15:05:25 <RRSAgent> RRSAgent has joined #hcls
15:05:25 <RRSAgent> logging to http://www.w3.org/2009/05/27-hcls-irc
15:06:03 <matthias_samwald> scribe: matthias_samwald
15:06:22 <matthias_samwald> TOPIC --- Datasets
15:06:39 <vassil_momtchev> vassil_momtchev has joined #HCLS
15:07:07 <matthias_samwald> rrsagent, scribe: matthias_samwald
15:07:07 <RRSAgent> I'm logging. I don't understand 'scribe: matthias_samwald', matthias_samwald.  Try /msg RRSAgent help
15:07:22 <matthias_samwald> jun: we created a mapping between TCM and Entrez gene
15:07:32 <matthias_samwald> i did some manual correction of the mapping
15:07:39 <matthias_samwald> ... i did some manual correction of the mapping
15:07:51 <matthias_samwald> ... anja also sent me some links today
15:07:58 <matthias_samwald> ... she also linked to SIDER, drugbank
15:08:12 <matthias_samwald> ... dataset quite well interlinked
15:09:19 <matthias_samwald> ... anja encountered performance problems with running SILK over remote SPARQL endpoints
15:10:37 <matthias_samwald> ... we have a rough idea of an interesting use-case in this area
15:11:01 <matthias_samwald> ... we managed to submit an abstract to the DILS poster/demo session, we will get feedback at the end of this month
15:11:23 <matthias_samwald> ... we investigate aTags to enrich the knowledge base with new statements
15:12:23 <matthias_samwald> anja: i did not put use-case on wiki, proposed another small use-case related to TCM today via mail, will put it on the wiki later
15:12:39 <matthias_samwald> ... for SILK, i had to put data into local SPARQL endpoint
15:13:16 <matthias_samwald> ... performance not really an issue, datasets are not updated that often, letting SILK run for some hours is not that bad in this case.
15:14:01 <matthias_samwald> ... had to use local SPARQL endpoint because public endpoints do not allow 7 million queries in a row...
15:14:58 <matthias_samwald> scribeNick: matthias_samwald
15:15:19 <matthias_samwald> anja: egon willighagen was excited about this new dataset
15:15:40 <matthias_samwald> ... matthias and peter ansell were also working on SIDER in parallel.
15:16:17 <matthias_samwald> ... i might also look into linking to LinkedCD
15:16:36 <matthias_samwald> susie: LinkedCT contains new drugs, will there be much side effects data?
15:17:54 <matthias_samwald> anja: there are also marketed drugs in LinkedCT
15:18:46 <matthias_samwald> matthias: i am almost finished with converting SIDER to aTags, i am re-using the DBpedia and OBO URIs directly, should be complementary to the conversion of Anja
15:19:14 <matthias_samwald> anja: I looked at the conversion script from peter ansell, don't know about the results
15:19:37 <matthias_samwald> susie: a next step will be to think about additional datasets
15:20:47 <matthias_samwald> bosse: i have not made progress with working on a query and identifying necessary datasets
15:22:53 <matthias_samwald> susie: we should be able to pose new interesting questions based on the LOD we created
15:23:10 <matthias_samwald> ... we are still lacking questions / necessary steps to utilize the data
15:24:00 <matthias_samwald> jun: in the wiki page we are not giving enough demonstrations. we are just giving a description on how things are done by browsing different websites -- but we wwant to show how linked data can be used!
15:24:27 <matthias_samwald> susie: bosse and i put together some top questions.
15:24:58 <Susie> http://esw.w3.org/topic/HCLSIG/LODD/Questions
15:26:05 <matthias_samwald> susie: (going through questions)
15:27:43 <matthias_samwald> anja: we can give a summarisation of all active ingredients a company is working on / marketing
15:28:09 <matthias_samwald> susie: can we link to pathways?
15:28:56 <matthias_samwald> ... there is pathway information in some Bio2RDF datasets
15:29:58 <matthias_samwald> matthias: the "Linked Life Data" datasets (LarKC / Astra Zeneca) should also have a lot of pathway data
15:32:09 <matthias_samwald> susie: genes and proteins are often linked interchangegably, this could be an entry point.
15:32:41 <matthias_samwald> vassil: hi, i am from ontotext, we are working with Bosse on Linking Life Data
15:32:54 <matthias_samwald> ... we can work on interlinking / sharing identifiers
15:33:21 <matthias_samwald> ... we can also look at user interfaces
15:33:39 <matthias_samwald> ... just querying with SPARQL does not help
15:33:56 <matthias_samwald> susie: i agree
15:34:43 <matthias_samwald> vassil: we are planning to work on user interfaces
15:35:39 <matthias_samwald> ... we should start from the other side -- developing interfaces for concrete tasks by researchers
15:36:23 <matthias_samwald> matthias: could we use Ontotext LifeSKIM?
15:36:47 <matthias_samwald> vassil: this is a bit more specialized, you cannot put arbitrary RDF into it
15:37:47 <matthias_samwald> susie: it's a chicken and egg problem. has anyone else thought about the right order?
15:37:54 <matthias_samwald> Zakim, who is talking?
15:37:54 <Zakim> sorry, matthias_samwald, I don't know what conference this is
15:39:07 <matthias_samwald> vassil: we are looking at Exhibit
15:39:31 <matthias_samwald> vassil: the idea is to run SPARQL queries, get back JSON, and render on screen
15:39:42 <matthias_samwald> ... we hope to see results in 1 month
15:42:01 <matthias_samwald> Zakim, list conferences
15:42:01 <Zakim> I see SW_HCLS(LODD)11:00AM, WAI_EOWG(BAD TF)11:00AM, SEC_WSCWG()11:00AM, HTML_Forms()10:45AM active
15:42:04 <Zakim> also scheduled at this time are W3C_(SearchComm)10:45AM, W3C_(ECTF)10:30AM, XML_Core()11:00AM, T&S_EGOV()11:00AM, XML_()11:00AM, Team_(SITE)11:00AM, MM_MMI(dialog)11:00AM,
15:42:06 <Zakim> ... GA_WebCGM()11:00AM
15:42:33 <matthias_samwald> Zakim, this is SW_HCLS(LODD)
15:42:33 <Zakim> ok, matthias_samwald; that matches SW_HCLS(LODD)11:00AM
15:43:31 <matthias_samwald> susie: (describes query 2 on the wiki page)
15:44:57 <matthias_samwald> ... it seems to be a broad question... aggregate everything around a compound
15:46:23 <matthias_samwald> ... questions 2 (How is this therapy/compound different from existing therapies/compounds) is too broad actually, i will move them down in the list
15:47:08 <matthias_samwald> ... question 3 (What are our patients saying about our drugs) has a strong text mining component
15:49:22 <ericP> Zakim, please dial ericP-office
15:49:22 <Zakim> ok, ericP; the call is being made
15:49:24 <Zakim> +EricP
15:49:35 <matthias_samwald> ... another question: Who are the key opinion leaders for the therapeutic area?
15:49:47 <matthias_samwald> vassil: we have  pubmed, but not citation informatoin
15:49:59 <matthias_samwald> matthias: we could ask anita de waard (elsevier)
15:50:07 <matthias_samwald> susie: i will ask anita
15:54:04 <matthias_samwald> ... question: Of drugs from either the same or different company for the same indication, are they approved in the same target region of interest – US or Global
15:54:12 <matthias_samwald> susie: is this possible in SPARQL
15:54:33 <matthias_samwald> ... ?
15:55:17 <matthias_samwald> eric: not possible in a single SPARQL query
15:55:36 <matthias_samwald> susie: this query seems to be quite tricky
15:55:52 <matthias_samwald> ... especially the part about geography
15:56:09 <matthias_samwald> bosse: the information is proprietary, but i am not totally sure
15:56:45 <matthias_samwald> ACTION ITEM -- have a look whether WHO has useful data about geography of approved drugs
15:57:27 <matthias_samwald> ACTION: bosse have a look whether WHO has useful data about geography of approved drugs
15:58:08 <matthias_samwald> susie: in two weeks we will see how successful we were in looking into these questions
15:59:10 <matthias_samwald> susie: question "are there natural alternatives to this drug?" -- can it be answered with the TCM dataset?
15:59:43 <matthias_samwald> jun: i am a bit worried about the user  interface for presenting query results, that might cost me more time
16:00:34 <matthias_samwald> ... we might need to add some new information (via aTags) to make it useful
16:01:57 <matthias_samwald> anja: you can use associations between genes and diseases, if a drug and a TCM drug are working on the same genes, this  might be a hint
16:02:35 <matthias_samwald> anja: we can define similarity, but we need to have a critical look at the validity
16:03:57 <matthias_samwald> jun: the TCM people also used pathway information to validate
16:04:58 <matthias_samwald> matthias: i can help in judging the validity
16:05:15 <matthias_samwald> TOPIC --- triplification challenge
16:05:43 <matthias_samwald> susie: maybe TCM?
16:05:50 <matthias_samwald> anja: we need use-cases
16:06:32 <matthias_samwald> bye!
16:06:34 <Zakim> - +1.610.651.aabb
16:06:36 <Zakim> - +46.4.63.3.aadd
16:06:37 <Zakim> - +03592490aacc
16:06:38 <Zakim> -??P14
16:06:39 <Zakim> - +049308385aaaa
16:07:27 <matthias_samwald> zakim, list attendees
16:07:29 <Zakim> As of this point the attendees have been +049308385aaaa, +1.610.651.aabb, +03592490aacc, +46.4.63.3.aadd, EricP
16:07:38 <matthias_samwald> rrsagent, generate minutes
16:07:38 <RRSAgent> I have made the request to generate http://www.w3.org/2009/05/27-hcls-minutes.html matthias_samwald
16:07:59 <matthias_samwald> rrsagent, set logs world-visible
16:09:02 <matthias_samwald> Zakim, bye
16:09:02 <Zakim> leaving.  As of this point the attendees were +049308385aaaa, +1.610.651.aabb, +03592490aacc, +46.4.63.3.aadd, EricP
16:09:02 <Zakim> Zakim has left #hcls
16:09:06 <matthias_samwald> rrsagent, bye
16:09:06 <RRSAgent> I see 1 open action item saved in http://www.w3.org/2009/05/27-hcls-actions.rdf :
16:09:06 <RRSAgent> ACTION: bosse have a look whether WHO has useful data about geography of approved drugs [1]
16:09:06 <RRSAgent>   recorded in http://www.w3.org/2009/05/27-hcls-irc#T15-57-27