<Joanne> Joanne here -- I'll be back in 2 minutes.

W3C HCLSIG - Translational Medicine group

<Joanne> am back

<Mary> It is Mary from knoesis center

<Joanne> Joanne is 518 276

<mscottm2> Just sent word about the Pharmacogenomics article through.

scribenick bobP

<micheldumontier> matthias: restructuring the article; we submitted a review paper first; needed to separate the research components

Matthias: Creating a nice outline, w detailed description of conversion
... how ontologies are created. Results section shows queries

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

Matthias: todo list at the top
... ID key competency, done. Others are not finished yet
... also should try to finalize next v. of TMO
... Michel and I have been extending TMO to describe genetic variety
... enhanced v of TMO could be a nice addition

<micheldumontier> +1 on OWL reasoning :)

Matthias: we can demonstrate onts plus reasoning in queries

<Joanne> +1 on OWL reasoning

<Joanne> +1 on enhanced version of TMO

<BobF> Is anyone else getting an echo from Matthias?

yes

<Joanne> yes on echo

<mscottm2> somebody needs to mute

<micheldumontier> lena: should we consider gene expression data?

Matthias: A, do not want to include gene expression data. It's about genetic varieties

<Lena> just muted myself

<Lena> also, i have a cold ...

Michel: Need to go thru use cases and verify sets

<Lena> me too

BobF: Can do

Joanne: Me too.

<micheldumontier> @action item: joanne, lena bobF and michel to look at use cases and verify the necessary data sets

<Joanne> I suggest we set up a separate call at a specific time to go through the use case

Michel: What does SNPPedia give us in addition to dbSNP?

BobF: Helpful to consider how easy to convert?

Michel: Talking about converting dbSNP. Would be different from representation of snpPedica
... TMO would be conforming (to dbSNP?)

BobF: snpPedia not all that amenable to conversion. Would be a challenge

Scott: Why is snpPedia hard?
... Crawling was taking a long time (dbSNP, right?)

<matthias_samwald> reconnecting...

<Lena> question to anyone that knows: how are the SNP in SNPedia identified and correlated to the diseases?

BobF: Mappings to ontologies?

Scott: Don't remember quite about RDF from SNPedia

BobF: Looked at SNPedia, did not see a good way to convert
... have you looked at mappings to ontology. Confidence in this?

Matthias: Looked at SNPedia RDF, not quite good, using semantic media wiki
... this is good, but does not (extend down to content?)
... there is basis info re...(dropping off)
... sum: some info in RDF so basic tasks can be achieved w SNPedid

<matthias_samwald> genewikiplus.org/

Matthias: Benjamin (Good?) GeneWikiPlus
... used info from SNPedia and linked w genewiki from wikipedia
... representation of genes and their properties. Combine genetics w variation.
... GeneWikiPlus might be a good starting point.

Michel: Extensions to TMO.

Matthias: Michel and I have worked on this, not finished
... need to find consensus on how to represent genetic variation
... maybe based on realist model. Worthwhile to have repr that is in line w basic...(faded)

<mscottm2> matthias can you write what you just said?

(just at the punchline too!)

Michel: Need to devote a whole call to extending TMO for genetic variation. Next week's call.

<micheldumontier> ACTION: item to next week will be about extending TMO [recorded in http://www.w3.org/2011/11/10-hcls2-minutes.html#action01]

ericP: Can get hold of i2b2 data, to compel them w interesting questions
... provide sparql access to i2b2, to show why to connect outside of i2b2

<micheldumontier> ACTION: item to joanne, lena bobF and michel to look at use cases and verify the necessary data sets [recorded in http://www.w3.org/2011/11/10-hcls2-minutes.html#action02]

Joanne: Can you get a sample of i2b2 data?

ericP: Must ask specific Q to stimulate

<micheldumontier> ACTION: item to develop TMO use case [recorded in http://www.w3.org/2011/11/10-hcls2-minutes.html#action03]

<micheldumontier> ihttp://www.w3.org/wiki/HCLSIG/Use_case/TMO_for_pharmacogenomics

Michel: Matthias started this use case
... need to develop the value proposition here

ericP: i2b2 can access phenotype data. Some sets for SNP data

<Lena> ericP: affymetrix (gene expression data) from i2b2

ericP: that's all within i2b2. So pathways, GO might not be needed

(ericP fading sometimes)

Scott: Do they have the SNP info?

ericP: Are there drug onts for adverse events

Scott: Tie to patient alleles

ericP: Some datasets have alleles.
... So patient pop, all taking drug in class, get to AEs
... might need drug hierarchies

Scott: Lots of stuff on AEs, like OMOP
... some of these efforts are doing things w. RDF
... i2b2 only in Oracle?
... one of possible couplings, look up SNP at sparql endpoint

<Joanne> https://i2b2.cchmc.org/faq#data1

Scott: in scenario where clinician is prescribing

Joanne: Link shows the stuff that's in i2b2
... primary use case is looking for patient cohorts, somewhat limited

<mscottm2> Something that I mentioned: OMOP http://omop.fnih.org/

Joanne: Sepsis use case

Matthias is back.

Michel: Next week will be TMO, and develop use case doc

<micheldumontier> http://www.w3.org/wiki/HCLSIG/pharmacogenomics_2012

<Lena> i can work on federating queries across the distributed endpoints... maybe with the help from eric :)

Matthias: Google doc, easy to generate a lot of text, hard to see forest for the trees

Scott: dbSNP. Going to have opportunity to set up endpoint
... are we waiting on this?

<Lena> also, it would be fun/relevant to add a visual interface (faceted browsing?) that will let clinicians (not just semantic web geeks!) build the relevant queries

BobF: We have gained access to Michel's server and uploaded
... also to a mySQL db
... We can provide the schema, w a script

(Rick is faded)

<micheldumontier> mysql database is accessble at http://s5.semanticscience.org/phpmyadmin/ login: tm-ro pass: tm

ericP: Query is more valuable than foreign keys

Scott: SQL queries as sparql, do we know the sql queries to pull up info re SNPs

Michel: Type of SNP, class, chromosome, allele, etc depending on which table
... but only a handful of facets here

BobF: If addition info required we can provide. This was just a first pass.

<Joanne> *** i have to leave now. I need a few minutes before my next telcon ***

<Lena> i don't see the clinical association... perhaps that's in a table that was not imported?

<Joanne> please contact me through email or phone for follow-up on the items we discussed. -- Joanne

<mscottm2> Space, the final frontier..

:)

<ericP> micheldumontier, do you have an SQL endpoint for that database?

<mscottm2> In general, using a speakerphone during teleconferences creates these types of interesting noise problems.

<Mary> Is there any Pharmacogenomics info in this db?

<ericP> (i.e. so i can mysql -u tm-ro -h some.machine -p 3305 ?)

<mscottm2> thanks all

<Lena> ericP: got my sparql gloves on, if you need help :)

<ericP> mysql -h s5.semanticscience.org

<Lena> hehe

<mscottm2> ciao

<micheldumontier> ok, it works now

<mscottm2> From MySQL Command Line Client, "connect s5.semanticscience.org" gives an error: "Error 1049 .. unknown database"

<mscottm2> database name?

<Lena> should be dbsnp, i think

<Lena> that's what's in phpmyadmin

<mscottm2> yeah, just looked up dbsnp - thanks

<micheldumontier> good?

<mscottm2> So, I need to combine dbsnp and s5.semanticscience.org with the 'use' command?

<mscottm2> trying to figure out how it wants parameters

<Lena> sp LOC would be the main table

<mscottm2> sp?

<Lena> so

<Lena> sorry :)

<Lena> LOC has the SNP symbol and the accession number, which we can use to look up the snp on entrez gene, i think

<Lena> let me check

<mscottm2> Nevermind - I'll figure out the mysql cmd line some other time. php interface is good. Yes, LOC appears to be the main table.

<Lena> NM_003636.2 exist in homologene

<Lena> checking now RDF homologene...

<Lena> i keep forgetting how to load the mysql port on swobjects...

<Lena> got it :-) --stem

<micheldumontier> we should make a wiki page that documents this entire dbsnp effort

<micheldumontier> from how bobF got the data into these tables, to the db configuration to the swobjects mapping/query files

<Lena> hum... homologene in bio2rdf seems to have nothing on NM_003636.2

<Lena> maybe I'm doing the query wrong...

<Lena> nothinkg on KCNAB2 either...

<mscottm2> can you remind me what that was?

<Lena> that is the very first SNP in the LOC table :)

<Lena> or rather gene symbol where that SNP exists

<mscottm2> tx

<mscottm2> voila, I am still a few clicks behind.

<Lena> if you lookup the value on the accession number on entrez, it exists only in two databases: homologene and gene expression omnibus

<Lena> micheldumontier: where do you think we can post this instead?

<Lena> i am just brainstorming here... it's nice to have an audience :-)

<Lena> mscottm2: for swobjects

<Lena> SPARQL.exe --stem http://biordf.org/dbSNP/ -S mysql://tm-ro@s5.semanticscience.org/dbsnp --serve http ://localhost:8001/dnsnp

<Lena> sparql endpoint with dnsnp up and running

<mscottm2> Wow! Really? Add that to the tutorial!

<mscottm2> where are the maps (SPARQL Constructs)?

<mscottm2> (sorry that I keep stepping away - single Papa the last few weeks. had to cook dinner for the kids during the TM call.)

<Lena> wait... no constructs yet :)

<Lena> still trying to figure out the queries :)

<Lena> had to cook dinner for the kids during the TM call. ==> that's why they invented fish sticks :P :P

<mscottm2> absolutely - we eat those regularly

<mscottm2> Got to chase the kids to bed now. If you figure out a query, please skype it to me. :)

<mscottm2> updating, rebooting, too so bye!

<Lena> micheldumontier: is it possible to remove the password from the mysql port... just for a few hours?

<Lena> i wanted to verify whether the problem is swobjects or my lack of knowledge of it :)

<mscottm2> cmd /query micheldumontier might get his attention but skype , Google chat , are better.

<micheldumontier> oh hey

<micheldumontier> oh ok

<micheldumontier> i can do this

<mscottm2> hey - cool

<mscottm2> ever generate the minutes?

<micheldumontier> done

<Lena> thanks :)

This is scribe.perl Revision: 1.136  of Date: 2011/05/12 12:01:43  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

No ScribeNick specified.  Guessing ScribeNick: bobP
Inferring Scribes: bobP
Default Present: +1.760.705.aaaa, Scott_Bauer, Bob_Powers, +46.7.08.13.aacc, michel, mscottm, matthias_samwald, Lena, Bosse, JoanneLuciano, +1.781.431.aaff, ericP, [IPcaller]
Present: +1.760.705.aaaa Scott_Bauer Bob_Powers +46.7.08.13.aacc michel mscottm matthias_samwald Lena Bosse JoanneLuciano +1.781.431.aaff ericP [IPcaller]

WARNING: No meeting title found!
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<dbooth> Meeting: Weekly Baking Club Meeting


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<dbooth> Chair: dbooth

Got date from IRC log name: 10 Nov 2011
Guessing minutes URL: http://www.w3.org/2011/11/10-hcls2-minutes.html
People with action items: item