246733 ("BIORDF")

I'll try again

<samwaldmatthias> i am ipcaller

<Susie> Olivier sends his regrets

<ericP> +004631776aaaa is Kirsten

BB: VK - review Action Items

<ericP> Scribenick: BillBug

VK: review Use Case (AD & PD) and look at demo script in more detail

SS: also

- review options for ISMB

- review JB SemWebTech pros

- review demo practical issues

VK: go SS

<vipul> Agenda

<vipul> Options for presenting at ISMB - Susie

SS: review ISMB presentation options

- bypass writing full-paper (time too short)

- Barb Bryant (ISMB chair) presented options

* send BMC Bioinform paper to highlights track

* PLoS track

* SIGs?

* organize Birds of Feather discussion (many BoF at ISMB)

VK: prioritize?

<alanr> Bill, you scribing?

Can I pass the baton to you, Alan?

<alanr> yes

SS

- 1) send BMC Bioinform

2) description of demo

3) BoF

4) SIG participation

5) PLoS Track

<scribe> done scribing

<samwaldmatthias> 21 - 25 of july

<vipul> Core Semantic Web benefits to highlight in the demo - John

<alanr> Advantages: Knowledge Representation

<alanr> 2) Knowledge integration

<alanr> - make sure consistent

<alanr> - deduce additional knowledge

<alanr> - in the case of OWL/RDF class hierarchy and class membership that is not explicitly declared

<alanr> - combine two "information resources" can use ontology to harmonize two resources

<alanr> - using rdms ontology becomes queries, new tables, possible constraints, but not well defined.

<alanr> - as opposed to OWL/RDF

<alanr> Problem: Pages on wiki immutable.

<alanr> ACTION: EricP to investigate problems with wiki [recorded in http://www.w3.org/2007/02/19-biordf-minutes.html#action01]

<alanr> Kei - multilayer representation, starting with annotation layer

<alanr> many sites are not structured. Adding annotation to sites would help with resource discovery

<vipul> q

<alanr> But: Standard vocabulary needed for this sort of annotation

<alanr> Kei - next layer: Integration

<alanr> allow users to interrelate concepts in meaningful ways

<alanr> in rdb: can supply foreign key, primary key but semantics has to be external - hard to discover relationship inside the rdb

<mscottm> agree with Kei - need to distinguish between domain semantics and data structure semantics.

<alanr> Beauty of semantic web is that it is describeed so machine can get at it.

<alanr> Third layer: Data available in OWL/RDF

<alanr> not only raw data - may not be that informative. Bill suggested distilled knowledge

<alanr> easier to integrate using SW technology.

<vipul> ack

<alanr> Bill, John: What pages were immutable?

<alanr> BillBug: Key thing: Semantics. Of minimal use unless we tie into shared formal semantic structures that people are already using.

<alanr> From controlled vocabularies to OBO Foundry.

<alanr> BillBug: Third dimension of Kei's is most important. Distilled knowledge resources *not* with data. Rather people mix them up.

<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

<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

<alanr> Semantics are not global - can't move from one RDB to another

<alanr> for a good time: sw dot neurocommons dot org slash map.html <don't circulate for now>

<alanr> John: Difference between prolog and OWL-DL. Decidable and computable. Compare to prolog/uml

here, here - JB!

<alanr> June: Sent mail to Don re: use case

<alanr> From EricN: re: clinical

<alanr> Alan,

<alanr> Here is a draft for a possible clinical angle to the HCLS demo...

<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:

<alanr> http://esw.w3.org/topic/HCLSIG/Drug_Safety_and_Efficacy/SDTM/Example_N3#Clinical_Data

<alanr> 2. Compile patient data for either:

<alanr> a. disease progression - base on symptomatic terminology such as EOAD or MCI for AD, and tremor, hyperkinetic dysarthia, or bradykinesia for PD

<alanr> or b. new drug trial - dosing, symptomatic response patterns over time + any observed adverse events (AE)

<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

<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)

<vipul> http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo

<alanr> - for PD: Cogentin, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=441352

<alanr> or Piribedil, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=198284

<alanr> 4. Use either set of data to show trends using a simple graph visualization (generic table to graph tool?)

<vipul> Maybe link it through from the demo wiki page?

<alanr> June discusses AD/PD Use case: Large, not intended to do all - more to pick from for demo.

<alanr> Layout: AD on left, data sources, Parallel PD use case. Some blank because they haven't been able to figure out parallels yet

<alanr> BillBug: Working on way of expressing specific assertions in narrow area , to use PATO to use phenotypic qualities.

<alanr> discussion at http://sourceforge.net/mailarchive/forum.php?thread_id=31662008&forum_id=35770

<alanr> BillBug: Means to move from June's description to formal representation

<alanr> vipul: Bill plz identify specific use cases he is representing. Bill: Linked to PD use case as existed in Sept/Oct

<alanr> is useful!

<alanr> Keep going!

<alanr> (Bill asks if people think this is useful - so he can decide how much effort to put into it)

<Don> Everyone...I just received an email back that the Use Case document exceeded the permitted size on the list.

<alanr> ACTION: Check feasibility of Bill's approach. All check out his examples. [recorded in http://www.w3.org/2007/02/19-biordf-minutes.html#action02]

<vipul> ACTION: Check feasibility of Bill's approach for focusing the use case [recorded in http://www.w3.org/2007/02/19-biordf-minutes.html#action03]

http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/SeedOntologyDetailedFollowup

<alanr> Action 2 is Don_Doherty

<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

<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

<alanr> K channel story, interferon gamma story. Too much to fold into one scenario

<alanr> Ask whether polymorphisms in channels associated with disease risks

<Don> Okay...people should be receiving the use case

<alanr> Got document.

<alanr> June: Mouse models/ does SNP exist in human.

<alanr> alan - just read about K channel SNP associated with deafness.

<alanr> Bill - idea about immunotherapy link. Bill could you plz elaborate on this to mailing list?

<Don> June...could we talk more about the Use Case on tomorrow's BIONT call?

<vipul> ACTION: Connect the benefits to the use case [recorded in http://www.w3.org/2007/02/19-biordf-minutes.html#action04]

<alanr> hearing loss discussion - http://sourceforge.net/mailarchive/forum.php?thread_id=31646450&forum_id=44607

<alanr> sw dot neurocommons dot org slash map.html

<alanr> ACTION: Susie to poll group on meeting before next SW Gathering [recorded in http://www.w3.org/2007/02/19-biordf-minutes.html#action05]

<ericP> hi all. account create is turned back on on the wiki

<ericP> but i may be telling you too late

<alanr> eric will you handle minutes generation please?

<alanr> rrsagent set minutes world-readable

<alanr> rrsagent set log world-readable

This is scribe.perl Revision: 1.127  of Date: 2005/08/16 15:12:03  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

Found ScribeNick: BillBug
Inferring Scribes: BillBug

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WARNING: No "Present: ... " found!
Possibly Present: Advantages Alan_Ruttenberg BB BillBug Bill_Bug But Don Don_Doherty IPcaller John JohnBarkley June June_Kinoshita Kei_Cheung Kirsten Layout MIT-G346 P0 Problem SS Scott_Marshall Scribenick Susie VK Vipul_Kashyap aabb aacc alanr ericP mscottm samwaldmatthias vipul
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy


WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 19 Feb 2007
Guessing minutes URL: http://www.w3.org/2007/02/19-biordf-minutes.html
People with action items: check connect ericp susie

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WARNING: No "Topic: ..." lines found!  
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<dbooth> Topic: Review of Amy's report