14:16:17 RRSAgent has joined #hcls2 14:16:17 logging to http://www.w3.org/2010/05/03-hcls2-irc 14:16:48 SD: Assay produces SWAN PrimaryData; ComputedData is a result of analysis; results in a Claim 14:17:11 SD: we have a very simple version of myExperiment at a high level - can David help us flesh it out? 14:17:49 Zakim, who is here? 14:17:49 sorry, mscottm, I don't know what conference this is 14:17:51 On IRC I see RRSAgent, Zakim, mscottm, Tim, sudeshna_, alex_, AlexPassant, ericP 14:18:07 Zakim, this is scidisc 14:18:07 sorry, mscottm, I do not see a conference named 'scidisc' in progress or scheduled at this time 14:18:12 SD: Use cases: (a) gene list from BioRDF; (b) Tim & I have been working on e.g. genetic association use case in Autism, e.g. GWAS; as next step let's take some of those studies and see how that use case maps out to the model 14:18:29 SD: again, David can we get some help on this fleshing out? 14:19:04 DN: some of the myExp fleshin gout is in the services and services provenance 14:19:51 SD: perhaps as action item we can work offline to take a particular genetic association study and model it here 14:20:00 DN: can provide some diagrams for the next call 14:20:44 SM: can DN confuse us just a little by saying what the sticky bits are? DN: what sticky bits? SM: what level do the models articulate? is there a big problem here? 14:21:02 DN: analyses done without myExp? 14:21:26 SM: how do we glue all this stuff together? 14:21:38 SM: as myExp is so much about services? 14:21:39 ssahoo2 has joined #HCLS2 14:21:58 SM: for example do you have stuff in myExp about GWAS? 14:22:57 DN: essentially workflow made up of interlinked processs - some effort to express what type each is - but limited - the "services" are more about WSDL, SOAP, etc - can we use BioCatalog here to classify the actual services themselves? 14:23:21 DN: hoepfully we there get the details on what services are really doing 14:25:22 Satya: how does description of service usable in contet of describing how an experiment is being conducted? 14:25:35 DN: ??? 14:26:27 Satya: in provenance community we have looked at limitations of services; what we need in context of experiment is in semantic annotations; more covered by OBI than by a service oriented ontology 14:28:34 Satya: what I'd look at is extend Taverna workflow model to add semantic annotations, extending Provenir - for these use cases may comncentrate more on domain aspects of these anayses 14:28:54 Provenir - an upper-level provenance ontology: http://wiki.knoesis.org/index.php/Provenir_Ontology 14:28:56 SD: we really lookijg at e.g. the kind of statistical analysis etc 14:29:02 SD: agree with Satya 14:29:46 SM: use case of descriinb experiments as workflows in the sense of "computable pieces & types of statistical analysis" but graph of workflow can allow you to find similar processes 14:30:04 SD: need to capture summary that susch and such statistical method was used 14:30:27 Satya: looking at computational processes - e.g. sequence extraction, stats analysis, etc 14:30:37 Autism was mentioned earlier - I've noticed that autism is being studied by NCBO: http://bmir.stanford.edu/publications/view.php/ontology_driven_data_integration_for_autism_research 14:30:58 DN: BioCatalog is based in manchester as well, like Satya's collaborators in Manchester 14:31:37 Satya: I interacted with the BioCatalog interface thing too 14:31:54 SD: what was the name of the effort, Satya? 14:32:03 Janus semantic provenance framework 14:32:14 SM extension of Provenir 14:32:24 SD: good discussion 14:32:52 SD: ACTION ITEM: work to define one particular use case to capture details of work flow for next call; 14:33:05 SD: Satya - can you update us on Microarray use case 14:34:05 Satya: The model you shared from Paolo - has many overlapps with OBI - lets use where that occurs - SD: can you show us the specific classes where you see overlap? 14:34:18 http://esw.w3.org/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext 14:34:34 SSatya: posted this - use case for micrarray use case from BioRDF 14:35:40 Satya: what we have done is primarily (Kei did this by hand) created scenario of this gene list as RDF graph, Jun and Satya created a schema taking concepts from OBI and other concepts at NCBO - lena has integrated with the DiseaseOme 14:36:01 http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint.php 14:36:17 diseasome dataset 14:36:22 Satya: this is the diseaseOme endpoint 14:36:37 Satya: can find a list of diesease associated with this gene 14:37:15 SD: looks like m-array use case you are working on in BioRDF group - lot of overlap - we can learn from each other - rather than direct use of each other's work - 14:37:19 david_newman has joined #hcls2 14:37:57 Satya: significant overlap but we didn't deal with Study, Rsearch Question, etc -= these are probably sepcific to scientific discourse 14:39:53 SD: action items: take on of the use cases & map onto the ontology - work out the workflow with correct semantic annotations and meets scientific needs 14:41:01 SD: can DN help - ? DN: can produce some diagrams for workflows - have a lot of other stuff going on - for next few weeks I'lldo some diagrams 14:41:01 SD: four weeks out 14:42:28 AG: question: everything hooks from myExp to computation - if I am doing insilico biology - everything under computation belongs to myExp - can this be something jsut run on my computer? shouldn't it be considered as a computational assay? 14:50:04 AG, SN & TC: discussion on whether this is true, whether there is such a thing as a computational Assay, is it the same as a physical laboratory Assay? 14:50:30 AG: whay should a computational experiment be different form a lab experiment? 14:51:01 Satya: what distinguishes in silico from in vivo? point is how well does the computational model mimic the natural world? 14:52:23 Paolo: OBI says exactly what TC said; Assay produces data from real world; DataTransformationis data to data 14:53:38 SM: what we're talking about is what you call something; point remains that there are processes that are going on here choices being made about storage of enzymes, conditions, temperatures, laser config, etc -- conutless factors have an effect - same holds for computational processes 14:56:02 Let's make a use case and see how it plays out instead of changing the model directly 14:57:12 TC: let's maintain the distinction between inductive and deductive 14:57:34 TC: let's have the people interested in computational experiments do a specific use case here 14:57:49 AG: fine with me - I will look at OBI 14:58:11 SM: this call shouldn't have four weeks intervals 15:07:36 Tim has joined #HCLS2 15:58:06 jasons has joined #hcls2 16:00:32 johnM has joined #hcls2 16:01:32 xiaoshu has joined #hcls2 16:02:01 no one talking? 16:03:19 is anybody else on the phone? 16:03:45 zakim, who is on the phone? 16:03:45 sorry, johnM, I don't know what conference this is 16:03:46 On IRC I see xiaoshu, johnM, jasons, RRSAgent, Zakim, mscottm, alex_, AlexPassant, ericP 16:03:54 zakim, this is TERM 16:03:54 ok, johnM; that matches SW_HCLS(TERM)12:00PM 16:04:49 zakim, who is here? 16:04:49 On the phone I see +1.919.846.aaaa, +1.919.445.aabb, John_Madden 16:04:50 On IRC I see xiaoshu, johnM, jasons, RRSAgent, Zakim, mscottm, alex_, AlexPassant, ericP 16:05:24 I'm 846 16:05:31 zakim, 1.919.445.aabb is xiaoshu 16:05:31 sorry, johnM, I do not recognize a party named '1.919.445.aabb' 16:05:32 Hi John 16:05:47 445 is me 16:05:59 still trying to dial in 16:06:06 zakim, +1.919.445.aabb is xiaoshu 16:06:06 +xiaoshu; got it 16:06:07 +mscottm 16:06:34 zakim, +1.919.846.aaaa is Jasons 16:06:34 +Jasons; got it 16:11:11 http://www.w3.org/blog/hcls 16:11:57 http://lists.w3.org/Archives/Public/public-semweb-lifesci/ 16:16:55 http://bioportal.bioontology.org/ 16:21:00 http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-551/oaei09_paper0.pdf 16:35:34 + +1.919.744.aacc 16:35:40 -Jasons 16:41:30 Carolina Data Warehouse for Health 16:43:56 http://caties.cabig.upmc.edu/ 16:44:24 http://www.dbmi.pitt.edu/faculty/crowley.html 16:47:27 Zakim, who is making noise? 16:47:39 mscottm, listening for 12 seconds I heard sound from the following: mscottm (33%) 16:48:15 - +1.919.744.aacc 16:48:56 In boston, most important topic was not missing the boat on electronic health records 16:53:08 xiaoshu has left #hcls2 16:53:13 -John_Madden 16:53:15 -mscottm 16:53:17 -xiaoshu 16:53:18 SW_HCLS(TERM)12:00PM has ended 16:53:20 Attendees were John_Madden, xiaoshu, mscottm, Jasons, +1.919.744.aacc 16:53:43 rrsagent, draft notes 16:53:43 I'm logging. I don't understand 'draft notes', johnM. Try /msg RRSAgent help 16:53:52 rrsagent, draft log 16:53:52 I'm logging. I don't understand 'draft log', johnM. Try /msg RRSAgent help 16:54:43 RRSAgent, please draft minutes 16:54:43 I have made the request to generate http://www.w3.org/2010/05/03-hcls2-minutes.html mscottm 16:54:52 RRSAgent, please make log world-visible 16:55:01 thanks scott 16:55:08 no prob (cut and paste ;) ) 16:55:16 cheers 16:55:23 cheers 16:55:46 johnM has joined #hcls2 19:01:03 Zakim has left #hcls2 19:22:41 sudeshna has joined #hcls2 19:23:24 sudeshna has left #hcls2