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

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 10 Sep 2012 18:18:58 +0200
Message-ID: <CACHzV2NRFUvCAtc518zZtD1VNLVB=+UdFLw8G0CTu8YTfTRZGw@mail.gmail.com>
To: linkedlifedatapracticesnote@googlegroups.com, Michael Miller <Michael.Miller@systemsbiology.org>
Cc: HCLS <public-semweb-lifesci@w3.org>
Hi Michael,

Yes, Michel is referring to the approach discussed in the "Translating
standards into practice" paper:
http://www.ncbi.nlm.nih.gov/pubmed/22449719

I grabbed one of his messages from an expressionrdf thread in July. In
fact, the next message in that thread was from you. :)

What I was considering was to expand a bit on the notion/definition of
semantic interoperability in the text of the Emerging Practices IG
note.

Cheers,
Scott

On Mon, Sep 10, 2012 at 5:08 PM, Michael Miller
<Michael.Miller@systemsbiology.org> wrote:
> 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 16:19:29 GMT

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