16:06:48 <RRSAgent> RRSAgent has joined #hcls2
16:06:48 <RRSAgent> logging to http://www.w3.org/2011/10/20-hcls2-irc
16:06:56 <michel> rrsagent, make logs public
16:08:30 <michel> boycer: has been lurking from LODD, interested in TM group
16:08:40 <bobP> scribenick bobP
16:08:48 <michel>  ... Drug Interaction Knowledge Base http://thedatahub.org/dataset/the-drug-interaction-knowledge-base
16:09:00 <michel>  ... developing use case with scientific discourse
16:09:10 <michel>  ... some work could be of benefit to this group
16:09:12 <bobP> boycer: Pieces of drug-interaction kb might be of interest here.
16:09:48 <boycer> http://www.ncbi.nlm.nih.gov/pubmed/15961986
16:10:27 <michel>  ... link shows abstract for an article that reports a human study on drug interaction
16:10:56 <michel>  ... concludes "Both clopidogrel and ticlopidine significantly inhibited the CYP2B6-catalyzed bupropion hydroxylation. "
16:11:35 <michel>  ... quantitative data in the results
16:11:37 <boycer> http://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?id=38646
16:12:06 <michel>  ... dailymed ; *the* resource for drug labeling
16:12:29 <michel>  ... structured product labeling 
16:12:44 <boycer> clopidogrel
16:12:44 <bobP> scribenick michel
16:12:50 <michel>  ... search for clopidogrel
16:13:04 <boycer> http://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?id=51831
16:13:05 <adrien> does not work here
16:13:55 <adrien> got it
16:14:11 <boycer> Therefore, the potential exists for a drug interaction between bupropion and drugs that are substrates of or inhibitors/inducers of the CYP2B6 isoenzyme (e.g., orphenadrine, thiotepa, cyclophosphamide, ticlopidine, and clopidogrel). 
16:14:20 <michel>  ... not found in the first, but is found in the second
16:14:56 <michel>  ... interaction not mentioned in one of these package inserts
16:15:29 <michel>  ... is it possible to build data using the semantic web so that this information is automatically propagated 
16:15:46 <michel>  ... built a prototype to give a mashup view
16:15:54 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/pi-mashup-example/dikb-label-mashup-escitalopram.html
16:16:21 <michel>  ... package insert for escitalopram
16:17:03 <michel>  ... can we use simple string matching techniques to match compound in labels; what are the claims, and link to a resource that supports or refutes the claim
16:17:57 <michel> zakim, who is making noise?
16:17:57 <Zakim> sorry, michel, I don't know what conference this is
16:18:06 <michel> zakim, this is hcls2
16:18:06 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
16:18:12 <michel> zakim, who is making noise
16:18:12 <Zakim> I don't understand 'who is making noise', michel
16:18:20 <michel> zakim, who is making noise?
16:18:33 <Zakim> michel, listening for 11 seconds I could not identify any sounds
16:18:45 <michel> zakim, who is here?
16:18:45 <Zakim> On the phone I see Scott_Bauer, +1.412.802.aaaa, +33.3.83.59.aabb, Bob_Powers, [IPcaller], +1.781.431.aacc, Scott_Bauer.a, ??P2
16:18:47 <bobP> ... whole sentence can be linked; click goes out to PubMed
16:18:47 <Zakim> On IRC I see RRSAgent, Zakim, BobF, michel, epichler, bobP, adrien, boycer, Lena_, ericP
16:19:15 <boycer> http://www.pitt.edu/~rdb20/data/DIKB-lightning-summary-05262010.pdf
16:19:49 <michel>  ... 5 slides about the drug interaction knowledge base
16:20:12 <michel>  ... how does this differ from drugbank? drugbank is a much larger project
16:20:53 <michel>  ... makes links to drug interactions, but no real evidence
16:21:04 <michel>  ...  dikb models the evidence for each of the claims
16:21:10 <bobP> ... DIKB is an evidential system, with evidence both for and against hypothises
16:22:09 <michel>  ... taxonomy of evidence (slide 3)
16:22:45 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html
16:22:57 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/
16:23:18 <boycer> http://dbmi-icode-01.dbmi.pitt.edu:2020/page/Drugs/escitalopram
16:23:18 <rkiefer> rkiefer has joined #HCLS2
16:23:22 <michel>  ... using D2R to make a SPARQL endpoint
16:24:27 <boycer> http://dbmi-icode-01.dbmi.pitt.edu:2020/resource/Assertions/448
16:25:08 <Lena_> drugs are not linked to drugbank? 
16:25:08 <boycer> http://dbmi-icode-01.dbmi.pitt.edu:2020/page/Evidence/534
16:26:16 <Lena_> no prob here
16:26:16 <bobP> Can you distinguish between inhibition of MOA or of, say, metabolism, of a given drug?
16:26:32 <adrien> works well here
16:27:12 <bobP> boycer: Not yet linked to drugbank, but working on 
16:27:20 <bobP> Lena: Can use SILK
16:27:40 <bobP> ... w partial string-matching or concatenation
16:28:24 <michel> boycer: for certain drugs, getting a lot of evidence regarding pharmacokinetics, etc
16:28:43 <michel>  ... HCLS use case - let's do this on a bigger scale - more complete view of drug package insert
16:28:45 <bobP> ... use case: proposing W3C use this at a larger scale to create more complete view of drug packaging
16:28:57 <bobP> ... to curate other drug sources
16:29:38 <michel>  ... if info in literature, would sources agree that the information existed
16:30:28 <michel> bobP: Can you distinguish between  MOA or metabolism, of a given drug?
16:31:20 <michel> boycer: pharmacokinetics - ADME ; MOA about targeting
16:31:53 <bobP> ... Metabolic Inhibition Pharmaco KB
16:32:47 <BobF> PK = what the body does to the drug; PD = what the drug does to the body; mech of action = how the drug works
16:32:58 <michel> boycer: could DIKB link to the TMO?
16:34:01 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl
16:34:17 <bobP> Michel: What to do with your ontology-of-evidence?
16:34:31 <boycer> http://www.ncbi.nlm.nih.gov/pubmed/19435613
16:34:31 <bobP> boycer: Wrote paper on this
16:35:00 <bobP> ... would like to see this become part of larger effort re scientific claims
16:35:42 <bobP> ... what is the study type? useful to users, to limit evidence for claims
16:36:00 <michel>  ... in vitro vs in vivo
16:36:03 <bobP> ... clinical care evidence different fro others
16:36:40 <bobP> ... tried also to automatically iterate thru evidence: Pharmacists were too conservative
16:37:46 <Lena_> can I use this in my projects? ;-)
16:37:59 <bobP> Michel, boycer: This is more epistemological
16:38:37 <bobP> Michel: HCLS long term strategy it to have a number of these ontologies to work together
16:38:58 <bobP> boycer: Use case does not require sophisticated evidence taxonomy
16:39:17 <bobP> ... just find an approach to mash-up w. labels
16:40:19 <bobP> boycer: Lena, complete for anti-depressants but not for some others
16:40:46 <bobP> ... complete for the drugs we have studied
16:41:50 <bobP> ... goal is to move resource to wikipedia w expert communities
16:42:11 <bobP> ... toward a clinical decision support tool in the long term.
16:42:20 <bobP> Michel: AMIA oral talk
16:42:33 <michel> https://docs.google.com/document/d/1b4eufZJp0BFVplCZE07ZZ6cFCMDoVBUjb_O_uIiYVEo/edit?hl=en_US
16:44:14 <BobF> reading now...
16:44:16 <Zakim> + +62427aadd
16:44:39 <mscottm> mscottm has joined #hcls2
16:47:59 <mscottm> Google doc being discussed?
16:48:39 <michel> https://docs.google.com/document/d/1b4eufZJp0BFVplCZE07ZZ6cFCMDoVBUjb_O_uIiYVEo/edit?hl=en_US
16:48:51 <mscottm> tx
16:49:20 <Lena_> can I be given access on the doc, please?
16:51:08 <mscottm> https://docs.google.com/document/d/1b4eufZJp0BFVplCZE07ZZ6cFCMDoVBUjb_O_uIiYVEo/edit?hl=en_US
16:51:21 <mscottm> oh, share privileges
16:58:55 <bobP> Michel: BobF has set up a truncated version of dbDNP
16:59:28 <bobP> BobF: Pulled down latest build, only for human and only for mapped well to chromosome
16:59:56 <bobP> ... then pulled out fields, attributes. Filtered down to a subset of the model
17:00:05 <michel> http://s5.semanticscience.org/phpmyadmin/
17:00:12 <bobP> ... can do another extraction, or maybe pull dynamically
17:00:27 <bobP> ... SNP ids, assoc genes, location, etc
17:01:04 <bobP> ... took info, put into Michel DB.
17:01:40 <bobP> Michel: Working from *far* south here
17:02:02 <bobP> Scott: Would like to do w SWObjects
17:02:09 <bobP> ... rather than D2R
17:02:24 <bobP> Michel: mySQL.
17:02:59 <bobP> Scott: What are SQL queries w SWObjects?
17:03:11 <bobP> Michel: Will describe this...
17:03:44 <bobP> Scott: SWObjects can create map, sparql-able RDF
17:04:37 <bobP> ... Lena has worked w SWObjects extensively
17:05:16 <bobP> Lena: Linking to mySQL. queries are ugly,
17:05:21 <BobF> db has 4 tables, fields include rsID, chromosome, SNP class, validation status, alleles, and info for associated genes
17:05:44 <bobP> ... so dream query, then map, can load SWObject w the dream query instead of SQL
17:05:51 <Zakim> - +62427aadd
17:05:54 <Lena_> can you hear me?
17:06:05 <adrien> yes :)
17:06:21 <bobP> Michel: Will make a read-only account
17:06:26 <BobF> Information about associated genes include: gene symbol, locus ID, mRNA accession, functional class, and (if it affects the protein sequence) protein accession, frame, residue
17:07:29 <bobP> Michel: Thanks to Richard for presentation.
17:07:40 <Zakim> -Scott_Bauer
17:07:59 <bobP> (Michel now broken up...)
17:08:00 <Zakim> -[IPcaller]
17:08:02 <Zakim> - +1.781.431.aacc
17:08:03 <adrien> michel, we can not here the end
17:08:08 <adrien> ear the end
17:08:14 <BobF> I need to run - thanks, all
17:08:15 <adrien> bye everyone
17:08:18 <Zakim> -Scott_Bauer.a
17:08:22 <epichler> bye
17:08:25 <Zakim> - +1.412.802.aaaa
17:08:29 <epichler> epichler has left #HCLS2
17:08:39 <michel> action item: michel to make read-only account to mysql database
17:08:39 <Zakim> - +33.3.83.59.aabb
17:09:06 <Zakim> -??P2
17:09:14 <michel> action item: lena / scott to create an SWObjects endpoint over the data, where the query is on the snpid - and get related data
17:10:11 <bobP> michel - is that a wrap?
17:13:47 <bobP> rrsagent, draft minutes
17:13:47 <RRSAgent> I have made the request to generate http://www.w3.org/2011/10/20-hcls2-minutes.html bobP
17:13:57 <bobP> rrsagent, make logs public
17:14:07 <Zakim> disconnecting the lone participant, Bob_Powers, in SW_HCLS(TMO)11:00AM
17:14:10 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:14:11 <Zakim> Attendees were Scott_Bauer, +1.412.802.aaaa, +33.3.83.59.aabb, Bob_Powers, [IPcaller], +1.781.431.aacc, +62427aadd
18:32:35 <Zakim> Zakim has left #hcls2