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Re: BioRDF Brainstorming -- Connecting the Health Care and Life Science KB to the Linking Open Data datasets

From: Matthias Samwald <samwald@gmx.at>
Date: Fri, 15 Feb 2008 14:44:55 +0100
Message-ID: <1C15987A77BE404385660849185BF3F4@tessellate>
To: <public-semweb-lifesci@w3.org>
Cc: "Richard Cyganiak" <richard@cyganiak.de>, "Hausenblas, Michael" <michael.hausenblas@joanneum.at>

I added yet another item to the BioRDF Brainstorming document [1].  Here is 
the text that can also be found and edited on the Wiki page:

___HCLS KB mapping to the open linked data repositories___

It would be great if two of the largest coherent Semantic Web structures, 
namely the HCLS Knowledge Base and the Linking Open Data datasets [2], could 
be mapped to each other.
Some possible anchors in the Linking Open Data (LOD) datasets:
 * DBpedia (besides label-matching, we could also make use of information 
like CAS number, Uniprot/Pubmed references etc. that are part of DBpedia)
 * W3C Wordnet
 * OpenCyc 1.0

Some possible anchors in the HCLS KB:
 * All of the OBO ontologies
 * MeSH in SKOS
 * NeuronDB

Since DBpedia is already mapped to most other datasets in the LOD 
collection, DBpedia would probably be our primary target for such mappings. 
Since the ontological foundation of most LOD datasets is relatively loose 
compared to most HCLS datasets, the mapping should not be done with 
owl:sameAs or owl:equivalentClass statements, but rather with softer 
statements such as rdfs:seeAlso. The only exception is OpenCyc, where a more 
stringent mapping with owl:equivalentClass is possible. A mapping between 
the SKOS version of MeSH and the SKOS version of Wikipedia categories could 
also receive special attention: we could use owl:sameAs (although this is 
discouraged by the SKOS specification) or the specialized SKOS mapping 

Furthermore, we should:
 * Learn about the guidelines for publishing RDF/OWL according to the 
practices agreed on by the Open Linked Data community [3]
 * Analyze which of the HCLS KB datasets are already in agreement with these 
 * Decide if some of our HCLS-oriented projects could benefit from adhering 
to these practices. This should NOT trigger a general discussion about URI 
issues and resolution mechanisms once again. At this point, we simply want 
to evaluate who in the HCLS community it motivated to published 'linked 

Even if we decide that adhering to the linked data practices is not of 
special interest to us, a mapping to the LOD datasets would still be very 
valuable in itself.

[1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Brainstorming
[2] http://richard.cyganiak.de/2007/10/lod/
[3] http://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/

Matthias Samwald

Semantic Web Company, Austria
DERI Galway, Ireland

----- Original Message ----- 
From: "Susie M Stephens" <STEPHENS_SUSIE_M@LILLY.COM>
To: <public-semweb-lifesci@w3.org>
Sent: Monday, February 04, 2008 6:05 PM
Subject: BioRDF Brainstorming

> I've created a Wiki page where people can propose projects for BioRDF to
> work on until the end of April [1]. It'd be great if you could post any
> ideas that you may have.
> Cheers,
> Susie
> [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Brainstorming
Received on Friday, 15 February 2008 13:45:21 UTC

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