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!
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