HCLSIG/PharmaOntology/Meetings/2010-12-16 Conference Call/minutes
Michel: Topic - AMIA submission
http://jointsummits2011.amia.org/tbi-2011-initial-call-proposals
Joanne: We can submit if in press, but not elsewhere. So OK
Michel: Still valid to go for the podium format.
Joanne: Trish did a poster last year.
...ask for podium, but if w/o time slot then might get poster.
Michel: So long as either you or Trish can attend, go ahead and write the 1 page abstract, I'll review
Michel: Topic - Working Groups
... create working groups of 3-4 people
... help keep TM active with different interests/expertise
... to domain experts and plumbers
ericP volunteers to be an animal model
Joanne: Front end would need a focus group
...need users with problems to solve
Tim is not experienced in the medical community
ericP hears from others that we like to do cool fun things, but not the boring necessary stuff
... important that we include participants that have a vested interest, and can bring the outcomes in
michel does Tim prefer tooling?
Tim likes plumbing.
Joanne: He does, and he's good at it too!
Joanne: technology needs to solve a stated problem
Michel: Challenge is to find those groups who have individuals who have a vested interest in tech
...to bring it back in-house, then hear back from them
...do we have the individuals or do we have to recruit?
Eric: We don't have a specific process when we have a broad group (?)
Michel: We can generate best-practices documents
Michel: Think about a new set of deliverables
... health records, animal models, pharmacogenetics
...to create a new set of objectives
Joanne: Want someone who is an early adopter
Michel: Patient records, data
-> File:Tmo-indivo-lebot-2010-Dec-16.pdf TMO Indivo plan
Tim: Sent a diagram
...Diagram shows patient data flow.
...pdf is a view of the world from an outsider's perspective
...will keep pushing down the Virtuoso .trig path
Michel: Reconvene Jan 6
Happy Holidays!
Topic - how to get the patient data
hg clone https://dvcs.w3.org/hg/TMO-Indivo
http://sourceforge.net/projects/swobjects/files/
102 files updated, 0 files merged, 0 files removed, 0 files unresolved
I have checked out the files.
I now have /Applications/Sparql.app
bash-3.2$ /Applications/Sparql.app/Contents/MacOS/Sparql --version dyld: Library not loaded: /opt/local/lib/mysql5/mysql/libmysqlclient.16.dylib
Referenced from: /Applications/Sparql.app/Contents/MacOS/Sparql Reason: image not found Trace/BPT trap
sudo mkdir -p /opt/local/lib/mysql5/mysql/
I see /Applications/Sparql.app/Contents/Frameworks/libmysqlclient.16.dylib
sudo ln -s /Applications/Sparql.app/Contents/mysql/libmysqlclient.16.dylib /opt/local/lib/mysql5/mysql/libmysqlclient.16.dylib
I did: sudo ln -s /Applications/Sparql.app/Contents/Frameworks/libmysqlclient.16.dylib /opt/local/lib/mysql5/mysql/
(Eric promises this will go away soon....)
bash-3.2$ l /opt/local/lib/mysql5/mysql/ total 8 lrwxr-xr-x 1 root admin 68 Dec 16 13:10 libmysqlclient.16.dylib -> /Applications/Sparql.app/Contents/Frameworks/libmysqlclient.16.dylib
bash-3.2$ /Applications/Sparql.app/Contents/MacOS/Sparql --version sparql version 1.0 . Revision 1355 modified 2010-12-06 22:49:13 -0500 (Mon, 06 Dec 2010) by ericprud. https://swobjects.svn.sourceforge.net/svnroot/swobjects/branches/sparql11
alias sparql=/Applications/Sparql.app/Contents/MacOS/Sparql
cd /demos/tmo/source/dvcs-w3-org/tmo-indivo-instances/version/c1cef20da460-hg/TMO-Indivo/syntheticPatients
trying 'make test'
got errors:
SPARQL ?= SPARQL
SPARQL -qd AD_PCHR_1-tmo.trig -e 'PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?mbox { ?s foaf:mbox ?mbox }' --compare tests/email_1.srt || echo AD_PCHR_1-tmo.trig\(0\): error !mbox /bin/sh: SPARQL: command not found
SPARQL=sparql make test
sparql -qd AD_PCHR_1-tmo.trig -e 'PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?mbox { ?s foaf:mbox ?mbox }' --compare tests/email_1.srt || echo AD_PCHR_1-tmo.trig\(0\): error !mbox /bin/sh: sparql: command not found AD_PCHR_1-tmo.trig(0): error !mbox
SPARQL=/Applications/Sparql.app/Contents/MacOS/Sparql make test
ALIASING BAD
bash-3.2$ SPARQL=/Applications/Sparql.app/Contents/MacOS/Sparql make test /Applications/Sparql.app/Contents/MacOS/Sparql -qd AD_PCHR_1-tmo.trig -e 'PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?mbox { ?s foaf:mbox ?mbox }' --compare tests/email_1.srt || echo AD_PCHR_1-tmo.trig\(0\): error !mbox
tests/q8_2.srt
PREFIX trans: <tag:eric@w3.org:2009/tmo/translator999#>
=-qd AD_PCHR_1-tmo.trig -e
q: quiet
d: data
=-e execute query string
What does .trig stand for?
qg pchr AD_PCHR_1-tmo.trig tests/q1.rq
g: loads into graph
/Applications/Sparql.app/Contents/MacOS/Sparql --help
d <file>: load file into default graph
g <graphName> <file>: load file into default graph graphName
AD_PCHR_1-tmo.trig
test: all $(MBOXES) $(Q1S) $(Q4S) $(Q6S)
we don't get to q8:
/Applications/Sparql.app/Contents/MacOS/Sparql -qd AD_PCHR_1-tmo.trig -e 'PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?mbox { ?s foaf:mbox ?mbox }' --compare tests/email_1.srt || echo AD_PCHR_1-tmo.trig\(0\): error !mbox /Applications/Sparql.app/Contents/MacOS/Sparql -qd AD_PCHR_2-tmo.trig -e 'PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?mbox { ?s
$(Q8S)
test: all $(MBOXES) $(Q1S) $(Q4S) $(Q6S) becomes "test: all $(MBOXES) $(Q1S) $(Q4S) $(Q6S) $(Q8S)"
(on line 67 of Makefile)
SPARQL=/Applications/Sparql.app/Contents/MacOS/Sparql make test
SPARQL=/home/eric/checkouts/swobjects/bin/sparql make test
a bad test:
AD_PCHR_2-tmo.trig:0: error: data tests/q8.rq:0: note: query tests/q8_2.srt:0: note: expected results
SPARQL=/Applications/Sparql.app/Contents/MacOS/Sparql make test || echo look back for an error
@$(SPARQL)
SW_HCLS(TMO)11:00AM has ended
Attendees were Bob_Powers, michel, EricP, Joanne_Luciano, lebot, +1.650.331.aabb
lebot, ~ test: += Q8S
~ silence make test except for errors
sorry, that was my commit
oops, forgot to push