15 Dec 2011

See also: IRC log




scribenick bobP

Matthias: Agenda: ICBO conference; looking at the google doc spreadsheet
... need to add terms to the spreadsheet

<matthias_samwald> https://docs.google.com/spreadsheet/ccc?key=0AiGT-vnkGcoLdEJrOTU4blAtME04S3plUW5XQ1FwcHc&hl=en_US

Matthias: there are -zero- new terms :)

<iker> yea

<JyotiPathak> jyotishman.mayo@gmail.com

Scott: Have heard good things about Trish's BioPortal

(you need an APIKey to send java agains it)

<JyotiPathak> This is the agenda of PSB 2012 meeting: http://psb.stanford.edu/schedule.pdf

<JyotiPathak> Is anyone familiar with this work from PSB 2012?

<JyotiPathak> The Extraction of Pharmacogenetic and Pharmacogenomic Relations – A Case Study Using PharmGKB Ekaterina Buyko, Elena Beisswanger, and Udo Hah

scribe: Trish was talking about the annotation features

Matthias: Any impression of these terms?

BobF: Will be looking at this

Matthias: Also db schema that you might have, to import to ontology

Scott: Q a set of tasks and terms required by those tasks
... various scenarios could be used to claim the terms and why

Matthias: Should use the warfarin use case
... also competency questions should give us some guidance

Scott: Previous documents, we have considered looking up various info pieces
... depending on clinical research or practice.
... TMO handles drugs pretty well. We need more on the patient side of things

BobF: What about overlap w other ontologies?

Matthias: PGx ont, Seq ont

BobF: Filter for the speadsheet?

Matthias: Let it all out.

Scott: "Don't develop ontologists' block!"
... can always import terms

Matthias: Onts can be created and never used; should try not to do
... Seq ont fine, but not compatible w OBO, makes it hard to do the kind of reasoning that we want
... TMO should be simple, broad aspects of pgx, pharma develop and clincial app in one coherent framework
... could be powerful in the end
... coherence between pharam dev, clincial app, general info re biomarkers

Jyoti: Looked at Disease Ontology, elements that can be linked here?

Matthias: Disease Ont OBO, hierarchy of diseases like ICD

Scott: Has good cross references to other onts; so it's the choice for referring to diseases
... swat4ls, seems to be the best disease ontology

Matthias: TMO has class Disease; can use class subsumption

<JyotiPathak> http://psb.stanford.edu/psb-online/proceedings/psb12/buyko.pdf

Matthias: do not want to go deep into the class structure of Dis Ont, just link in

<mscottm2> Hi Michel - we've discussed adding terms to TMO and just now, human disease ontology

Jyoti: Goal is to add new classes, not individuals?

Matthias: Can be both, modeling and representations most can be classes
... urge to add some terms to the spreadsheet
... will try to incorporate terms
... should try to represent some significant data, like warfarin data
... place individual patient into their appropriate subclasses
... OWL reasoning will be tested for usefulness

<matthias_samwald> https://docs.google.com/document/d/1Ww8snzxs9N-uJjq1y4kLZFm-LKIgkcnJtKT0M2PPnZA/edit?hl=en_US

Matthias: this link is a good pattern to start the next paper

<michel> +1

Matthias: Jan 15 is deadline

<JyotiPathak> +1

BobF: +1

ericP: +1 geekiness

<JyotiPathak> +1 interested for ICBO

Michel from Chile! Build from the document?

Matthias: Copy and paste, what we are trying to do with extended TMO
... but don't mention data conversion, not biomarker pipelines
... just broad paper on how to make ontologies useful

Jyoti: Reasoning use case, demonstrate on patient-level?

Matthias: Entire thing might be happening 10 years from now.
... genetic testing will be more common than today; more and more data re variants
... want to represent the meanings. Now clinical practice is very broad
... hypothetical scenario, things will be more complicated than the first-line treatment of today

<michel> +q what will we do for evaluation?

<michel> +q to discuss evaluation

Matthias: have Alz that has these 100 biomarkers that might be relevant plus medications
... 100 classes of patients here, maybe require distinct treatments
... medications might be dependant on these biomarkers
... so there are pre-defined classes of patients; trying to find molecular subclasses and diseases

(cannot capture the whole tour-de-force description here from Matthias!)

Jyoti: Present results too? Grand scheme of things?

Matthias: Yes, try to get as far as we can. Might be able to demonstrate in small setting
... create small mock-up of scenario and small mock-up of patient
... should be enough for proof of concept for OWL reasoning for this purpose

ericP: Cases that benefit from OWL, those that might not
... how to factor decisions for CDS people
... publisher has CDS data, offer to clinics

Iker(?): We should try to focus on clinical practice

scribe: we see the whole text (but this does not make it all the way to the rules?)

ericP: Compatible with this idea?

Matthias: Do not want to focus strictly on OWL reasoning, but build an RDF framework

ericP: Would like to separate use cases w simple sparql from those that can use OWL DL reasoning
... this w/o OWL, this w OWL, and here is the cost

Iker: "We can get far w reasoning", but not always true
... fragmenting the use cases has some merit to it

Scott: Start w info retrieval like ericP, then also what we can do w reasoning
... should delineate sparql and sparql+reasoning
... might consider for the big-Pgx-paper

Matthias: OWLim

<iker> OWLIM has also some limitations

<iker> mainly regarding scaling

Matthias: should not directly compare sparql vs owl
... how to best combine owl reasoning w sparql magic

ericP: Try to get both tracks going at once?

Scott: Trajectory was already along these lines. Pt, drug, disease
... then pivot on facets, can find the path
... information retrieval perspective is the start, w sparql endpoints for dbSNP, SNPedia
... focus on the relations, info retrieval is a motivation
... need not address sparql vs owl
... then OWL on top would be great

<iker> ericP, do you have a couple of minutes after the call?

(bobP -1)

<JyotiPathak> ICBO deadline seems to be Jan 31st, not Jan 15th

<JyotiPathak> http://www.kr-med.org/icbofois2012/dates.htm


Matthias: Next telco on Dec 22!

Scott: Look at the galley proofs!

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.136 (CVS log)
$Date: 2011/12/15 18:01:15 $

Scribe.perl diagnostic output

[Delete this section before finalizing the minutes.]
This is scribe.perl Revision: 1.136  of Date: 2011/05/12 12:01:43  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

No ScribeNick specified.  Guessing ScribeNick: bobP
Inferring Scribes: bobP

WARNING: No "Topic:" lines found.

WARNING: No "Present: ... " found!
Possibly Present: BobF Bob_Powers IPcaller Jyoti JyotiPathak MacTed Matthias Scott Scott_Bauer aaaa bobP ericP https iker matthias_samwald michel mscottm2
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy

WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting

WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 15 Dec 2011
Guessing minutes URL: http://www.w3.org/2011/12/15-hcls2-minutes.html
People with action items: 

WARNING: No "Topic: ..." lines found!  
Resulting HTML may have an empty (invalid) <ol>...</ol>.

Explanation: "Topic: ..." lines are used to indicate the start of 
new discussion topics or agenda items, such as:
<dbooth> Topic: Review of Amy's report

[End of scribe.perl diagnostic output]