- From: M. Scott Marshall <mscottmarshall@gmail.com>
- Date: Mon, 10 Sep 2012 18:18:58 +0200
- 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 UTC