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Re: proposed COI call Wed 4 Sep

From: Deborah L. McGuinness <dlm@cs.rpi.edu>
Date: Wed, 4 Sep 2013 03:54:45 -0400
Message-ID: <5226E745.2080306@cs.rpi.edu>
To: <public-semweb-lifesci@w3.org>
I will not be able to make the call at 7:30 but we are very interested 
in the nanopublications angle as well as the provenance angle.
our recent paper at dils [1] lays out a bit of the background and as has 
been pointed out, jim mccusker's thesis work is pushing these ideas forward.

[1] **McCusker, J.<http://tw.rpi.edu/web/person/JamesMcCusker>, Lebo, 
T.<http://tw.rpi.edu/web/person/TimLebo>, Krauthammer, 
M.O.<http://tw.rpi.edu/web/person/MichaelKrauthammer>, and McGuinness, 
D.L.<http://tw.rpi.edu/web/person/Deborah_L_McGuinness> 2013. Next 
Generation Cancer Data Discovery, Access, and Integration Using Prizms 
and Nanopublications <http://tw.rpi.edu/web/doc/mccusker_dils2013>. In 
Proceedings of Ninth International Conference on Data Integration in the 
Life Sciences <http://tw.rpi.edu/web/event/dils2013> (July 11-12 2013, 
Montreal, Quebec). http://tw.rpi.edu/web/doc/mccusker_dils2013


Deborah L. McGuinness, Ph.D.
Tetherless World Senior Constellation Chair
Professor of Computer and Cognitive Science
Rensselaer Polytechnic Institute
105 8th St.
Troy, NY 12189
518 276 4404

On 9/3/2013 6:58 PM, Sajjad Hussain wrote:
> Hi Kerstin,
> Good to hear your thoughts about terminology mapping, and adopting 
> Nanopublications schema to deal with mapping provenance issues. Please 
> see my response in-line:
> On 9/3/13 8:50 AM, Kerstin Forsberg wrote:
>> Hi Eric,
>> Thanks for the link to the RIM RDF tutorial, will read with great 
>> interest.
>> I'll not able to join tomorrow. Two thoughts re. mappings.
>> - How to align this with the interest in getting RDF (SKOS) versions 
>> directly from source (eg we have a good interaction with MedDRA MSSO 
>> about this).
>> - Mapping provenance
>> The justification and attribution of the mappings (between 
>> concept/terms) are key to trust them. At the ICBO conference earlier 
>> this summer we discussed the idea of turning for example the mappings 
>> in the Bioportal into Nanopublications based on some great work by 
>> Jim McCusker. So that the Bioportal mappings stated as 
>> skos:closeMatch also would have the justification of them as being 
>> the results of using the LOOM lexical algorithm. An alternative would 
>> be to treat mappings as linksets as done by Open PHACTS and provide 
>> the justification for the links/mappings (between entities) as part 
>> of the linkset description in VoID. Alasdair Gray is working on a 
>> nice proposal 1) on this based on the W3C HCLS task force for dataset 
>> discovery and description that Michel lead.
> Here, it would be interesting to distinguish mappings into three 
> categories and their possible provenance measures:
> 1) Manually defined mappings: In the Nanopublications schema, 
> provenance is captures by the property nanopub:hasProvenance which 
> ties to the property nanopub:hasSupporting, which could capture the 
> mappings curation information (e.g. creator, author, version, rights etc)
> 2) (semi-)automatically found mappings: You have already discussed 
> this case above. So in the case, the information about the LOOM 
> lexical algorithm could be described using nanopub:hasSupporting 
> property in Nanopublications--or alternatively using the Open PHACTS 
> approach ...
> 3) Inferred mappings via reasoning: New mappings can be inferred via a 
> reasoning process (i.e terminology reasoning). In this case, a 
> reasoning proof (i.e. set of inference steps under a rule-based 
> reasoning) can very well be suited to provide some provenance 
> information.
> Just to make my point clear, I would like to share an concrete case:
> Test-case:
> --------
>  ICD-9-CM code (999.4) <---exactMatch --> SNOMED-CT code (213320003) 
> <---exactMatch --> MedDRA code (10067113), for details see 
> term-mapping-example.png and example-term-map.n3.
> Results:
> -----
>  - ICD-9-CM code (999.4) <---exactMatch --> MedDRA code (10067113), 
> because skos:exactMatch is a transitive property.
> A) The proof of this inferred mapping is shown in 
> example-term-map-proof.n3
> B) An abstract or summary of the reasoning results are shown in 
> example-term-map-ances.n3, which gives an overview information about 
> which of the asserted facts (i.e. asserted mappings) were used to 
> derive this inferred mapping.
> C) Finally, an example Nanopublication describing this inferred 
> mapping is shown in example-term-map-nano.n3, where the reasoning 
> information from A) and B) are treated to provide some provenance 
> information as two supporting graphs ":NanoPub_1_Supporting_1" and 
> ":NanoPub_1_Supporting_2". Interestingly :NanoPub_1_Supporting_2 can 
> be validated by a proof-checker--such as cwm 
> (http://www.w3.org/2000/10/swap/doc/cwm) or euler 
> (http://eulersharp.sourceforge.net/).
> I plan to attend the COI call Wed 4 Sep.
> Kind Regards,
> Sajjad
> *****************************************************
>> On 3 sep 2013, at 07:39, Eric Prud'hommeaux <eric@w3.org 
>> <mailto:eric@w3.org>> wrote:
>>> Emory proposed that we meet tomorrow at 7:30am US Eastern to make
>>> progress on shared terminology mappings. That's 4:30 for west-coasters
>>> so if anyone's attending from there, we can split the call into
>>> 30 mins on term mapping when Emory can make it and
>>> 30 minutes on outreach material at the regular time 3.5 hours later.
>>> Please reply with scheduling constraints and I'll do my best to
>>> accomodate.
>>> minutes of prior meetings:
>>> http://www.w3.org/2013/07/12-hcls-minutes
>>> http://www.w3.org/2013/07/18-hcls-minutes
>>> http://www.w3.org/2013/08/07-hcls2-minutes
>>> proposed agenda:
>>> updates on collab between TAPS and SALUS on sharing terminology mappings
>>>  [Conor, Gökçe, Emory]
>>> education/outreach material, e.g.
>>> http://www.w3.org/2013/HCLS-tutorials/RIM/
>>> http://www.w3.org/2013/C-CDA/IJ.xml
>>>  more stuff from SMART
>>> Please RSVP so I can get a head count for the bridge reservation.
>>> Call will be from 11:30-12:30 UTC (07:30 EDT) (13:30 CET)
>>> using the Zakim Bridge: +1.617.761.6200, with
>>> Conference Code: 4257 ("HCLS")
>>> For text, we will use the IRC channel #hcls on irc.w3.org 
>>> <http://irc.w3.org> port 6665.
>>> Please try out <http://irc.w3.org/> if you don't have an IRC client.
>>> -- 
>>> -ericP
Received on Wednesday, 4 September 2013 07:56:12 UTC

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