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 <e...@w3.org
<mailto:e...@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
