HCLSIG/PharmaOntology/Meetings/2011-07-14 Conference Call/Minutes

* Now talking on #hcls2
* Topic for #hcls2 is: #hcls2 pharmacogenomics paper
* Topic for #hcls2 set by michel at Thu Jun 30 11:59:50 2011
* mscottm (marshall@81.69.36.208) has joined #hcls2
* Zakim (rrs-bridgg@128.30.52.169) has joined #hcls2
<mscottm> Zakim, who is here?
<Zakim> sorry, mscottm, I don't know what conference this is
<Zakim> On IRC I see mscottm, BobP, ericP
<mscottm> Zakim, this is tmo
<Zakim> ok, mscottm; that matches SW_HCLS(TMO)11:00AM
<BobP> scribenick BobP
<Zakim> +??P29
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* epichler (ad4c1522@207.192.75.252) has joined #HCLS2
<Zakim> + +1.781.431.aaaa
<BobP> Scott: On the way to making a clinical query work
<BobP> ... want to do patient data from pharmGKB, by Monday?
<BobP> ... Adrien replied
<BobP> ... Adrien has warfarin text-mined relations in RDF
<BobP> ... pharmGKB could go quickly
* michel (c13ece97@78.129.202.38) has joined #hcls2
<Zakim> +??P10
<michel> zakim, ??P10 is michel
<Zakim> +michel; got it
<BobP> ... (talking re RPI hackathon)
<BobP> Michel: Can take over pharmGKB mapping
<BobP> ... add column headers from pharmGKB, add to TMO
<BobP> ... will add script to TMO svn
<iker> two interesting data sources from PharmGKB
<iker> https://www.pharmgkb.org/do/serve?objCls=PhenotypeDataset&objId=PA135603152#tabview=tab0
<BobP> Scott: pdfs can go into dropBox
<iker> https://www.pharmgkb.org/do/serve?objId=PA161845844&objCls=PhenotypeDataset#tabview=tab0
<BobP> Elgar: Can set up dropbox
<BobP> that was fast too!
<BobP> Michel demonstrating lightning fast facility w Google
* michel - lol
<BobP> Scott: Admiring Iker's query
<BobP> ... walk-through w competency questions
<ericP> Zakim, please dial ericP-office
<Zakim> ok, ericP; the call is being made
<Zakim> +EricP
<BobP> ... clinical is covered. Remains: drug development pharma mining example
<BobP> ... ideally we describe how solution links out
<BobP> Scott: Center of paper has shifted, but we can describe a pharma ex
<BobP> ... vicinity of gene or related genes; easy to move from one aspect to another
<BobP> ... on the shelf for now.
<michel> zakim, who is making noise
<Zakim> I don't understand 'who is making noise', michel
<BobP> ericP's mike is not noisy
<BobP> ericP: Looking at Iker's query, w replies
<BobP> Iker: Not making use of SWObjects
<BobP> ... just Xferred dbSNP to RDF
<BobP> ... can KB for this be added to TMO KB?
<BobP> ... w TMO KB, I can upload
<BobP> Scott: Can find homes for dbSNP and for warfarin data.
<BobP> ... should be able to refer to KB separately as well as together
<BobP> Iker: Should extend TMO, or use another ont, for mappings?
<BobP> Scott: Mapping to semantics can happen w SWObjects?
<BobP> ericP: Here's how I can construct IRIs in proper form. Iker, do you want to materialize?
<BobP> ... URL construction can be done in several ways
<BobP> ... if sparql technique doesn't work, then we need to think
<BobP> Iker: (discussing tech w ericP)
<BobP> ... datamined one line at a time(?)
<BobP> ... used D2R2. Issue is, chromosome maps to local vocabulary
<BobP> ericP: Issue is not tech, but which vocabs to settle on.
<BobP> Iker: Found a vocab for SNPs
<BobP> Scott: For choosing terms: gene variant-specific terms would come from our own TMO
<BobP> ... once stabilized, then ericP does mappings
<BobP> ... long term, most sustainable approach is to create mapping to SWObjects
<BobP> ... rather than materialize
<BobP> ericP: Change in schema, we would have to adjust anyways
<BobP> ... tools already exist
<BobP> ... prefer to use my tools, more expressive now
<BobP> Iker: D2R fully materialized it
<BobP> Scott: As long as we know it;s working, we can write about it.
<BobP> ... but we should move more toward sustainable solutions
<BobP> ... if NIH has sparql endpoints, then they can move toward happiness w us
<BobP> ericP: Can use sqlServer itself
<BobP> (microsoft taking hits here :-)
<BobP> Scott: ericP you have got the most agile solutions
<BobP> ... already have materialized RDF for sparql query
<BobP> ericP: Next step, figure out schemas for SNPs.
<Zakim> -EricP
<BobP> Michel: Adding more terms from TMO, some from SO. Has terminology
<ericP> Zakim, please dial ericP-office
<Zakim> ok, ericP; the call is being made
<Zakim> +EricP
<BobP> Michel: W. list of types, then can add to TMO
<BobP> ericP: TMO or SO?
<BobP> Michel: SO is substantially larger. Either case necessitates mapping.
<BobP> ... ontological commitment. Real entity or info entity?
<BobP> ... SO commits you to info content, w TMO we can use realist ont
<BobP> ericP: SO lots of fringe?
<BobP> Michel: Can use mireot to extract minimal ontology, just hierarchy.
<BobP> ... real problem is that chromosome is an information content entity
<BobP> ericP: Matters in some universe? Proteins as aggregate vs specific prot in a cell
<BobP> Michel: There are experiments w individual molecules!
<BobP> ericP: Just spell it differently?
<BobP> Michel discussing property sillinesss issues down the info path
<BobP> ericP: Happy to stick w informational solution
<BobP> Michel: Statements about the nature of genes, doen't make sense re info
<BobP> Elgar asking about the choice
<mscottm> good answer!
<BobP> ... inclined to do it this way too
<BobP> Michel: One KB material, other KB info, then disjoint and we have to deal with this eventually anyway
<BobP> ... if pick SO to do mapping, that's OK for now.
<BobP> Scott: Readers of this paper, assuming pgx apps, won't notice the difference
<BobP> ... no difference at the query level
<BobP> ericP: asking about classes vs individuals
<BobP> Michel: Semantics communicates to the user the kinds of things they're dealing w in their KB.
<BobP> ... recall that we started w modelling question
<BobP> ericP: +1
<BobP> Scott: Community curated ontology in your email?
<BobP> ... don't have to decide on SO yet?
<BobP> Michel: Will add terms to TMO for now.
<BobP> Elgar: Would suggest to go w material entities
<BobP> Michel: Safe bet, we have our terminology under our control
<BobP> ... we can map everything in dbSNP...
<BobP> ericP: -1 Fragmentation of semweb, distinctions should be demonstrated by use cases
<BobP> Michel: kebbi has material molecular things, but we have disjoint things
* mscottm agrees with ericP on the principle of reuse and the need for a use case that demonstrates the need for a different model
<BobP> ericP: Say, new use case exceeds expressivity of model
<BobP> ... sort of minimalist, but decisions have already been made.
* michel the reuse is satisfied by mapping
<BobP> Elgar: We have already followed this paradigm in TMO
<BobP> ... we chose to use TMO protein class
<BobP> ... would have preferred to use mappings to other onts
<BobP> ... might have pulled in SO terms
<BobP> ericP: Agree, consistent.
<BobP> Michel: Updating TMO in svn, not webProtege
<BobP> Elgar: webProtege seems to be a one-time dump
<BobP> Michel: Can put up owl-doc version, or ontoB(?)
<michel> another ontology viewer: http://www.ontobee.org/
<BobP> Michel: Need list of types to use
<Zakim> -EricP
<mscottm> Zakim, who is here
<Zakim> mscottm, you need to end that query with '?'
<mscottm> Zakim, who is here?
<Zakim> On the phone I see Bob_Powers, mscottm, ??P29, +1.781.431.aaaa, michel
<Zakim> On IRC I see michel, epichler, iker, Zakim, mscottm, BobP, ericP
<mscottm> Can anybody hear me?
<Zakim> -michel
<mscottm> thanks all! bye!
<Zakim> -mscottm
<epichler> dropped voice connection - see you Sun - e2
<Zakim> - +1.781.431.aaaa
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<BobP> rrsagent, draft minutes
<BobP> zakim, who is here?
<Zakim> On the phone I see Bob_Powers, ??P29
<Zakim> On IRC I see michel, iker, Zakim, mscottm, BobP, ericP
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<BobP> rrsagent, draft minutes
<mscottm> Oops - I'm afraid that I forgot to invite RRSAgent.
<Zakim> -Bob_Powers
<BobP> oh
* michel has quit (Quit: http://www.mibbit.com ajax IRC Client)
<BobP> i can email the minutes
<mscottm> Thanks!