From: Nicolas Le N. <le...@eb...> - 2007-06-27 09:15:28
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>> 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 Exactly. This is why there should be only one entry for UniProt, as there is one for EC. >> 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 Yes. Absolutely. But there are multiple "databases". This is the whole problem of those xrefs. Do-they represent the namespaces or the resources. >> 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. Yes ... but it is not supposed to physically exist. So it is not really a "Location". It is just a unique string associated to a data type. But it avoids some confusion we can find with name, like GO's CGD that could be the acronym of Candida Genome Database, but also of the Cattle Genome Database. >> 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? This is an example. MIRIAM Resources can be used in different ways. One thing we will implement is the access to the associated webservices, so a software could decide to launch a molecule viewer when encountering a PDB URI rather than building an hyperlink. -- 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... |