Re: [Obo-relations] [Obo-discuss] Draft document on OBO id and URI policy
Ward Blondé
Dear OBO URI drafters,
I see in the OBO Foundry Identifier Policy that it is the intention to
make OBO and OWL entirely interconvertible in the future. I have some
questions about how things are arranged for relations. It seems nothing
special is said about relations until now in
https://docs.google.com/View?docID=0Acx6Blq96uycZHpwcm5td18wZGtkMmdiZ3Y&revision=_latest
Especially about the difference between relation types at the class
level (as they are used in OBO) and the instance level (object
properties as used in OWL-DL). These are clearly different things, e.g.
part_of is the inverse of has_part at the instance level, but not at the
class level. Can I assume that the URI that follows logically from the
URI Policy denotes the relation type at the instance level (the
owl:ObjectProperty)? So:
http://purl.obolibrary.org/obo/part_of rdf:type owl:ObjectProperty for
the direct semantics of OWL??
Is there any way to have URIs for class level relation types from these
basic instance relation types? Like e.g.
http://purl.obolibrary.org/obo/class_rel/part_of ??
The latter cannot be used anywhere in OWL-DL, but continuing the work on
Metarel, I am trying to make such relation types of use within OWL Full.
Which means they would also need a URI. And because everything that
exists deserves a URI... :-)
Regards,
Ward
Alan Ruttenberg wrote:
> As discussed in last year's OBO foundry meeting, we've drafted a
> document describing the proposed policy, going forward, for mapping
> ids of OBO ontologies in OBO format to URIs.
>
> The draft document is at
>
> https://docs.google.com/View?docID=0Acx6Blq96uycZHpwcm5td18wZGtkMmdiZ3Y&revision=_latest
> <https://docs.google.com/View?docID=0Acx6Blq96uycZHpwcm5td18wZGtkMmdiZ3Y&revision=_latest>
>
> It's drafting has been a collaborative effort - please see
> acknowledgement at the end of the document.
>
> It is intended that once the document is finalized we will be working
> on a new embedding of OBO in OWL, using the proposed URI scheme, and
> taking advantage of the features of OWL 2.
>
> If you would like to have write access to the document so as to
> include comments in line, or help improve it, please let me know.
> Otherwise comments by any modality are welcome.
>
> Regards,
> Alan
> (yes, I'm aware that there is still a FIXME in the document)
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Alan Ruttenberg
>
>
> Dear OBO URI drafters,
>
> I see in the OBO Foundry Identifier Policy that it is the intention to
> make OBO and OWL entirely interconvertible in the future. I have some
> questions about how things are arranged for relations. It seems nothing
> special is said about relations until now in
> https://docs.google.com/View?docID=0Acx6Blq96uycZHpwcm5td18wZGtkMmdiZ3Y&revision=_latest
>
> Especially about the difference between relation types at the class
> level (as they are used in OBO) and the instance level (object
> properties as used in OWL-DL). These are clearly different things, e.g.
> part_of is the inverse of has_part at the instance level, but not at the
> class level. Can I assume that the URI that follows logically from the
> URI Policy denotes the relation type at the instance level (the
> owl:ObjectProperty)? So:
> http://purl.obolibrary.org/obo/part_of rdf:type owl:ObjectProperty for
> the direct semantics of OWL??
>
> Is there any way to have URIs for class level relation types from these
> basic instance relation types? Like e.g.
> http://purl.obolibrary.org/obo/class_rel/part_of ??
>
> The latter cannot be used anywhere in OWL-DL, but continuing the work on
> Metarel, I am trying to make such relation types of use within OWL Full.
> Which means they would also need a URI. And because everything that
> exists deserves a URI... :-)
Hello Ward,
There are plans to have this distinction be made in the next release
of RO/BFO. This is an issue distinct to the URI policy, which only
addresses the questions of how to map OBO format ids to URIs for OBO
Foundry ontologies and other ontologies that are planned to be
submitted or whose developers wish to take advantage of the
infrastructure that is being developed to support the URIs.
-Alan
Ward Blondé
Hello Alan,
Thanks for your answer. Still it is not entirely clear to me which URIs
are recommended to be used in OWL-DL files (so at the instance level).
This one:
http://purl.obolibrary.org/obo/part_of ?
In the owl file of OBI, I find also this:
http://www.obofoundry.org/ro/ro.owl#part_of
as well as OBI-specific relation types like:
http://purl.obolibrary.org/obo/OBI_0000312 <!-- is_specified_output_of -->
All these stand in places for relation types at the instance level
(object properties).
David Osumi-Sutherland
re: URIs for OBO relations:
I believe that Chris Mungall has generated more conventional OBO IDs
instance and type level OBO relations. He's currently on vacation -
he'll be back on the 20th. He should be able to let you and others on
this list know when and where these will be released.
Cheers,
David
David Osumi-Sutherland, PhD
Curator/ Ontologist
FlyBase / Virtual Fly Brain
Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge, CB2 3EH, UK
Tel: +44 (0)1223 333 963
Fax: +44 (0)1223 766 732