On May 24, 2007, at 11:36 AM, William Bug wrote:
Hi Alan,
Here's the GO/NCBO/Berkeley list that Chris Mungall curates (a page
I'm certain you've been to many times):
http://www.berkeleybop.org/ontologies/
As you know, it contains - among a host of other XML-based formats
- XML-serialized OWL & RDF versions of most all OBO ontologies, as
well as an extensive collection of mappings (also available in RDF
& OWL).
Rather than going through and copy & pasting ALL the OWL & RDF
links into a text file, I thought I just send this reminder and cc
to Chris, as he may have other ideas about how to get these into
the NC repository that don't include error-prone copy & pasting or
require someone to write a scraper for this page.
NC? My acronym buffer is full - do I know this one?
It would also be worth other members of HCLS IG pitching in to help
give you some sense of priorities for these files. I could give
you my sense of that - but that may be less inclusive than we
really want for future HCLS IG demos or NC efforts in general.
In terms of scraping the page, everything is pretty regularized
(and probably algorithmically generated, if I know Chris).
For the ontologies themselves, the URL template appears to be:
http://www.berkeleybop.org/ontologies/obo-all/<ontology_name>/
<ontology_name>.owl
http://www.berkeleybop.org/ontologies/obo-all/<ontology_name>/
<ontology_name>.rdf
The RDF is pretty much legacy pseudo-RDF, from our first attempt to
do GO in RDF many years ago - I would ignore this
You can also fetch by ID-space prefix; for example
<BASE-URL> /owl/ <IDspace>
There isn't always a 1-1 mapping; for example GO is one IDspace and 3
ontologies. So
<BASE-URL> /obo-all/biological_process/biological_process.owl
is a subset of
<BASE-URL> /owl/GO
<BASE-URL> can be either purl.org/obo or http://www.berkeleybop.org/
ontologies. The former is the basis for the stable URIs as it is
independent of hosting location
For the inter-ontology maps, the URL template appears to be:
http://www.berkeleybop.org/ontologies/obo-all/
<ontology1_xp_ontology2>/< ontology1_xp_ontology2 >.owl
http://www.berkeleybop.org/ontologies/obo-all/<
ontology1_xp_ontology2 >/< ontology1_xp_ontology2 >.rdf
'xp' for 'cross-product', I assume.
yes, 'cross product' is the name that seems to have stuck for this
kind of intra and inter ontology combinatorial definitions.
it's not quite as regular as you make out - for example, it is just
mammalian_phenotype_xp because
mammalian_phenotype_xp_pato_xp_go_xp_chebi_xp_mouse_anatomy would be
too much
Note for the xps, there is also a separate imports file;
<BASE-URL> / <a_xp_b> / <a_xp_b>.imports.{owl,obo}
eg
http://www.berkeleybop.org/ontologies/obo-all/go_xp_chebi/
go_xp_chebi.imports.owl
Which is nothing but a collection of import statements. I realise
that this is a different strategy from the semweb norm whereby you
include the import in the main owl file, but I think in general its
easier to do late coupling than late decoupling hence the decision.
Also I'm not keen on mixing imperative parser directives in with
declarative ontological statements.
be warned these xp files are at the draft stage, reasoning over them
will give you some unusual results
So to create a priority list, we'd just need the name of the
ontology. Everything else could be done algorithmically.
Cheers,
Bill
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
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