From: Erick A. <eri...@gm...> - 2011-03-31 13:22:39
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Hi Mikel, actually, in practice we are only going to be walking from the varietas rank till the order rank so that the team working on a given crop data could "navigate" (through the ranks) to another (related) crop data. However, in a visualisation application, we thought of displaying the entire path to the root for a given species PLUS the corresponding taxa ranks... cheers, Erick 2011/3/31 Mikel Egaña Aranguren <me...@fi...>: > Hi; > > Taxonomical knowledge representation is still an issue, and something > that will be quite important with the growth of Linked Data, since taxa > seem like the natural hubs for life sciences in the Linked Data cloud. > > Biological taxonomy is tricky for many reasons > (http://bioinformatics.oxfordjournals.org/content/24/13/i313.full) but > it needs to be solved soon. > > Now, Erick, I can see for example querying for all the "subtaxa" of > mammalia, but why would you want to query the subranks of class? > > Cheers > > > > On og., 2011.eko marren 31a 13:30, Peter Midford wrote: >> Hi Erick, >> Why do you think that the ranks themselves should be hierarchical? Saying that a particular species is_a particular genus (or is part_of a genus) is different from saying the ranks themselves are related in that way. Both TAXRANK and the rank terms in the NCBI taxonomy are intended to be used as annotation properties or tags, it's not clear what reasoning you would expect to do with them. >> >> Peter >> >> On Mar 31, 2011, at 3:46, Erick Antezana wrote: >> >>> Hi, >>> >>> is there an ontology "out there" capturing the taxonomy ranks (e.g. >>> species, genus) and their relationships? >>> >>> I found the "Taxonomic rank vocabulary" @ BioPortal >>> (http://purl.bioontology.org/ontology/TAXRANK); however, it is a sort >>> of flat collection of terms... >>> >>> Likewise, the "NCBI organismal classification" >>> (http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy) >>> captures the ranks but no "hierarchy" among them... >>> >>> I am looking for something that would place for instance genus below >>> family and above species... >>> >>> thanks, >>> Erick >>> >>> ------------------------------------------------------------------------------ >>> Create and publish websites with WebMatrix >>> Use the most popular FREE web apps or write code yourself; >>> WebMatrix provides all the features you need to develop and >>> publish your website. http://p.sf.net/sfu/ms-webmatrix-sf >>> _______________________________________________ >>> Obo-taxonomy mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-taxonomy >> Peter E. Midford >> Phenoscape Ontology Curator >> Pet...@gm... >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Create and publish websites with WebMatrix >> Use the most popular FREE web apps or write code yourself; >> WebMatrix provides all the features you need to develop and >> publish your website. http://p.sf.net/sfu/ms-webmatrix-sf >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > -- > Mikel Egaña Aranguren, PhD > http://mikeleganaaranguren.com > > Marie Curie post-doc at Ontology Engineering Group, UPM > http://www.oeg-upm.net/ > > > ------------------------------------------------------------------------------ > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > |