HCLSIG/PharmaOntology/Meetings/2009-11-12 Conference Call

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Conference Details

  • Date of Call: Thursday November 12 2009
  • Time of Call: 12:00 - 1:00pm ET
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: +33.4.89.06.34.99 (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 42572 ("HCLS2").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC)
  • Mibbit instructions: go to http://www.mibbit.com/chat and click the server link. Enter irc.w3.org:6665 into that box, enter a nickname, and enter #HCLS2 for the channel
  • Duration: 1h
  • Convener: Susie

Agenda

  • Ontology Update - Colin
  • * questions: (1) names - spacy or underliny? (2) what issues have been raised by data loading? (3) what to do about "outcome", "treatment safety", etc?
  • Diagnostic Data - Michel
  • PCHR Data - Susie
  • Data Loading and Mapping - Michel
  • Paper (intro, intro box, UI, etc.) - All
  • AOB

Minutes

Attendees: Chris, Jim, Colin, Bosse, Michel, Joshua, Matthias, EricM, EricP, Christi, Trish, Elgar, Susie

in attendance: Susie, Chris, Colin, Bosse, Jim, Matthias, Michel, Joshua Phillips, Eric Miller, Trish, Elgar

susie: agenda - Colin to do ontology, Michel to do diagnostic data, Susie to do pchr data, Michel to do data loading and mapping

colin: have updated with role relations, Elgar's questions

colin: spaces or underlines?

susie: happy whichever?

elgar: underlines preferred

elgar: inconsistency between versions of protege - looks nicer with underlines but is mostly cosmetic

trish: it's a problem if the human-readable name is being used as the rdf id

trish: what are we usinf for names

colin: both rdfs:label and iao:IAO_115

susie: we need to make a choice - my bias to underscores

susie: can you guys take this offline? ACTION

colin: to bear in mind - what issues have been raised by data loading, if any?

colin: what to do about unassigned terms like "health outcome"?

susie: happy for you to pursue business about lifestyle

susie: would like to capture "health outcome"

susie: how did they respond?

colin: does the patient data have outcomes in it?

susie: in the multiple annual medicals

colin: so the outcome proceeds from the difference between successive encounters

susie: also correlation between snps/lifestyle and encounters

trish: is the concern that there are orphan classes?

colin: wondering what people think

susie: since outcome and safety are two of the most important things

elgar: we should make up our minds, given we have bfo

trish: tentatively place w/ curation status

all: agreed

colin: susie - do we have data that maps on to safety

susie: i'd like to add adverse events - could map on to safety

chris: i'll think about that

susie: we have SIDER

susie: are the patient records realistic?

colin: safety difficult as absence of bad things happening

elgar: general understanding is negative effects

chris: worth further discussion

bosse: not an adverse drug effect because may not be caused by a drug

susie: colin - are happy to get together w/ bosse, elgar & chris about safety

colin: yes

susie: DIAGNOSTIC DATA

susie: ------------------

michel: have taken text from panel 2, passed it through NCBO Annotator

michel: http://tm.semanticscience.org/describe/?url=http://bio2rdf.org/tmo:panel2/ffcdde6da9ecaa4a

michel: rdf'ified results

michel: link above tells us about "amygdala"

michel: linkage to ontology nebulous because lack information about meaning and where it came from

michel: once i understand how that works can load concepts into endpoint

susie: trish - does this supersede what you've done?

trish: did something similar but was a more specific subset. have been in touch w/ michel and maryann martone

elgar: trish - i put two random pubmed abstracts through annotator and was disappointed; did i use it correctly? is there documentation on entity recognition?

trish: just looks for preferred name + synonyms

elgar: do i have to select ontologies explicitly?

trish: there is a 'select all' option

susie: seems we're on track

susie: FAKE PATIENT DATA

susie

susie: Chris has put a lot of work into the different patients

susie: i have been updating Patient One (the template) - want to look at it one more time before publishing

susie: bosse - you've signed up for patient 3

bosse: much harder than i expected - where do i get drug code

chris: just NDC

susie: I was following Peter Kos - also asked him re genomic information but he had to go to 3 web sites

susie: keep as simple as possible

susie: bosse - keep plugging away

susie: Peter Kos has volunteered to fill in some of the gaps - hopefully by splitting load we can get it done quicker

chris: genomic section difficult

susie: some of the genotyping can be repeated across patients

christi: I got the lab results in

christi: doing Downs Syndrome example

susie:christi has made great progress, anja has flu, matthias?

matthias: very complicated - bit puzzled about how xml should be structured

chris: how do we compare?

susie: getting uploaded to wiki

susie: jim - what progress?

jim: have been working but lack access to wiki

susie: jim- could you do patient 4?

jim: sure

susie: definitely making progress though more of a task than I'd expected. but very worthwhile

jim: happy to do xslt

susie: look at patient one

chris: what one do i start on?

susie: christi's

susie: DATA LOADING AND MAPPING

michel: just waiting for patient data - need to think about mapping - in paper?

colin: that was me

michel: colin - do you need help with mapping?

colin: let me know how you get on

michel: just in paper at moment so let's migrate that to google doc

colin: OK

susie: PAPER

susie: goal to move paper into Word and make edits there on Monday

susie: Elgar - you'd volunteered to make SW box

elgar: have descriptions and definitions for about terms; too long

susie: anja was working on data sources; for ui we'll talk about 1. pubby and 2. what we'd like to see.

susie: chris says the veterans' association system is one that physicians like - bosse is leading on openvista (OS version of this)

susie: goal to make web client that looks like openvista. Eric Miller (attached) interested in doing a mockup

susie: bosse - what update?

bosse: have added section to paper; missing anja's contribution

susie: thinking of having a breakout group

susie: eric - anything to add

eric: getting bearings and finding out where assets live

bosse: eric - look at what we have in the document

susie: will invite eric to have access

bosse: one question - one of the challenges is identifiers

bosse: shouldn't we mention identifiers as a challenge?

susie: URIs will be in box and also text about SW approach, but no discussion about common URIs

susie: challenges of reconciling identifiers

susie: good progress; should be really good paper

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