tag:blogger.com,1999:blog-16081779.post2216376147246776920..comments2023-10-28T09:24:38.420+01:00Comments on iPhylo: Wiki modelling - Part 3Roderic Pagehttp://www.blogger.com/profile/00269598293846172649noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-16081779.post-56693616344018736462009-02-02T23:26:00.000+00:002009-02-02T23:26:00.000+00:00Pete,NCBI ids are widely used as taxon URIs, partl...Pete,<BR/><BR/>NCBI ids are widely used as taxon URIs, partly because they are stable (something biodiversity databases have -- until recently -- failed to ensure), and partly because they are connected to data that people care about - sequences. They also have the advantage of providing a single "view" of what each taxon is (although that view may change over time).<BR/><BR/>I haven't thought about this much, but I would lean to the idea that taxonomic names should have URIs (they are essentially tags), that we are interested in information tagged with those names, and that some people/agencies/organisations will provide a view on what is (or isn't) included in a particular taxon. Those views that people find useful (e.g., NCBI taxon ids) will get used. I personally don't find debates about the existence of taxa terribly illuminating.<BR/><BR/>Re TreeBASE, the nearest I've come across are the URL API links described at http://www.treebase.org/treebase/urlapi.htmlRoderic Pagehttps://www.blogger.com/profile/00269598293846172649noreply@blogger.comtag:blogger.com,1999:blog-16081779.post-2383233658140367972009-02-02T20:55:00.000+00:002009-02-02T20:55:00.000+00:00The NCBI taxon id works in a way similar to the Ge...The NCBI taxon id works in a way similar to the GeoSpecies ID's in that the ID stays the same despite changes in nomenclature. I would use this except that there is no NCBI ID for most species. There needs to be a sequence for there to be an NCBI ID.<BR/><BR/>In this sense, the NCBI ID and GeoSpecies ID are compatible types of OTU's.<BR/><BR/>It seems that the genomics people are already using forms of the NCBI ID as Species URI's<BR/><BR/>This gets into what makes a good species URI.<BR/><BR/>I think that there is a species and different scientists publish taxonomic hypotheses for that species. <BR/><BR/>It seems that most others see this the other way around. <BR/><BR/>They see it from this perspective. There are publications (each with a slightly different meaning for the species they discuss). They point these at each other merge etc. and create an identifier.<BR/><BR/>Is this a useful, meaningful identifier? Maybe for publications and as additional information related to species concepts, but not something I would use to tie specimens to a operational taxonomic unit (OTU).<BR/><BR/>RelatedTopic: I have treebaseID's in the GeoSpecies database, but I have not figured out the best way to express them. Do you have a standard URI?Pete DeVrieshttps://www.blogger.com/profile/13883413416016252154noreply@blogger.com