15:59:46 <RRSAgent> RRSAgent has joined #hcls
15:59:46 <RRSAgent> logging to http://www.w3.org/2009/03/05-hcls-irc
16:00:13 <mscottm> Zakim, who is on the phone?
16:00:13 <Zakim> On the phone I see EricP, helena, mscottm, johnM
16:00:20 <ericP> Zakim, johnM has johnM, MarryKennedy, CoryH
16:00:20 <Zakim> +johnM, MarryKennedy, CoryH; got it
16:00:47 <Zakim> +oliver
16:00:55 <Zakim> + +1.510.381.aaaa
16:01:00 <Zakim> +Kingsley_Idehen
16:01:03 <curoli> zakim, oliver is curoli
16:01:03 <Zakim> +curoli; got it
16:01:15 <Zakim> + +1.617.395.aabb
16:01:21 <kidehen> kidehen has joined #hcls
16:01:25 <matthias_samwald> still trying to dial in...
16:01:45 <Zakim> + +46.4.67.7.aacc
16:02:20 <Zakim> - +1.510.381.aaaa
16:02:37 <mscottm> Bosse Andersson
16:02:49 <ericP> Zakim, +46.4.67.7.aacc is Bosse
16:02:50 <Zakim> +Bosse; got it
16:02:53 <Zakim> +??P4
16:03:00 <jun> jun has joined #hcls
16:03:03 <mscottm> http://esw.w3.org/topic/HCLSIG/Meetings/2009-03-05_Conference_Call
16:03:03 <matthias_samwald> Zakim ??P4 is matthias_samwald
16:03:06 <Zakim> +Jun
16:03:12 <Zakim> +??P5
16:03:21 <ericP> Zakim, +1.617.395.aabb is KevinDoyle
16:03:21 <Zakim> +KevinDoyle; got it
16:03:25 <matthias_samwald> Zakim, ??P4 is matthias_samwald
16:03:25 <Zakim> +matthias_samwald; got it
16:03:27 <mscottm> Zakim, who is on the phone?
16:03:27 <Zakim> On the phone I see EricP, helena, mscottm, johnM, curoli, Kingsley_Idehen, KevinDoyle, Bosse, matthias_samwald, Jun, ??P5
16:03:32 <Zakim> johnM has johnM, MarryKennedy, CoryH
16:03:52 <Ratnesh> Ratnesh has joined #HCLS
16:04:05 <ericP> Zakim, ??P5 is SimonJupp
16:04:05 <Zakim> +SimonJupp; got it
16:04:25 <ericP> ericP has changed the topic to: http://esw.w3.org/topic/HCLSIG/Meetings/2009-03-05_Conference_Call
16:06:26 <ericP> topic: News Updates by BioRDF, COI, LODD, Pharma Ontology, Scientific Discourse, Terminology - All 
16:06:32 <seanb> seanb has joined #HCLS
16:06:36 <Zakim> +Kei_Cheung
16:06:59 <Zakim> +??P9
16:07:23 <kei> kei has joined #HCLS
16:07:34 <ericP> Zakim, ??P9 Ratmesh
16:07:34 <Zakim> I don't understand '??P9 Ratmesh', ericP
16:07:37 <ericP> Zakim, ??P9 is Ratmesh
16:07:37 <Zakim> +Ratmesh; got it
16:07:38 <Ratnesh> zakim, ??P9 is me
16:07:38 <Zakim> I already had ??P9 as Ratmesh, Ratnesh
16:07:53 <ericP> scribenick: mscottm
16:07:57 <mscottm> Welcome Sean!!
16:08:03 <banderss> banderss has joined #HCLS
16:08:31 <ericP> Zakim, Ratmesh is really Ratnesh
16:08:31 <Zakim> +Ratnesh; got it
16:09:13 <Zakim> +??P11
16:09:18 <seanb> Zakim, ??P11 is me
16:09:18 <Zakim> +seanb; got it
16:09:19 <mscottm> Kei: C-SHALS presentation last week, good opportunity for networking, meeting went well.
16:10:07 <Kevin> Kevin has joined #HCLS
16:10:35 <Kevin> Kevin has left #HCLS
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.
16:10:46 <KevinDoyle> KevinDoyle has joined #HCLS
16:11:00 <sjupp> sjupp has joined #HCLS
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.
16:13:41 <Zakim> +Eric_Neumann
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
16:17:06 <eneumann> eneumann has joined #HCLS
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
16:22:19 <aliman> aliman has joined #hcls
16:23:20 <ericP> KevinDoyle: (terranode)
16:23:32 <Zakim> +Alistair
16:23:36 <ericP> s/terranode/teranode/
16:23:42 <johnM> welcome Alistair
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
16:37:25 <Zakim> + +1.617.710.aadd
16:37:33 <Zakim> -KevinDoyle
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?
16:41:32 <Zakim> +??P18
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 http://www4.wiwiss.fu-berlin.de/bizer/pub/lod-datasets_2009-03-05_colored.png (colored graphic)
16:49:25 <mroos> mroos has joined #hcls
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?
17:01:16 <Zakim> -Eric_Neumann
17:01:42 <mscottm> John: OWL will always be correct.
17:02:14 <Zakim> -matthias_samwald
17:02:33 <Zakim> -Kingsley_Idehen
17:02:34 <Zakim> -mscottm
17:03:06 <Zakim> - +1.617.710.aadd
17:03:06 <Ratnesh> bye
17:03:10 <Zakim> -Bosse
17:03:12 <Zakim> -Ratnesh
17:03:14 <Zakim> -Kei_Cheung
17:03:15 <KevinDoyle> KevinDoyle has left #HCLS
17:03:19 <Zakim> -curoli
17:03:23 <Zakim> -Jun
17:04:05 <matthias_samwald> matthias_samwald has left #hcls
17:13:36 <mroos> bye
17:13:38 <Zakim> -seanb
17:13:40 <Zakim> -SimonJupp
17:13:43 <Zakim> -EricP
17:13:44 <Zakim> -Alistair
17:13:44 <Zakim> -??P18
17:14:26 <Zakim> -helena
17:15:37 <sjupp> sjupp has left #HCLS
17:18:14 <HelenaDeus> anobody still there? eric mentioned there were more people interested in managing user permissions in RDF.
17:18:46 <epichler> epichler has joined #hcls
17:19:14 <HelenaDeus> if possible, I'd like to know who has been doing work related to that and what they have been doing :-)
17:19:26 <Zakim> disconnecting the lone participant, johnM, in SW_HCLS()11:00AM
17:19:31 <Zakim> SW_HCLS()11:00AM has ended
17:19:33 <Zakim> Attendees were EricP, helena, mscottm, johnM, MarryKennedy, CoryH, +1.510.381.aaaa, Kingsley_Idehen, curoli, Bosse, Jun, KevinDoyle, matthias_samwald, SimonJupp, Kei_Cheung,
17:19:35 <Zakim> ... Ratnesh, seanb, Eric_Neumann, Alistair, +1.617.710.aadd
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23:54:42 <RRSAgent> logging to http://www.w3.org/2009/03/05-hcls-irc
23:56:43 <mscottm> RRSAgent, please draft minutes
23:56:43 <RRSAgent> I have made the request to generate http://www.w3.org/2009/03/05-hcls-minutes.html mscottm
23:56:58 <mscottm> RRSAgent, please make log world-visible
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