 
> 
> Work Tel : Bureau (41 21)785 93 35; FAX +8544 
> *Mobile Phone 1     41-78-690-3643
> 
> Molecular Nutrition (Team 35), Nestlé Research Center, 
> Vers-Chez-Les-Blanc, 1000 Lausanne (26), Switzerland  
> 
> 
> 
> 
> 
> > -----Original Message-----
> > From:	Mace,Catherine,LAUSANNE,NRC/NT 
> > Sent:	jeudi, 8. novembre 2001 14:54
> > To:	Roberts,Matthew-Alan,LAUSANNE,NRC/NT
> > Subject:	RE: GO & SwissProt
> > 
> > 
> > Example 1
> > NM_006329 analysis fibulin 5 Hs.11494;AF093118  
> > 
> > SwissProt
> > FUNCTION: PROMOTES ADHESION OF ENDOTHELIAL CELLS THROUGH INTERACTION OF
> > INTEGRINS AND THE RGD MOTIF. COULD BE A VASCULAR LIGAND FOR INTEGRIN
> > RECEPTORS AND MAY PLAY A ROLE IN VASCULAR DEVELOPMENT AND REMODELING. 
> > SUBCELLULAR LOCATION: SECRETED. 
> > TISSUE SPECIFICITY: EXPRESSED PREDOMINANTLY IN HEART, OVARY, AND COLON BUT
> > ALSO IN KIDNEY, PANCREAS, TESTIS, LUNG, AND PLACENTA. NOT DETECTABLE IN
> > BRAIN, LIVER, THYMUS, PROSTATE, OR PERIPHERAL BLOOD LEUKOCYTES. 
> > SIMILARITY: CONTAINS 6 EGF-LIKE DOMAINS. 
> > 
> > GO: integrin ligand cell-cell matrix adhesion extracellular matrix soluble
> > fraction Extracellular excluding cell wall Angiogenesis 
> > 
> > Example 2
> > NM_001758 analysis cyclin D1 PRAD1 parathyroid adenomatosis 1, Hs.82932,
> > M73554 
> > 
> > FUNCTION: ESSENTIAL FOR THE CONTROL OF THE CELL CYCLE AT THE G1/S (START)
> > TRANSITION. 
> > SUBUNIT: INTERACTS WITH THE CDK4 AND CDK6 PROTEIN KINASES TO FORM A
> > SERINE/THREONINE KINASE HOLOENZYME COMPLEX. THE CYCLIN SUBUNIT IMPARTS
> > SUBSTRATE SPECIFICITY TO THE COMPLEX. 
> > DISEASE: INVOLVED IN B-LYMPHOCYTIC MALIGNANCY (PARTICULARLY MANTLE-CELL
> > LYMPHOMA (MCL)) BY A CHROMOSOMAL TRANSLOCATION T(11;14)(Q13;Q32) THAT
> > INVOLVES CCND1 AND IMMUNOGLOBULIN GENE REGIONS (BCL1 ONCOGENE). ACTIVATION
> > OF CCND1 MAY BE ONCOGENIC BY DIRECTLY ALTERING PROGRESSION THROUGH THE
> > CELL CYCLE. 
> > DISEASE: INVOLVED IN A SUBSET OF PARATHYROID ADENOMAS BY A CHROMOSOMAL
> > TRANSLOCATION T(11;11)(Q13;P15) THAT INVOLVES CCND1 AND THE PARATHYROID
> > HORMONE (PTH) ENHANCER (PRAD1 ONCOGENE). 
> > SIMILARITY: BELONGS TO THE CYCLIN FAMILY. CYCLIN D SUBFAMILY. 
> > 
> > GO: none 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Katherine Mace, PhD
> > Team leader, Metabolic and Genetic Regulation
> > Nestlé Research Center
> > PO Box 44, CH-1000 Lausanne 26
> > Tel: +41 21 785 87 99
> > Fax: +41 21 785 85 44
> > e-mail: catherine.mace at rdls.nestle.com  
> > 
> > 
> > 
> > ----------
> > From: 	Roberts,Matthew-Alan,LAUSANNE,NRC/NT
> > Sent: 	Thursday, November 8, 2001 10:40 AM
> > To: 	Mace,Catherine,LAUSANNE,NRC/NT
> > Subject: 	FW: GO & SwissProt
> > 
> > Catherine,
> > 
> > Can you give me a few specific examples of the discrepencies you found
> > between GO and the SwissProt "function"? I will then pass on this to the
> > GO editor who seems to want to look into the issue.
> > 
> > -----Original Message-----
> > From: Midori Harris [mailto:midori at ebi.ac.uk] 
> > Sent: mercredi, 7. novembre 2001 18:02
> > To: Roberts,Matthew-Alan,LAUSANNE,NRC/NT
> > Cc: gofriends at genome.Stanford.EDU
> > Subject: Re: GO & SwissProt
> > 
> > 
> > Hello,
> > 
> > The assignment of GO terms to gene products can be done by several
> > dirrerent methods; some methods make use of SwissProt keywords already
> > associated with a SwissProt entry, while other methods are independent of
> > SwissProt annotation.
> > 
> > It would help us address your question in more detair if you could provide
> > some examples of the discrepancies between SwissProt functions and GO
> > terms.
> > 
> > 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 Wed, 31 Oct 2001 matthew-alan.roberts at rdls.nestle.com wrote:
> > 
> > > 
> > > We are currently using GO to classify & group our microarray results.
> > Some
> > > people in our organization have seen discrepencies with the  "function"
> > > listed in the comments of a SwissProt entry. Can anyone comment about
> > the
> > > utility or comparability of the SwissProt "function" and the function
> > > assigned by GO classification? Furthermore, is the GO entry in someway
> > based
> > > on the SwissProt database??
> > > 
> > > Best Regards, Matthew A. Roberts- Project Leader Nutritional Genomics
> > > "Leave your drugs in the chemists pot if you can heal the patient with
> > > food!"
> > >                                              - HIPPOCRATES, the Father
> > > of Medicine 
> > > 
> > > Work Tel : Bureau (41 21)785 93 35; FAX +8544 
> > > *Mobile Phone 1     41-78-690-3643
> > > 
> > > Molecular Nutrition (Team 35), Nestlé Research Center, 
> > > Vers-Chez-Les-Blanc, 1000 Lausanne (26), Switzerland  
> > > 
> > > 
> > > 
> > > 
> > > -----Original Message-----
> > > From: Mike Cherry [mailto:cherry at genome.Stanford.EDU]
> > > Sent: mercredi, 31. octobre 2001 03:26
> > > To: gofriends at genome.Stanford.EDU
> > > Subject: CVS : schema & software directories
> > > 
> > > 
> > > GO CVS repository clean-up is continuing.
> > > 
> > > The old and out of date go/schema and most of the sub-directories in
> > > go/software have been deleted from the repository.  Two directories
> > > remain in software, SGD for the Perl scripts used by SGD and
> > > Python/MGI for the source of the MGI browser.
> > > 
> > > The GO database software and schema is available from
> > > 
> > >   http://www.fruitfly.org/annot/go/database
> > > 
> > > and soon from sourceforge.
> > > 
> > > -Mike
> > > 
> > > 
> > > --
> > > This message is from the GOFriends moderated mailing list.  A list of
> > public
> > > announcements and discussion of the Gene Ontology (GO) project.
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> > > 
> > > 
> > > --
> > > This message is from the GOFriends moderated mailing list.  A list of
> > public
> > > announcements and discussion of the Gene Ontology (GO) project.
> > > Problems with the list?           E-mail:
> > owner-gofriends at geneontology.org
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> > > 
> > 
> > 
> > 
> 



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