Fwd: proposed COI call Wed 4 Sep

[Jim McCusker]

For your interest.

Jim

---------- Forwarded message ----------
From: Sajjad Hussain <sajjad....@crc.jussieu.fr>
Date: Tue, Sep 3, 2013 at 6:58 PM
Subject: Re: proposed COI call Wed 4 Sep
To: Kerstin Forsberg <kerstin.l...@gmail.com>
Cc: Eric Prud'hommeaux <er...@w3.org>, "public-sem...@w3.org" <public-sem...@w3.org>, Charlie Mead <charli...@yahoo.com>, Josh Mandel <jma...@gmail.com>, Hans Constandt <ha...@ontoforce.com>, Christel Daniel <christe...@crc.jussieu.fr>, Mustafa Yuksel <mus...@srdc.com.tr>, Gokce Banu Laleci Erturkmen <go...@srdc.com.tr>, Erick Von Schweber <er...@surveyorhealth.com>, "Solbrig, Harold R." <Solbrig...@mayo.edu>, Stan Huff <Stan...@imail.org>, "Jiang, Guoqian, M.D., Ph.D." <Jiang....@mayo.edu>, "Emory Fry (Google Drive)" <ea...@gmx.com>, Conor Dowling <conor-...@caregraf.com>, David Booth <da...@dbooth.org>, Jos De Roo <jos....@agfa.com>

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 <er...@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 port 6665.

Please try out <http://irc.w3.org/> if you don't have an IRC client.

--

-ericP

--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.m...@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu

--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.m...@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu