See also: IRC log
<Joanne> Joanne here -- I'll be back in 2 minutes.
<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! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <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[End of scribe.perl diagnostic output]