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16:04:32 <bobP> scribenick bobP
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16:05:00 <matthias_samwald> https://docs.google.com/document/d/1bsJ3YWuH1k3gdXtSN2PXfmUIavtR-hDXhHMn0bKB5pk/edit?hl=en_US
16:05:01 <bobP> Michel: Write short special report, then consider the new charter
16:05:09 <bobP> :)
16:05:31 <bobP> Michel: Scott concerned w timing, Matthias requirements
16:06:18 <bobP> Matthias: Agreed on using this kind of data type Special report 1000-3000 words
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16:06:31 <bobP> ... google doc started
16:06:35 <mscottm> About how many pages is that?
16:07:11 <bobP> ... from the viewpoint of normal research, personalized med, we can say that semweb is niche area
16:07:42 <bobP> ... requirement for future medicine, article should give overview of problems that motivate
16:08:02 <bobP> ... also non-experts need a good overview of what we are suggesting
16:08:32 <bobP> ... brief enough to focus on ideas and mission
16:09:21 <bobP> ... Outline in google doc is summary, not really an abstract
16:09:45 <bobP> ... one section is required for future perspectives, where most of text should go
16:10:06 <ericP> Zakim, please dial ericP-office
16:10:06 <Zakim> sorry, ericP, I don't know what conference this is
16:10:09 <bobP> ... looks out 5-10 years, how semantics, text-mining etc will play
16:10:14 <ericP> Zakim, this is hcls
16:10:14 <Zakim> ok, ericP; that matches SW_HCLS(TMO)11:00AM
16:10:18 <ericP> ciao
16:10:30 <ericP> Zakim, please dial ericP-office
16:10:30 <Zakim> ok, ericP; the call is being made
16:10:31 <Zakim> +Don_Doherty
16:10:53 <ericP> Zakim, please dial ericP-office
16:10:54 <Zakim> ok, ericP; the call is being made
16:10:55 <Zakim> +EricP
16:11:15 <bobP> ... we can agree on high level statement, then go on discussing how pharma would be involved
16:11:28 <bobP> ... and integrated into clinical decision support
16:12:03 <bobP> ... can also present ontologies, say how we expect pieces of puzzle to fit in infrastructure
16:12:23 <bobP> ... over next two weeks
16:12:35 <bobP> Michel: Good, like the high-levelness and tone
16:12:46 <bobf> Is there a deadline for the submission?
16:13:00 <bobP> ... interesting to present what semweb can do
16:13:16 <bobP> ... pasted in resources at heart of integration
16:13:24 <bobP> ... should also have a figure
16:13:47 <bobP> ... don't know the value of including everything
16:14:03 <bobP> Matthias: Have already reduced table somewhat
16:14:59 <bobP> Michel: Figure: variation, response, pop genetics, diseases and treatment
16:15:27 <bobP> ... table has raw data, as terms and onts to leverage or describe
16:16:16 <bobP> ... maybe illustrate the RDF-like character, or a concept map about relationships
16:17:05 <ericP> i don't feel qualified to answer
16:17:09 <bobP> Scott: Solves the hesitation in the model
16:17:35 <bobP> ... position paper, put it out there, then continue in research
16:17:54 <bobP> ... should mention gene-variant concept in this paper anyway
16:18:24 <bobP> Michel: Starts w future perspective, can talk re resources and how can be exploited
16:18:51 <bobP> Michel: Need to come up w model on how to make contributions
16:19:03 <bobP> ... suggest one or two people to write first draft
16:19:16 <bobP> ... message needs to be highly focused
16:19:37 <bobP> ... Matthias and I to write first draft?
16:19:47 <bobP> ... by next week - Yes.
16:20:00 <bobP> ... next Thu will have coherent draft
16:20:09 <mscottm> Scott was referring specifically to the 'gene variant pipeline' concept from Matthias in the earlier draft as nice to include in the position paper.
16:20:39 <bobP> d'accord
16:21:12 <bobP> Michel: Talk re research heading.
16:21:38 <bobP> ... Summary of competency questions
16:21:55 <bobP> ... have gone through competency questions
16:22:09 <bobP> Matthias: Have a table.
16:22:11 <michel> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US
16:22:43 <bobP> Michel: Need to finish relevant datasets
16:23:04 <bobP> ... also need application and data services need to be filled out
16:23:21 <bobP> Matthias: We could try to use extended version of TMO
16:23:54 <bobP> ... owl reasoning on top to classify a particular patient into a stratification(?)
16:24:42 <bobP> Michel: Task, create nec and suff conditions for classification
16:24:51 <bobP> Matthias: Should agree on extension of TMO
16:25:28 <bobP> ... while ago I worked on this; should have a separte call (to nail this down)
16:25:39 <bobP> Michel: Data representation
16:26:07 <bobP> Matthias: TMO is realist-based, another is generic RDF-izaiton, not nec the same
16:26:31 <bobP> ... should do both in parallel, but with connections
16:27:05 <bobP> ... generic RDF, then try to map to TMO that can be condensed for reasoning
16:27:34 <bobP> Scott: Going back to original implementation, how to represent SNPs etc
16:28:07 <bobP> ... more viable form of representation,..
16:28:38 <bobP> ... need a way to represent SNPs in relation to patients
16:29:01 <bobP> ... relation drug/snp/dosage/phenotype
16:29:17 <bobP> Michel: Overarching diagram, maybe continue developing
16:29:31 <bobP> ... how data are connected should be explicit for us
16:29:44 <bobP> ... need to review that diagram
16:30:28 <bobP> ... Had started a diagram w types and relations between them
16:30:56 <bobP> ... now we understand how things are connected and hence how to construct querie
16:31:26 <bobP> Matthias: Diagram for shot paper needs high-level concepts
16:32:02 <bobP> Michel: Linked data ontology project needs specific enties, etc
16:32:19 <Zakim> - +46.4.63.3.aacc
16:32:33 <bobP> Matthias: Diagram + Protege, two different tracks?
16:32:50 <bobP> Scott: top-down vs bottom-up
16:33:02 <Zakim> + +46.4.63.3.aaee
16:33:16 <bobP> Michel: Ontology is implementation, to think about info. It's the artifact.
16:33:29 <bobP> ... diagram is conceptual, how things ought to be.
16:33:46 <bobP> ... also shows how to construct queries
16:34:08 <bobP> Scott: Diagram shows info requirements; then move to ontology
16:34:27 <bobP> Michel: If we agree on diagram, then we move to ontology
16:35:00 <bobP> ericP: Interface, pattern 1 -> pattern 2, so picture shows pattern 2?
16:35:05 <bobP> Michel: Yes.
16:35:43 <michel> diagram: https://docs.google.com/drawings/d/1OaqlmiTbIAkgHM6kCV-4xbRddHJiN1YZkCWdNHvwiGI/edit?authkey=CIT4rcwM&hl=en_US&authkey=CIT4rcwM
16:36:06 <bobP> Scott: Will be working ont -> sparql; some things better handled in owl?
16:36:27 <bobP> ... patient instances are in KB
16:36:30 <iker> my regrets but i must leave
16:36:36 <Zakim> -??P17
16:36:42 <bobP> ... TMKB, using next to dbSNP
16:37:22 <bobP> Scott: Any possibility of getting clinical data or sample SNP?
16:37:40 <bobP> Matthias: SNP datasets are out there, also genomes
16:38:02 <bobP> ... need work to extract. In public domain
16:38:45 <bobP> Scott: No machine learning. Need realistic forms of data
16:39:08 <bobP> Matthias: Cool to create view of patients w 500K data points!
16:39:24 <bobP> Scott: (scared?) but could work!
16:39:59 <bobP> ... SNPs that are relevant to treatment, assume identified early
16:40:27 <bobP> Matthias: Can have combinations of SNPs that have special meaning
16:41:18 <Zakim> -EricP
16:41:25 <ericP> Zakim, please dial ericP-office
16:41:25 <Zakim> ok, ericP; the call is being made
16:41:27 <Zakim> +EricP
16:43:09 <bobP> Scott: Machine learning in addition to these other connections?
16:43:43 <bobP> Michel: Focus on table of competency questions
16:43:57 <mscottm> Scott was seeking assurance that we won't be attempting machine learning at this stage. :)
16:44:14 <bobP> yes :)
16:45:00 <bobP> Michel: Add competency questions, one by one.
16:45:47 <bobP> Scott: Synch w dbSNP. Next level might be to get sql dump on disk
16:46:05 <bobP> ericP: Iker and I both worked on this.
16:46:55 <bobP> ... scripts complicated. Saw ftp site etc, easy to get a little bit, but dbSNP is huge
16:47:38 <bobP> ... wget() does not do the whole thing
16:48:12 <bobP> ... Oxford has scripts, which included sources
16:48:55 <bobP> Scott: Oxford has given a way to load into mySQL, brought Iker to them
16:49:25 <bobP> ... ideally us SWObjects w database connector
16:49:46 <bobP> ... once working, we could talk sparql endpoint for dbSNP
16:50:16 <bobP> ericP: Representative sample would be awesome
16:50:45 <bobP> ... now foreign keys declared
16:51:35 <bobP> bobf: Can help guide though the schema
16:52:21 <bobP> ericP: For one use case, we can work through which columns we need
16:53:03 <bobP> Matthias: dbSNP does not answer specific clincial questions
16:53:35 <bobP> ... know different SNPs available, different alleles and percentages in hapmap
16:53:56 <bobP> ... but don't need to know all the references etc
16:54:49 <mscottm> +1
16:54:53 <bobP> bobf: Show semweb capabilities or create new knowledge?
16:55:27 <bobP> ... pgx people are wary of inferring too strongly!
16:55:49 <bobP> ericP: Goal is to say, using semweb will make your job easier.
16:56:07 <bobP> ... maybe recapitulate and existing paper
16:56:26 <bobP> bobf: List of resources here is a really good start
16:56:58 <bobP> ... here are areas of discrepancies, ..., and here is how we would solve this
16:57:36 <bobP> Michel: dbSNP use case to connect data. SNP -> other resources connection is important
16:58:30 <bobP> ... relations sequences, gene products, pop variation etc. Need use cases to drive this.
16:59:27 <bobP> Scott: By making available in RDF, can integrate across datasets. SNP db different from drug db
17:00:07 <bobP> ... usable in clinical research, pharma. All in one software landscape.
17:00:57 <bobP> Michel: Matthias and I on first draft. Please add a use case to the table.
17:01:27 <Zakim> -??P5
17:01:28 <Zakim> -Don_Doherty
17:01:28 <Zakim> -Bob_Powers
17:01:29 <Zakim> -Scott_Bauer
17:01:33 <Zakim> - +1.781.431.aabb
17:01:36 <Zakim> - +46.4.63.3.aaee
17:01:49 <Zakim> - +33.3.83.59.aaaa
17:02:00 <bobP> rrsagent, draft minutes
17:02:00 <RRSAgent> I have made the request to generate http://www.w3.org/2011/09/15-hcls2-minutes.html bobP
17:02:16 <bobP> rrsagent, make logs public
17:04:59 <Zakim> - +31.62.427.aadd
17:05:00 <Zakim> -EricP
17:05:00 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:05:02 <Zakim> Attendees were +33.3.83.59.aaaa, Bob_Powers, Scott_Bauer, +1.781.431.aabb, +46.4.63.3.aacc, +31.62.427.aadd, Don_Doherty, EricP, +46.4.63.3.aaee
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