17:01:24 <RRSAgent> RRSAgent has joined #hcls2
17:01:24 <RRSAgent> logging to http://www.w3.org/2011/12/15-hcls2-irc
17:01:31 <matthias_samwald> zakim, this is hcls
17:01:31 <Zakim> ok, matthias_samwald; that matches SW_HCLS(TMO)11:00AM
17:01:37 <matthias_samwald> zakim, who is here?
17:01:37 <Zakim> On the phone I see Bob_Powers, [IPcaller]
17:01:39 <Zakim> On IRC I see RRSAgent, Zakim, matthias_samwald, bobP, MacTed, ericP
17:01:49 <iker> iker has joined #hcls2
17:01:52 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
17:01:52 <Zakim> +matthias_samwald; got it
17:01:55 <Zakim> + +1.215.239.aaaa
17:02:09 <Zakim> +Scott_Bauer
17:03:10 <Zakim> +mscottm2
17:04:01 <mscottm2> mscottm2 has joined #hcls2
17:05:04 <JyotiPathak> JyotiPathak has joined #hcls2
17:06:51 <bobP> scribenick bobP
17:07:24 <bobP> Matthias: Agenda: ICBO conference; looking at the google doc spreadsheet
17:07:47 <bobP> ... need to add terms to the spreadsheet
17:07:51 <matthias_samwald> https://docs.google.com/spreadsheet/ccc?key=0AiGT-vnkGcoLdEJrOTU4blAtME04S3plUW5XQ1FwcHc&hl=en_US
17:08:34 <bobP> ... there are -zero- new terms :)
17:08:45 <iker> yea
17:09:06 <JyotiPathak> jyotishman.mayo@gmail.com
17:10:36 <Zakim> +Scott_Bauer.a
17:10:41 <BobF> BobF has joined #hcls2
17:11:17 <bobP> Scott: Have heard good things about Trish's BioPortal
17:11:57 <bobP> (you need an APIKey to send java agains it)
17:12:29 <JyotiPathak> This is the agenda of PSB 2012 meeting: http://psb.stanford.edu/schedule.pdf
17:12:47 <JyotiPathak> Is anyone familiar with this work from PSB 2012?
17:12:49 <JyotiPathak>  The Extraction of Pharmacogenetic and Pharmacogenomic Relations – A  Case Study Using PharmGKB Ekaterina Buyko, Elena Beisswanger, and Udo Hah
17:12:54 <bobP> ... Trish was talking about the annotation features
17:14:00 <bobP> Matthias: Any impression of these terms?
17:15:10 <bobP> BobF: Will be looking at this
17:15:44 <bobP> Matthias: Also db schema that you might have, to import to ontology
17:16:11 <bobP> Scott: Q a set of tasks and terms required by those tasks
17:16:29 <bobP> ... various scenarios could be used to claim the terms and why
17:16:41 <bobP> Matthias: Should use the warfarin use case
17:16:57 <bobP> ... also competency questions should give us some guidance
17:17:38 <bobP> Scott: Previous documents, we have considered looking up various info pieces
17:18:02 <bobP> ... depending on clinical research or practice.
17:18:24 <bobP> ... TMO handles drugs pretty well. We need more on the patient side of things
17:18:39 <bobP> BobF: What about overlap w other ontologies?
17:18:59 <bobP> Matthias: PGx ont, Seq ont
17:19:14 <bobP> BobF: Filter for the speadsheet?
17:19:24 <bobP> Matthias: Let it all out.
17:19:27 <Zakim> +ericP
17:20:04 <bobP> Scott: "Don't develop ontologists' block!"
17:20:15 <bobP> ... can always import terms
17:20:52 <bobP> Matthias: Onts can be created and never used; should try not to do
17:21:25 <bobP> ... Seq ont fine, but not compatible w OBO, makes it hard to do the kind of reasoning that we want
17:22:02 <bobP> ... TMO should be simple, broad aspects of pgx, pharma develop and clincial app in one coherent framework
17:22:12 <bobP> ... could be powerful in the end
17:22:33 <bobP> ... coherence between pharam dev, clincial app, general info re biomarkers
17:23:05 <bobP> Jyoti: Looked at Disease Ontology, elements that can be linked here?
17:23:35 <bobP> Matthias: Disease Ont OBO, hierarchy of diseases like ICD
17:23:53 <michel> michel has joined #hcls2
17:24:08 <bobP> Scott: Has good cross references to other onts; so it's the choice for referring to diseases
17:24:32 <bobP> ... swat4ls, seems to be the best disease ontology
17:24:52 <bobP> Matthias: TMO has class Disease; can use class subsumption
17:25:00 <Zakim> +[IPcaller]
17:25:08 <michel> zakim, [IPcaller] is michel
17:25:08 <Zakim> +michel; got it
17:25:11 <JyotiPathak> http://psb.stanford.edu/psb-online/proceedings/psb12/buyko.pdf
17:25:18 <bobP> ... do not want to go deep into the class structure of Dis Ont, just link in
17:25:57 <mscottm2> Hi Michel - we've discussed adding terms to TMO and just now, human disease ontology
17:27:51 <bobP> Jyoti: Goal is to add new classes, not individuals?
17:28:23 <bobP> Matthias: Can be both, modeling and representations most can be classes
17:29:13 <bobP> ... urge to add some terms to the spreadsheet
17:29:31 <bobP> ... will try to incorporate terms
17:30:20 <bobP> ... should try to represent some significant data, like warfarin data
17:30:38 <bobP> ... place individual patient into their appropriate subclasses
17:31:06 <bobP> ... OWL reasoning will be tested for usefulness
17:31:37 <matthias_samwald> https://docs.google.com/document/d/1Ww8snzxs9N-uJjq1y4kLZFm-LKIgkcnJtKT0M2PPnZA/edit?hl=en_US
17:32:30 <bobP> ... this link is a good pattern to start the next paper
17:32:49 <michel> +1
17:32:57 <bobP> ... Jan 15 is deadline
17:33:05 <JyotiPathak> +1
17:33:16 <bobP> BobF: +1
17:33:35 <bobP> ericP: +1 geekiness
17:34:20 <JyotiPathak> +1 interested for ICBO
17:35:46 <bobP> Michel from Chile!  Build from the document?
17:36:29 <bobP> Matthias: Copy and paste, what we are trying to do with extended TMO
17:36:54 <bobP> ... but don't mention data conversion, not biomarker pipelines
17:37:07 <bobP> ... just broad paper on how to make ontologies useful
17:37:35 <bobP> Jyoti: Reasoning use case, demonstrate on patient-level?
17:38:02 <bobP> Matthias: Entire thing might be happening 10 years from now.
17:38:28 <bobP> ... genetic testing will be more common than today; more and more data re variants
17:38:54 <bobP> ... want to represent the meanings. Now clinical practice is very broad
17:39:27 <bobP> ... hypothetical scenario, things will be more complicated than the first-line treatment of today
17:39:45 <michel> +q what will we do for evaluation?
17:40:01 <michel> +q to discuss evaluation
17:40:03 <bobP> ... have Alz that has these 100 biomarkers that might be relevant plus medications
17:40:31 <bobP> ... 100 classes of patients here, maybe require distinct treatments
17:40:47 <bobP> ... medications might be dependant on these biomarkers
17:41:18 <bobP> ... so there are pre-defined classes of patients; trying to find molecular subclasses and diseases
17:41:49 <bobP> (cannot capture the whole tour-de-force description here from Matthias!)
17:42:10 <bobP> Jyoti: Present results too? Grand scheme of things?
17:42:36 <bobP> Matthias: Yes, try to get as far as we can. Might be able to demonstrate in small setting
17:43:02 <bobP> ... create small mock-up of scenario and small mock-up of patient
17:43:25 <bobP> ... should be enough for proof of concept for OWL reasoning for this purpose
17:43:46 <bobP> ericP: Cases that benefit from OWL, those that might not
17:44:05 <bobP> ... how to factor decisions for CDS people
17:44:27 <bobP> ... publisher has CDS data, offer to clinics
17:45:00 <bobP> Iker(?): We should try to focus on clinical practice
17:46:39 <bobP> ... we see the whole text (but this does not make it all the way to the rules?)
17:46:56 <bobP> ericP: Compatible with this idea?
17:47:35 <bobP> Matthias: Do not want to focus strictly on OWL reasoning, but build an RDF framework
17:48:13 <bobP> ericP: Would like to separate use cases w simple sparql from those that can use OWL DL reasoning
17:48:31 <bobP> ... this w/o OWL, this w OWL, and here is the cost
17:49:01 <bobP> Iker: "We can get far w reasoning", but not always true
17:49:12 <bobP> ... fragmenting the use cases has some merit to it
17:49:41 <bobP> Scott: Start w info retrieval like ericP, then also what we can do w reasoning
17:49:59 <bobP> ... should delineate sparql and sparql+reasoning
17:50:30 <bobP> ... might consider for the big-Pgx-paper
17:51:00 <bobP> Matthias: OWLim
17:51:12 <iker> OWLIM has also some limitations
17:51:21 <iker> mainly regarding scaling 
17:52:20 <bobP> ... should not directly compare sparql vs owl
17:52:36 <bobP> ... how to best combine owl reasoning w sparql magic
17:54:02 <bobP> ericP: Try to get both tracks going at once?
17:54:53 <bobP> Scott: Trajectory was already along these lines. Pt, drug, disease
17:55:09 <bobP> ... then pivot on facets, can find the path
17:56:04 <bobP> ... information retrieval perspective is the start, w sparql endpoints for dbSNP, SNPedia
17:56:34 <bobP> ... focus on the relations, info retrieval is a motivation
17:56:44 <bobP> ... need not address sparql vs owl
17:56:55 <bobP> ... then OWL on top would be great
17:58:37 <iker> ericP, do you have a couple of minutes after the call?
17:59:01 <bobP> (bobP -1)
17:59:06 <JyotiPathak> ICBO deadline seems to be Jan 31st, not Jan 15th
17:59:08 <JyotiPathak> http://www.kr-med.org/icbofois2012/dates.htm
17:59:08 <bobP> :(
18:00:18 <bobP> Matthias: Next telco on Dec 22!
18:00:35 <bobP> Scott: Look at the galley proofs!
18:00:54 <Zakim> -Scott_Bauer.a
18:00:55 <Zakim> -Bob_Powers
18:00:57 <Zakim> -Scott_Bauer
18:01:10 <bobP> rrsagent, draft minutes
18:01:10 <RRSAgent> I have made the request to generate http://www.w3.org/2011/12/15-hcls2-minutes.html bobP
18:01:20 <bobP> rrsagent, make logs public
18:01:22 <Zakim> -michel
18:02:58 <ericP> alan yagoda
18:03:33 <mscottm2> tx
18:05:11 <mscottm2> good luck!
18:05:12 <Zakim> -mscottm2
18:18:38 <Zakim> -matthias_samwald
18:20:17 <Zakim> - +1.215.239.aaaa
18:20:19 <Zakim> -ericP
18:20:20 <Zakim> SW_HCLS(TMO)11:00AM has ended
18:20:22 <Zakim> Attendees were Bob_Powers, matthias_samwald, +1.215.239.aaaa, Scott_Bauer, mscottm2, ericP, michel
20:07:29 <Zakim> Zakim has left #hcls2