16:03:10 <RRSAgent> RRSAgent has joined #biordf
16:03:10 <RRSAgent> logging to http://www.w3.org/2007/02/19-biordf-irc
16:03:12 <Susie> Susie has joined #BioRDF
16:03:13 <BillBug> 246733 ("BIORDF")
16:03:23 <ericP> Zakim, this will be BioRDF
16:03:23 <Zakim> ok, ericP, I see SW_HCLS(BioRDF)11:00AM already started
16:03:31 <BillBug> I'll try again
16:03:36 <vipul> zakim, who's on the call?
16:03:36 <Zakim> On the phone I see +004631776aaaa, +1.781.620.aabb, Vipul_Kashyap, [IPcaller], Don_Doherty, +1.301.366.aacc
16:04:01 <Zakim> +EricP
16:04:12 <samwaldmatthias> i am ipcaller
16:04:16 <Zakim> +Bill_Bug
16:04:19 <Zakim> -Bill_Bug
16:04:30 <ericP> Zakim, IPcaller is samwaldmatthias 
16:04:30 <Zakim> +samwaldmatthias; got it
16:04:48 <Zakim> +Bill_Bug
16:04:58 <ericP> Zakim, +1.781.620.aabb is Susie 
16:04:58 <Zakim> +Susie; got it
16:05:05 <vipul> zakim, who's on the call?
16:05:05 <Zakim> On the phone I see +004631776aaaa, Susie, Vipul_Kashyap, samwaldmatthias, Don_Doherty, +1.301.366.aacc, EricP, Bill_Bug
16:05:42 <Zakim> +Kei_Cheung
16:05:53 <Susie> Olivier sends his regrets
16:06:13 <ericP> Zakim, +1.301.366.aacc JohnBarkly
16:06:13 <Zakim> I don't understand '+1.301.366.aacc JohnBarkly', ericP
16:06:22 <ericP> Zakim, +1.301.366.aacc is JohnBarkley
16:06:23 <Zakim> +JohnBarkley; got it
16:07:26 <ericP> +004631776aaaa is Kirsten
16:07:34 <ericP> zakim, +004631776aaaa is Kirsten
16:07:34 <Zakim> +Kirsten; got it
16:07:51 <vipul> Zakim, pick up a scribe
16:07:51 <Zakim> I don't understand 'pick up a scribe', vipul
16:07:58 <ericP> Zakim, please pick a victim
16:07:58 <Zakim> Not knowing who is chairing or who scribed recently, I propose Bill_Bug
16:08:40 <ericP> Meeting: BioRDF
16:08:47 <BillBug> BB: VK - review Action Items
16:08:51 <ericP> Scribenick: BillBug 
16:09:26 <BillBug> VK: review Use Case (AD & PD) and look at demo script in more detail
16:09:46 <Zakim> +[MIT-G346]
16:10:08 <BillBug> SS: also
16:10:10 <BillBug>   - review options for ISMB
16:10:11 <BillBug>   - review JB SemWebTech pros
16:10:13 <BillBug>   - review demo practical issues
16:10:16 <BillBug> VK: go SS
16:11:23 <Zakim> +June_Kinoshita
16:11:30 <alanr> alanr has joined #biordf
16:11:39 <vipul> Agenda
16:11:39 <alanr> zakim, who is on
16:11:39 <Zakim> I don't understand 'who is on', alanr
16:11:49 <alanr> zakim, who is on the call?
16:11:49 <Zakim> On the phone I see Kirsten, Susie, Vipul_Kashyap, samwaldmatthias, Don_Doherty, JohnBarkley, EricP, Bill_Bug, Kei_Cheung, [MIT-G346], June_Kinoshita
16:12:00 <vipul> Options for presenting at ISMB - Susie
16:12:09 <BillBug> SS: review ISMB presentation options
16:12:11 <BillBug>   - bypass writing full-paper (time too short)
16:12:13 <alanr> zakim, [MIT-G346] is Alan_Ruttenberg
16:12:13 <Zakim> +Alan_Ruttenberg; got it
16:12:13 <BillBug>   - Barb Bryant (ISMB chair) presented options
16:12:15 <BillBug>       * send BMC Bioinform paper to highlights track
16:12:16 <BillBug>       * PLoS track
16:12:18 <BillBug>       * SIGs?
16:12:19 <BillBug>       * organize Birds of Feather discussion (many BoF at ISMB)
16:12:21 <BillBug> VK: prioritize?
16:12:29 <alanr> Bill, you scribing?
16:12:41 <BillBug> Can I pass the baton to you, Alan?
16:12:45 <alanr> yes
16:13:16 <BillBug> SS
16:13:18 <BillBug>   - 1) send BMC Bioinform
16:13:20 <BillBug>    2) description of demo
16:13:21 <BillBug>    3) BoF
16:13:23 <BillBug>    4) SIG participation
16:13:24 <BillBug>    5) PLoS Track
16:13:26 <BillBug> done scribing
16:13:55 <samwaldmatthias> 21 - 25 of july 
16:14:18 <vipul> Core Semantic Web benefits to highlight in the demo - John
16:14:23 <Zakim> +??P0
16:14:23 <ericP> ericP has changed the topic to: BIONT/BioRDF weekly telecon -- agenda: http://lists.w3.org/Archives/Public/public-semweb-lifesci/2007Feb/0088
16:14:44 <alanr> Advantages: Knowledge Representation
16:14:57 <ericP> Zakim, ??P0 is alanr 
16:14:57 <Zakim> +alanr; got it
16:15:16 <alanr> 2) Knowledge integration
16:15:24 <alanr>  - make sure consistent
16:15:30 <alanr>  - deduce additional knowledge
16:15:53 <alanr>  - in the case of OWL/RDF class hierarchy and class membership that is not explicitly declared
16:15:54 <Zakim> -alanr
16:16:23 <alanr>  - combine two "information resources" can use ontology to harmonize two resources
16:16:57 <alanr>  - using rdms ontology becomes queries, new tables, possible constraints, but not well defined.
16:17:04 <alanr>  - as opposed to OWL/RDF
16:17:07 <Zakim> +Scott_Marshall
16:17:13 <BillBug> q+
16:17:13 <alanr> zakim, who is on the call?
16:17:14 <Zakim> On the phone I see Kirsten, Susie, Vipul_Kashyap, samwaldmatthias, Don_Doherty, JohnBarkley, EricP, Bill_Bug, Kei_Cheung, Alan_Ruttenberg, June_Kinoshita, Scott_Marshall
16:17:31 <mscottm> mscottm has joined #biordf
16:17:46 <alanr> Problem: Pages on wiki immutable.
16:17:57 <alanr> Action: EricP to investigate problems with wiki
16:18:24 <alanr> Kei - multilayer representation, starting with annotation layer
16:18:51 <alanr> many sites are not structured. Adding annotation to sites would help with resource discovery
16:19:02 <ericP> q+ to advise "semantics of RDBs not expressed in SQL and not globally distinguishable". saying there are no semantics my annoy RDB folks
16:19:18 <vipul> q
16:19:25 <alanr> But: Standard vocabulary needed for this sort of annotation
16:19:27 <vipul> q?
16:19:57 <alanr> Kei - next layer: Integration
16:20:14 <alanr> allow users to interrelate concepts in meaningful ways
16:20:35 <BillBug> q+
16:20:46 <alanr> in rdb: can supply foreign key, primary key but semantics has to be external - hard to discover relationship inside the rdb
16:20:56 <mscottm> agree with Kei - need to distinguish between domain semantics and data structure semantics.
16:21:03 <alanr> Beauty of semantic web is that it is describeed so machine can get at it.
16:21:31 <alanr> Third layer: Data available in OWL/RDF
16:22:01 <alanr> not only raw data - may not be that informative. Bill suggested distilled knowledge
16:22:10 <alanr> easier to integrate using SW technology.
16:22:35 <BillBug> q+
16:22:38 <vipul> ack
16:22:46 <alanr> Bill, John: What pages were immutable?
16:23:00 <vipul> ack BillBug
16:24:05 <alanr> BillBug: Key thing: Semantics. Of minimal use unless we tie into shared formal semantic structures that people are already using.
16:24:13 <alanr> From controlled vocabularies to OBO Foundry.
16:25:44 <Don> q+
16:26:01 <alanr> BillBug: Third dimension of Kei's is most important. Distilled knowledge resources *not* with data. Rather people mix them up.
16:26:37 <alanr> e.g. if you do text mining but don't do it in terms defined by these already extant ontologies then you lose the value
16:27:32 <vipul> ack ErcP
16:27:41 <ericP> ack ericP 
16:27:41 <Zakim> ericP, you wanted to advise "semantics of RDBs not expressed in SQL and not globally distinguishable". saying there are no semantics my annoy RDB folks
16:28:32 <alanr> Semantics are not global - can't move from one RDB to another
16:29:23 <vipul> ack Don
16:29:41 <alanr> for a good time: sw dot neurocommons dot org slash map.html <don't circulate for now>
16:31:20 <alanr> John: Difference between prolog and OWL-DL. Decidable and computable. Compare to prolog/uml
16:31:27 <BillBug> here, here - JB!
16:31:56 <alanr> June: Sent mail to Don re: use case
16:33:05 <alanr> From EricN: re: clinical
16:33:06 <alanr> Alan,
16:33:06 <alanr> Here is a draft for a possible clinical angle to the HCLS demo...
16:33:06 <alanr> 1. Extend PD/AD demo to include clinical study data from patients, using DSE's draft RDF model based on CDISC's SDTM standard:
16:33:06 <alanr> http://esw.w3.org/topic/HCLSIG/Drug_Safety_and_Efficacy/SDTM/Example_N3#Clinical_Data
16:33:07 <alanr> 2. Compile patient data for either:
16:33:09 <alanr>     a. disease progression - base on symptomatic terminology such as EOAD or MCI for AD, and tremor, hyperkinetic dysarthia, or bradykinesia for PD
16:33:12 <alanr> or b. new drug trial - dosing, symptomatic response patterns over time + any observed adverse events (AE)
16:33:14 <alanr> 3. If drug trial, then links to PubChem drug information would be useful: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound
16:33:17 <alanr>   - for AD:  Cognex, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2723754 (images- http://pubchem.ncbi.nlm.nih.gov/image/structurefly.cgi?cid=2723754)
16:33:17 <vipul> http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo
16:33:20 <alanr>   - for PD: Cogentin, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=441352
16:33:22 <alanr>      or Piribedil, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=198284
16:33:24 <alanr> 4. Use either set of data to show trends using a simple graph visualization (generic table to graph tool?)
16:34:34 <vipul> Maybe link it through from the demo wiki page?
16:37:22 <alanr> June discusses AD/PD Use case: Large, not intended to do all - more to pick from for demo.
16:38:37 <vipul> q?
16:39:20 <BillBug> q+
16:39:35 <alanr> Layout: AD on left, data sources, Parallel PD use case. Some blank because they haven't been able to figure out parallels yet
16:39:39 <vipul> ack BillBug
16:39:46 <alanr> q+ alanr re: Progress on image aspect of demo
16:40:06 <alanr> q+ alanr to talk about progress on image aspect of demo
16:41:07 <alanr> BillBug: Working on way of expressing specific assertions in narrow area , to use PATO to use phenotypic qualities.
16:42:32 <alanr> discussion at http://sourceforge.net/mailarchive/forum.php?thread_id=31662008&forum_id=35770
16:43:16 <alanr> BillBug: Means to move from June's description to formal representation
16:43:47 <alanr> vipul: Bill plz identify specific use cases he is representing. Bill: Linked to PD use case as existed in Sept/Oct
16:44:51 <alanr> is useful!
16:44:55 <alanr> Keep going!
16:46:10 <alanr> (Bill asks if people think this is useful - so he can decide how much effort to put into it)
16:47:26 <Don> Everyone...I just received an email back that the Use Case document exceeded the permitted size on the list.
16:47:58 <alanr> Action: Check feasibility of Bill's approach. All check out his examples.
16:48:47 <vipul> Action: Check feasibility of Bill's approach for focusing the use case
16:49:10 <BillBug> http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/SeedOntologyDetailedFollowup
16:49:51 <alanr> Action 2 is Don_Doherty
16:51:12 <alanr> June - initial thoughts on where to show benefits re: use case. Would like to integrate 3 databases. 1) SWAN 2) Genomic, e.g. expression. 3) NeuronDB and associated databases
16:51:35 <ericP> ESW wiki has account creation temporarily turned off due to spamming prob. i wonder if we can temporarily temporarily turn it on so folks can create their accounts
16:52:17 <alanr> K channel story, interferon gamma story. Too much to fold into one scenario
16:52:52 <alanr> Ask whether polymorphisms in channels associated with disease risks
16:52:56 <Don> Okay...people should be receiving the use case
16:53:13 <alanr> Got document.
16:53:58 <alanr> June: Mouse models/ does SNP exist in human. 
16:54:50 <vipul> q?
16:54:52 <alanr> alan - just read about K channel SNP associated with deafness.
16:56:25 <alanr> Bill - idea about immunotherapy link. Bill could you plz elaborate on this to mailing list?
16:56:49 <Zakim> -Kirsten
16:57:32 <Don> June...could we talk more about the Use Case on tomorrow's BIONT call?
16:58:13 <vipul> Action: Connect the benefits to the use case 
16:58:20 <alanr> hearing loss discussion - http://sourceforge.net/mailarchive/forum.php?thread_id=31646450&forum_id=44607
16:58:52 <alanr> sw dot neurocommons dot org slash map.html
16:59:13 <BillBug> BillBug has joined #biordf
16:59:48 <Zakim> -Scott_Marshall
17:01:24 <Zakim> -Bill_Bug
17:01:25 <Zakim> -Susie
17:01:27 <Zakim> -Vipul_Kashyap
17:01:28 <Zakim> -Kei_Cheung
17:01:29 <Zakim> -JohnBarkley
17:01:30 <Zakim> -samwaldmatthias
17:01:31 <Zakim> -Don_Doherty
17:01:32 <Zakim> -June_Kinoshita
17:01:34 <alanr> Action: Susie to poll group on meeting before next SW Gathering
17:01:40 <Zakim> -EricP
17:01:50 <alanr> Zakim, prepare minutes
17:01:50 <Zakim> I don't understand 'prepare minutes', alanr
17:01:59 <ericP> hi all. account create is turned back on on the wiki
17:02:05 <ericP> but i may be telling you too late
17:02:11 <alanr> RRSAgent, prepare minutes
17:02:11 <RRSAgent> I'm logging. I don't understand 'prepare minutes', alanr.  Try /msg RRSAgent help
17:02:22 <alanr> eric will you handle minutes generation please?
17:03:19 <alanr> rrsagent, draft minutes
17:03:19 <RRSAgent> I have made the request to generate http://www.w3.org/2007/02/19-biordf-minutes.html alanr
17:03:45 <alanr> rrsagent set minutes world-readable
17:04:50 <alanr> rrsagent set log world-readable
17:05:00 <alanr> rrsagent, set log world-readable
17:05:15 <alanr> RRSAgent, set log world-readable
17:05:34 <alanr> rrsagent, draft minutes
17:05:34 <RRSAgent> I have made the request to generate http://www.w3.org/2007/02/19-biordf-minutes.html alanr
17:06:40 <Zakim> disconnecting the lone participant, Alan_Ruttenberg, in SW_HCLS(BioRDF)11:00AM
17:06:43 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:06:46 <Zakim> Attendees were Vipul_Kashyap, Don_Doherty, EricP, Bill_Bug, samwaldmatthias, Susie, Kei_Cheung, JohnBarkley, Kirsten, June_Kinoshita, Alan_Ruttenberg, alanr, Scott_Marshall
17:08:12 <ericP> RRSAgent, please make log world-readable
17:08:43 <ericP> though i note from before: 2007-02-19T17:05:00Z <alanr> rrsagent, set log world-readable
17:08:46 <ericP> 2007-02-19T17:05:00Z <RRSAgent> I have made the request, alanr
17:09:27 <alanr> ok looks good now. Bye