Re: [Obo-discuss] Resource URI:s

[Nicolas Le N. <le...@eb...>]

Hi,

Something similar actually already exists, although based on URNs and not
PURLs. In order to support the MIRIAM guidelines on model annotations, the
MIRIAM resources have been created, that provide a unique way to identify
data-types (and not resources. Several data resources can provide the same
data, and several data types can be provided by the same data resource).
The idea is rather than providing lists of URIs, like LSIDs, offering a
system to build and resolve URI. The system was initially meant to serve
the community of modelers, but its flexibility and genericity now
attracted a more diverse user-base (e.g. the PSI consortium).

Development and maintenance of MIRIAM resources is supported by a funding
from the EU, as part of the preparation of ELIXIR, the European
Infrastructure of Bioinformatics.

More info at:
http://www.ebi.ac.uk/miriam/

Several OBO ontology are already in MIRIAM Database (to build a URI to a
term, replace $ID by the identifier of this term)

ChEBI:                    urn:miriam:obo.chebi:$ID
Evidence codes:           urn:miriam:obo.eco:$ID
Gene Ontology:            urn:miriam:obo.go:$ID
Systems Biology Ontology: urn:miriam:obo.sbo:$ID

You can see MIRIAM URIs in action in the following article:
http://www.nature.com/nbt/journal/v26/n10/abs/nbt1492.html

Best regards,

PS: This message is purely informative and not intended to start a flame
war PURL Vs URI or any other technical debate :-)


> Hello Tore,
>
> At the first meeting of the OBO Foundry in July we resolved to do
> exactly this, and are in the process of implementing the solution.
> Have a look at
> http://ashby.csail.mit.edu/presentations/ColonizationOfTheSemanticWebByOBOFoundry.pdf
>
> We're also working on a regularization of dbxrefs.
>
> Regards,
> Alan
>
> 2008/10/28 Tore Eriksson <tor...@po...>:
>> Hello everybody,
>>
>> I am using the OBO ontologies in owl format and would like to propose a
>> clean-up of the URI:s that represent ontology entries. Due to what I can
>> only assume is a lack of a "standard" URI for each resource, people seem
>> to create their own ones using their own domains. I am fully aware that
>> having multiple URI:s for the same resource is not a problem in it self,
>> but I do think avoiding an explosion in identifiers would be preferable
>> in the long run.
>>
>> As an example, I have encoutered the following URI:s for GO:0000001
>>
>> <http://purl.org/obo/owl/GO#GO_0000001> - OBO owl format
>> <http://www.geneontology.org/go#GO:0000001> - OBO rdf format
>> <http://purl.obo.org/gene_ontology/GO_0000001> - old OBO?
>> <http://purl.uniprot.org/go/0000001> - UniProt
>> <http://bio2rdf.org/go:0000001> - bio2rdf
>>
>> I am fully aware that the last three are out of OBO jurisdiction, and I
>> am
>> only listing them here for completeness. As for the first two, the URI:s
>> changes depending on the file format, and I was unable to find any
>> owl:sameAs triple that link the two together.
>>
>> Furthermore, the relationship ontology in owl does not follow the above
>> pattern but uses a different URI format:
>>
>> <http://www.obofoundry.org/ro/ro.owl#part_of> - OBO owl format
>> <http://www.geneontology.org/go#OBO_REL:part_of> - OBO rdf format
>>
>> This makes me a little apprehensive that in the future it might be
>> rerouted
>> to
>>
>> <http://purl.org/obo/owl/RO#part_of>
>>
>> without notice.
>>
>> I am aware that there are multiple groups working on the same problem
>> and
>> that there will always be some divergence, but I would like to propose
>> three things:
>>
>> * Change the rdf format to use the same URI:s as the owl format.
>> * Add an owl:sameAs pointing to the old rdf URI to the owl format files.
>> * Show what URI patterns are the standard ones to promote reuse.
>>
>> Regards
>>
>> Tore
>>
>> _______________________________________________________________
>> <> dc:creator [
>>   foaf:name "Tore Eriksson",
>>             "$B%H!<%l!!%(%j%/%=%s(B"@jp;
>>   foaf:mbox_sha1sum "2bd9291b301f112775e118f96eb63314594b1a86";
>>   foaf:workplaceHomepage <http://www.taisho.co.jp/> ].
>>
>>
>>
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-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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