17:00:20 <RRSAgent> RRSAgent has joined #hcls2
17:00:20 <RRSAgent> logging to http://www.w3.org/2011/11/10-hcls2-irc
17:00:28 <michel> rrsagent, make logs public
17:01:34 <fuogo> fuogo has joined #hcls2
17:01:55 <bobP> bobP has joined #hcls2
17:02:26 <matthias_samwald> zakim, this is hcls
17:02:26 <Zakim> ok, matthias_samwald; that matches SW_HCLS(TMO)11:00AM
17:02:27 <Zakim> +Bob_Powers
17:02:48 <micheldumontier> micheldumontier has joined #hcls2
17:02:51 <Zakim> + +1.518.276.aabb
17:03:01 <Zakim> + +46.7.08.13.aacc
17:03:03 <micheldumontier> zakim, this is tmo
17:03:03 <Zakim> micheldumontier, this was already SW_HCLS(TMO)11:00AM
17:03:07 <Zakim> ok, micheldumontier; that matches SW_HCLS(TMO)11:00AM
17:03:08 <Joanne> Joanne has joined #hcls2
17:03:21 <Joanne> Joanne here -- I'll be back in 2 minutes.
17:03:50 <Zakim> +[IPcaller]
17:04:06 <Zakim> - +46.7.08.13.aacc
17:04:07 <mscottm2> mscottm2 has joined #hcls2
17:04:13 <micheldumontier> zakim, [IPcaller] is michel
17:04:13 <Zakim> +michel; got it
17:04:29 <Zakim> + +62427aadd
17:04:41 <Zakim> +??P31
17:04:45 <Zakim> + +46.7.08.13.aaee
17:05:14 <micheldumontier> topic: W3C HCLSIG - Translational Medicine group
17:05:22 <Joanne> am back
17:05:39 <micheldumontier> zakim, who is here?
17:05:47 <Zakim> On the phone I see +1.760.705.aaaa, Scott_Bauer, ??P19, Bob_Powers, +1.518.276.aabb, michel, +62427aadd, ??P31, +46.7.08.13.aaee
17:05:52 <Mary> It is Mary from knoesis center
17:06:02 <Joanne> Joanne is 518 276
17:06:15 <Zakim> On IRC I see mscottm2, Joanne, micheldumontier, bobP, fuogo, RRSAgent, Zakim, bbalsa, Mary, matthias_samwald, Lena, ericP
17:06:29 <mscottm2> Zakim, +62427aadd is mscottm
17:06:38 <Zakim> +mscottm; got it
17:06:51 <matthias_samwald> zakim, ??P19 is matthias_samwald
17:07:00 <Lena> zakim, ??P31 is Lena 
17:07:03 <Joanne> zakim, +1.518.276.aabb is Joanne
17:07:04 <Zakim> +matthias_samwald; got it
17:07:13 <bbalsa> zakim, +46.7.08.13.aaee is Bosse
17:07:14 <Zakim> +Lena; got it
17:07:16 <Zakim> +Joanne; got it
17:07:22 <Zakim> +Bosse; got it
17:07:39 <Joanne> zakim, Joanne is JoanneLuciano
17:07:39 <Zakim> +JoanneLuciano; got it
17:08:20 <mscottm2> Just sent word about the Pharmacogenomics article through.
17:08:43 <Zakim> +Scott_Bauer.a
17:08:57 <BobF> BobF has joined #hcls2
17:09:51 <Zakim> + +1.781.431.aaff
17:10:00 <bobP> scribenick bobP
17:10:08 <micheldumontier> matthias: restructuring the article; we submitted a review paper first; needed to separate the research components
17:10:18 <epichler> epichler has joined #HCLS2
17:10:52 <bobP> Matthias: Creating a nice outline, w detailed description of conversion
17:11:20 <bobP> ... how ontologies are created. Results section shows queries
17:11:32 <micheldumontier> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US
17:11:38 <bobP> ... todo list at the top
17:12:02 <bobP> ... ID key competency, done. Others are not finished yet
17:12:18 <bobP> ... also should try to finalize next v. of TMO
17:12:37 <bobP> ... Michel and I have been extending TMO to describe genetic variety
17:12:50 <bobP> ... enhanced v of TMO could be a nice addition
17:13:14 <micheldumontier> +1 on OWL reasoning :)
17:13:19 <bobP> ... we can demonstrate onts plus reasoning in queries
17:14:56 <Zakim> +ericP
17:15:36 <Joanne> +1 on OWL reasoning
17:15:43 <Joanne> +1 on enhanced version of TMO
17:15:50 <BobF> Is anyone else getting an echo from Matthias?
17:15:54 <bobP> yes
17:15:58 <Joanne> yes on echo
17:16:07 <mscottm2> somebody needs to mute
17:16:46 <micheldumontier> lena: should we consider gene expression data?
17:16:47 <bobP> Matthias: A, do not want to include gene expression data. It's about genetic varieties
17:16:59 <Zakim> -matthias_samwald
17:17:11 <Lena> just muted myself
17:17:17 <Lena> also, i have a cold ...
17:18:17 <bobP> Michel: Need to go thru use cases and verify sets
17:18:26 <Lena> me too
17:18:29 <bobP> BobF: Can do
17:18:45 <bobP> Joanne: Me too.
17:18:56 <micheldumontier> @action item: joanne, lena bobF and michel to look at use cases and verify the necessary data sets
17:19:30 <Joanne> I suggest we set up a separate call  at a specific time to go through the use case
17:19:42 <bobP> Michel: What does SNPPedia give us in addition to dbSNP?
17:20:00 <bobP> BobF: Helpful to consider how easy to convert?
17:20:38 <bobP> Michel: Talking about converting dbSNP. Would be different from representation of snpPedica
17:20:59 <bobP> ... TMO would be conforming (to dbSNP?)
17:21:18 <bobP> BobF: snpPedia not all that amenable to conversion. Would be a challenge
17:21:29 <matthias_samwald> matthias_samwald has joined #hcls2
17:21:39 <bobP> Scott: Why is snpPedia hard?
17:22:07 <bobP> Scott: Crawling was taking a long time (dbSNP, right?)
17:22:08 <matthias_samwald> reconnecting...
17:22:11 <Lena> question to anyone that knows: how are the SNP in SNPedia identified and correlated to the diseases? 
17:22:20 <bobP> BobF: Mappings to ontologies?
17:22:40 <Zakim> +[IPcaller]
17:23:15 <bobP> Scott: Don't remember quite about RDF from SNPedia
17:23:38 <bobP> BobF: Looked at SNPedia, did not see a good way to convert
17:24:00 <bobP> ... have you looked at mappings to ontology. Confidence in this?
17:24:32 <bobP> Matthias: Looked at SNPedia RDF, not quite good, using semantic media wiki
17:25:00 <bobP> ... this is good, but does not (extend down to content?)
17:25:22 <bobP> ... there is basis info re...(dropping off)
17:26:17 <bobP> ... sum: some info in RDF so basic tasks can be achieved w SNPedid
17:26:34 <matthias_samwald> genewikiplus.org/
17:26:40 <bobP> ... Benjamin (Good?) GeneWikiPlus
17:27:07 <bobP> ... used info from SNPedia and linked w genewiki from wikipedia
17:27:37 <bobP> ... representation of genes and their properties. Combine genetics w variation.
17:28:31 <bobP> ... GeneWikiPlus might be a good starting point.
17:30:54 <bobP> Michel: Extensions to TMO.
17:31:14 <bobP> Matthias: Michel and I have worked on this, not finished
17:31:41 <bobP> ... need to find consensus on how to represent genetic variation
17:32:19 <bobP> ... maybe based on realist model. Worthwhile to have repr that is in line w basic...(faded)
17:32:23 <Zakim> -[IPcaller]
17:32:26 <mscottm2> matthias can you write what you just said?
17:32:48 <bobP> (just at the punchline too!)
17:33:35 <bobP> Michel: Need to devote a whole call to extending TMO for genetic variation. Next week's call.
17:33:40 <micheldumontier> action item: next week will be about extending TMO
17:34:12 <bobP> ericP: Can get hold of i2b2 data, to compel them w interesting questions
17:34:39 <bobP> ... provide sparql access to i2b2, to show why to connect outside of i2b2
17:34:50 <micheldumontier> action item: joanne, lena bobF and michel to look at use cases and verify the necessary data sets
17:35:04 <bobP> Joanne: Can you get a sample of i2b2 data?
17:35:33 <bobP> ericP: Must ask specific Q to stimulate
17:35:34 <micheldumontier> action item: develop TMO use case
17:36:21 <micheldumontier> ihttp://www.w3.org/wiki/HCLSIG/Use_case/TMO_for_pharmacogenomics
17:36:26 <bobP> Michel: Matthias started this use case
17:36:40 <bobP> ... need to develop the value proposition here
17:37:17 <bobP> ericP: i2b2 can access phenotype data. Some sets for SNP data
17:37:34 <Lena> ericP: affymetrix (gene expression data) from i2b2
17:37:57 <bobP> ... that's all within i2b2. So pathways, GO might not be needed
17:38:27 <bobP> (ericP fading sometimes)
17:39:12 <bobP> Scott: Do they have the SNP info?
17:39:39 <bobP> ericP: Are there drug onts for adverse events
17:39:48 <bobP> Scott: Tie to patient alleles
17:40:07 <bobP> ericP: Some datasets have alleles.
17:40:29 <bobP> ... So patient pop, all taking drug in class, get to AEs
17:41:07 <bobP> ... might need drug hierarchies
17:41:25 <bobP> Scott: Lots of stuff on AEs, like OMOP
17:41:50 <bobP> ... some of these efforts are doing things w. RDF
17:42:02 <bobP> Scott: i2b2 only in Oracle?
17:42:51 <bobP> ... one of possible couplings, look up SNP at sparql endpoint
17:43:04 <Joanne> https://i2b2.cchmc.org/faq#data1
17:43:12 <bobP> ... in scenario where clinician is prescribing
17:43:42 <bobP> Joanne: Link shows the stuff that's in i2b2
17:44:10 <bobP> ... primary use case is looking for patient cohorts, somewhat limited
17:44:16 <mscottm2> Something that I mentioned: OMOP http://omop.fnih.org/
17:45:04 <bobP> Joanne: Sepsis use case
17:45:17 <Zakim> +[IPcaller]
17:45:31 <bobP> Matthias is back.
17:46:17 <bobP> Michel: Next week will be TMO, and develop use case doc
17:46:22 <micheldumontier> http://www.w3.org/wiki/HCLSIG/pharmacogenomics_2012
17:48:46 <Lena> i can work on federating queries across the distributed endpoints... maybe with the help from eric :)
17:49:12 <bobP> Matthias: Google doc, easy to generate a lot of text, hard to see forest for the trees
17:50:01 <bobP> Scott: dbSNP. Going to have opportunity to set up endpoint
17:50:11 <bobP> ... are we waiting on this?
17:50:12 <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 
17:50:37 <bobP> BobF: We have gained access to Michel's server and uploaded
17:50:46 <bobP> ... also to a mySQL db
17:52:02 <bobP> BobF: We can provide the schema, w a script
17:52:12 <bobP> (Rick is faded)
17:52:30 <micheldumontier> mysql database is accessble at http://s5.semanticscience.org/phpmyadmin/  login: tm-ro pass: tm
17:52:59 <bobP> ericP: Query is more valuable than foreign keys
17:55:08 <bobP> Scott: SQL queries as sparql, do we know the sql queries to pull up info re SNPs
17:55:45 <bobP> Michel: Type of SNP, class, chromosome, allele, etc depending on which table
17:55:57 <bobP> ... but only a handful of facets here
17:56:17 <bobP> BobF: If addition info required we can provide. This was just a first pass.
17:56:37 <Joanne> *** i have to leave now. I need a few minutes before my next telcon *** 
17:56:46 <Lena> i don't see the clinical association... perhaps that's in a table that was not imported?
17:57:16 <Joanne> please contact me through email or phone for follow-up on the items we discussed.  -- Joanne
17:57:21 <Zakim> -JoanneLuciano
17:57:25 <mscottm2> Space, the final frontier..
17:57:35 <bobP> :)
17:57:49 <ericP> micheldumontier, do you have an SQL endpoint for that database?
17:58:11 <mscottm2> In general, using a speakerphone during teleconferences creates these types of interesting noise problems.
17:58:11 <Mary> Is  there any Pharmacogenomics info in this db?
17:58:34 <ericP> (i.e. so i can mysql -u tm-ro -h some.machine -p 3305 ?)
17:58:41 <Zakim> -[IPcaller]
17:58:59 <Zakim> - +1.781.431.aaff
17:59:16 <mscottm2> thanks all
17:59:20 <Lena> ericP: got my sparql gloves on, if you need help :)
17:59:22 <Zakim> -Bosse
17:59:26 <Zakim> -Scott_Bauer
17:59:42 <ericP> mysql -h s5.semanticscience.org
18:00:21 <Zakim> -Bob_Powers
18:01:27 <epichler> epichler has left #HCLS2
18:02:12 <Zakim> - +1.760.705.aaaa
18:06:30 <Zakim> -Scott_Bauer.a
18:06:33 <Zakim> -ericP
18:06:34 <Zakim> -michel
18:06:47 <Lena> hehe
18:06:48 <micheldumontier>  rrsagent, draft minutes 
18:06:48 <RRSAgent> I have made the request to generate http://www.w3.org/2011/11/10-hcls2-minutes.html micheldumontier
18:06:53 <mscottm2> ciao
18:06:55 <micheldumontier> rrsagent, make log world-visible
18:07:01 <Zakim> -mscottm
18:08:41 <Zakim> -Lena
18:08:43 <Zakim> SW_HCLS(TMO)11:00AM has ended
18:08:45 <Zakim> Attendees were +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]
18:11:14 <micheldumontier> ok, it works now
18:17:17 <mscottm2> From MySQL Command Line Client, "connect s5.semanticscience.org" gives an error: "Error 1049 .. unknown database"
18:18:38 <mscottm2> database name?
18:19:06 <Lena> should be dbsnp, i think
18:19:20 <Lena> that's what's in phpmyadmin
18:19:45 <mscottm2> yeah, just looked up dbsnp - thanks
18:20:23 <micheldumontier> good?
18:20:51 <mscottm2> So, I need to combine dbsnp and s5.semanticscience.org with the 'use' command?
18:21:09 <mscottm2> trying to figure out how it wants parameters
18:22:23 <Lena> sp LOC would be the main table
18:22:41 <mscottm2> sp?
18:23:12 <Lena> so
18:23:15 <Lena> sorry :)
18:23:42 <Lena> LOC has the SNP symbol and the accession number, which we can use to look up the snp on entrez gene, i think
18:23:45 <Lena> let me check
18:23:50 <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.
18:24:47 <Lena> NM_003636.2 exist in homologene
18:25:01 <Lena> checking now RDF homologene... 
18:25:30 <Lena> i keep forgetting how to load the mysql port on swobjects... 
18:26:12 <Lena> got it :-) --stem
18:28:08 <micheldumontier> we should make a wiki page that documents this entire dbsnp effort
18:29:02 <micheldumontier> from how bobF got the data into these tables, to the db configuration to the swobjects mapping/query files
18:30:02 <Lena> hum... homologene in bio2rdf seems to have nothing on NM_003636.2
18:30:08 <Lena> maybe I'm doing the query wrong... 
18:31:00 <mscottm2> mscottm2 has joined #hcls2
18:31:18 <Lena> nothinkg on KCNAB2 either... 
18:31:56 <mscottm2> can you remind me what that was?
18:37:13 <Lena> that is the very first SNP in the LOC table :)
18:37:33 <Lena> or rather gene symbol where that SNP exists
18:38:38 <mscottm2> tx
18:39:15 <mscottm2> voila, I am still a few clicks behind.
18:41:49 <Lena> if you lookup the value on the accession number on entrez, it exists only in two databases: homologene and gene expression omnibus
18:42:24 <Lena> micheldumontier: where do you think we can post this instead?
18:42:43 <Lena> i am just brainstorming here... it's nice to have an audience :-)
18:45:43 <Lena> mscottm2: for swobjects 
18:45:47 <Lena> SPARQL.exe --stem http://biordf.org/dbSNP/ -S mysql://tm-ro@s5.semanticscience.org/dbsnp --serve http ://localhost:8001/dnsnp
18:46:21 <Lena> sparql endpoint with dnsnp up and running
18:51:38 <mscottm2> Wow! Really? Add that to the tutorial!
18:52:09 <mscottm2> where are the maps (SPARQL Constructs)?
18:53:25 <mscottm2> (sorry that I keep stepping away - single Papa the last few weeks. had to cook dinner for the kids during the TM call.)
18:57:01 <Lena> wait... no constructs yet :)
18:57:11 <Lena> still trying to figure out the queries :)
18:57:28 <Lena> had to cook dinner for the kids during the TM call. ==> that's why they invented fish sticks :P :P
19:03:21 <mscottm2> absolutely - we eat those regularly
19:04:00 <mscottm2> Got to chase the kids to bed now. If you figure out a query, please skype it to me. :)
19:05:05 <mscottm2> updating, rebooting, too so bye!
19:05:32 <Lena> micheldumontier: is it possible to remove the password from the mysql port... just for a few hours?
19:05:54 <Lena> i wanted to verify whether the problem is swobjects or my lack of knowledge of it :)
19:07:44 <mscottm2> cmd   /query micheldumontier might get his attention but skype , Google chat , are better.
19:07:51 <micheldumontier> oh hey
19:08:14 <micheldumontier> oh ok
19:08:15 <micheldumontier> i can do this
19:08:16 <mscottm2> hey - cool
19:08:19 <Zakim> Zakim has left #hcls2
19:08:44 <mscottm2> ever generate the minutes?
19:08:46 <micheldumontier> done
19:09:05 <Lena> thanks :)
19:09:12 <micheldumontier> rrsagent, draft minutes 
19:09:12 <RRSAgent> I have made the request to generate http://www.w3.org/2011/11/10-hcls2-minutes.html micheldumontier
19:09:35 <mscottm2> tx, bye!
19:15:06 <Lena> success!
19:15:13 <Lena> query to retrieve accession numbers:
19:15:16 <Lena> select ?acc where { _:LOC <http://biordf.org/dbSNP/LOC#symbol> "KCNAB2" ;        <http://biordf.org/dbSNP/LOC#mma_acc> ?acc ; }
19:15:34 <Lena> (for one gene)
19:29:41 <Lena> micheldumontier: once more dbsnp tables are loaded, please let me know; there's not much this query can do withouth either 1) accession number being described somewhere with links to OMIM or any other disease references and 2) the tables that contain the information the links the SNP to the disease in dbSNP
19:30:01 <micheldumontier> i don't have any more
19:30:06 <micheldumontier> i got these from bobP
19:30:15 <micheldumontier> so, we need to ask him for the tables
19:31:27 <Lena> there's a group that apparently povides mysql dump for one table at a time - https://cgsmd.isi.edu/dbsnpq/downloads.php#dbSNPdownloadsTables
19:32:19 <Lena> i was trying to see if someone provide a mysql port open so that we did not have to overload your servers... but could not find it yet
19:36:29 <ericP> lena, are you doing all the work for me?
19:36:34 <ericP> you rock!
19:36:51 <micheldumontier> where is the sparql endpoint?
19:37:16 <Lena> so far... only on my machine
19:37:26 <Lena> let me document the workflow somewhere... one sec
19:39:01 <Lena> https://docs.google.com/document/d/1UJK9GPqnd3z7fl38s19UPyP3wblMoTlcmlw261L1ETc/edit?hl=en_US
19:45:04 <Lena> i found something about the accession numbers on sindice... trying that next
19:56:47 <Lena> ericP: apparently ucsc genome browser also contains SNP data
19:56:51 <Lena> http://biostar.stackexchange.com/questions/1333/dbsnp-best-way-to-obtain-data-on-snps
19:57:04 <Lena> and we know THAT has a mysql port open :-) :-)
20:03:43 <ericP> cooool
20:32:28 <Lena> ericP: trying this: BIND(fn:substring(?acc, 1, 9) as ?accession)
20:32:40 <Lena> but this is what I get:
20:33:00 <Lena> "http://www.w3.org/2005/xpath-functions#substring"
20:33:08 <Lena> weird, huh?
20:39:04 <Lena> ericP: also (sorry for being the bearer of bad news)... wrapper need to be added for services like sindice
20:39:05 <Lena> SERVICE <http://sparql.sindice.com/> produced error: ResultSet constructor: no parser for mediatype "text/html"
20:54:44 <ericP> Lena, roger
20:55:02 <Lena> the fn:substring error is strange... 
20:55:16 <Lena> that one was fixed when we worked on the gene express api
20:55:28 <ericP> "http://www.w3.org/2005/xpath-functions#substring" is the error message?
20:55:41 <Lena> no... it's the output of the queyr!
20:55:57 <Lena> s/queyt/query
20:56:02 <Lena> s/queyr/query
20:56:07 <ericP> some poor variable got bound to "http://www.w3.org/2005/xpath-functions#substring" ?
20:56:12 <ericP> that's really odd
20:56:38 <Lena> and no matter where I cut the string, it allways gives me the complete uri for the xpath function
20:57:06 <ericP> truly bizarre
20:59:54 <ericP> sparql -D -e 'SELECT ?s (SUBSTR(?o, 2, 5) AS ?x) WHERE { ?s <http://usefulinc.com/ns/doap#shortdesc> ?o }'
20:59:57 <ericP> +----+---------+
21:00:00 <ericP> | ?s | ?x      |
21:00:02 <ericP> | <> | " sema" |
21:00:05 <ericP> +----+---------+
21:00:09 <ericP> that seems about right
21:00:13 <ericP> what's that query di for you?
21:01:08 <ericP> (btw, i have a theory: that it's giving an error on the substr of an IRI (which perhaps it is supposed to do), but it's not the kind of error which simply says "ignore this row")
21:07:02 <Lena> trying now
21:07:28 <Lena> that one worked
21:07:59 <Lena> can I ask you to peek at the query that I am trying?
21:08:12 <Lena> tired eyes can't debug very well :)
21:08:25 <ericP> where is it?
21:08:45 <ericP> (lots of urls back in the history)
21:13:15 <Lena> select ?accession where { _:LOC <http://biordf.org/dbSNP/LOC#symbol> 'KCNAB2' ; <http://biordf.org/dbSNP/LOC#mma_acc> ?acc .  BIND(fn:substring(xsd:string(?acc), 1,9) as ?accession) }
21:13:20 <ericP> tx
21:19:11 <Lena> and... :)
21:19:26 <Lena> (curiosity)
21:21:10 <ericP> got distracted
21:21:14 <ericP> back on the mission
21:22:26 <ericP> want to paste in those prefixes, just 'cause i'm a slacker
21:29:26 <Lena> PREFIX fn: <http://www.w3.org/2005/xpath-functions#> select ?accession where { _:LOC <http://biordf.org/dbSNP/LOC#symbol> 'KCNAB2' ; <http://biordf.org/dbSNP/LOC#mma_acc> ?acc .  BIND(fn:substring(?acc, 1,9) as ?accession) } limit 10
21:30:52 <ericP> and the data which that queries?
21:32:08 <ericP> phone call?
21:32:19 <ericP> hmm, google voice, perhaps?
21:33:54 <ericP> you can work around this with something like IF (isLiteral(?o), SUBSTR(?o, 2, 5), "XX")
21:36:28 <Lena> oh.. sorry
21:36:31 <Lena> data... 
21:36:36 <Lena> google voice ok
21:37:57 <Lena> sparql --stem http://biordf.org/dbSNP/ -S mysql://tm-ro@s5.semanticscience.org/dbsnp --serve http://localhost:8001/dnsnp
21:48:26 <ericP> uname -a
21:48:26 <ericP> Linux eric-ubu 3.0.0-12-generic #20-Ubuntu SMP Fri Oct 7 14:56:25 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
21:48:49 <Lena> Linux ubuntu 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 19:00:26 UTC 2011 i686 GNU/Linux 
23:45:49 <mox601> mox601 has joined #HCLS2