From: Chris M. <cj...@fr...> - 2007-06-27 00:19:05
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On Jun 26, 2007, at 2:59 PM, Nicolas Le Novere wrote: > This is an interesting problem, that is more general than taxonomical > information. There is maybe a confusion between a type of data, and > the > resources that distribute it. And I think the GO Database > Abbreviations > falls in this trap. The data-type is a shared namespace. I'm not sure I follow. The abbreviation indicates the authority/ database that owns the ID-space, not who the various organisations are that redistribute the data > For instance enzyme nomenclature is distributed by EBI IntEnz, SBI > enzyme, > KEGG ENZYME etc. But the identifiers are always EC:x.x.x.x > Same for PIR/SwissProt/TrEMBL ids (UniProt id), PubMed/Medline, etc. But the EC is the organisation in charge of assigning identifiers within the EC ID-space > (interestingly, for UniProt ids, GO DA provides four redundant > entries, > with four different namespaces, linked to the same resource. But > for EC, > only one is listed, and not the master-copy, which is IntEnz) I'd say we could collapse a few of the UniProt entries. Perhaps the primary URL for EC could be changed too. We really need a dedicated list for this. > In the present case, NEWT and NCBI taxonomy share the same identifier > namespace, and therefore the data type is not really an NCBI one. I always thought the NCBI were the authority for this particular ID- space. If it's a collaborative venture then the primary URL should really reflect this. Or are you just saying the NEWT browser is another way to browse the same information? If so then it's easy to add an alternate URL > In MIRIAM Resources, we deprecated the root URI > "http://www.ncbi.nlm.nih.gov/Taxonomy/" and created > "http://www.taxonomy.org/" (no flame on URIs looking like URLs please) Not sure what you mean. That URI *is* a URL. > see: > http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb? > section=browse&data=MIR:00000006 > > So http://www.taxonomy.org/#9606 can redirect to > http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi? > mode=Info&id=9606 > or > http://www.ebi.ac.uk/newt/display?search=9606 ok, so all that's required is an alternate URL for retrieving a different html view of the same information? > according the user's liking. > >> Some of the translations in the OBO Download Matrix are experimental, >> including the NCBI taxon one. >> >> You're right in that the GO-sanctioned IDspace for this resource is >> 'taxon' >> http://www.geneontology.org/cgi-bin/xrefs.cgi >> >> (this may change when the IDspace directory migrates to becoming a >> shared GO/NCBI/UniProt resource) >> >> I chose NCBITaxon to reflect the source (NCBI are not the only source >> of organismal classification taxons - but let's not get into that >> now) and also to reflect the fact that the identifier for an OBO/OWL >> class has information structured in a different way than the source >> records. >> >> On Jun 26, 2007, at 10:48 AM, Aaron Gussman wrote: >> >>> On the OBO Foundry main page it says the NCBI organismal >>> classification >>> Prefix is "taxon" but on the OBO Download Matrix, the >>> ncbi_taxonomy.obo file has term ids of the form "id: NCBITaxon:2". >>> Should it be "taxon:" or "NCBITaxon:"? >>> >>> Thanks, >>> Aaron >>> >>> >>> -------------------------------------------------------------------- >>> -- >>> --- >>> This SF.net email is sponsored by DB2 Express >>> Download DB2 Express C - the FREE version of DB2 express and take >>> control of your XML. No limits. Just data. Click to get it now. >>> http://sourceforge.net/powerbar/db2/ >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >> >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> > > > -- > Nicolas LE NOVERE, Computational Neurobiology, > EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 > 1SD, UK > Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074 > http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:nle...@ho... > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > |