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Re: [Obo-discuss] Ontology about molecular markers
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From: Erick A. <eri...@gm...> - 2009-10-19 09:02:48
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Hi Pankaj, thanks for the links, they are very useful. In the Biodiversity site I have also found: http://www.bioversityinternational.org/fileadmin/bioversity/publications/pdfs/1082.pdf On the other hand, I was wondering whether the list of concepts you refer to ("We have used some of these concepts in a controlled vocabulary format (not ontology).") is accessible somewhere? thanks, Erick 2009/10/3 Pankaj Jaiswal (OSU) <jai...@sc...>: > I think its a mixed bag of concepts. If its only for the markers then as > Judy has pointed out may objects are in the SO. In the list below some items > are not markers, but methods/analysis. So do you think we can define a > markers as something that one can have a locus on a map? If so you have > molecular markers and qualitative/quantitative markers. See some of the work > done by Bioversity International (former IPGRI) in this reference, though > not in the ontology format > (http://www.bioversityinternational.org/index.php?id=19&user_bioversitypublications_pi1[showUid]=2789). > > You may also be interested in looking at the Gramene database's QTL and > Marker subsections. We have used some of these concepts in a controlled > vocabulary format (not ontology). Here's an example of a QTL > http://gramene.org/db/qtl/qtl_display?qtl_accession_id=AQEZ001 > > Pankaj > > Erick Antezana wrote: >> >> Hi Judy, >> >> yes, some terms like for instance: >> >> score >> QTL >> AFLP >> maker >> trait >> variation >> genotype >> breeding >> polymorphism >> marker >> ... >> >> maybe some of them should be in a different ontology (such as SO, or some >> might be already captured by OBI?) >> >> >> regarding the relationships, something like: >> >> >> is_flanked_by (flanking marker) >> is_associated_to (associated marker) >> has_sequence (source sequence) >> ... >> >> >> Again, it is a very rough naming, but the idea would be to capture those >> elements in an ontology (or several) which could support the annotation of >> markers, experiments based on makers, etc. >> >> thanks, >> Erick >> >> 2009/9/30 Judith Blake <Jud...@ja... >> <mailto:Jud...@ja...>> >> >> Hi Erick, >> >> What kind of terms were you thinking of? Could you give an example >> or two? >> >> There is the Sequence Ontology that provides terminology for >> sequence features? >> >> There is the Protein Ontology that provides for protein and complex >> terms? >> >> Etc. >> >> Judy >> >> >> >> On 9/30/09 4:19 AM, "Erick Antezana" <eri...@gm... >> <http://eri...@gm...>> wrote: >> >> Hello, >> >> I was wondering whether somebody is working (building, >> collecting terms, etc) on an ontology dedicated to capture >> and/or deal with molecular marker terms, their relationships, >> etc. If so, could you please point out to any related resource? >> >> thanks, >> Erick >> >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart >> your >> developing skills, take BlackBerry mobile applications to market and >> stay >> ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> http://p.sf.net/sfu/devconf >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> <mailto:Obo...@li...> >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9-12, 2009. Register now! >> http://p.sf.net/sfu/devconf >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > > -- > Pankaj Jaiswal > Assistant Professor > Dept. of Botany and Plant Pathology > 3082 Cordley Hall > Oregon State University > Corvallis, OR, 97331-2902, USA > > Ph.: +1-541-737-8471 > Fax: +1-541-737-3573 > Web: www.gramene.org > www.plantontology.org > > |