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Re: Adding addition OWL & RDF artifacts to the NC RDF repository

From: Chris Mungall <cjm@fruitfly.org>
Date: Thu, 24 May 2007 12:03:49 -0700
Message-Id: <307005D6-EA97-46F8-8B85-D528CFC6B9A1@fruitfly.org>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, Alan Ruttenberg <alanruttenberg@gmail.com>, Rees Jonathan <jar@mumble.net>
To: William Bug <William.Bug@DrexelMed.edu>


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)
>
>
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>
>
>
>
Received on Thursday, 24 May 2007 19:04:07 UTC

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