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15:06:01 <matthias_samwald> zakim, this is hcls
15:06:01 <Zakim> ok, matthias_samwald; that matches SW_HCLS()11:00AM
15:06:06 <matthias_samwald> zakim, who is here
15:06:07 <Zakim> matthias_samwald, you need to end that query with '?'
15:06:11 <matthias_samwald> zakim, who is here?
15:06:11 <Zakim> On the phone I see Bob_Powers, [IPcaller], Tony, michel
15:06:14 <Zakim> On IRC I see BobF, RRSAgent, Zakim, matthias_samwald, michel, bobP, MacTed, ericP
15:06:27 <michel> Meeting: W3C HCLS – Clinical Decision Support
15:06:37 <michel> Chair: Matthias Samwald
15:06:53 <michel> scribenick: Michel
15:07:03 <michel> AMIA submission
15:07:22 <michel> matthias: put down ideas on a google doc
15:07:35 <bobP> hey, i can scribe
15:07:37 <michel> https://docs.google.com/file/d/0ByGT-vnkGcoLSkhzVDRYd2x6bkU/edit
15:07:58 <Zakim> +[GVoice]
15:08:00 <bobP> scribenick: bobP
15:08:27 <bobP> Matthias: Suggestion by Bob Freimuth to look into immunogenetics
15:09:01 <bobP> ... AMIA page is limited to one page, tried to squeeze
15:09:31 <bobP> ... feedback +1 from Michel
15:09:35 <Zakim> +[IPcaller.a]
15:09:47 <bobP> ... (reading... :)
15:10:56 <bobP> ... some PGx related developments in G-group
15:11:18 <bobP> ... we should move these discussions to hcls
15:11:22 <bobP> Michel: +1
15:11:55 <bobP> Michel: also +1 on one-pager for AMIA
15:12:16 <bobP> ... "very well done"
15:13:39 <bobP> Michel, Matthias discussing .doc commenting on G-drive
15:14:08 <bobP> BobF: "This is well written" and plenty of material
15:14:29 <bobP> ... do we have a comprehensive dataset that can be mined
15:14:53 <mscottm> mscottm has joined #hcls
15:15:06 <bobP> ... confirm, that we have an example, w/o convering everything?
15:15:07 <Zakim> +mscottm
15:15:25 <bobP> Matthias: We have converted clincally relevent subsets
15:15:29 <Zakim> +harryh
15:15:44 <bobP> ... for PGx, focus on (?) for genes
15:16:07 <bobP> ... plus PharmaGKB clinically relevant SNPs
15:16:24 <bobP> ... plus Michel has a selection for conversion to RDF
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15:16:42 <bobP> Michel: SNPs have been converted.
15:16:57 <bobP> BobF: Focus is large :)
15:17:31 <bobP> Michel: We can provide data for SNPs and phenotypic datatypes
15:17:45 <bobP> ... would like to get reasoning going over these data
15:18:18 <bobP> BobF: Given this scope, wording is +1
15:18:41 <bobP> Matthias: Will do minor edits w feedback and submit
15:18:51 <bobP> BobF: Thanks!
15:21:58 <bobP> Matthias: Agenda: Potential use case of immunogenetics
15:22:31 <bobP> ... IGx might indeed be an addional use case w PGx
15:23:01 <bobP> ... IGx small number of genes 3-10 from human leukocyte antigen genes
15:23:15 <bobP> ... few, but high variety of sequences
15:23:36 <bobP> ... almost every nucleotide can vary
15:24:06 <bobP> ... BobF can we infer alleles?
15:24:54 <bobP> ... still looking; would be interesting to see how our approach could work here
15:25:37 <bobP> BobF: IGx came to me from NMDP Nat'l Marrow Donor Program
15:26:05 <bobP> ... central for bone marrow and HLA typing, 1M patients/year
15:26:44 <bobP> ... tech challenge w HLA is interesting, less than a dozen, pseudogenes etc, are designed to be highly variable
15:26:56 <bobP> ... tremendous genetic variability
15:27:13 <bobP> ... throw this on everyone's radar
15:27:41 <bobP> ... post-translational mod, regulation, how they dimerize on cell surface
15:27:59 <bobP> ... translplant scenerio has to account for all of this
15:28:33 <bobP> ... NMDP came to Mayo for data modeling, w flexibility and manage thru time
15:29:04 <bobP> ... one of issues is that seq tech is improving, moved into whole geneome, next-gen
15:29:21 <bobP> ... impact on def of alleles becomes now quite complicated
15:29:35 <bobP> ... no longer talking about one or two wrt ref seq
15:29:48 <bobP> ... but dozens of variants
15:30:05 <bobP> ... the *allele nomenclature will not scale to this challenge
15:30:35 <bobP> ... now faced w data integration w patients w missing, old data
15:30:55 <bobP> ... so open world assumption may fill this
15:31:10 <bobP> ... algorithms for matches may need this
15:31:33 <bobP> ... IGx suited in many ways for semweb. How to proceed?
15:32:17 <bobP> Scott: Harkening back, part of project in IGx, French group doing xml
15:32:50 <bobP> ... group had lots of interesting IGx xml
15:33:08 <bobP> ... data are threre, but how to harvest as semweb
15:33:46 <bobP> ... should we start a KB from this legacy?
15:34:04 <bobP> BobF: Novel alleles are being discovered going forward
15:34:36 <bobP> ... challenges in enumerating alleles: can have indel events and other re-arrangements that make things *really* complicated
15:34:50 <bobP> ... canonical approaches will not cover the space
15:35:18 <bobP> ... emphasize that challenge comes from next-gen seq, novel variants at extremely large scale
15:35:43 <bobP> ... how to store + go back and interpret in a phenotypically relevant way
15:36:16 <bobP> BobF: NMDP has invited me down to workshop
15:36:37 <bobP> ... dedicated to developing datastandards for next-gen
15:37:07 <bobP> ... lots of vendors, there will be an ongoing effort by the group
15:37:16 <matthias_samwald> example of a full HLA sequence http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?B*15:15
15:37:45 <bobP> ... scope of standards, from metadata, to more intricate governance over data changing monthly
15:38:37 <bobP> ... lots of the right people and stakeholders, gravitating to traditional approaches :{
15:38:50 <bobP> Michel: An opportunity :)
15:39:17 <bobP> BobF: We could have a dramatic impact on how this community functions.
15:39:50 <bobP> bobP: (asking the right question is the most important step :)
15:40:00 <BobF> http://www.ebi.ac.uk/imgt/hla/ambig.html
15:40:28 <bobP> Matthias: Seq above 1089 nucleotides for a single allele
15:40:47 <bobP> BobF: This is an underestimate, since that's for coding sequence only
15:41:00 <bobP> ... there is intronic plus (?) se
15:41:31 <bobP> ... avg is 5K seq per gene, accounting for this other content
15:41:32 <BobF> intronic + flanking sequence
15:41:59 <bobP> Matthias: Think of as a seq of fixed length?
15:42:29 <bobP> ... should look into insertions and deletions also
15:42:44 <bobP> ... looking, all of seqs have same length
15:43:25 <bobP> BobF: Yes, generally true for class 1, but class 2 genes have a different structure
15:44:05 <bobP> ... true generally for open reading frames, but class 1 and class 2 differ in all this, different proteins
15:44:29 <bobP> Scott: Given huge amount of variance, exp class 2, can we use SNPs here??
15:45:12 <bobP> ... have a sense that HLA has so much variation, would be hard to establish a reference population for SNP analysis
15:46:05 <bobP> BobF: (not an expert, but) There are relatively finite number (not nec small) of alleles that are inherited thru generations
15:46:22 <bobP> ... other sites are novel variants that occur sporadically, can be inherited
15:46:39 <bobP> ... they are designed to be highly variable
15:46:48 <bobP> ... mutated quite rapidly
15:47:13 <bobP> Matthias: But there is dbSNP data for these HLA genes
15:47:26 <BobF> http://hla.alleles.org/alleles/index.html
15:47:36 <bobP> BobF: Yes, but dbSNP not authoritative for HLA
15:48:09 <bobP> ... > 8100 alleles in these databases, but not always haplotypes so the combinations will explode rapidly
15:48:17 <BobF> http://www.ebi.ac.uk/imgt/hla/ambig.html
15:50:13 <bobP> ... page for ambiguous calls
15:50:14 <BobF> B*07:02:01G+B*07:05:03	vs B*07:02:11+B*07:05:01G
15:50:44 <bobP> ... string indicates a given patient genotype, two diff haplotype combinations
15:50:58 <BobF> B*07:67N
15:51:08 <Zakim> -harryh
15:51:08 <bobP> ... but no way to tell the difference, so nomenclature is fudged as above
15:51:54 <bobP> ... trying to adopt nomenclature that will account for this, but running out of ways to lexically describe all this
15:52:07 <bobP> Michel: Why are haplotypes ambiguous?
15:52:08 <matthias_samwald> link describing the naming: http://hla.alleles.org/nomenclature/naming.html
15:52:55 <bobP> BobF: Gets back to phases. Take first set of allele defined on one strand, other allele on other strand
15:53:25 <bobP> ... ambiguous to tell from only genotype. Has implications for what gets expressed on the cell surface
15:53:43 <bobP> ... we cannot completely disambiguate the alleles yet
15:54:33 <bobP> (Michel and BobF going deep)
15:55:10 <bobP> BobF: Classical phasing problem is whether variant is on one strand of the other
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15:55:25 <bobP> ... one, two, three polymorphs, can work out the phasing
15:55:45 <bobP> ... but will large numbers it becomes very difficult to disambiguate
15:56:08 <bobP> Michel: king of getting it
15:56:47 <bobP> (looking up the 1000-word figure)
15:57:04 <bobP> (kind of getting it :)
15:57:26 <bobP> Matthias: Timeline?
15:57:53 <bobP> BobF: Group agrees that they need data standard
15:58:41 <bobP> ... have expressed that semweb, inferencing tech for allele calls might be a way to start
15:59:14 <bobP> ... month or so to frame, then feed them interim solutions over a few months
15:59:26 <bobP> ... pilot solutions 1Q13
15:59:59 <bobP> Matthias: New use case before PGx is done?
16:00:31 <bobP> ... scalability of owl reasoners. IGx seems to be an order of magnitude greater than PGx
16:01:09 <bobP> BobF: Solving this would solve PGx too. HLA is the king of all genetic loci in this regard.
16:01:19 <bobP> :)
16:01:28 <ericP> cheers all
16:01:29 <Zakim> -Tony
16:01:30 <Zakim> -mscottm
16:01:31 <Zakim> -michel
16:01:32 <Zakim> -Bob_Powers
16:01:36 <Zakim> -[IPcaller]
16:01:58 <bobP> rrsagent, draft minutes
16:01:58 <RRSAgent> I have made the request to generate http://www.w3.org/2012/10/11-hcls-minutes.html bobP
16:02:08 <bobP> rrsagent, make logs public
16:02:14 <Zakim> -[GVoice]
16:02:21 <ericP> et voila
16:07:14 <Zakim> disconnecting the lone participant, [IPcaller.a], in SW_HCLS()11:00AM
16:07:16 <Zakim> SW_HCLS()11:00AM has ended
16:07:16 <Zakim> Attendees were Bob_Powers, [IPcaller], Tony, michel, [GVoice], mscottm, harryh
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