scribenick bobP

<matthias_samwald> https://docs.google.com/document/d/1bsJ3YWuH1k3gdXtSN2PXfmUIavtR-hDXhHMn0bKB5pk/edit?hl=en_US

Michel: Write short special report, then consider the new charter

:)

Michel: Scott concerned w timing, Matthias requirements

Matthias: Agreed on using this kind of data type Special report 1000-3000 words
... google doc started

<mscottm> About how many pages is that?

Matthias: from the viewpoint of normal research, personalized med, we can say that semweb is niche area
... requirement for future medicine, article should give overview of problems that motivate
... also non-experts need a good overview of what we are suggesting
... brief enough to focus on ideas and mission
... Outline in google doc is summary, not really an abstract
... one section is required for future perspectives, where most of text should go
... looks out 5-10 years, how semantics, text-mining etc will play

<ericP> ciao

Matthias: we can agree on high level statement, then go on discussing how pharma would be involved
... and integrated into clinical decision support
... can also present ontologies, say how we expect pieces of puzzle to fit in infrastructure
... over next two weeks

Michel: Good, like the high-levelness and tone

<bobf> Is there a deadline for the submission?

Michel: interesting to present what semweb can do
... pasted in resources at heart of integration
... should also have a figure
... don't know the value of including everything

Matthias: Have already reduced table somewhat

Michel: Figure: variation, response, pop genetics, diseases and treatment
... table has raw data, as terms and onts to leverage or describe
... maybe illustrate the RDF-like character, or a concept map about relationships

<ericP> i don't feel qualified to answer

Scott: Solves the hesitation in the model
... position paper, put it out there, then continue in research
... should mention gene-variant concept in this paper anyway

Michel: Starts w future perspective, can talk re resources and how can be exploited
... Need to come up w model on how to make contributions
... suggest one or two people to write first draft
... message needs to be highly focused
... Matthias and I to write first draft?
... by next week - Yes.
... next Thu will have coherent draft

<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.

d'accord

Michel: Talk re research heading.
... Summary of competency questions
... have gone through competency questions

Matthias: Have a table.

<michel> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US

Michel: Need to finish relevant datasets
... also need application and data services need to be filled out

Matthias: We could try to use extended version of TMO
... owl reasoning on top to classify a particular patient into a stratification(?)

Michel: Task, create nec and suff conditions for classification

Matthias: Should agree on extension of TMO
... while ago I worked on this; should have a separte call (to nail this down)

Michel: Data representation

Matthias: TMO is realist-based, another is generic RDF-izaiton, not nec the same
... should do both in parallel, but with connections
... generic RDF, then try to map to TMO that can be condensed for reasoning

Scott: Going back to original implementation, how to represent SNPs etc
... more viable form of representation,..
... need a way to represent SNPs in relation to patients
... relation drug/snp/dosage/phenotype

Michel: Overarching diagram, maybe continue developing
... how data are connected should be explicit for us
... need to review that diagram
... Had started a diagram w types and relations between them
... now we understand how things are connected and hence how to construct querie

Matthias: Diagram for shot paper needs high-level concepts

Michel: Linked data ontology project needs specific enties, etc

Matthias: Diagram + Protege, two different tracks?

Scott: top-down vs bottom-up

Michel: Ontology is implementation, to think about info. It's the artifact.
... diagram is conceptual, how things ought to be.
... also shows how to construct queries

Scott: Diagram shows info requirements; then move to ontology

Michel: If we agree on diagram, then we move to ontology

ericP: Interface, pattern 1 -> pattern 2, so picture shows pattern 2?

Michel: Yes.

<michel> diagram: https://docs.google.com/drawings/d/1OaqlmiTbIAkgHM6kCV-4xbRddHJiN1YZkCWdNHvwiGI/edit?authkey=CIT4rcwM&hl=en_US&authkey=CIT4rcwM

Scott: Will be working ont -> sparql; some things better handled in owl?
... patient instances are in KB

<iker> my regrets but i must leave

Scott: TMKB, using next to dbSNP
... Any possibility of getting clinical data or sample SNP?

Matthias: SNP datasets are out there, also genomes
... need work to extract. In public domain

Scott: No machine learning. Need realistic forms of data

Matthias: Cool to create view of patients w 500K data points!

Scott: (scared?) but could work!
... SNPs that are relevant to treatment, assume identified early

Matthias: Can have combinations of SNPs that have special meaning

Scott: Machine learning in addition to these other connections?

Michel: Focus on table of competency questions

<mscottm> Scott was seeking assurance that we won't be attempting machine learning at this stage. :)

yes :)

Michel: Add competency questions, one by one.

Scott: Synch w dbSNP. Next level might be to get sql dump on disk

ericP: Iker and I both worked on this.
... scripts complicated. Saw ftp site etc, easy to get a little bit, but dbSNP is huge
... wget() does not do the whole thing
... Oxford has scripts, which included sources

Scott: Oxford has given a way to load into mySQL, brought Iker to them
... ideally us SWObjects w database connector
... once working, we could talk sparql endpoint for dbSNP

ericP: Representative sample would be awesome
... now foreign keys declared

bobf: Can help guide though the schema

ericP: For one use case, we can work through which columns we need

Matthias: dbSNP does not answer specific clincial questions
... know different SNPs available, different alleles and percentages in hapmap
... but don't need to know all the references etc

<mscottm> +1

bobf: Show semweb capabilities or create new knowledge?
... pgx people are wary of inferring too strongly!

ericP: Goal is to say, using semweb will make your job easier.
... maybe recapitulate and existing paper

bobf: List of resources here is a really good start
... here are areas of discrepancies, ..., and here is how we would solve this

Michel: dbSNP use case to connect data. SNP -> other resources connection is important
... relations sequences, gene products, pop variation etc. Need use cases to drive this.

Scott: By making available in RDF, can integrate across datasets. SNP db different from drug db
... usable in clinical research, pharma. All in one software landscape.

Michel: Matthias and I on first draft. Please add a use case to the table.

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