16:04:30 <RRSAgent> RRSAgent has joined #hcls2
16:04:30 <RRSAgent> logging to http://www.w3.org/2010/10/28-hcls2-irc
16:05:02 <matthias_samwald> zakim, this is hcls
16:05:02 <Zakim> ok, matthias_samwald; that matches SW_HCLS(TMO)11:00AM
16:05:06 <ericP> Zakim, please dial ericP-office
16:05:06 <Zakim> ok, ericP; the call is being made
16:05:08 <Zakim> +EricP
16:05:15 <ericP> Zakim, who is here?
16:05:15 <Zakim> On the phone I see Bob_Powers, Joanne_Luciano, +46.4.63.3.aaaa, +1.317.655.aabb, ??P22, ??P27, +1.781.431.aacc, EricP
16:05:17 <Zakim> On IRC I see RRSAgent, joanne, epichler, bbalsa, michel, soroush, matthias_samwald, Zakim, ericP
16:07:19 <soroush_> soroush_ has joined #HCLS2
16:07:43 <matthias_samwald> i volunteer for scribing.
16:07:47 <michel> thanks
16:07:50 <matthias_samwald> scribenick: matthias_samwald
16:08:16 <matthias_samwald> joanne: in the last telecon, chime summarized some of his work.
16:08:37 <matthias_samwald> ... the information did not have enough detail to tell us which mapping would be right, because there was not enough information.
16:09:30 <ericP> 1 person with 3 bodies?
16:10:13 <matthias_samwald> ... a sample from the same age/date/gender from a different location. we imagined a situation where supplies are short. we decided we did not have the authority to decide about identity. 
16:10:42 <matthias_samwald> ... the patient data is ambiguous.
16:11:01 <Zakim> +mscottm
16:11:31 <matthias_samwald> ... the different options should be presented in the paper to the readers.
16:13:32 <michel> ericP is this a model problem, or a data input problem?
16:14:00 <matthias_samwald> joanne: question: "when it happens, what are the possible causes?"
16:15:25 <matthias_samwald> scott: a question when you are trying to map is, are you starting with the correct term -- as a recommendation, there should be disambiguation built into the interface. if a clinican is labeling a clinical report, they should be offered many choices to help them disambiguate.
16:15:53 <soroush_> soroush_ has joined #HCLS2
16:16:04 <matthias_samwald> joanne: another issue is when the categories are too narrow.
16:16:53 <matthias_samwald> ... if the annotator has to record something that has not been seen before, it will not be recorded/annotated.
16:17:19 <matthias_samwald> ... you have to expect that unusual / unexpected things will need to be captured.
16:17:30 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/Data/MappingDataToSNOMED
16:18:07 <matthias_samwald> michel: i have made a mapping to SNOMED terms on the wiki.
16:18:35 <ChristiDenney> ChristiDenney has joined #hcls2
16:19:15 <matthias_samwald> scott: alignment is a different process than data entry.
16:19:32 <matthias_samwald> scott: but the underlying decisions that need to be made are probably similar.
16:20:13 <Bob> Bob has joined #hcls2
16:20:19 <matthias_samwald> michel: regarding the mapping table on the wiki -- what does our coverage look like?
16:21:06 <matthias_samwald> ... how many patient records do not have any matches, what are we proposing to do about it?
16:21:28 <matthias_samwald> joanne: the table... is the data from all patients combined?
16:21:37 <matthias_samwald> michel: don't know, chime gave me the link.
16:21:44 <Bob> Michel: Summary of last week's meeting?
16:21:44 <Bob>  <Bob> Joanne: Went thru Chime's record, discussed what could not be matched
16:21:44 <Bob>  <Bob> ... decided that it was important not to make inferences where they didn't exist
16:21:44 <Bob>  <Bob> ... granularization didn't have enough detail
16:21:44 <Bob>  <Bob> ... Second case was where inference was not warranted
16:21:45 <Bob>  <Bob> ... influenza case had sample coming from same...but different parts of body
16:21:47 <Bob>  <Bob> ... different modes of taking samples, but we didn't have authority to infer
16:21:49 <Bob>  <Bob> Eric: Is this a modelling question?
16:21:51 <Bob>  <Bob> Joanne: Data are ambiguous
16:21:53 <Bob>  <Bob> ... this is what Chime was working on last week
16:21:55 <Bob>  <Bob> ... answering Eric: these are the kinds of things that do come up
16:21:57 <Bob>  <Bob> Eric: We get to resolve the ambiguities, port to Indivo, more modelling, bugs are in Indivo
16:21:59 <Bob>  <Bob> ... yes there's value in disussing in the paper, since people will encounter this
16:22:01 <Bob>  <Bob> ... but those are resolvable bugs in our model etc
16:22:03 <Bob>  <Bob> ... Invdivo model carries these interpretations, gives a concrete example
16:22:05 <Bob>  <Bob> ... prepares people for encountering these, point out to reader that these can be fixed
16:22:07 <Bob>  <Bob> Scott: Disambiguation? There will always be cases where data themselves have not be disambiguating
16:22:09 <Bob>  <Bob> ... need to have disambiguation built into the interface, at the clinician front end
16:22:13 <Bob>  <Bob> Joanne: Two thumbs up!
16:22:15 <Bob>  <Bob> Scott: If you've done that then minimizes noise later on
16:22:17 <Bob>  <Bob> Joanne: If categories are too narrow, as in galaxies, people need to be able to record that things have not been seen before
16:22:20 <Bob>  <Bob> ... want to make sure that unusual things can be noted
16:22:22 <Bob>  <Bob> Scott: Yes, this also should be captured
16:22:24 <Bob>  <Bob> Michel: Q about mapping of terms
16:22:26 <Bob> Joanne: We can look at coverage
16:22:32 <Bob> (above section was at beginning of call!)
16:22:37 <matthias_samwald> oh, i was scribing here as well!
16:22:58 <matthias_samwald> okay, you take over!
16:23:04 <Bob> (I was off on hlcs2!)
16:23:44 <mscottm> mscottm has joined #hcls2
16:23:46 <Bob> Joanne: Map to more than one snomed category, but there weren't that many cases like this
16:23:58 <matthias_samwald> scribenick: Bob
16:24:36 <Bob> Michel: Q is more tech, In patient data conversion we were keeping track of labels
16:25:04 <Bob> Eric: Going Indivo to TMO?
16:25:22 <Bob> ... Will the Indivo xml carry these IDs? Yes
16:25:41 <Bob> ... this is place where tests are not carefully done yet
16:25:51 <Bob> ... rest of these tests have interesting modeling questions
16:26:12 <Bob> ... Indivo writes down a code w coding system, units, etc.
16:26:27 <Bob> ... combination of coding and ids gives you snomed
16:26:40 <Bob> ... But we want to start picking away at these, modeling w TMO
16:27:19 <Bob> ... too many, so we bring them in slowly, elevate some of them to our first-class way
16:27:34 <Bob> ... can start putting in further information
16:27:57 <Bob> ... goal here is to take bp, figure out mechanics
16:28:10 <Bob> ... problem is that some test results are not structured
16:28:37 <Bob> ... also have very structured tests, but some are just values
16:29:00 <Bob> ... ex: had to make up a genetic test, result
16:29:15 <Bob> Michel: Share the structure?
16:29:58 <Bob> Eric: This came up early b/c w SNPs
16:30:55 <Bob> ... genotyping SNPs
16:31:18 <Zakim> - +46.4.63.3.aaaa
16:31:39 <ericP> https://dvcs.w3.org/hg/TMO-Indivo/file/3334734509e9/syntheticPatients/AD_PCHR_1.xml#l702
16:32:00 <Zakim> + +46.4.63.3.aadd
16:32:31 <Bob> ... these are tests w lots of structure
16:34:04 <Bob> Discussion of what is deep in this representation...
16:34:39 <michel> http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp&cmd=search&term=rs72547528
16:35:19 <michel> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=72547528
16:35:19 <Zakim> + +1.302.598.aaee
16:35:36 <Bob> Michel: See C/T, chromosome, position, etc
16:36:50 <Bob> Michel: This is analogous to term-mapping, in that there is no corresponding record in dbSNP
16:37:14 <Bob> ... needs to be formalization, but up to you whether to embed
16:37:47 <Bob> Eric: Alan R. had raised Q, to what degree are we capturing all the information?
16:38:22 <Bob> ... there are laws re capturing data, etc, so we can't throw anything away
16:39:14 <Bob> Michel: Next-gen seq, how to get back to raw data from annotation?
16:40:01 <Bob> Scott: We can throw down challenge to Indivo re SNPs
16:40:48 <Bob> Eric: Clinics have laws that say you have to do all this, but EHRs are not motivated to
16:41:22 <Bob> Scott: Maybe a placeholder in our data to enable this capability
16:42:00 <Bob> ... going back to low level from high level, sort of a reverse use case
16:42:13 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/Diagrams
16:42:31 <Bob> Michel: Here is the diagram to represent elements in the first query
16:42:57 <Bob> ... describe visually the query and identify elements in our KB
16:43:27 <Bob> ... query is largely described in relation rather than in type
16:43:46 <Bob> ... could be domain and range restrictions, but we haven't done that
16:44:06 <Bob> ... we had discussion re specialization of relations
16:44:13 <Trish> Trish has joined #HCLS2
16:44:18 <Bob> ... Will RDF still have this structure?
16:44:43 <Bob> Eric: Yes, roughly.  If something better, then would use it
16:45:07 <Bob> ... would like to have the extra predicates so consumers don't have to constrain by type
16:45:17 <Bob> ... use where I can
16:45:50 <Bob> Michel: We have in linked-data: specific predicates sitting in one namespace
16:46:14 <Bob> Eric: We need some inference if we are over-specializing our predicates
16:46:59 <Bob> Michel: Coarse relations, use them in different combinations
16:47:10 <Bob> ... we should create a mapping of relations
16:47:27 <Bob> Eric: We can do this in specific use cases
16:48:07 <Bob> ... point out that there can be more general use cases, what can be queried w/o inference
16:48:22 <Bob> Joanne: Use cases is what drives the TMO
16:48:39 <Bob> Eric: Yes, this would be the prize if we can show
16:49:08 <Bob> Michel: TMO isn't playing a big role if we don't really use predicate mappings
16:49:31 <michel> use case - query the dataset   - use dataset specific types/relations
16:49:39 <michel> use case - query all datasets - use TMO types/relations
16:49:44 <michel> but requires mappings
16:49:46 <Bob> Eric: Use case: get query across datasets, but can still ask intelligent questions
16:49:49 <michel> at the type and relation level
16:51:22 <Bob> Eric: Do we get to ask readers for more general queries?
16:52:07 <Bob> ... maybe say that these are questions for the community, OK as an interest group
16:52:36 <Bob> Michel: Contrast two different queries w different predicate formulations
16:53:22 <Bob> Scott: Chime's queries were from wiki, not aligned w TMO?
16:54:19 <Bob> ... should we change queries or TMO or both, from last week's call
16:54:39 <Bob> Michel: Some of this is just in patient data, not in TMO
16:55:14 <Bob> ... before: mapping at type-level, we could query the type but could not do it w relation
16:57:09 <Bob> Michel: Scott, we want to contrast sparql within-dataset, against TMO types and relations across all datasets that are aligned
16:57:45 <Bob> ... LODD we could query irrespective of which dataset, we did not have relation mapping
16:58:23 <Bob> ... objects, individuals call for relations, we want to query on these sorts of predicates
16:59:06 <Bob> Eric: LODD certain amount of coding to make things similar, so queries get similar units, etc
16:59:35 <Bob> Michel: One query for a union across datasets
16:59:53 <Bob> Eric: How general can you get before there is no useful unified query
17:00:06 <Bob> ... Ex: BP need normalization
17:00:42 <Bob> ... what query can we get in this non-normalized form?  (excellent point) "Head-scratching time."
17:01:20 <Bob> Michel: Take the paper that we had, start adding in new work.
17:01:41 <Bob> Eric: We can point out about EHR integration
17:02:10 <Zakim> - +46.4.63.3.aadd
17:03:40 <Zakim> - +1.317.655.aabb
17:05:31 <Bob> Michel: Want to convey that linked-data play nicely in the whole business space
17:06:44 <Trish> agree, at least for now no need to include SNP data but point to source
17:07:28 <Bob> ... Nobody is going to undertake the whole process to convert everything
17:08:10 <Bob> ... they can just take their own part. SNP is a good example.
17:08:35 <Zakim> -mscottm
17:08:57 <mscottm> hand of God?
17:08:58 <mscottm> ;)
17:08:59 <Trish> need to move to next call
17:09:04 <michel> yup
17:09:04 <mscottm> bye
17:09:07 <michel> bye
17:09:10 <matthias_samwald> (i need to leave, bye!)
17:09:14 <Zakim> -??P27
17:09:17 <Trish> i can work on some MS items
17:09:27 <Zakim> - +1.302.598.aaee
17:09:53 <Zakim> -EricP
17:09:54 <Zakim> -??P22
17:09:55 <Zakim> -Bob_Powers
17:09:56 <Zakim> - +1.781.431.aacc
17:09:56 <Zakim> -Joanne_Luciano
17:09:57 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:09:59 <Zakim> Attendees were Bob_Powers, Joanne_Luciano, +46.4.63.3.aaaa, +1.317.655.aabb, +1.781.431.aacc, EricP, mscottm, +46.4.63.3.aadd, +1.302.598.aaee
17:28:51 <matthias_samwald> matthias_samwald has joined #hcls2
17:57:07 <michel> rrsagent, draft minutes
17:57:07 <RRSAgent> I have made the request to generate http://www.w3.org/2010/10/28-hcls2-minutes.html michel
17:57:17 <michel> rrsagent, make log world-visible
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