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06:25:44 <Helen> test
06:26:02 <Helen> zakim, who
06:26:10 <ivan> no zakim, helen
06:26:39 <Helen> hi
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06:32:21 <ivan> Scribe: Helen
06:32:32 <ivan> Topic: HCLSIG F2F, first day
06:32:41 <ivan> Chair: Eric Neumann
06:33:22 <Helen> participants introduction, list of names and afflications to be recorded later
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06:38:42 <Helen> Eric, suggests to Joanthan to give a intro of science commons to the group
06:39:38 <Helen> espcially in publication, in using leagal tags
06:40:44 <Helen> Eric N, main goal is to generate public documents about this HCLS's activities, artifacts by the end of the year, 
06:41:27 <Helen> Objectives: focused, direct activities in task areas, 
06:41:52 <Helen> cross-task collabboration, dynamic interaction, 
06:42:21 <ivan> Present: Helen Chen, Agfa; Dirk Colaert Agfa; Ray Hookway, HP; Alan Ruttenberg, Milleneum Pharmaceutrecal; Bo Anderson, AZ; Kersin Forsberg, AZ; Ivan Herman, W3C; Scott Marshall, UvA; Jonathan Rees, Science Commons; Donald Doherty, Brainstage Research; Vipul Kashyup, Parners Healthcare; Eric Neumann, Teranode; Joanne Luciano, U of Manchester; Keu Cheung, Yale Center for Medical Information; Susie Stephens, Oracle; Chimezie Ogbuji, Cleveland Clinic
06:42:30 <Helen> HCLS is focused on best practices, not standards, also identify areas to push to the other Semantic Web areas
06:43:07 <Helen> put demos, senarios to illustrate issues, also demo at a large scale, how semantic web can work
06:43:51 <Helen> generate documents to interact with other initiatives, to see what can be done with semantic web. 
06:44:29 <Helen> Important to specify the roadmap for the group in the remaining year, more focused activities
06:45:06 <Helen> HCLS Timeline (draft), 
06:46:23 <Helen> 1/07 timeframe: Draft best practices, (demonstrations - BioRDF, BioOnt, ACPP, DSE),( LS URI - Code Base, Tec Help?)
06:46:36 <Helen> Collect specific proposals for demostrations, 
06:46:45 <Helen> define areas for best practices definitions
06:47:11 <Helen> Joanne, want to know the specific charters of the group
06:47:32 <Helen> Eric N: orginal charter is too big and vague, 
06:48:33 <Helen> Ivan: this is an interest group, not a working group, 
06:48:49 <Helen> working group is more for deliverables, timelines, 
06:49:24 <Helen> IG group is loosely connnected, 
06:50:12 <Helen> at W3C, need to produce working draft regularly, not scienctific publication, 
06:50:38 <Helen> states what we know, what we have for public comments, 
06:51:01 <Helen> Eric N, need to publish the work of this IG group in the near future
06:51:27 <Helen> Ivan: publish  "W3C working draft"
06:52:54 <Helen> Ivan: Next May, by the end of this IG's time, the charter has to be renew, and may generate enough interests for other groups
06:53:42 <Helen> Dirk C. suggests identifiy publishing date and task for each TF group at this meeting
06:54:40 <Helen> Ivan: the deadline of the draft is ISWC 
06:55:08 <Helen> Ivan: each group to "elect" editor of these publication
06:56:18 <Helen> Eric: if any issues are important to healthcare and life science area, but not standarized yet, need to put in sceniaros, and requirements
06:56:45 <Helen> Kei: SPARQL, on the table?
06:57:03 <Helen> Chimezie: named graph, is on the discussion yesterday
06:57:38 <Helen> Don: RDF vs. OWL, heavy weight, light weight semantics, alternatives
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06:58:41 <Helen> advises, what kinds of questions RDF and OWL each best suited for 
06:59:04 <Helen> Vipul: use of rules, 
06:59:18 <Helen> Eric: driving with scenarios, 
06:59:53 <Helen> Alan: between owl and RDF, always use OWL (personal view)
07:00:29 <Helen> Eric: Day One Agenda
07:05:04 <Helen> http://esw.w3.org/topic/HCLS/F2F/Agenda
07:05:19 <ivan_> Present: Matthias Samwald, U of Wien
07:05:45 <Helen> Update on Semantic Web Activities By Ivan, no slides
07:06:27 <Helen> Happening now: core infrastructures: SPARQL, RIF
07:08:08 <Helen> SPARQL: progress quickly on recommendation stage, however, new technic problems identified, new public documents will be published soon, and goes back to the recommendation candidate phase again
07:08:41 <Helen> a number of implementations, Jena, Oracle (might have one soon),
07:09:32 <Helen> RIF group: complicated tasks, reconcile a number of theories. 
07:09:42 <Helen> F2F planed before ISWC
07:10:23 <Helen> GRDDL group, might be very relavant to HCLS IG, 
07:11:25 <Helen> HTML -> RDF, standard way to abstract information, when annotate data, consider this technology
07:13:00 <Helen> Former SW Best Practice and Implementation group, published a number of documents worth looking at
07:13:08 <mscottm> ^ standard way to _extract_ information embedded in microformats
07:13:14 <Helen> last week just published "time ontology",
07:13:27 <Helen> group reactivated again, last week first Tcon
07:13:48 <Helen> continue working on modeling problems, patterns, 
07:14:20 <Helen> HCLS important to have bridges with this group, 
07:14:50 <Helen> two relavent areas of this group to HCLS: 
07:17:09 <Helen> RDFa: more vigor micro-format, can be seen as a serialized RDF (?) http://www.w3.org/TR/xhtml-rdfa-primer/
07:17:37 <Helen> linked to GRDDL 
07:20:08 <Helen> Ivan: Micro format and RDFa have the same goal, should show the example
07:21:42 <Helen> New interest grooup education and out-reach, chaired by Susie, educations
07:23:52 <Helen> Ivan: public perception on SW being complicated, only people with certain background can use, this group is to educate people on using simply SW technology to do their work
07:26:01 <Helen> New interest group: coordination group, weekly Tcon, discuss issues raised in one group, that might be relavent to other groups
07:26:43 <Helen> also coordinate W3C with other non W3C organizations
07:27:40 <Helen> Eric is regularly attending this group to make aware HCLS issues to other groups. 
07:28:48 <Helen> one issue: in need of a system tools to bridge Rational DB and RDF
07:29:38 <Helen> a number of implentations in IBM, Oracle, etc. but might have a workshop on this topic next year
07:30:31 <Helen> issue: review and extension of RDF specification
07:31:06 <Helen> issue: Uncertainty in RDF?
07:31:28 <Helen> will be a workshop at ISWC, planning an incubator group on this topic
07:32:17 <Helen> Eric N: lots of confussion around this topic, would be better to get clear use cases, 
07:33:14 <Helen> Ivan: could give a intro on what has been done in uncertainty reasoning
07:34:26 <Helen> issue: need a layer between RDF and OWL lite, 
07:35:55 <Helen> so people don't need to have owl reasoner to use SW
07:37:05 <Helen> W3C resouce constraints, so need to postpone creation of some interest groups
07:37:52 <Helen> Joanne, Vipul, Eric: HCLS continuously provide use cases for these issues. 
07:39:30 <Helen> Kei: any interest in data-mining, structured data (? intension)
07:40:57 <Helen> Ivan: W3C is not a research body, need to see if there is possibility to standardize, otherwise, the topic will not be on the agenda
07:41:10 <Helen> Dirk: any work on workflow?
07:41:41 <Helen> Ivan: no right now, might be in rule group,
07:42:05 <Helen> Scott: how about web service?
07:42:46 <Helen> Ivan: not SW activity, done at web service space, 
07:43:33 <Helen> just published SW description of WSDL
07:44:18 <Helen> Scott: also wants to add semantic data on workflow
07:45:10 <Helen> no mechanism to state semantic data on port
07:45:35 <Helen> Short presentation from TFs
07:45:47 <Helen> BIORDF group, by Susie
07:47:07 <Helen> Review charter: 
07:47:12 <Helen> participants
07:47:48 <Helen> Neuroscience focus: Heerogenous data, interfaces, disease docus
07:48:36 <Helen> Tasks: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks
07:52:49 <Helen> Matthias Samwalo joined meeting and made introduction
07:53:36 <Helen> Publication: Semantic web meets e-neuroscience: an RDF use case
07:54:36 <Helen> Report: Converting biological information to the W3C Resouce Description Framework (RDF): Experience with Entrez Gene
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07:55:42 <Helen> Ivan: collect all reports and publications made by IG groups and members on the HCLS page
07:56:29 <Helen> BioRDF goals:
07:57:26 <Helen> http://esw.w3.org/topic/BioRDF_Top_Level_Task
08:00:00 <Helen> Ivan: a huge number of tasks, hard to manage at the IG level
08:01:20 <Helen> susie: some tasks have been completed, need to make a "completed tasks" list
08:02:14 <Helen> Eric N: initial stage, many people join in on topics they familiar with
08:03:23 <Helen> now need to focus on a number of topics that yield results
08:04:06 <Joanne> Would it make sense to narrow to one disease focus? Also, it's hard to see what if any dependencies exist on the list of active tasks.
08:04:46 <Joanne> Focus Focus Focus
08:05:40 <Helen> Susie: top priority is to generate a URI document, time to start building a demo
08:06:01 <Helen> Ivan: plus other working documents, reports from the group
08:07:50 <Helen> Vipul: BIONT group review
08:10:51 <Helen> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/
08:10:59 <Helen> Work so far:
08:11:17 <Helen> Use case for Parkinson's disease
08:11:48 <Helen> A seed ontology for Parkinson's Disease based on the cullular and molecular biologist perspective
08:12:13 <Helen> identification of pre-exisitng ontologies for "cross-link" into the seed ontology
08:12:42 <Helen> colloaboration opportunities
08:12:47 <Joanne> (backup a bit) - question raised and will be discussed later, is tackling the URI issue something that HCLSIG should take on or something HSLSIG should push back to W3C?
08:13:04 <Helen> thanks, Joanne
08:13:35 <Joanne> no problem!
08:13:40 <Helen> BIONT and BIORDF
08:14:00 <Helen> Collaboration with ACPP task force, 
08:14:12 <Helen> Next steps: 
08:14:21 <Helen> collaborations and real demo
08:15:24 <Helen> Eric: map data instances to conceptual ontology
08:16:19 <Joanne> ACCP stands for what?
08:16:31 <Helen> Vipul: two types of mapping: ont - ont (ACPP ont - RIM ont for example), and instnace to high level ont
08:16:31 <Joanne> I mean ACPP 
08:16:33 <Helen> ACPP
08:16:43 <Helen> Adaptable clinical pathways and protocols
08:17:28 <Joanne> Thanks!
08:17:50 <Helen> Ivan: ont management would be an issue, need to discuss with deployment group, 
08:18:11 <Helen> if the IG group puts out ont, need to consider how to maintain them
08:18:57 <Helen> Vipul: if the ont from this group has values, it will be rolled out to other spaces and maintained.
08:20:48 <Helen> Scott: Any OBO OWL Repository?
08:21:14 <Helen> Vipul: intension to use OBO to host the ont.
08:21:35 <Helen> Dirk: wonder if it is the goal for IG to produce ontologies
08:21:54 <Helen> Vipul, Eric: only for the purpose of demos
08:22:19 <Helen> emphasis on bridging pieces, no too concern about completeness
08:22:36 <Helen> Kei: does OBO has data?
08:23:12 <Helen> Scott: OBO only for ontologies, not for data
08:24:46 <Helen> break
08:24:49 <Helen> finally!
08:36:08 <vipul> BIONT Presentation is available at:
08:36:13 <vipul> http://esw.w3.org/topic/HCLS/OntologyTaskForce?action=AttachFile&do=get&target=AmsterdamF2FStatus.ppt
08:39:40 <ivan_> 04 01Present: Helen Chen, Agfa; Dirk Colaert Agfa; Ray Hookway, HP; Alan Ruttenberg, Milleneum Pharmaceutrecal; Bo Anderson, AZ; Kersin Forsberg, AZ; 01,08ivan01,99 Herman, W3C; Scott Marshall, UvA; Jonathan Rees, Science Commons; Donald Doherty, Brainstage Research; Vipul Kashyup, Parners Healthcare; Eric Neumann, Teranode; Joanne Luciano, U of Manchester; Keu Cheung, Yale Center for Medical Information; Susie Stephens, Oracle; Chimezie Ogbuji, Cleveland Clinic
08:39:48 <eneumann> joining...Jurg  Hachlenburg, U Dresden
08:40:16 <eneumann> ACPP presentation- Helen Chen... 
08:40:18 <ivan_> scribe: Eric
08:40:20 <mscottm> Joerg Hakenberg
08:40:29 <ivan_> ScribeNick: eneumann
08:42:18 <eneumann> ... trim down large charter: have a descriptive mechanism for medical knowledge, in order to support reasoning
08:42:53 <eneumann> ... also, support personal information of patients
08:44:44 <eneumann> ...handle variances in clinical pathways, ala rules, for decision support
08:46:19 <eneumann> ...clinical use cases, radiology, coronary artery bypass graft (CABG) 
08:47:09 <eneumann> ... main constructs: patient states, tasks, preconditions, postconditions, goals, preferences
08:47:52 <Joanne> (for the record.... A clinical pathway is a patient-focused tool, which describes the timeframe and sequencing of routine, predictable multidisciplinary interventions and expected patient outcomes, for a group of patients with similar needs. From http://www.ottawahospital.on.ca/hp/dept/nursing/pathways/index-e.asp
08:49:20 <Joanne> Joanne has joined #hcls
08:49:28 <Joanne> OWL-S  http://www.daml.org/services/owl-s/1.0/
08:49:38 <eneumann> Question regarding OWL-S: http://www.daml.org/services/owl-s/
08:52:00 <eneumann> ... OWL-S can be used as a process model-- caveat that it may not be supported next year when funding at UMD goes away
08:53:05 <eneumann> ... need to include triples that may not yet be factual, but are interpretations
08:55:16 <eneumann> ...  important issues: exclusion and scoped negation, temporal concepts, weighted (probabilities) conditions, pre-position of knowledge body (evidence)
08:57:42 <eneumann> Drug Safety and Efficacy - Eric's presentation...
09:03:25 <Helen> test
09:04:42 <Helen> Helen has joined #hcls
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09:04:57 <Helen> ACPP presentation http://esw.w3.org/topic/HCLS/ACPPTaskForce/Telecons?action=AttachFile&do=get&target=ACPPProgress
09:04:59 <ivan_> zakim, this is hcls
09:04:59 <Zakim> ivan_, I see SW_HCLS(f2f)3:00AM in the schedule but not yet started.  Perhaps you mean "this will be hcls".
09:08:01 <ivan_> zakim, this will be hcls
09:08:02 <Zakim> ok, ivan_; I see SW_HCLS(f2f)3:00AM scheduled to start 128 minutes ago
09:08:57 <jar> jar has joined #hcls
09:10:33 <eneumann> .... http://esw.w3.org/topic/HCLS/F2F/DrugSafety
09:12:14 <Zakim> SW_HCLS(f2f)3:00AM has now started
09:12:21 <eneumann> ... need to follow up on new SPF std (based on HL7 RIM)
09:13:58 <eneumann> URI resolution in ontologies - Alan Ruttenberg
09:19:43 <eneumann> ...What goes wrong with URLs
09:20:44 <eneumann> ... content disappears, server disappears, content is too slow, too big, what format, info resource or not
09:26:36 <Helen> Minor correction: It is SPL (Structured Product Label) not SPE
09:26:38 <Helen> http://www.fda.gov/oc/datacouncil/spl.html
09:26:44 <eneumann> ...LSID definition
09:27:29 <eneumann> ...http-range14: using the result code; type 303 may point to metadata
09:28:03 <eneumann> ... content negotiation, server offers list
09:29:50 <eneumann> ... short statements from John Barkley, Matthias Samwald, and Phil Lord 
09:30:44 <eneumann> ... distinguish information from non-information
09:33:09 <eneumann> ... Kei: identifiable and gettable, overlap, but not the same
09:38:13 <eneumann> ...uri with hash
09:39:36 <eneumann> ...how to avoid 'late solutions'; knowing more ahead of time
09:43:00 <eneumann> ...alternative: using OWL to represent URI info
09:47:37 <eneumann> ...InfoRes vs NotAnInfoRes
09:47:55 <eneumann> Unchanging InfoRes vs EvolveableInfoRes
09:50:39 <Joanne> Information resources can be obtained over the wire (gettable) - so a person isn't an information resource, but their webpage is (may be)
09:51:33 <eneumann> ... how to define versioning-- source authority dependent
09:51:48 <Joanne> proposes versioning semantics in an ontology because they are context depentent
09:52:07 <Joanne> argues we don't need named graphs to do this
09:56:11 <eneumann> ....RetrievalMethod: Transform, SPARQL, WebService...
09:57:16 <eneumann> ...multiple retrieval methods, company specific
10:01:59 <eneumann> ......classes of InfoRes's
10:02:31 <Joanne> these examples may not be part of an upper (shared) ontology
10:05:50 <eneumann> ...NotAnInfoResto an InfoRes: seeAlso, foaf:homepage, subjectOf_
10:10:12 <eneumann> ... do not share "bare URIs'
10:13:06 <eneumann> ... how to resolve "clothed URIs" with RESTfulness?
10:14:26 <Joanne> can use "bare" URIs in private
10:15:51 <Joanne> some discussion now is - what is a bare URI? (jonathan rees)
10:18:02 <Joanne> Chimezie had some comments I couldn't capture
10:18:28 <Joanne> Kai - how do we manage/certify trust?
10:20:39 <Zakim> SW_HCLS(f2f)3:00AM has ended
10:20:40 <Zakim> Attendees were 
10:29:26 <dturi> dturi has joined #HCLS
10:35:03 <dturi> I managed to get an account and join. Daniele
11:24:32 <dturi> Please let me know when I can call in.
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11:32:31 <Dirk> Dirk has joined #HCLS
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11:45:03 <eneumann> hi zakim
11:45:13 <ivan_> zakim, this is hcls
11:45:13 <Zakim> ivan_, I see SW_HCLS(f2f)3:00AM in the schedule but not yet started.  Perhaps you mean "this will be hcls".
11:45:22 <ivan_> zakim, this will be hcls
11:45:22 <Zakim> ok, ivan_; I see SW_HCLS(f2f)3:00AM scheduled to start 285 minutes ago
11:49:18 <Zakim> SW_HCLS(f2f)3:00AM has now started
11:50:27 <Joanne> Discussion about whether to address URIs or not.
11:50:41 <Joanne> Ivan is proposing various options
11:50:55 <Joanne> Susie suggests we create a pros and cons document
11:51:31 <Joanne> Alan (personally) doesn't want to be handed an LSID and doesn't want to support an LISD, suggests poll group and that he suggested another alternative
11:51:52 <Joanne> Advocates we said we see no reason to use LSIDs and leave it at taht
11:52:09 <jar> jar has joined #hcls
11:52:29 <jar> alan: lsids *are* our problem since we're likely to be handed them.. so we should take a side
11:52:37 <Joanne> Welcome JAR - I can post previous scribe since beginning on skype if you'd like
11:53:10 <jar> hi joanne. i think scribing to the chat works pretty well. do you agree?
11:53:11 <Joanne> Dirk - what makes life sciences so special that we need our own ID
11:54:03 <Joanne> yes, - you don['t get the history and I started scribing before you signed on, I was only suggesting skype so you could see what I'd aldready captured.
11:56:31 <Joanne> continuting .. Scott made note to Dirk that LSIDs are not exclusively for Life Science
11:57:00 <Joanne> Ivan says Henry has a meeting today or tomorrow with Sean Martin (missed some before)
11:57:49 <Joanne> Alan summarizing Eric - get consensus within this group and review before it goes out. although it may be public already
11:58:03 <ivan_> http://www.w3.org/2001/tag/doc/URNsAndRegistries-50
11:58:24 <Helen> Helen has joined #hcls
11:58:42 <Joanne> the document is public
11:58:57 <Helen> Joanne, can you send the link again?
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11:59:20 <Joanne> Helen, what link?
12:00:00 <dturi> http://www.w3.org/2001/tag/doc/URNsAndRegistries-50
12:00:01 <Joanne> Make sure those that are or have been vocal about LSIDs summarizing what we just said and send mail to them and to Henri.
12:00:16 <Joanne> Hi Daniele!
12:00:36 <dturi> hi joanne
12:00:53 <Joanne> Welcome.  Will you be dialing in?
12:01:06 <dturi> i'm already connected
12:01:15 <Joanne> I meant on audio.
12:01:20 <dturi> yes
12:01:25 <Joanne> Great!
12:01:27 <jar> ivan: argument at tag level is whether lsid's live in a separate uri space
12:01:49 <jar> ivan: and that's separate from the question of whether they should be used at all
12:02:00 <Joanne> Ivan asks how widely they are used today (LSIDs)
12:02:15 <dturi> we use them for all the entities in mygrid
12:02:18 <Joanne> Eric - NCI have had internal battles and have adopted them
12:02:46 <Joanne> Ivan - Interest group needs to take a stand: rubbish, if possible use through http, etc. there must be a clear statement.
12:03:06 <Joanne> Eric - we've had our own internal disccussion and find it difficult to address all the issues
12:03:30 <Joanne> If we can't get through this at this meeting, then dpn
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12:06:37 <Zakim> I've been running since Aug 21; seems I need a restart
12:07:02 <Zakim> bot restart in 1 minute
12:07:28 <jar> Joanne: likes alan's ideas...
12:07:47 <ivan_> ScribeNick: jar
12:07:54 <Joanne> Joanne has joined #hcls
12:07:55 <dturi> what's alan's idea?
12:08:14 <jar> kei: 80% but we need to be clear on meaning of versions, articulate use cases .  
12:08:49 <jar> (to dturi: from this morning's presentation - express info about resources in owl / rdf)
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12:09:05 <dturi> thank you
12:09:25 <jar> alan: action item:  describe use case where lsid is too heavyweight
12:09:46 <jar> eric: make a draft and circulate it
12:09:59 <Joanne> put together draft of this idea, publish it at as a draft, accept and expect public comments
12:11:21 <Joanne> two issues - articulate cases where the URI ontology is necessary and where it isn't 
12:11:34 <Joanne> 2nd - discuss it with LSID community
12:11:54 <Joanne> side benefit - will have a better mechanism for resolution
12:12:22 <Joanne> there are big pieces of what LSIDs do but they have insprired what is in Alan's proposal
12:12:25 <Joanne> Susie,
12:13:19 <Joanne> Susie -not a big fan of LSIDs, but.... (missed it - check with susie)
12:13:38 <Joanne> Name is always the same in LSIDs - not same with ARC (?)
12:13:50 <dturi> ARK
12:14:25 <Joanne> thanks Daniele - feel free to jump in and scribe if you can hear and capture the arguments.  I"m not that fast
12:14:49 <dturi> different names for the same thing in ARK - which might cause problems
12:16:01 <Joanne> LSIDs independent of domain name - an advantage
12:16:30 <Joanne> If Entrez published all their IDs as LSIDs and provided a resolver, then
12:17:26 <Joanne> if they changed (servers? organizatinos?) the resolver would still resolve and it would still work
12:17:58 <Joanne> Matthias - likes his own (more lightweight) proposal best
12:18:43 <Joanne> simple http url (Matthias cont'd)
12:19:24 <Joanne> Ivan - caveat - SPRQL doesn't exist - what he relies on is OWL, a recommendation and considered Stable. SPRQL is a draft. there is a difference,.
12:19:50 <Joanne> Need a draft of how Matthias prposal woarks
12:19:52 <Joanne> works
12:21:05 <Joanne> Chimezie - hard to follow discussion - wants to see clear examples 
12:21:50 <Joanne> Helen - No need for LSID - URI model with HTTP seems to be enough
12:22:19 <jar> helen: preference for generic web architecture, current structure
12:24:12 <Joanne> Dirk - not involved in discussion and no technical opion. Philosophical - Simplist solution
12:24:47 <Joanne> Peson from HP..  Against LSID because LS isn't special, Also against more infrastructure
12:25:02 <Joanne> Joerg - No Opinion
12:26:29 <jar> kei: compare alan's thing to swmantic web services.  alan agrees
12:27:55 <jar> kirsten like 'eat your own medicine' aspect
12:28:33 <jar> scott: lsid is a problem for interoperatbility wsp. w.r.t. owl
12:29:02 <jar> scott: look at alan's email of may 9'th, id's for entrez entries
12:29:50 <jar> scott: does the new proposal address the needs in that email?
12:31:35 <jar> scott: maybe redo these examples in the new context
12:33:34 <Joanne> Jar:  not enough representation from those who have 1st hand experience with LSIDs
12:36:57 <jar> vipul: we need a separation of concerns - make requirements, then hand them off
12:38:41 <dturi> I agree that lightweight is better if possible
12:39:00 <dturi> There are concerns for us about versioning
12:39:01 <Joanne> Eric - abstains
12:39:21 <dturi> And about the use of foreign authorities
12:39:45 <dturi> I have heard nothing about the latter so far
12:40:06 <Joanne> Eric considers every authority foreigh
12:40:08 <dturi> third party authorities
12:40:09 <Joanne> more?
12:40:18 <Joanne> an example?
12:40:27 <dturi> so that you don't need to own the data
12:40:38 <dturi> to say something about it
12:41:17 <dturi> mygrid could add metadata to lsids produced by ncbi
12:41:38 <Joanne> let me know when you're done.
12:41:46 <dturi> ok
12:41:57 <dturi> cannot hear
12:42:02 <Joanne> ok done or ok you'll let me know
12:42:08 <dturi> finished
12:42:17 <Joanne> thank you!
12:43:12 <Joanne> Eric neuman's slide...
12:43:49 <Joanne> Depicts and example of his take from what Alan saids
12:44:45 <Joanne> Is Gene concept, Uni Gene ID?  Is it a non-information resource?
12:44:53 <Joanne> Example is:
12:45:13 <Joanne> Information Resource (Data Record - (Entrez Gene))
12:45:54 <Joanne> has link labeled "seeAlso" to a Non-information resource (Gene Concept - UniGene ID?)
12:46:33 <Joanne> Data Record (MIPS) has a seeAlso link to Gene Concept UniGene ID? (Same node mentioned above)
12:47:09 <Joanne> Data Record (EBI) has a seeAlso link to Gene Concept UniGene ID? (Same node as mentioned above)
12:47:59 <Joanne> Summary - for nodes with 3 seeAlso relations pointing to Gene Concept UniGene ID? node
12:48:15 <Joanne> the "?" is part of the name of the node in Eric's daiagram
12:50:13 <jar> eric: should we (as a group) talk about conceptual models? e.g. what is a gene, or how do gene db's relate to one another
12:52:59 <jar> alan: it's fine to talk about "the thing that db record N refers to" without taking a stand on what that thing is
12:54:05 <jar> eric: wants to drive preparation of a document, before ISWC (nov 5)
12:54:40 <jar> eric is chief editor, with help from others
12:56:14 <mscottm> <small bio break>
12:56:29 <dturi> shall stay online?
12:57:26 <vipul> URL for Ontology presentation is given below
12:57:30 <vipul> http://esw.w3.org/topic/HCLS/F2F/BioRDFBIONT?action=AttachFile&do=get&target=AmsterdamF2F.ppt
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13:01:02 <Joanne> test
13:07:47 <Don> Parkinson's disease ontology
13:08:48 <Don> http://esw.w3.org/topic/HCLS/ParkinsonUseCase
13:10:04 <ivan_> zakim, who is here?
13:10:04 <Zakim> sorry, ivan_, I don't know what conference this is
13:10:05 <Zakim> On IRC I see Kei, Zakim, Joanne, samwaldmatthias, Susie, mscottm, Helen, jar, eneumann, Dirk, ivan_, vipul, RRSAgent, Don
13:18:44 <Don> Non-domain expert building of ontology
13:19:01 <Don> Look at information queries
13:20:17 <Joanne> test
13:21:09 <Don> Testing using queries potentially show design issues
13:21:38 <Don> Modeling as binary relationship or classes
13:22:14 <Don> Performance is a consideration in approach
13:22:34 <Don> Disease as dynamic process or a static class
13:23:58 <Don> Requirements driven
13:28:13 <Don> modeling constructs depend on the way you use your ontologies
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13:28:42 <kei> test
13:29:25 <Don> obo wants to model "reality"
13:30:18 <Don> Hi Kei!
13:30:58 <kei> <Chimezie>it's a matter of perspective
13:31:16 <kei> <Dirk> model disease as a process
13:31:24 <kei> <Alan>disesae and diagnosis are not the same
13:31:35 <kei> <Scott>one needs to know the stage of disease
13:31:42 <Helen> this is no obsolute "reality", it is all about perspective and scope
13:31:45 <kei> <Chimezie>model something one is asking. It also depends on the needs and there is no point of model something one doesn't need
13:32:43 <jar> vipul: doesn't want to pay attention to barry smith until we know what real problem he's trying to solve (mistake fixed)
13:32:45 <kei> <kerstin>model common things
13:33:26 <kei> <alan>use case to model a variety of domains?
13:33:59 <Don> <vipul> queries are the use cases
13:34:28 <kei> <vipul>modelin  subclasses vs., instances (t-box vs. a-box)
13:34:38 <Don> <alan> nominals break the boundaries between ABoxes and TBoxes
13:34:54 <kei> <vipul>performance is a determining factor
13:36:01 <kei> <Ivan>current reasoners are efficient with t-box (or large a-box and small t-box)
13:36:59 <kei> <vipul>owl-lite is similar to SQL
13:37:36 <kei> <alan>a-box is fine with pellet
13:38:38 <Don> <vipul> what level do you model?
13:38:52 <ivan_> ScribeNick: kei
13:39:10 <kei> <vipul>how to relate concepts at the right level
13:39:25 <Don> <vipul> trying to come up with principles including level to model relationships
13:39:45 <Don> <vipul> data and queries are important drivers of ontologies
13:41:24 <Don> <vipul> uncertainty plays a central role in science
13:41:51 <Don> <Dirk> there is a way to model uncertainty in OWL
13:41:58 <kei> <dirk>we need to consider carefully how to model uncertainty
13:42:44 <kei> <Ivan>reification in rdf is problematic
13:43:05 <kei> <Ivan>the current rdf semantics ignore reification
13:45:19 <kei> <alan>one can make statement about statement that is not true
13:45:34 <kei> <Ivan>named graph can be an alternative
13:47:24 <Don> <eric> not only uncertainty, also what are your axiomatic assumptions
13:47:45 <kei> <Ivan>one community is bayesian network and the other is fuzzy-logic-based
13:50:26 <kei> <vipu> multiple domains and ranges can be model explicitly by derived classes using union or intersection "and" or "or"
13:50:46 <Don> <vipul> handling default values of OWL properties
13:51:11 <Don> <alan> true defaults are not represented in OWL right now
13:51:53 <kei> <Helen>no rules are used in the ontology design
13:52:32 <Don> <vipul> we could propose rule based systems to solve these problems
13:52:55 <kei> <Ivan>n3 is one set of rules
13:52:58 <Don> <vipul> we want to cross link to other ontologies
13:53:17 <Don> <alan> only way right now is to use owl:Imports
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13:56:49 <kei> <scott>for modeling purposes protective vs. symptomatic
13:57:21 <kei> <eric> mechanism modeling will change over time and then molecular level
13:57:37 <kei> <Don>it's causuality
13:58:19 <Don> <scott> how to create an ontology to support your view of your experimental results
13:59:17 <kei> <scott>evolution of ontology is an important issue
14:00:50 <kei> <vipul>map the ontological design to existing data generated in the biordf group
14:00:56 <Don> <dirk> is there anything that can generalize across domains
14:02:34 <kei> <Ivan>identify the problems and communicate with the rules group
14:03:17 <kei> <Helen>compare different problems based on what criteria
14:03:20 <Don> <helen> hard to evaluate which choice is best...how to compare
14:03:57 <Don> <alan> how to know when your ontology is good
14:06:11 <Don> <helen> results depend on how tools are optimized
14:06:45 <Don> <kei> evaluation is a topic of research
14:07:54 <Don> <eric> think about if the data are available in RDF and/or OWL, what advantages would that provide
14:08:19 <Don> <eric> try the bridging piece first!
14:08:53 <Don> <ivan> wants dates and names...when will you be done!
14:31:39 <kei> <Kei>there is a possbility of submitting an invited paper to a special issue of bmc bioinformatics (we can describe different activities in HCLSIG)
14:32:15 <Don> <helen> Capture medical knowledge in OWL, etc.
14:32:19 <kei> <Helen> we can use rules to capture semantics for supporting medical decision making
14:33:15 <Don> <helen> sequence of execution is important in ER
14:34:26 <kei> <Helen>describes a thrombolysis use case
14:35:08 <Don> <vipul> are you describing a workflow?
14:35:19 <Don> <helen> no...not a workflow
14:36:12 <Don> <helen> treatment sequence for thrombosis patient
14:38:19 <Don> <helen> decision support system
14:38:59 <kei> <vipul> is this a task model driven by knowledge
14:39:37 <kei> <Helen>it's an architecture argument
14:40:52 <Don> <helen> ontology should map to SnoMed
14:41:11 <kei> <vipul>should patients have more properties
14:41:55 <Don> <helen> not the group's task to exhaustively define patient states
14:42:00 <kei> <helen>loinc and snomed concepts can be borrowed
14:44:05 <kei> <Helen>patients states include operational states
14:47:48 <kei> <Dirk>there is a lack of temporal modeling in ontology
14:48:59 <Don> <vipul> we don't want to confound temporal and normalization issues
14:56:16 <Don> <vipul> OWL-S includes precondition and postcondition concepts
14:56:36 <Don> <vipul> implementing functionality of a planner
14:56:47 <kei> <Chimezie>the same things can be implemented using existing rule-based systems
14:57:38 <kei> <Chimezie><Alan>process, planning, production systems?
15:01:09 <kei> <alan>planning systems employ pre-conditions and post-conditions to formulate plans
15:02:03 <kei> <Alan>is the system working?
15:02:11 <kei> <Helen>yes
15:02:52 <Don> <chimezie> CABG Coronary Artery Bypass Graft
15:03:17 <Don> <chimezie> DLP Description Logic Programming
15:05:48 <kei> <vipul>any relationship with SWRL?
15:06:05 <Don> <chimezie> SWRL and DLP are nearly the same
15:06:55 <Don> <helen> the query is ultimately a set of rules
15:11:44 <kei> <dirk>why not using part-of in the anatomical ontology
15:12:45 <kei> <chimezie>HL7 uses a two-level approacn
15:12:56 <Don> <vipul> given this modeling approach, what diseases are you able to cover
15:13:13 <Don> <alan> disease severity is a judgement
15:13:15 <kei> <chimezie>FMA is very complex
15:14:29 <kei> <chimezie>clinical records need to be considered also
15:15:53 <Don> <chimezie> been developing a patient record ontology for about 3 years
15:16:31 <Don> <chimezie> need to model numeric comparisons
15:17:00 <Don> <chimezie> used rules
15:17:17 <kei> <vipul>xml can handle numeric classifications
15:18:44 <kei> <vipul>are controlled vocabularies used?
15:19:15 <kei> <chimezie>yes, but there are problems with string-based vocabularies
15:21:00 <kei> <vipul>how counting is done?
15:23:37 <kei> <vipul>hl7 includes the notion of value set
15:24:39 <kei> <helen>HL7 is not concerned about qualifiers
15:27:26 <kei> <chimezie>controlled vocabulary vs. classifications
15:28:39 <kei> <chimezie>use of property values
15:28:56 <kei> <Alan>one can define enumerated classes
15:30:20 <Don> <chimezie> what situations are best for controlled vocabularies
15:33:06 <eneumann> ACTION: Assess whether enumerable classes can be used to handle controlled vocabularies ala HL7 qualifiers
15:34:00 <kei> <chimezie>computational issues related to the enumerated class construct
15:34:13 <eneumann> ACTION: Eric+Alan, Draft best practice proposal around URI resolution using ontologies, goal before Nov 6th.
15:35:07 <Don> <alan> usually there is something behind a string that is of use
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15:41:23 <Don> <chimezie> how we go about decision support
15:45:49 <Don> <vipul> this is essentially statistical reasoning
15:46:35 <kei> <vipul>very thin on semantic reasoning
15:48:02 <kei> <eric>need to wrap and thank to all presenters 
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15:48:17 <ivan_> rrsagent, draft minutes
15:48:17 <RRSAgent> I have made the request to generate http://www.w3.org/2006/10/03-hcls-minutes.html ivan_
15:49:20 <Don> rrsagent, draft minutes
15:49:20 <RRSAgent> I have made the request to generate http://www.w3.org/2006/10/03-hcls-minutes.html Don
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