01:01:41 jar has joined #hcls 13:54:29 RRSAgent has joined #hcls 13:54:29 logging to http://www.w3.org/2007/11/09-hcls-irc 13:54:38 zakim, who is here? 13:54:38 sorry, eneumann, I don't know what conference this is 13:54:39 On IRC I see RRSAgent, Zakim, eneumann, AdrianP, chimezie, matthiassamwald, ericP 13:54:53 zakim, this is hcls 13:54:53 ok, eneumann; that matches SW_HCLS(TPAC)8:30AM 13:55:01 zakim, who is here? 13:55:01 On the phone I see ??P4 13:55:02 On IRC I see RRSAgent, Zakim, eneumann, AdrianP, chimezie, matthiassamwald, ericP 13:55:51 jar has joined #hcls 13:57:39 Zakim, who is here 13:57:39 ericP, you need to end that query with '?' 13:57:42 Zakim, who is here? 13:57:42 On the phone I see ??P4 13:57:43 On IRC I see jar, RRSAgent, Zakim, eneumann, AdrianP, chimezie, matthiassamwald, ericP 13:57:49 Zakim, ??P4 is matthiassamwald 13:57:49 +matthiassamwald; got it 13:57:57 mscottm has joined #hcls 13:58:11 Zakim, who is on the phone 13:58:11 I don't understand 'who is on the phone', ericP 13:58:26 Zakim, matthiassamwald is f2f 13:58:26 +f2f; got it 13:59:42 daboo has joined #hcls 13:59:46 Susie has joined #hcls 14:00:35 +??P8 14:00:55 Zakim, matthiassamwald is ??P8 14:00:55 sorry, matthiassamwald, I do not recognize a party named 'matthiassamwald' 14:01:13 Zakim, f2f has Chimezie, Susie, eneumann,Tonya, GeorgeAllen, vipul, ronan, jyotishman, scottM, michel, joanne, bron, TNBhat, DavidB, DanCorwin, Jonathan, Andria, MarcusCollins, 14:01:13 +Chimezie, Susie, eneumann, Tonya, GeorgeAllen, vipul, ronan, jyotishman, scottM, michel, joanne, bron, TNBhat, DavidB, DanCorwin, Jonathan, Andria, MarcusCollins; got it 14:01:48 Zakim, f2f has ericP 14:01:48 +ericP; got it 14:01:58 Zakim, who is here? 14:01:58 On the phone I see f2f, ??P8 14:02:00 f2f has ericP 14:02:01 On IRC I see Susie, dbooth, mscottm, jar, RRSAgent, Zakim, eneumann, AdrianP, chimezie, matthiassamwald, ericP 14:02:04 zakim, ??P8 is Zakim, matthiassamwald is ??P8 14:02:05 I don't understand '??P8 is Zakim, matthiassamwald is ??P8', dbooth 14:02:36 Zakim, ??P8 is matthiassamwald 14:02:41 +matthiassamwald; got it 14:02:56 impressive! ;) 14:03:12 the audio signal is hardly understandable at the moment, though. 14:03:18 scribe: ericP 14:03:37 tonya: still feel like i have to do my legacy work at Partners 14:03:47 ... need more tool development 14:04:00 ... tool customization is huge 14:04:15 ... it's still easier to use legacy tools 14:04:48 ... pain is that when i use those tools, i will need to build it again 14:05:06 vipul: i've not been able to articulate the long-term savings 14:05:20 tonya: Partners has a two year trajectory 14:05:45 ... when we started tool investment, i had a small budget 14:06:07 ... had to barter for resources and show resultes to keep project alive 14:06:27 eneumann: early discussion of ROIs 14:06:46 ... we said "here are *possible* ROIs" 14:07:16 ... we shouldn't try, as HCLS, to push developers 14:07:37 ... we should instead identify a pain point that we can address in less than two years 14:07:57 ... bridges business case 14:08:13 Topic: intro 14:08:47 eneumann: Susie learnd the outreach lessons 14:10:48 Joanne: decided as a group to select something, which may not align with each participants' focus 14:11:15 scottM: @@missed@@ 14:12:01 eneumann: we have matured and developed a common language 14:12:27 ... we started as an IG 'cause we didn't know what we would produce 14:12:46 ... we can now spin off WGs producing rec-track documents 14:14:19 topic: BioRDF 14:14:41 jluciano has joined #hcls 14:14:49 hello! 14:14:49 michel has joined #hcls 14:14:50 http://esw.w3.org/topic/HCLS/F2F/2007/11/Agenda?action=AttachFile&do=get&target=BioRDF.ppt 14:15:50 matthias - can you hear Susie ok? 14:16:00 -> http://esw.w3.org/topic/HCLS/F2F/2007/11/Agenda?action=AttachFile&do=get&target=BioRDF.ppt BioRDF review [Susie] 14:16:57 -matthiassamwald 14:17:30 [slide 1-2] 14:17:31 I guess that means no. :) 14:17:46 The audio is hardly understandable. 14:18:21 Zakim, please dial ericP-mobile 14:18:21 ok, ericP; the call is being made 14:18:23 +EricP 14:18:59 -EricP 14:19:11 scribing... SUsie: focused more on bench side than bedside 14:19:42 matthiassamwald, susie moved closer to phone. i dialed in and it was ok for me 14:22:18 [slide 8] 14:22:22 i'll try again 14:22:28 jar: list needs Ray Hookway 14:22:52 +??P8 14:23:22 yes, sounds better. 14:25:13 eneumann: KB has one mapping -- others possible 14:25:41 ... Q: will everyone have their own mapping, or is it a shared ontology 14:26:02 Susie: Q: dev KB in what direction? 14:26:12 ... .. include chem data 14:26:28 ... .. FeDeRate data 14:26:48 ... .. good practice for contributing 14:26:59 eneumann: would like to see chem data 14:27:42 ... can invite IUPAC to join us to develop INCHI URIs 14:28:16 ... use case: companies merging 14:29:17 george: [raised issue of pattented chems] 14:29:50 eneumann: only have to worry if police can knock on your door for writing down the chemical 14:30:16 alanr: 10 mins on chem during KB talk? 14:30:31 [yes] 14:31:23 Topic: Adaptice Clinical Protocols and Pathways 14:31:33 Topic: Adaptice Clinical Protocols and Pathways [Chimezie] 14:31:41 alanr has joined #hcls 14:34:31 lots of noise, i understand about 1/4 of what is said 14:35:16 vipul: we are discovering scenarios at Partners where we want forward-chained inference 14:35:36 tonya: we spend more time getting data to engine than waiting for the engine to do inference 14:36:02 chimezie: can do inference over a subset of the data 14:36:22 tonya: we are thinking about state-management 14:36:40 ... cash inference state 14:37:08 vipul: that cashing required regardless of forward/backward direction 14:37:42 tonya: typically computer arrives at a conclusion discards them 14:37:58 chimezie: these are non-academic problems 14:39:14 ... trying to see what of our needs can be captured in ontologies and what in rules 14:40:02 matthias - I'm afraid that I only moved the polycom(telcon apparatus) toward Chimezie just as he finished. 14:40:12 eneumann: this area had been active during the first year 14:40:28 vipul: inclusion/exclusion criteria is a big overlap 14:40:55 there is less noise now. thanks! 14:43:04 chimezie: helen and i were concearned that our need for a value proposition didn't reflect exactly in this work 14:43:36 q+ 14:43:46 AdrianP: @@missed@@ 14:44:29 AdrianP: ACPP should collaborate with RIF. 14:44:31 vipul: attempt to steer OWL1.1 from our use cases leads to resisitance 14:45:00 ... though chair (alanr) has addressed that 14:45:35 Susie: it's time to work with RIF 14:45:47 [agreement -- noted that Adrian is in RIF] 14:46:27 alanr: the OWL WG has a specific charter 14:46:35 ... that said, we want use cases 14:46:52 ... there are multiple avenues for working with OWL WG and general community 14:47:08 ack alanr 14:47:12 ... lots of interest in temporal reasoning 14:47:31 ... use case work involves reducing to the technical nugget 14:47:49 ACPP usecases: http://esw.w3.org/topic/HclsigDscussionTopics/HclsSubGroupACPP/Stroke 14:48:00 http://esw.w3.org/topic/HCLS/ACPPTaskForce/GuidelinesIndicationsForCABG 14:48:03 ... re chimezie's comment about what's missing, can we take sets of your [tonya's] rules 14:48:29 tonya: there weren't sufficient cycles to vet 14:48:55 ... we not very proscriptive when we do decision support 14:49:41 ... we try to make the machine notify the clinician as early as possible. can get then get negative feedback from the clinician 14:50:08 george: this [business rules] is low hanging fruit 14:50:30 vipul: we could develop and share rule archetypes 14:50:50 AdrianP: lots of industry vendors who would like use cases 14:51:25 tonya: we are working with Ilog, but found their expressivity inssuffient for our needs 14:52:52 ... if we have 50 rules for, say, a goal lipid, we don't want to have to sequence them 14:53:32 ... their model required attention to clinically irrelevent sequencing 14:54:02 [tabled] 14:54:17 Topic: Drug Safety and Efficacy 14:54:57 [slide 26 (or so) from yesterday's slides] 14:55:29 Bron Kissler: [introduction] was orig member of CDISC 14:55:48 ... my interests are in SDTM and where semweb works with this 14:56:09 eneumann: this is an XML standard. we didn't want to duplicate this work 14:57:28 SDTM = Study Data Tabulation Model 14:57:40 eneumann: non-trivial to build a large KB 14:57:56 ... can we get *some* data and work on visualization? 14:58:13 ... worked with Phizer 14:58:35 ... merged data with Similie's Babel converter 14:58:52 s/Phizer/Pfizer/ 14:59:30 eneumann: we're still using strings here (more work to do) 14:59:52 [shows Ehibit of example JSON RDF] 15:00:57 eneumann: can, for instance, look only at "severe" event data 15:01:25 ... data was synthesized Pfizer patient data 15:02:45 http://simile.mit.edu/exhibit/ 15:02:45 eneumann: the RDF graph has the variation in patient data and interface adds these facets automatically 15:03:07 http://eneumann.org/exhibit/clinicaldemo 15:03:11 -> http://simile.mit.edu/exhibit/ Exhibit homepage 15:03:52 [eneumann demos selecting for adverse events] 15:04:13 +q 15:04:47 -> http://eneumann.org/exhibit/clinicaldemo Semantic Web Clinical Trials Demo 15:05:38 AdrianP: interface? 15:05:43 eneumann: Javascript 15:06:28 chimezie: we spent 2 hours working up an Exhibit interface. get's great wow-factor 15:06:43 mscottm: scalability? 15:07:24 eneumann: chokes around 1k records 15:07:34 ... trying to get dev resources for this project 15:08:44 ... Exhibit solves say 60% of interface needs as is, but can be extended with statistical functions 15:10:16 Draft note on DSE at http://www.w3.org/2001/sw/hcls/Note_DSE_20071108.html 15:10:25 -> http://www.w3.org/2001/sw/hcls/Note_DSE_20071108 Drug Safety and Efficacy Note on CDISC's Study Data Tabulation Model (SDTM) 15:11:05 eneumann: interested in CDISC's extensions to model genomics 15:11:15 ... new information can be added to STDM 15:12:46 Bron: when you get into regulatory docs, your adoption speeds up 15:15:40 biont talk begins 15:16:07 idea was to collaborate across the groups 15:16:38 ontology best practice to be shared and driven by the other tasks 15:16:46 A number of presentations were given 15:17:04 developed 3 use cases 15:17:14 scribe: alanr 15:17:28 topic: Biont 15:17:41 parkinsons, combined AD use case , patient recruitment use case 15:17:53 +??P10 15:18:44 COI followed from BIONT 15:19:14 POMR developed during ACPP. Ont group looked at this. 15:19:21 Helen chen's ACPP ontology 15:19:38 -> http://esw.w3.org/topic/HCLS/F2F/2007/11/Agenda?action=AttachFile&do=get&target=BIONT-Slides.ppt Biont Report 15:20:25 discussion of difference between clinical research and clinical trials 15:20:44 Parkinson's disease ontology worked on at Amsterdam F2F 15:21:00 POMR = Problem oriented medical records 15:21:30 interacting with biordf was "interesting time" 15:21:51 -> http://esw.w3.org/topic/HCLS/OntologyTaskForce/POMR POMR wiki page 15:22:21 Contrast top down versus bottom up in BioRDF 15:22:46 Lot of momentum on BioRDF ont development, BioONT stepped back 15:23:17 Slide discusses a variety of issues with ontology development 15:23:23 -> http://purl.org/cpr/owl Latest CPR ontology (was POMR ontology) 15:23:55 direction -> feed back to OWL 1.1 group or SWD group 15:24:13 Slide discusses POMR best practices 15:24:28 summarized by Chimezie 15:24:43 no "concepts" allowed. 15:27:50 -> http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf Barry smith on cognitive concepts versus universals / defined classes 15:27:51 some discussion of issues around ontology construction 15:28:33 EricN SKOS versus OWL wants to be discussed 15:28:41 time for a break! 15:28:59 There is a real problem with figuring out how to represent time 15:29:05 scaling issues for OWL 15:29:39 Eric asks whether TBOX or ABOX 15:30:06 Next issue: How to work with ontologies and programming languages such as Java 15:31:00 :) 15:31:12 Vipul: interoperability - how do we make these systems work together over the next few years as both will be present 15:32:15 Tentative proposals: 1) Technical division 2) Application driven 15:32:23 for moving forward 15:32:52 biont and biordf need to be combined into one group 15:33:23 Proposed reorg: Discovery, Development, Secondary use if Healthcare Data 15:34:09 Alan agrees 15:35:19 -??P8 15:36:02 -??P10 15:36:31 Summary slides prepared initially by Susie, Ericp, Alan, added to by EricN 15:41:10 jar has joined #hcls 16:07:14 Zakim, please dial ericP-mobile 16:07:14 ok, ericP; the call is being made 16:07:15 +EricP 16:07:45 -EricP 16:08:02 +[IPcaller] 16:11:00 zakim, who is here? 16:11:00 On the phone I see f2f, [IPcaller] 16:11:01 f2f has ericP 16:11:02 On IRC I see jar, Susie, dbooth, mscottm, RRSAgent, Zakim, eneumann, AdrianP, chimezie, matthiassamwald, ericP 16:11:47 alanr has joined #hcls 16:11:53 michel has joined #hcls 16:12:02 topic: HCLS rechartering questionnaire 16:12:37 ericp: about w3c chartering process. community comes to w3c, proposes a charter 16:12:48 i.e. w3c proposes a charter. 16:13:35 ericp: question was how to most effectively use the energy that was out there? 16:15:03 ericp: we contacted many people & got many thoughtful responses 16:16:19 ericp: respondents were categorized, as a check on the survey 16:18:55 ericp: clumps - pharma, academia, vendor; w3c members/nonmembers 16:20:02 alanr: business development and WG spinoffs as specific activities of the IG 16:20:32 joanne: what is diff btwn interest group and working group? 16:22:25 alanr: IG scope is quite varied. could be just an irc channel; rare to do sw development as we did; but it's up to us really 16:23:30 ericn: this IG can be a generator [incubator] of WGs, maybe 16:23:46 s/, maybe// 16:29:36 (for some reason, the audio quality has become worse again during the break) 16:31:41 matthias, the ploycom got moved away from the projector (with loud fan) and onto a table. and the speaker is standing further away from it. 16:32:04 ericp: join working groups are possible. e.g. w3c has worked jointly with ietf 16:32:34 ericp: we could do things with CDISC if we wanted to. 16:35:35 alanr: we can build on what we've done so far - the charter should allow us to 16:36:27 Zakim, f2f has Chimezie, Susie, eneumann,Tonya, GeorgeAllen, vipul, ronan, jyotishman, scottM, michel, joanne, bron, TNBhat, DavidB, DanCorwin, Jonathan, Andria, MarcusCollins, ericP 16:36:28 ericP was already listed in f2f, ericP 16:36:30 +Chimezie, Susie, eneumann, Tonya, GeorgeAllen, vipul, ronan, jyotishman, scottM, michel, joanne, bron, TNBhat, DavidB, DanCorwin, Jonathan, Andria, MarcusCollins; got it 16:37:28 susie: more work with pharma space, personalized medicine (efficacy & safety) 16:38:12 susie: no silos please 16:40:02 (earlier, vipul talked about the idea of organizing vertically, by project/problem, not by kind-of-task, e.g. ontologies, uris) 16:40:42 ericp: there's a sweet point between thining and typing 16:40:54 s/thining/thinking 16:42:08 topic: (shifted a while back) what should the rechartered group do & organize itself 16:46:47 q+ ericN 16:46:51 q+ 16:47:36 ack chimezie 16:50:29 ack ericN 16:50:42 alanr has joined #hcls 16:52:02 -[IPcaller] 16:52:19 ack ericP 16:53:49 q? 16:53:51 q+ 16:53:57 q+ alanr 16:55:25 ack alanr 16:58:29 q+ george 17:00:22 ack george 17:00:24 alanr: are you still scribing, jar? 17:00:55 joanne: does the charter have to be done by end of day today? 17:01:10 alanr: a few weeks, maybe 17:01:19 discussion of liaisons 17:01:24 q+ 17:01:52 q+ to say that our current structures reflect our experiences of accountability 17:01:56 q+ 17:02:19 scottm: ... 17:02:26 ack ericP 17:02:26 ericP, you wanted to say that our current structures reflect our experiences of accountability 17:02:30 q+ 17:02:43 ack ericP 17:02:48 ack Susie 17:02:50 ericp: it has to be someone's job to reach out 17:03:08 susie: how does CDISC do this? 17:03:39 CDISC industry advisory board get to select seats on BoD 17:03:56 ack chimezie 17:04:04 FDA is not on CDISC board, just observers 17:04:35 chime: liaison and advisory roles very important - need to identify stakeholders 17:04:55 q+ vipul 17:04:55 q+ 17:05:10 chime: we should be pulling in people who have lots of experience e.g. Rector 17:05:47 q+ alanr 17:05:47 ack vipul 17:06:14 q+ to ask how do we make the case of what's in it for them (the early adopters) to participate 17:06:45 vipul: how to bake some kind of outreach process into charter? [sorry vipul I'm sure I got this wrong -jar] 17:07:07 vipul: everyone comes for "value" 17:07:09 q? 17:07:34 vipul: why do they not see value? 17:07:35 q+ 17:07:43 vipul: analyze this 17:07:44 ack mscottm 17:08:22 scottm: involvement from manchester important - we don't have it as much as we'd like - carol g 17:09:11 ack alanr 17:09:12 ack alanr 17:09:14 scottm: how to involve more europeans and more early adopters 17:09:24 q- ericP 17:09:55 alanr: we should say something in the charter about this kind of activity being a task 17:10:20 joanne: "scout" 17:10:22 ack dbooth 17:10:22 dbooth, you wanted to ask how do we make the case of what's in it for them (the early adopters) to participate 17:10:26 ack dbooth 17:10:46 q+ 17:10:50 dbooth: how do we make the case for participation in this group? 17:10:57 q- susie 17:11:09 s/the case/the case to early adopters/ 17:11:32 ericp: wants people to be confident that the charter will do what they want it to do 17:11:40 breaking for lunch now 17:11:43 George's idea is that we have a Semantic Cooperation Outreach and Understanding Taskforce (SCOUT) 17:48:42 Susie has joined #hcls 18:03:23 alanr has joined #hcls 18:04:58 +??P0 18:05:44 eneumann has joined #hcls 18:06:11 zakim, ??P0 is MikeTravers 18:06:11 +MikeTravers; got it 18:07:07 jar has joined #hcls 18:09:03 jluciano has joined #hcls 18:12:20 i'm not scribing - who is? 18:13:51 mscottm has joined #hcls 18:14:01 did we get an introduction to Mike Travers ? 18:14:15 perhaps i'll ask for that after susie's talk 18:14:22 susie: chose Alzheimer's Disease as application 18:14:46 ... lot's of different resources combined in a knowledgebase of RDF 18:15:12 ... all entities are assigned URI's and stored in RDF/OWL in a triplestore 18:15:25 Topic: Knowledge Base 18:15:39 ... queried using SPARQL and visualization tools for result sets 18:16:19 ... openlink virtuoso used as triplestore, HP provided hardware for server 18:17:08 alan: we're going to walk through the demo, then go into some of the ontology and data integration issues 18:18:13 ... also will look at an application that Alan built at millenium that is being rebuilt/revived 18:18:15 ACTION: alanr will post his presentation to wiki 18:18:40 and IRC (notes) please 18:19:32 ... ask a specific question with semantic web and look at specific answers 18:19:54 ... example question: Biological processes in dendrites? 18:21:54 ... example of the SPARQL query using GO identifier and looking at label 18:23:28 ... example view of GO classes with names and definitions 18:24:34 ... possible to get same information with a GET 18:25:36 ... concentrated signal transduction and active in Pyramidal Neurons (known to be damaged in Alzheimer's) 18:26:05 concentrated ^ *on* signal transduction 18:26:19 ... web search returns too much info 18:26:47 ... interested in genes related to above signal transduction 18:28:18 Mesh: Pyramidal Neurons -> Pubmed: Journal Articles -> Entrez Gene (GeneRIFs): Genes -> GO: Signal Transduction 18:29:47 ... i.e. SPARQL query spans the above four data sources 18:29:50 ... looking at result set, many genes are related to Alzheimer's 18:31:25 ... Alan's question: create a system that will let us prioritize siRNA's provided that there are materials for studying them. 18:32:22 ... Allen Brain Atlas, mouse brain cuts stained for gene expression, 20K genes, 400K high res images 18:33:33 ... screen scraped (!) 18:34:06 ... interface built on Google Maps API to browse images 18:35:05 ... a couple of pages of code (!) 18:36:10 ... BIRN can "view source", use our code in MBAT, just like people learning by using other's html 18:37:03 ... Eric N. built a result browser in Exhibit that pulls in images and genomic context, transcription region, etc. 18:39:35 question from vipul: have you done anything with ranking results? 18:40:02 ... answer: no. That's something that text mining groups can help with. 18:43:00 question from michel: did you consider using bio2rdf? 18:43:33 answer: decided not to - wanted to be careful about the statements we were making 18:46:04 alan: shows quote from Matthias Samwald that says we haven't reached the common language yet because our query demands detailed knowledge about the heterogeneous data sources, alas: there is a lot of mapping to be done still 18:46:22 s/alan/alas/^ 18:48:45 alan: about instances: "objects", particulars, independent continuants - "fully present at every time when it exists" 18:49:01 vipul, using multiple ontologies manifests in differently expressed queries 18:49:11 examples furnished upon request 18:49:53 ... Instances (2): "properties" (dependent continuants) 18:50:22 ... Instances (3): Processes "Takes place (unfolds) over a period of time" 18:51:36 question from Joann: do I have to be present for a walk in the woods? 18:52:07 answer from George: it depends on what plants you found along the way. :) 18:54:49 ... classes, roles 18:55:12 ... Words mash up functions and objects (peptide example) 18:56:00 ... Normalized representations dissect words 18:56:23 -> http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Alan Rector and Ontology Normalization 18:58:20 ... PeptideHormone defined in RDF/OWL (graph shown with sentence) 19:01:15 ... URI substituted for things in graph 19:02:19 -> http://obofoundry.org/cgi-bin/detail.cgi?id=relationship RO - Relation ontology 19:03:08 ... 'triples' view of graph : inventory of all triples represented by graph 19:03:16 sstephen has joined #hcls 19:03:35 ro:has_role - from BFO 19:07:47 alan: possible answers to the "Ugly OWL RDF" problems: Macros, Rules as transformation mechanisms 19:08:39 ... Paris: Activity center analysis 19:10:24 ... analyze subgraphs based on pathways instead of single genes 19:11:42 ... background about demo: 350M triples in Openlink Virtuoso (~20Gb) 19:12:15 ... commodity hardware, biggest so far is MeSH associations to articles (200M triples) 19:15:06 ... looking at OWLIM http://www.ontotext.com/owlim/big/index.html 19:15:11 q? 19:15:57 q+ vipul 19:16:02 q+ mscottm 19:16:09 ack vipul 19:16:58 ack mscottm 19:18:31 q+ Bron 19:18:51 q- Bron 19:18:56