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RE: [linkedlifew3cnote] [LLD] Fwd: Michel's semantic interoperability definitions

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Mon, 10 Sep 2012 08:08:05 -0700
Message-ID: <d9edba7abf92e77a9f603f9c56652a99@mail.gmail.com>
To: linkedlifedatapracticesnote@googlegroups.com, HCLS <public-semweb-lifesci@w3.org>
hi all,

> Note, I brought up wanting to integrate some definitions that Michel
> had brought up.

i might be off base here but :

> 3. semantic interoperability - establish SPARQL-based transformations
> of each source to a global schema

sounds like what the BioRDF paper laid the groundwork for?

cheers,
michael

> -----Original Message-----
> From: linkedlifedatapracticesnote@googlegroups.com
> [mailto:linkedlifedatapracticesnote@googlegroups.com] On Behalf Of M.
> Scott Marshall
> Sent: Monday, September 10, 2012 7:58 AM
> To: linkedlifedatapracticesnote@googlegroups.com; HCLS
> Subject: [linkedlifew3cnote] [LLD] Fwd: Michel's semantic
interoperability
> definitions
>
> In discussions about finishing touches on the Emerging Practices IG
> Note, I brought up wanting to integrate some definitions that Michel
> had brought up. I have finally located the text that I keep referring
> to. :) See below.
>
> Cheers, Scott
>
> ---------- Forwarded message ----------
> From: Michel Dumontier <michel.dumontier@gmail.com>
> Date: Mon, Jul 9, 2012 at 7:32 PM
> Subject: Re: GXA RDF
> To: expressionrdf@googlegroups.com
> Cc: jupp@ebi.ac.uk
>
>
> Ok,
>  so, i'm planning to add a mapping table - from a generalized concept
> to the specific vocabularies in which that concept is defined. Now,
> the list of terms immediately supports the goal of semantic
> annotation, but it falls short in terms of semantic interoperability.
> One of the things that we can do is mimic what we did for the TMO work
> - we added terms to the TMO with formalized mappings (rdfs:subClassOf,
> owl:equivalentClass) to those target terminologies, and could then use
> the TMO classes to query data that was annotated with *any* of the
> terminologies.  This is fine for simple concept-based data retrieval,
> but is very poor for structured queries, where each of the source data
> has a different topology.  Approaches like that of BioPAX helps
> marshal structurally and semantically varying data into one coherent
> form (FWIW). We can, however, facilitate this "global schema mapping"
> through SPARQL construct queries that lifts the data from one source
> to the target.  So here's the list of options with increasing work:
>
> 1. semantic annotation - list terms in use and/or corresponding terms
> using BioPortal
>  * benefit: users know where to look for terms of interest to them and
> will provide some kind of semantically annotated data
> 2. terminological mapping - formalized the equivalance/subclass
> relations among terms
>  * benefit: users know that any of the terms can be used to annotate
> and query their data (at the type level)
> 3. semantic interoperability - establish SPARQL-based transformations
> of each source to a global schema
> * benefit: users can query any data using a common formalization of
those
> data
>
> m.
Received on Monday, 10 September 2012 15:08:30 GMT

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