HCLSIG/Meetings/2009-03-05 Conference Call

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Conference Details

  • Date of Call: Thursday March 5, 2009
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 Greenwich Mean Time (GMT), 17:00 Central European Time (CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Scott, Susie


  • AOB


Attendees: Scott, EricP, helena, johnM, MaryKennedy, CoryH, curoli, Kingsley_Idehen, Matthias_samwald, Bosse Andersson, jun, KevinDoyle, Ratnesh, SimonJupp, seanb, Kei_Cheung, EricN, alistair Miles, mroos

16:10:38 [mscottm]

   ..following up on the query federation work, we are considering the Special Issue of BMC Bioinformatics, contacted editors about deadline extension to give us a fighting chance.

16:11:07 [mscottm]

   ..Need to think about the F2F meeting in the BioRDF group.

16:12:24 [mscottm]

   Eric (COI): showed demo at C-SHALS about patient eligibility making use of pushing SPARQL queries through to mySQL databases

16:12:46 [mscottm]

   ..Helen, Holger, and Eric are still working on the demo.

16:13:28 [mscottm]

   Bosse (LODD): got paper back, working on incorporating the reviewer's comments, need to think about F2F.

16:14:20 [mscottm]

   John (PharmaOnto): garbled (sorry!).

16:15:03 [johnM]

   NIH Challenge Grants announcement: http://grants.nih.gov/grants/funding/challenge_award/Omnibus.pdf (esp. pp 128ff)

16:15:09 [mscottm]

   John (Terminology): had a good presentation at C-SHALS, AIDA is being extended with new features, MeSH SKOS has been added to server.

16:15:47 [mscottm]

   johnM (AOB): Check this out, relevant to HCLS IG: http://grants.nih.gov/grants/funding/challenge_award/Omnibus.pdf

16:16:09 [mscottm]

   ..it's a large collection of NIH grant descriptions

16:16:13 [ericP]

   -> http://grants.nih.gov/grants/funding/challenge_award/Omnibus.pdf call for NIH Challnge Grants proposals

16:17:20 [ericP]

   topic: introductions

16:20:51 [ericP]

   -> http://www.w3.org/2009/Talks/0205-skos-egp/ skos use case slides

16:20:54 [mscottm]

   Intro (HelenaDeus): Grad student at UTexas interested in SW use cases

16:22:11 [[[KevinDoyle]]]

   I have joined these meetings a few times, but it has been a few months since I was last on a call

16:23:51 [ericP]

   KevinDoyle: platform for SW systems for lifcesci market

16:23:57 [ericP]

   ... on top of 11g

16:24:00 [mscottm]

   Intro (Sean Bechhofer, UManchester, involved in SW for many years - [scott paraphrases]

16:24:34 [ericP]

   aliman: Alistair Miles

16:24:44 [ericP]

   ... work with flyweb at Manchester

16:24:55 [ericP]

   ... worked with SWBP, developing skos

16:25:03 [jun]

   I think flyweb is from Oxford

16:25:23 [ericP]

   topic: skos intro [ aliman ]

16:25:49 [mscottm]

   Intro (Simon Jupp): Comes to us from UManchester, works for Robert Stevens, can provide information about SKOS tools (worked on SKOS editor for Protege)

16:25:53 [ericP]

   aliman: used to describe existing classification schemes which are not full-fledged ontologies

16:26:22 [ericP]

   ... useful when creating a new ont when you just want to provide navigation framework

16:26:33 [ericP]

   ... last call WG Aug or Oct last year

16:26:48 [ericP]

   ... last call WG 29 Aug 2008

16:26:58 [ericP]

   ... waiting i18n to submit comments

16:27:09 [ericP]

   ... hope for CR very shortly -- following a call for implementations

16:27:25 [seanb]

   -> http://www.w3.org/2006/07/SWD/SKOS/reference/20081001/ (SKOS editor's draft)

16:27:27 [ericP]

   ... excited to hear about our use of skos

16:27:57 [ericP]

   johnM: most folks here are using 2004 skos

16:28:10 [aliman]

   -> http://www.w3.org/TR/2005/WD-swbp-skos-core-guide-20051102/ 2005 SKOS Core Guide

16:29:02 [ericP]

   aliman: 2005 SKOS Core Guide is about to go to candidate rec

16:29:09 [ericP]

   ... basic overview hasn't changed

16:29:25 [ericP]

   ... new skos abstract synopsis breaks down the skos modules:

16:29:29 [ericP]

   ... .. concepts

16:29:41 [ericP]

   ... .. labeling with plain literals in natural language

16:29:48 [ericP]

   ... .. notations -- lexical code

16:29:51 [ericP]

   ... .. []

16:30:01 [ericP]

   ... .. mapping between concepts

16:30:10 [ericP]

   ... .. grouping into concept schemes

16:30:39 [ericP]

   ... mapping and notations modules are new

16:31:04 [mscottm]

   aliman: SKOS is broken into many modules: e.g. language, concept schemes, mapping, document properties, Semantic relations, etc.

16:31:18 [ericP]

   ... appendix skosxl for describing more about lexical entities

16:31:49 [ericP]

   ... RDF literals can't be subjects in RDF

16:32:03 [ericP]

   ... you either need to do some tricks, or identify them in another way

16:32:24 [ericP]

   ... skoxsl can say that "x" is a transliteration of "y"

16:32:53 [ericP]

   ... defn for skos:broader was transitive in 2005

16:33:07 [ericP]

   ... no longer transitive, but has a transitive super property

16:33:22 [ericP]

   ... eases getting at direct hierarchale relations

16:33:57 [mscottm]


16:34:16 [ericP]

   -> http://www.w3.org/2009/Talks/0205-skos-egp/ skos v.s. owl

16:34:24 [ericP]

   topic: skos vs. owl

16:34:54 [johnM]

   "Weakened Ontologies vs. Qulaified Ontolgies"

16:36:03 [eneumann]

   Evolving use-case for SKOS: as a central thesauri repository that can be used by text-mining applications to produce normalized (concept uri) output

16:39:19 [eneumann]

   ... within one pharma company, this is producing usable terminologies many times more efficiently than if OWL was being used.

16:41:09 [mscottm]

   ericP (slide2): some rdfs reasoning that you can do, asks Alistair if you can do that with SKOS

16:41:23 [seanb]


16:41:29 [kidehen]

   is it safe to say: SKOS is to Phenotype what OWL is to Gentotype?

16:41:45 [mscottm]

   Alistair: answers yes, with skos:broaderTransitive

16:42:26 [mscottm]

   ..can connect Fido with Animal via transitive relations

16:42:31 [kidehen]

   so SKOS is for ABox oriented categorization/classification (even folksonomy structure) and OWL for the TBox

16:45:58 [eneumann]

   SKOS best for descriptive forms where knowledge is limited, e.g., phenotypes and symptoms

16:46:17 [aliman]

   FYI from http://www.w3.org/TR/2008/WD-skos-reference-20080829/#L1045 -- """

16:46:18 [aliman]

   To make the "knowledge" embedded in a thesaurus or classification scheme explicit in any formal sense requires that the thesaurus or classification scheme be re-engineered as a formal ontology. In other words, some person has to do the work of transforming the structure and intellectual content of a thesaurus or classification scheme into a set of formal axioms and facts. This work of...

16:46:20 [aliman]

   ...transformation is both intellectually demanding and time consuming, and therefore costly. Much can be gained from using thesauri etc. "as-is", as informal, convenient structures for navigation within a subject domain. Using them "as-is" does not require any re-engineering, and is therefore much less costly.

16:46:21 [aliman]


16:49:17 [kidehen]

   note release of the latest LOD cloud bubble diagram: http://www4.wiwiss.fu-berlin.de/bizer/pub/lod-datasets_2009-03-05.html (clickable version) and lod-datasets_2009-03-05_colored.png (colored graphic)

16:52:16 [eneumann]

   SKOS -> OWL does appear to be a practical evolutionary approach within orgs

16:54:49 [mscottm]

   Alistair: two approaches: start with SKOS and eventually create an OWL copy, updating the mirrors

16:55:33 [mscottm]

   ..2) is mix the models, start with SKOS, add rdfs relation between SKOS concepts, e.g. rdfs:subClass

16:56:37 [mscottm]

   Sean (?): I would like to see use cases for these approaches.

16:58:54 [mscottm]

   ericP: OWL punning isn't a problem in SKOS (slide6)

16:59:34 [kidehen]

   When it is superficial (phenotypical) errors aren't costly

17:00:07 [kidehen]

   or aren't as costly as when they are genotypical (OWL)

17:00:09 [mscottm]

   Sean: How do I know when the machine is telling me something wrong?

17:00:47 [mscottm]

   ericP: Would the machine have been able to make any decisions using SKOS anyway?

17:01:42 [mscottm]

   John: OWL will always be correct.

17:03:15 [[[KevinDoyle]]]

   KevinDoyle has left #HCLS

17:18:14 [[[HelenaDeus]]]

   anobody still there? eric mentioned there were more people interested in managing user permissions in RDF.

http://www.w3.org/2009/03/05-hcls-minutes.html mscottm