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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>
Hi
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

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
tw.rpi.edu

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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