simple question

[Tanya Berardini]

Dear Aurelien,

I see now where the problem arose.  When you download the Ontology.tgz
file from Gramene from the site you describe, this includes the three GO
ontologies as well as the plant anatomy and developmental stages
ontologies.  The GO ontologies should be identical with those you can
download from GO consortium site. In this case, it appears that the files
have gone out of sync.

As Midori mentioned in her prior email, the GO term hemoglobin GO:0005833
has been renamed 'hemoglobin complex' with the same GO id in order to
better reflect the fact that this is a component term.  This should be
reflected in the next update that Gramene does to its database. (Correct
me if I'm wrong, Gramene folks.)

Hope this clarifies matters.

Regards,

Tanya


On Thu, 21 Nov 2002, abarre wrote:

> I know that plant have hemoglobin (like the leghemoglobin). My trouble
> was to see this term in the plant ontology and not in the
> gene ontology !
> I use the latest release of the Plant Ontologie, download on
> www.gramene.org.
> (ftp://ftp.gramene.org/pub/gramene/gramene_database)
>
>
>   **
>
> Hemoglobin in Plant Ontology :
> id=5382
> accession = 0005833
>
> * 0003673 : * Gene_Ontology
> <javascript:popup('info.php?info_type=1&term_id=1&nom=Gene_Ontology',(screen.width*0.7),(screen.height*0.7))>
>
> ===== * 0005575 : * cellular_component
> <javascript:popup('info.php?info_type=1&term_id=5135&nom=cellular_component',(screen.width*0.7),(screen.height*0.7))>
>
> ======= * 0005623 : * cell
> <javascript:popup('info.php?info_type=1&term_id=5136&nom=cell',(screen.width*0.7),(screen.height*0.7))>
>
> ========   * 0005622 : * intracellular
> <javascript:popup('info.php?info_type=1&term_id=5180&nom=intracellular',(screen.width*0.7),(screen.height*0.7))>
>
> =========== * 0005737 : * cytoplasm
> <javascript:popup('info.php?info_type=1&term_id=5268&nom=cytoplasm',(screen.width*0.7),(screen.height*0.7))>
>
> ============ * 0005829 : * cytosol
> <javascript:popup('info.php?info_type=1&term_id=5362&nom=cytosol',(screen.width*0.7),(screen.height*0.7))>
>
> ============== * 0005833 : * hemoglobin
> <javascript:popup('info.php?info_type=1&term_id=5382&nom=hemoglobin',(screen.width*0.7),(screen.height*0.7))>
>
>
>
>
> thanks for your answer !
>
>
> Tanya Berardini wrote:
>
> >Dear Aurelien,
> >
> >TAIR is part of the consortium that has been developing the Plant
> >Ontologies (anatomy and developmental stages).  Which plant ontology are
> >you using that contains the term hemoglobin, what is the term ID and from
> >where did you download the ontology? Your answers to these questions will
> >help me to track down the source of your problem.
> >
> >By the way, plants do have hemoglobin genes.  See :
> >
> >1:  Hunt PW, Watts RA, Trevaskis B, Llewelyn DJ, Burnell J, Dennis ES,
> >Peacock WJ. Related Articles, Links
> >
> >Expression and evolution of functionally distinct haemoglobin genes in
> >plants.
> >Plant Mol Biol. 2001 Nov;47(5):677-92.
> >PMID: 11725952 [PubMed - indexed for MEDLINE]
> >
> >2:  Watts RA, Hunt PW, Hvitved AN, Hargrove MS, Peacock WJ, Dennis ES.
> >Related Articles, Links
> >
> >A hemoglobin from plants homologous to truncated hemoglobins of
> >microorganisms.
> >Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10119-24.
> >PMID: 11526234 [PubMed - indexed for MEDLINE]
> >
> >3:  Trevaskis B, Watts RA, Andersson CR, Llewellyn DJ, Hargrove MS, Olson
> >JS, Dennis ES, Peacock WJ. Related Articles, Links
> >
> >Two hemoglobin genes in Arabidopsis thaliana: the evolutionary origins of
> >leghemoglobins.
> >Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):12230-4.
> >PMID: 9342391 [PubMed - indexed for MEDLINE]
> >
> >(among others)
> >
> >
> >Regards,
> >
> >Tanya Berardini
> >
> >On Wed, 20 Nov 2002, abarre wrote:
> >
> >
> >
> >>Hi,
> >>
> >>I was looking for the terl present in Plnat Ontology and not in Gene
> >>Ontology.
> >>Among the list, there's "hemoglobin". For me the hemoglobin is not a
> >>specific term of plant !!!!
> >>
> >>This term is really absent in latest release of Gene Ontology but was
> >>present in the precedent (as cellular component, GO:0005833) !
> >>Something change in blood composition ? I thought it had become OBSOLETE
> >>in this case !
> >>
> >>
> >>
> >>
> >>
> >
> >-------------------------------------------------------------------------------
> >Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
> >The Arabidopsis Information Resource	FAX: (650) 325-6857
> >Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
> >Department of Plant Biology		URL: http://arabidopsis.org/
> >260 Panama St.
> >Stanford, CA 94305
> >-------------------------------------------------------------------------------
> >
> >
> >
>
>
>

-------------------------------------------------------------------------------
Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------