16:00:47 <RRSAgent> RRSAgent has joined #hcls2
16:00:47 <RRSAgent> logging to http://www.w3.org/2011/06/09-hcls2-irc
16:00:50 <matthias_samwald1> zakim, this is hcls
16:00:50 <Zakim> ok, matthias_samwald1; that matches SW_HCLS(TMO)11:00AM
16:00:57 <matthias_samwald1> zakim, who is here?
16:00:57 <Zakim> On the phone I see Bob_Powers, +1.714.616.aaaa, ??P22
16:00:58 <Zakim> On IRC I see RRSAgent, Zakim, Fred, BobP, matthias_samwald1, ericP
16:01:08 <matthias_samwald1> zakim, ??P22 is matthias_samwald
16:01:08 <Zakim> +matthias_samwald; got it
16:01:35 <Adrien> Adrien has joined #HCLS2
16:02:09 <matthias_samwald1> zakim, +1.714.616.aaaa is Fred
16:02:10 <Zakim> +Fred; got it
16:02:25 <iker> iker has joined #hcls2
16:03:14 <Zakim> +??P50
16:03:25 <BobP> scribenick BobP
16:03:35 <Zakim> + +33.3.83.59.aabb
16:03:35 <iker> zakim. P50 it is me
16:04:05 <matthias_samwald1> zakim, ??P50 is iker
16:04:05 <Zakim> +iker; got it
16:04:30 <matthias_samwald1> zakim, +33.3.83.59.aabb is adrien
16:04:30 <Zakim> +adrien; got it
16:06:45 <matthias_samwald1> http://www.w3.org/wiki/HCLSIG/PharmaOntology/Meetings/2011-06-09_Conference_Call
16:07:53 <BobP> Matthias: Agenda: text mining, from spreadsheet to RDF
16:08:13 <BobP> ... Iker has posted RDF
16:08:48 <BobP> Not really useful to xform spreadsheet to RDF
16:09:29 <BobP> Iker: Have put up new RDF
16:09:59 <BobP> ... did not understand spreadsheet quite, but did try to xform
16:10:15 <BobP> ... consequences from pubmed articles?
16:10:32 <Joanne> Joanne has joined #hcls2
16:10:48 <BobP> ... there are some fields w numerals, other fields w/o meaning
16:11:02 <BobP> (there's a terrible echo)
16:11:52 <BobP> ... did not find all info in the spreadsheet
16:11:52 <Zakim> +Joanne_Luciano
16:12:40 <BobP> Matthias: The tool for spreadsheet in google docs also capable of xforming to RDF
16:13:36 <BobP> Two outputs, so can see both
16:14:58 <BobP> Matthias: Iker, you are using Google refine, may want to use G refine again in future
16:15:28 <BobP> Matthias: Agenda: Ontology. Wiki has two arenas for ont development
16:16:02 <BobP> ... webProtege, and dedicated Google doc where Michel has collected ideas for axioms, etc
16:16:40 <BobP> ... Michel and I have been collaborated, but on the separate platforms
16:17:08 <BobP> ... work-in-progress. Tried to describe genes, SNPs, etc under TMO.
16:17:41 <BobP> ... not as abstract entities, but as material entities w. partonomy, haplotypes, nucleotypes etc
16:18:10 <BobP> ... accounted for polymorphism across organisms; genetics compatible w TMO
16:18:39 <BobP> ... difficult to do this. Under heavy development. Question whether we can really do it this way.
16:19:12 <BobP> ... maybe represent all of this as some kind of information artifact rather than material.
16:19:52 <BobP> Adrien: Will look. How do you re-use SeqOnt?
16:20:23 <BobP> Matthias: Seems like we are still experimenting to forumlate as TMO-ish
16:20:58 <iker> my regrets but i must leave, I apologize
16:21:00 <BobP> ... SeqOnt talks about sequences, in the abstract. Matierially it introduces interesting problems.
16:21:08 <Zakim> -iker
16:21:40 <matthias_samwald1> https://docs.google.com/document/d/1BeaU3VJW1S_R3eB5ncrcW9wJ-lMU4xdmxCdjH8E0i5s/edit?hl=en_US
16:21:41 <BobP> ... difference bet gene and allele. Represent all as material then difference between gene and allele starts to disappear
16:22:05 <BobP> ... You can see here some of the things that Michel came up with.
16:22:34 <Joanne> 10 minute warning.  Am at EBI and leaving in 10 minutes.
16:22:43 <BobP> ... if all material entities, then notion of gene starts to disappear
16:22:48 <BobP> Hi Joanne!
16:23:20 <BobP> Matthias: This gives the notion of what some of the issues are.
16:23:27 <Joanne> my update:  I looked at my notes of what I converted and they are too low level to present.  Tim (used his tool) has not been available and I haven't had time to run through his documentation (I needed the brief)
16:23:52 <BobP> ... not wanted to re-invent the allele
16:23:53 <Joanne> So, i've not made any progress other than the raw conversion of the warfarin data to RDF
16:24:09 <Joanne> (sorry to have this in-line, but.... all i can do at the moment)
16:24:29 <BobP> ... in year or so we might want to represent more soph than SNPs, like inversions, deletions and the like.
16:24:35 <Joanne> on the other hand, i have started to read the papers that Elgar got from Michel on the prediction methods for warfarin dosing
16:25:09 <BobP> Scope of ontology, are we extending to personalized medicine?
16:25:39 <BobP> Matthias: Might want to re-name ont? There has been some discussion exchange on this.
16:26:09 <BobP> ... major trouble is to avoid modelling too much into basic biology.
16:26:41 <BobP> ... SeqOnt, etc, contain lots and lots of individual things, but lose focus.
16:27:11 <BobP> ... should keep focus on developing treatments. Perspective would help us.
16:27:45 <BobP> ... Protege rich client seems to work pretty well.
16:27:48 <BobP> +q
16:28:31 <BobP> ... Iker might provide us with individual accounts
16:29:14 <BobP> Matthias: Agenda: conversion
16:29:36 <BobP> Joanne: Tim Lebo has been travelling
16:30:02 <BobP> ... looking at papers on predicitve modeling for warfarin dosing
16:32:59 <BobP> Matthias: Agenda: snpPedia is a gold mine of data, on Semantic Media Wiki
16:33:18 <BobP> ... snpPedia available as RDF; will try to crawl and host
16:33:58 <BobP> ... with some clean-up this might be a very useful dataset
16:34:21 <BobP> ... they are curating mostly by hand
16:35:14 <matthias_samwald1> LDspider
16:35:31 <BobP> ... next steps, to look into linked data crawlers like LDspider
16:36:14 <BobP> Matthias: Agenda, conversion of other data; should think about other kinds of data that we have not yet discussed
16:37:18 <BobP> ... pretty sure that dbSNP has been RDF-ized
16:37:50 <BobP> ... Michel has already RDF-ized pharmGKB; relation to which ontologies?
16:38:44 <BobP> ... will probably discuss some more. Genotator dataset of gene-disease relationships
16:38:54 <BobP> ... project at Harvard
16:38:59 <matthias_samwald1> http://genotator.hms.harvard.edu/geno/
16:39:32 <BobP> ... snpPedia, etc should be our primary targets at the moment.
16:40:19 <BobP> ... some version of OMIM is in LOD
16:40:47 <BobP> ... not re-formulate to our ont, just link
16:41:55 <BobP> Matthas: Sparql endpoint development
16:42:46 <BobP> ... Iker started to create a KB, but not on the call anymore;
16:43:20 <BobP> Joanne: RPI has enormous expertise in this area; can get help here
16:43:51 <BobP> Matthias: Want to aggregate all of KB data at a central sparql?
16:44:08 <BobP> Joanne: But we can federate, need not be all at one place.
16:44:32 <BobP> Matthias: Yes and no. Tech for federation not yet perfect.
16:44:52 <BobP> Joanne: Can issue sparql against different sources
16:45:37 <BobP> Matthias: For demo purposes, works better to have all in one KB
16:45:53 <BobP> ... can use DERI and Michel endpoints
16:47:36 <BobP> Matthias: Sustainability is an issue
16:47:48 <BobP> Joanne: RPI can sustain across three years for sure
16:48:21 <BobP> Matthias: Discuss off-line
16:49:20 <BobP> Fred: Thought about a clinical use case in the Google doc
16:49:53 <Adrien> I don't see the doc on google doc
16:50:03 <BobP> ... deals w interaction between warf, aspirin and plavix, w stent
16:50:44 <BobP> ... use case creates a real-life dilemma for physician
16:51:07 <BobP> ... to prevent cardiac events vs bleeding. An area that is problematic now.
16:52:41 <BobP> Adrien: Can be useful. We have to be able to use this; if we can succeed here.
16:53:00 <BobP> Matthias: Realistic and tricky enough to warrant computerized clinical decision support
16:53:23 <BobP> ... complex, should ideally take care of interaction between medications
16:53:46 <BobP> Fred: If limiting to warfarin only, SNPs are already catalogued
16:54:08 <BobP> ... situation is not complex w warf alone
16:54:28 <BobP> ... interaction with other factors make it more subtle
16:55:21 <BobP> Matthias: Two levels of soph: 1) system shows a single alert w SNP, plus another alert for drug interactions
16:55:51 <BobP> ... different alerts are separated. But combined risk is not estimated.
16:56:14 <BobP> ... more sophisticated 2) combined risk.
16:56:33 <BobP> ... less soph would leave reasoning to the doctor.
16:56:53 <BobP> ... should we unify alerts and report to doctor?
16:57:55 <BobP> Fred: Drug interactions already have DBs; situation where physician gets additional info
16:58:24 <BobP> ... but would not want to make a hard-and-fast <determination>
16:58:46 <BobP> ... but make physician aware of genetic risk would be useful
16:59:39 <BobP> Matthias: Might have to make trade-off. Drug interaction more important than SNPs?
17:00:09 <BobP> ... even if not perfect, sometimes easier is more useful
17:00:26 <Joanne> I need to go.  regrets! and thanks! 
17:00:37 <Adrien> Bye Joanne
17:00:39 <Joanne> thanks everyone
17:00:43 <BobP> ... KB should have drug interactions in, as well a pgx
17:00:50 <Zakim> -Joanne_Luciano
17:01:11 <BobP> ... agenda item to look at drug interactions
17:01:46 <Zakim> -Bob_Powers
17:01:48 <Zakim> -Fred
17:01:49 <Zakim> -adrien
17:01:55 <matthias_samwald1> RRAagent, please draft minutes
17:02:03 <matthias_samwald1> RRSagent, please draft minutes
17:02:03 <RRSAgent> I have made the request to generate http://www.w3.org/2011/06/09-hcls2-minutes.html matthias_samwald1
17:02:38 <matthias_samwald1> RRSAgent, please set logs world-visible 
17:02:49 <Zakim> -matthias_samwald
17:02:51 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:02:52 <Zakim> Attendees were Bob_Powers, matthias_samwald, Fred, iker, adrien, Joanne_Luciano
17:03:51 <matthias_samwald1> zakim, bye
17:03:51 <Zakim> Zakim has left #hcls2
17:03:59 <matthias_samwald1> RRSagent, bye
17:03:59 <RRSAgent> I see no action items