See also: IRC log
<michel> ScribeNick: bobP
<mscottm2> can't hear you - Michel?
<BobF> severely breaking up
<matthias_samwald> this was noisy AND breaking up.
scribenick bobP
Matthias: Michel and I extended TMO, targeted to represent...
(Michel is talking from an advanced com center)
<mscottm2> LOL
Matthias: after a lot of
consideration, edited classes for genetic variantion
... also edited other classes of a general nature
... look at TMO as it is on BioPortal
... namespace of TMO is identical to that used to enhance
<matthias_samwald> http://bioportal.bioontology.org/ontologies/1461
Matthias: so all of changes went
live to BioPortal :)
... maybe we should reconsider the authoritative source
Michel: +1 to controlled releases
Matthias: It is going to a
release file
... latest on BioPortal 1.02
<michel> http://bioportal.bioontology.org/ontologies/46121?p=terms
bobP sees it
Joanne sees it
Matthias: Tried to follow the
realist approach; variation is not an abstract entity like
sequence
... this approach tried to build on established principles;
represent as material entity
Joanne: Working from authoritative source?
Matthias: Mixture. Looked at DBs
and how they representetd variation
... dbSNP also has short indels(?) etc
... still quite open. Is this approach good?
... also, how to represent more detail?
... Ex class region w SNP. Originally from Michel, represent
right down to nucleotide level
... SNP would be a subclass of nucleotide (?)
... concerned that this might not be practical. Gets complex
beyond simple SNP
... propose to identify SNP thru datatype property, as a
sequence stream
... go w. the more normal way that SNPs are represented in real
DBs
<Joanne> "as strings of characters"
BobF: Q Current models for
variants. SNPs need a reference sequence
... how does that fit here?
Matthias: Refer to loci w/in
genome where loci have relation to reference genomes
... found in relation to reference. Would suggest we find ont
rep that is independent of standard geneome
... in context of surrounding DNA
<michel> https://docs.google.com/document/d/1BeaU3VJW1S_R3eB5ncrcW9wJ-lMU4xdmxCdjH8E0i5s/edit?hl=en_US
Matthias: but may be useful to keep relation to reference genome
Michel: We did consider where
this residue is a SNP, partOf some reference genome
... that's a way to make the connection
<BobF> The NCI Life Sciences DAM may be a useful reference: http://ncientarch.info/sandbox/LSDAM2_2_1/
Matthias: SNP would go out the material branch; reference would go out the information entity branch
Michel: Need to make connection( didn't quite get this)
BobF: Been working w NCI on
modeling molecular entities,
... in this model we do address these issues
ericP: Guide us?
<BobF> http://ncientarch.info/sandbox/LSDAM2_2_1/
<ericP> http://ncientarch.info/sandbox/LSDAM2_2_1/
<Joanne> http://ncientarch.info/sandbox/LSDAM2_2_1/
<Lena> @matthias_samwald: if found "reference genomic sequence"@en in the tmo, it this what you meant?
<Joanne> http://ncientarch.info/sandbox/LSDAM2_2_1/
(my image is very narrow!)
Joanne: This works for me +1
Scott: TMO has DNA-region-w-SNP
<ericP> would that look like this in turtle ? [ a NucleicAcidSequenceFeature ] NucleicAcidPhysicalLocation [ a NucleicAcidSequence ] .
Scott: would mke SNP a property of a region
Joanne: SNP needs more than one nucleotide reference
<ericP> or in RDFS: { :NucleicAcidPhysicalLocation rdfs:domain :NucleicAcidSequenceFeature ; rdfs:range :NucleicAcidSequence . }
Matthias: Want to create this ont
from scratch on top of TMO?
... analyzed SO a lot; claims to have everything figured
out.
... but hard to understand
Joanne: Q (didn't get)
Matthias: SNP needs a population.
Use the knowledge to give special meaning to regions of the
genome
... liturature tries to avoid mutation (answer to Helen's
Q)
Michel: Seq, feature, what are
you trying to say?
... actually we have a different molecular material?
... is it really a feature of a sequence?
Matthias: Everything based on
individual, w specific regions etc. Then create
universals
... to group individuals
BobF: Two different levels of
granularity here
... ultimately we are talking about a physically different DNA,
should be treating like a physical entity
... from patient's perspective, show me what proceeds from this
reality(?)
... different from looking at populations, different
perspectives
ericP: Does one of these align more closely? Are use cases similar?
BobP: Both perspectives, but
could not drill into this area as much as would have
liked
... LSDAM, will be taking these considerations back
... tried to come up w high level use cases, so successful for
these
... but instantated in different ways for different use
cases
Michel: TMO distinguishes between
physical and sequences
... we do have both concepts, both are useful.
... what are individuals composed of?
... we do geno- and phenotyping both
BobF: LSDAM is looking at a translation to OWL
ericP: Opportunity here
Matthias: Could apply a Xform to
RDF
... TMO trying to do in this more complicated way, w ont
principles
... advantages for reasoning, etc; disadvantage makes things
complicated
... putting this realist view on top
BobF: LSDAM used UML b/c of the
existing infrastructure
... would welcome the input from OWL experts here
Scott: Taking ont approach so we
can use reasoning as well as easy integration
... choice should be tested against a reasoning task
... want a concrete set of test cases, to reason over patient
data etc
... would help us ground the conversation
Matthias: Should try to carry
this on, try a prototye
... OWL reasoning to classify patients
... practically, different models give confusion on variation
in individuals vs in populations
Lena: Patient instance of population?
Matthias: No. A population is a specific entity.
Lena: Patient part of a cohort, so patient could be an instance of cohort class.
BobF: Cohort could be a kind of cohort
(!) kind of popultion
Michel: TMO, would want to assign
attributes to populations
... can have cohorts of studies, etc. Averages over
individuals, as opposed to specific characteristic
Matthias: Should agree on community process to address this.
Scott: We started w use cases for
sparql queries
... Michel put up axioms for ethnicity
... clinical decision support, might not make a difference for
which way to go.
Michel: DrugBank geno-pheno all
in OWL. Can gain from clear formalization
... mixing categories then we can't leverage from what we
have
... want to go beyond just linked data.
ericP: If we write down in LD vs If we write down formally
Lena: Linked data will have new stuff, should be able to express in TMO
Scott: ...different demands
Matthias: TMO approach now is
ontological; vs put up raw RDF
... suggest end of Jan 2012
Scott: Pgx paper, there are prods
from reviewers
... want more material. Want what we're working on now!
... PGx for Future Medicine
Lena has bragging rights. We await!
<matthias_samwald> try to document all SPARQL endpoints and datasets you create on http://www.w3.org/wiki/HCLSIG/pharmacogenomics_2012 !!
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) Found ScribeNick: bobP Inferring Scribes: bobP WARNING: No "Topic:" lines found. WARNING: No "Present: ... " found! Possibly Present: BobF BobP Bob_Powers IPcaller Joanne JoanneLuciano Joanne_Luciano Joseph_Scheuhammer Lena Mary Matthias Michel P0 P27 RickKiefer Scott Scott_Bauer ScribeNick adrien ericP https iker matthias_samwald 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 Got date from IRC log name: 17 Nov 2011 Guessing minutes URL: http://www.w3.org/2011/11/17-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]