17:01:45 <RRSAgent> RRSAgent has joined #hcls2
17:01:45 <RRSAgent> logging to http://www.w3.org/2011/11/17-hcls2-irc
17:01:51 <michel> rrsagent, make logs public
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17:02:11 <michel> Chair: michel
17:02:17 <michel> ScribeNick: bobP
17:02:27 <michel> zakim, this is tmo
17:02:27 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
17:02:35 <michel> zakim, who is here?
17:02:37 <Zakim> On the phone I see Scott_Bauer, Joseph_Scheuhammer, Bob_Powers, Joanne_Luciano, [IPcaller]
17:02:38 <Zakim> On IRC I see matthias_samwald, RRSAgent, Zakim, adrien, michel, bobP, Mary, RickKiefer, ericP
17:02:38 <Joanne> Joanne has joined #hcls2
17:03:28 <BobF> BobF has joined #hcls2
17:03:45 <Zakim> +Scott_Bauer.a
17:04:13 <Zakim> + +62427aaaa
17:04:21 <mscottm2> mscottm2 has joined #hcls2
17:05:10 <Zakim> +[IPcaller.a]
17:05:27 <mscottm2> can't hear you - Michel?
17:05:37 <Zakim> -[IPcaller.a]
17:05:41 <BobF> severely breaking up
17:05:51 <matthias_samwald> this was noisy AND breaking up.
17:08:27 <bobP> scribenick bobP
17:08:53 <Zakim> +??P27
17:09:00 <bobP> Matthias: Michel and I extended TMO, targeted to represent...
17:09:29 <RickKiefer> RickKiefer has joined #hcls2
17:09:34 <bobP> (Michel is talking from an advanced com center)
17:09:58 <mscottm2> LOL
17:10:11 <michel> michel has joined #hcls2
17:10:21 <bobP> Matthias: after a lot of consideration, edited classes for genetic variantion
17:10:42 <bobP> ... also edited other classes of a general nature
17:10:58 <bobP> ... look at TMO as it is on BioPortal
17:11:15 <bobP> ... namespace of TMO is identical to that used to enhance
17:11:26 <matthias_samwald> http://bioportal.bioontology.org/ontologies/1461
17:11:37 <bobP> ... so all of changes went live to BioPortal :)
17:12:08 <bobP> ... maybe we should reconsider the authoritative source
17:12:36 <bobP> Michel: +1 to controlled releases
17:12:43 <iker> iker has joined #hcls2
17:13:10 <bobP> Matthias: It is going to a release file
17:13:41 <bobP> ... latest on BioPortal 1.02
17:13:57 <michel> http://bioportal.bioontology.org/ontologies/46121?p=terms
17:14:14 <bobP> bobP sees it
17:14:37 <Zakim> +[IPcaller.a]
17:15:06 <bobP> Joanne sees it
17:16:03 <bobP> Matthias: Tried to follow the realist approach; variation is not an abstract entity like sequence
17:16:21 <JoanneLuciano> JoanneLuciano has joined #hcls2
17:16:43 <bobP> ... this approach tried to build on established principles; represent as material entity
17:17:15 <bobP> Joanne: Working from authoritative source?
17:17:41 <bobP> Matthias: Mixture. Looked at DBs and how they representetd variation
17:18:04 <bobP> ... dbSNP also has short indels(?) etc
17:18:24 <bobP> ... still quite open. Is this approach good?
17:18:40 <bobP> ... also, how to represent more detail?
17:19:03 <Zakim> +EricP
17:19:28 <bobP> ... Ex class region w SNP. Originally from Michel, represent right down to nucleotide level
17:20:12 <bobP> ... SNP would be a subclass of nucleotide (?)
17:20:18 <Zakim> +??P0
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17:20:42 <bobP> ... concerned that this might not be practical. Gets complex beyond simple SNP
17:21:07 <bobP> ... propose to identify SNP thru datatype property, as a sequence stream
17:21:27 <bobP> ... go w. the more normal way that SNPs are represented in real DBs
17:21:46 <Joanne> "as strings of characters"
17:22:14 <bobP> BobF: Q Current models for variants. SNPs need a reference sequence
17:22:28 <bobP> ... how does that fit here?
17:22:54 <bobP> Matthias: Refer to loci w/in genome where loci have relation to reference genomes
17:23:33 <bobP> ... found in relation to reference. Would suggest we find ont rep that is independent of standard geneome
17:23:47 <bobP> ... in context of surrounding DNA
17:24:05 <michel> https://docs.google.com/document/d/1BeaU3VJW1S_R3eB5ncrcW9wJ-lMU4xdmxCdjH8E0i5s/edit?hl=en_US
17:24:11 <bobP> ... but may be useful to keep relation to reference genome
17:24:39 <bobP> Michel: We did consider where this residue is a SNP, partOf some reference genome
17:24:53 <bobP> ... that's a way to make the connection
17:25:04 <BobF> The NCI Life Sciences DAM may be a useful reference:  http://ncientarch.info/sandbox/LSDAM2_2_1/
17:26:27 <bobP> Matthias: SNP would go out the material branch; reference would go out the information entity branch
17:26:57 <bobP> Michel: Need to make connection( didn't quite get this)
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17:28:42 <bobP> BobF: Been working w NCI on modeling molecular entities,
17:28:54 <bobP> ... in this model we do address these issues
17:29:10 <bobP> ericP: Guide us?
17:29:20 <BobF> http://ncientarch.info/sandbox/LSDAM2_2_1/
17:29:20 <ericP> http://ncientarch.info/sandbox/LSDAM2_2_1/
17:29:39 <Joanne> http://ncientarch.info/sandbox/LSDAM2_2_1/
17:30:10 <Lena> @matthias_samwald: if found  "reference genomic sequence"@en in the tmo, it this what you meant?
17:30:52 <Joanne> http://ncientarch.info/sandbox/LSDAM2_2_1/
17:31:13 <bobP> (my image is very narrow!)
17:33:00 <bobP> Joanne: This works for me +1
17:33:24 <bobP> Scott: TMO has DNA-region-w-SNP
17:33:31 <ericP> would that look like this in turtle ? [ a NucleicAcidSequenceFeature ] NucleicAcidPhysicalLocation [ a NucleicAcidSequence ] .
17:33:40 <bobP> ... would mke SNP a property of a region
17:34:20 <bobP> Joanne: SNP needs more than one nucleotide reference
17:34:20 <ericP> or in RDFS: { :NucleicAcidPhysicalLocation rdfs:domain :NucleicAcidSequenceFeature ; rdfs:range :NucleicAcidSequence . }
17:34:44 <bobP> Matthias: Want to create this ont from scratch on top of TMO?
17:35:06 <bobP> ... analyzed SO a lot; claims to have everything figured out.
17:35:16 <bobP> ... but hard to understand
17:35:51 <bobP> Joanne: Q (didn't get)
17:36:23 <bobP> Matthias: SNP needs a population. Use the knowledge to give special meaning to regions of the genome
17:37:41 <bobP> ... liturature tries to avoid mutation (answer to Helen's Q)
17:37:58 <bobP> Michel: Seq, feature, what are you trying to say?
17:38:21 <bobP> ... actually we have a different molecular material?
17:38:40 <bobP> ... is it really a feature of a sequence?
17:39:18 <bobP> Matthias: Everything based on individual, w specific regions etc. Then create universals
17:39:31 <bobP> ... to group individuals
17:40:18 <bobP> BobF: Two different levels of granularity here
17:40:57 <bobP> ... ultimately we are talking about a physically different DNA, should be treating like a physical entity
17:41:24 <bobP> ... from patient's perspective, show me what proceeds from this reality(?)
17:41:47 <bobP> ... different from looking at populations, different perspectives
17:42:07 <bobP> ericP: Does one of these align more closely? Are use cases similar?
17:42:31 <bobP> BobP: Both perspectives, but could not drill into this area as much as would have liked
17:42:46 <bobP> ... LSDAM, will be taking these considerations back
17:43:04 <Zakim> -[IPcaller.a]
17:43:21 <bobP> ... tried to come up w high level use cases, so successful for these
17:43:41 <bobP> ... but instantated in different ways for different use cases
17:44:08 <bobP> Michel: TMO distinguishes between physical and sequences
17:44:33 <bobP> ... we do have both concepts, both are useful.
17:44:44 <bobP> ... what are individuals composed of?
17:45:07 <bobP> ... we do geno- and phenotyping both
17:45:40 <bobP> BobF: LSDAM is looking at a translation to OWL
17:45:52 <bobP> ericP: Opportunity here
17:46:10 <bobP> Matthias: Could apply a Xform to RDF
17:46:48 <bobP> ... TMO trying to do in this more complicated way, w ont principles
17:47:20 <bobP> ... advantages for reasoning, etc; disadvantage makes things complicated
17:47:37 <bobP> ... putting this realist view on top
17:48:09 <bobP> BobF: LSDAM used UML b/c of the existing infrastructure
17:48:26 <bobP> ... would welcome the input from OWL experts here
17:48:50 <bobP> Scott: Taking ont approach so we can use reasoning as well as easy integration
17:49:15 <bobP> ... choice should be tested against a reasoning task
17:49:33 <bobP> ... want a concrete set of test cases, to reason over patient data etc
17:49:43 <bobP> ... would help us ground the conversation
17:50:19 <bobP> Matthias: Should try to carry this on, try a prototye
17:50:29 <bobP> ... OWL reasoning to classify patients
17:51:07 <bobP> ... practically, different models give confusion on variation in individuals vs in populations
17:51:22 <bobP> Lena: Patient instance of population?
17:51:49 <bobP> Matthias: No. A population is a specific entity.
17:52:26 <bobP> Lena: Patient part of a cohort, so patient could be an instance of cohort class.
17:52:41 <bobP> BobF: Cohort could be a kind of cohort
17:52:55 <bobP> (!) kind of popultion
17:53:22 <bobP> Michel: TMO, would want to assign attributes to populations
17:53:59 <bobP> ... can have cohorts of studies, etc. Averages over individuals, as opposed to specific characteristic
17:54:19 <bobP> Matthias: Should agree on community process to address this.
17:56:18 <bobP> Scott: We started w use cases for sparql queries
17:56:29 <bobP> ... Michel put up axioms for ethnicity
17:57:03 <bobP> ... clinical decision support, might not make a difference for which way to go.
17:58:06 <bobP> Michel: DrugBank geno-pheno all in OWL. Can gain from clear formalization
17:58:30 <bobP> ... mixing categories then we can't leverage from what we have
17:58:45 <bobP> ... want to go beyond just linked data.
17:59:12 <bobP> ericP: If we write down in LD vs If we write down formally
17:59:47 <bobP> Lena: Linked data will have new stuff, should be able to express in TMO
18:00:02 <bobP> Scott: ...different demands
18:00:44 <bobP> Matthias: TMO approach now is ontological; vs put up raw RDF
18:01:38 <Zakim> -Joanne_Luciano
18:01:40 <bobP> ... suggest end of Jan 2012
18:02:32 <bobP> Scott: Pgx paper, there are prods from reviewers
18:03:04 <bobP> ... want more material. Want what we're working on now!
18:03:21 <bobP> ... PGx for Future Medicine
18:04:39 <bobP> Lena has bragging rights.  We await!
18:05:38 <matthias_samwald> try to document all SPARQL endpoints and datasets you create on http://www.w3.org/wiki/HCLSIG/pharmacogenomics_2012 !!
18:07:06 <Mary> Mary has left #hcls2
18:07:17 <Zakim> -Joseph_Scheuhammer
18:09:21 <Zakim> -[IPcaller]
18:09:27 <michel> rrsagent, draft minutes
18:09:27 <RRSAgent> I have made the request to generate http://www.w3.org/2011/11/17-hcls2-minutes.html michel
18:09:34 <Zakim> -??P27
18:09:41 <michel> rrsagent, make log world-visible
18:11:34 <Zakim> -Scott_Bauer.a
18:19:17 <Zakim> -Bob_Powers
18:22:44 <Zakim> -??P0
18:22:46 <Zakim> -EricP
18:22:48 <Zakim> - +62427aaaa
18:22:56 <Zakim> -Scott_Bauer
18:22:58 <Zakim> SW_HCLS(TMO)11:00AM has ended
18:23:00 <Zakim> Attendees were Scott_Bauer, Joseph_Scheuhammer, Bob_Powers, Joanne_Luciano, [IPcaller], +62427aaaa, EricP
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