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? Preferably your harmonizing with the existing work and that
the final approach is scriptable from the UMLS and doesn't require
curation.
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el. See
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the agreed-upon format to the GPC Honest Broker.
''The status of that document isn't entirely clear, but planning
conservatively...''
This implies deploying the data builder (#87) at all participating sites.
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omment:
Laurel,
In tomorrow's teleconference, please poll sites for their guestimate of
when they can have the data builder deployed for use in the breast cancer
survey.
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has a
starting AUI path of A6321000.A1582
Please see attached the code and also cc'ing Tim Meyer from our team in
case of questions related to the code.
Let me know if you need anything else.
Thanks,
Supreet
}}}
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this?:
"HH will point to documentation and will experimentally flip the server
side conversion flag to measure any performance difference"
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use
cases for this tool down the line for other cohorts, we can certainly take
on that project. Knowing that will help inform our work prioritization.
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cancer survey. And yes, that's only the first of many planned uses of the
technique; see DataSecurity#providing-data. So please do provide an
estimate for deployment at CMH.
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eks; January completion.
- 28 Feb 2015
- Wisconsin - February; delay because of holiday
- Minnesota - Begin work in January; February completion.
- UTSW - February; determining where to install
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Comment:
clarifying priorities for milestone:bc-survey-cohort-def
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paying attention when that ticket got closed; I really think one of these
other options that you considered is the right one" isn't cool.)
I hope this explanation addresses the need for...
Laurel will create a ticket for the process of approving terminology; will
hand it off to Phil
=> huhickman
Comment:
Justin, it helps to tell trac that you're handing the ball to Hubert.
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the unit code conversion is in the CRC Design
document, section 3.2.2. I will attach the pages to this ticket, and
attach some timing results as well.
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rsion in SQL for the
various possible convertible units in the metadata_xml field.
The default setting is OFF, and i2b2 assumes that the facts are stored in
normalized units.
It would be interesting for another site to repeat the timing experiment
as well.
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he's using.
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a. JC/UNMC: will poll users by next week
b. Bonnie/UMN: will poll users
c. other sites are encouraged to do likewise
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ussion 1/6. Please only allow end users to submit poll
responses.
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code similar to [https://bitbucket.org/njgraham
/pcori-annotated-data-dictionary pcori-annotated-data-dictionary] to build
CDM tables using PCORI CDM paths.
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.org/njgraham/pcori-annotated-data-
dictionary/src/1c1c0f980377bbd1adbe839edf84d8de92f5b1de/CDM_transform.sql?at=default
CDM_transform.sql] we used for the ETL Annotated Data Dictionary. Instead
of using the `path_map` file to map from PCORI to HERON terms, it could
just query the PCORI hierarc
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Query: "HISPANIC@09:01:26"
[1.7 secs]
Compute Time: 1 secs
Number of patients for "HISPANIC@09:01:26"
patient_count: 721
}}}
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exist
in the heron code base. I've been conservative in adding in indexes as we
go along.
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| Blocked By:
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---+
Changes (by dconnolly):
* milestone: data-quality2 => data-domains2
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diagnosis.
After review v1 vs v2 – I would recommend v1
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you estimated end of 2014 for production deployment; how did that
turn out?
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oposed GPC demographics
terminology and diagnosis modifiers to central desktop under the GPC i2b2
metadata folder. Could you load it onto Babel for me?
also Tuesday, December 23, 2014 1:36 PM
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le of the output?
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HackathonTwo, we worked on a
[https://docs.google.com/presentation/d/1Mqtsyxk4x8zrOM0e9EaruZIPH9sEwI_0zAC2Cmw9w6c/edit?usp=sharing
GPC CDM ETL] presentation.
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/
p.s. you'll be sending it to Iowa via https://redcap.kumc.edu/ ; see #211
for details.
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institution's Honest Broker. You
will upload the file to the survey.
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Batch modification to #174, #202, #192, #207 by dconnolly:
priority to minor
Comment:
not critical for the Jan 16 checkpoint
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Batch modification to #145, #146, #201, #160 by dconnolly:
milestone to drn-basic-query
Comment:
factoring milestone:drn-basic-query out of milestone:data-domains2
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Batch modification to #106, #31, #132, #159 by dconnolly:
milestone to cohort-char1
Comment:
phasing out milestone:data-agg1
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:
• jquery_ref.patch
• plugin_config.patch
Any requests for clarification can be sent to
finamore@mcrf.mfldclin.edu
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cript console for error
messages? We had some problems with non-standard javascript that chrome
rejected earlier.
A call or some screensharing might be worthwhile. I'm not free just now,
though.
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w_error);
};
}}}
Re `icefish2.gif`, see ticket:87#comment:56. It's not used in the new data
builder design; I should get rid of the broken reference.
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ess
with the CentOS stock 2.6 on our server)
I still need to clean things up but we're operational enough to generate
files.
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alled and can generate sqlite files - so
for UNMC, we won't be going to the interim route.
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erSaga#i2b2
-vm-dep), but perhaps your configuration is different?
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or: demo
How can I move into production mode and specify the "data_builder" account
instead for this access. Thanks.
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ndex.php http:.../PMService/ demo
demouser
}}}
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b` tables are blank, will that interfere
with your being able to extract our data for the purposes of the breast
cancer cohort selection?
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G
the relevant parts out. I think the relationship between the query
definition and the variable table is pretty straightforward.
If necessary, just give me the XML query definition that you ran and I'll
compute it.
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Batch modification to #109, #157 by dconnolly:
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but am not 100% sure.
Thank you.
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t.
[[BR]]
We had some i2b2 issues, so we had to build run the query manually, then
convert it to sqlite. Hence, hence our job and variable tables are empty.
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ion: => fixed
Comment:
Done: KUMC, WISC, UNMC, UTHSCSA, UTSW
tracked as separate tickets:
[[TicketQuery(id=217|218|168|205)]]
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closing #202.
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If you have shared
it, please let me know where.
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rs expect.
Jim
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: | Blocked By:
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---+---
Changes (by campbell):
* status: assigned => closed
* resolution: => fixed
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out the different options!
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environment.
See also [https://botbot.me/freenode/gpc-
dev/2015-01-23/?msg=30299978&page=1 #gpc-dev log].
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#x27;ll stand by
w.r.t. data builder approach until I see some data.)
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and in the expected format using the interim
builder. Still waiting to hear from our site PI that we can share the
data.
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sed
* resolution: => fixed
Comment:
UIOWA submitted data in the relevant format and UMN's issues are better
tracked as #110.
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riority to minor since I heard this
is a possibility being considered and not a definite plan/request.''
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g over my "accepted" tickets; I am
completely swapped out. Maybe the most useful thing to do is declare
victory and re-open this if we find reason to do more work on it?
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ort characterization
exercise?
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in comment:19.
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[https://bitbucket.org/njgraham/gpc-pcornet-cdm gpc-
pcornet-cdm] but compatible with Microsoft SQL Server.
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vey-redcap-als
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Gpc-dev@listser
edu/pipermail/gpc-dev/2014q1/09.html FW:
PCORnet: Draft Common Data Model 1.0]
\\Russ Waitman Wed Mar 19 15:12:02 CDT 2014
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|
-+-
Changes (by dconnolly):
* priority: major => minor
* milestone: morning-star => drn-basic-query
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Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/182#comment:5>
gpc
|
-+-
Changes (by dconnolly):
* priority: minor => major
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/182#comment:6>
gpc-informatics <http://informatics.gpcnetwork.org/>
edite the process. No update.
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/143#comment:4>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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Gpc-dev@
:
Blocking: |
---+
Changes (by lv):
* status: closed => reopened
* resolution: fixed =>
Comment:
Forgot to reopen this, as it's active.
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/143#
l send correspondence to the GPC PopMedNet Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/14#comment:36>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Net
Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/161#comment:9>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
___
Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/162#comment:6>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
___
e will send correspondence to the GPC PopMedNet Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/148#comment:19>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Net
eenlee will send correspondence to the GPC PopMedNet Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/166#comment:7>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Net
l send correspondence to the GPC PopMedNet Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/147#comment:7>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Net
eenlee will send correspondence to the GPC PopMedNet Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/163#comment:8>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Net
MedNet Administrators
to guide this process forward (likely 2/3/15 or so).
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/164#comment:6>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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