HCLSIG/Meetings/2009-03-05 Conference Call
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 #: +33.4.89.06.34.99 (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
Agenda
- News Updates by BioRDF, COI, LODD, Pharma Ontology, Scientific Discourse, Terminology - All
- C-SHALS trip report - Susie
- Intro SKOS, Summary of SKOS developments - Alistair Miles (Oxford)
- Use cases for representing data in SKOS vs OWL - Eric
http://www.w3.org/2009/Talks/0205-skos-egp/
- AOB
Minutes
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]
http://www.w3.org/2009/Talks/0205-skos-egp/
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]
semantics!
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(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.