Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  closed
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:  fixed
 Keywords:|  Blocked By:  259, 281, 306
 Blocking:|
--+--
Changes (by dconnolly):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Tom, feel free to polish the write-up more as you see fit, but this is
 done to my satisfaction.

 If you think it's worth more group attention, go ahead and re-open it.

 For follow-up work, see milestone:data-quality-q3

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 306
 Blocking:|
--+--

Comment (by mish):

 Results from UNMC and UTSCSA have3 been incorporated in the REDCap
 database. Partial results from CMH have also been integrated.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 306
 Blocking:|
--+--
Changes (by mish):

 * blockedby:  259, 281, 306, 309 => 259, 281, 306


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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+-
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 306, 309
 Blocking:|
--+-

Comment (by mish):

 I've started the [https://docs.google.com/document/d/1lECK43_tp-
 PblFtGIbFLvaJGq14Q9Miugcspe5A8Hr0/edit  write up] and hope to be finished
 this week.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+---
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306, 309
 Blocking:|
--+---

Comment (by bos):

 Replying to [comment:20 mish]:
 >  (UTHSCSA perhaps??)

 Yes, we should have results posted by Wednesday. Sorry, results have
 delayed by my attendance at the PMN conference.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+---
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306, 309
 Blocking:|
--+---

Comment (by bos):

 Replying to [comment:13 dconnolly]:
 > I don't think I understand the question. Why would you change the age
 ranges, Angela?

 Sorry, please allow me to retract the question. It was based on a faulty
 assumption after looking at the input file but before looking at the SQL
 code.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+---
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306, 309
 Blocking:|
--+---

Comment (by mish):

 Here are the results so far:

 || ||=Qa Base Results   =||=Qa Base Percentages =||=Qa Base Results=||= Qa
 Base Percentages =||=Qa Bc Results   =||=Qa Ob Results
 =||=Qa Base Results=||= Qa Base Percentages=||= Qa Bc Results=||=   Qa
 Ob Results=||=   Qa Term Matching=||=Qa Pcori Report+||
 || ||=2014 Q4   =||=2014 Q4=||= 2015 Q1 =||=2015 Q1=||= 2015 Q1=||=
 2015 Q1=||= 2015 Q2=||= 2015 Q2=||= 2015 Q2 =||=2015 Q2
 =||=2015 Q2 =||=2015 Q2||
 ||CMH||X||X||X||X|| ||X|| || || || || ||  ||
 ||KUMC||X||X||X||X||X||X|| || || || || || ||
 ||MCRF||X||X||X||X||X||X||X||X||X||X||X||X||
 ||MCW||X||X|| || || || || || || || || ||  ||
 ||UIOWA||X||X|| || || || || || || || || || ||
 ||UMN||X||X||X||X||X||X||X||X||X||X||X||X||
 ||UNMC||X||X||X||X||X||X|| || || || || || ||
 ||UTHSCSA||X||X||X||X||X||X|| || || || || || ||
 ||UTSW||X||X||X||X||X||X|| || || || || || ||
 ||WISC||X||X||X||X||X||X||X||X||X||X||X||X||

 I have heard from KUMC (Nathan) and they hope to have results in yet this
 week. I need to start the write up soon. Are there any other sites I
 should wait for before starting (UTHSCSA perhaps??) This Friday is the
 absolute latest for getting your data in before I start trying to draw
 some conclusions.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+---
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306, 309
 Blocking:|
--+---

Comment (by mish):

 I believe it was intended as Diagnosis w/ valid icd9's.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+---
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306, 309
 Blocking:|
--+---

Comment (by bos):

 In [https://bitbucket.org/jvanschyndle/gpc-2015-q2-qa-
 
files/src/1b9cf89ef8bdec77c474e2ed8adfe1b6e0ac910a/Q2_2015_GPC_QA.sql?at=default
 Q2_2015_GPC_QA.sql], `/* Encounters with No ICD 9 Code */` uses the result
 of `'num_valid_icd9'` which hasn't yet been populated. Am I missing
 something?

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by lv):

 One other note: our Age Bucket counts were very low initially. We
 identified a grouping issue where Netezza was joining results and SQL was
 selecting the first result it found.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by mish):

 For comment 2 above, REDCap was incorrectly expecting an integer, not a
 number. It worked fine for us (i.e. 0), so I missed it. Sorry, that's been
 fixed.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by lv):

 Few issues with importing our data:
 1. Some Dates were incorrectly formatted. Fixed.
  - obesity_max_admit_date
  - obesity_max_birth_date
  - obesity_min_admit_date
  - obesity_min_birth_date

 2. obesity_per_pat_proc_cpt_99381_87 didn't like our output of 2.76;
 Deleted this to get the file to load.
 3. NULL = "The value you provided could not be validated because it does
 not follow the expected format. Please try again." Fixed.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  bos
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--
Changes (by dconnolly):

 * owner:  dconnolly => bos


Comment:

 I don't think I understand the question. Why would you change the age
 ranges, Angela?

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by bos):

 The age breakdowns in this QA query differ from our GPC terms, e.g.
 `age_10_19` instead of `age_10_17`. Are we supposed to change this to the
 age range concepts used at our site?

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by mish):

 It appears as if I have permissions to fix this oversight. You should be
 able to access the Data Import Tool now.

 As a side note: ensure that Record ID is set to all upper case. I noticed
 that after running the script, mine was "Wisc" instead of "WISC". A simple
 edit corrected that.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by jdale):

 We have the file ready with the records stored as separate columns but I
 can't find where in the REDCap project to upload/import the file?  Can you
 advise?  Thanks.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by mish):

 UPLOAD process...

 You can either hop onto to the [https://redcap.gpcnetwork.org/|gpcnetwork
 redcap server] and try to upload the results for yourself, or send the
 results to Tom and he can upload them for you. Big bonus points for
 uploading them yourself.

 A couple of notes:
 * Not everyone has registered their InCommons accounts yet.
 * On import, don't forget to set the upload paramter:
  * ''Record format: The file to be uploaded has its records stored as
 separate **Columns**''

 -TM

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[Dan Connolly]

I'd like to see this "which loinc code do we use for BP?" issue escalated to 
its own ticket.

On Jul 14, 2015 1:29 PM, GPC Informatics  wrote:
#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by lv):

 MCRF ran the scripts in < 4 hours (run incrementally, so may be less total
 time) on SQL server.

 What's the process to submit results: REDCap, Email to Tom, something
 else?

 After validating, the zero/null results seem appropriate. In some cases we
 have raw data that we might be able to use to fill calculated values.

 Example:
 \i2b2\LP29694-4\LP29696-9\LP146111-2\72165-4\72165-4: Pediatric systolic
 blood pressure percentile per age, gender and height [0 facts; 0 patients]

 *SUGGESTION:
 \i2b2\LP29694-4\LP32525-5\LP96828-6\72225-6\29545-1\8480-6\(8480-6:
 Systolic blood pressure [12308605 facts; 749329 patients])

 *COULD THE PERCENTILE BE CALCULATED OFF OF THE VALUES PROVIDED BY THIS???

 One other note: in some cases we have a term that's used in the query, but
 we're not using it in our data. Could likely swap these if 1559-6 is
 approximately the same as 1557-8?

 \i2b2\LP29693-6\LP7784-4\1557-8\1557-8: Fasting glucose [0 facts; 0
 patients]

 *SUGGESTION: \i2b2\LP29693-6\LP7784-4\1558-6\ (1558-6: Fasting glucose
 [398797 facts; 150656 patients])

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290, 306
 Blocking:|
--+--

Comment (by lv):

 MCRF ran the scripts in < 4 hours (run incrementally, so may be less total
 time) on SQL server.

 What's the process to submit results: REDCap, Email to Tom, something
 else?

 After validating, the zero/null results seem appropriate. In some cases we
 have raw data that we might be able to use to fill calculated values.

 Example:
 \i2b2\LP29694-4\LP29696-9\LP146111-2\72165-4\72165-4: Pediatric systolic
 blood pressure percentile per age, gender and height [0 facts; 0 patients]

 *SUGGESTION:
 \i2b2\LP29694-4\LP32525-5\LP96828-6\72225-6\29545-1\8480-6\(8480-6:
 Systolic blood pressure [12308605 facts; 749329 patients])

 *COULD THE PERCENTILE BE CALCULATED OFF OF THE VALUES PROVIDED BY THIS???

 One other note: in some cases we have a term that's used in the query, but
 we're not using it in our data. Could likely swap these if 1559-6 is
 approximately the same as 1557-8?

 \i2b2\LP29693-6\LP7784-4\1557-8\1557-8: Fasting glucose [0 facts; 0
 patients]

 *SUGGESTION: \i2b2\LP29693-6\LP7784-4\1558-6\ (1558-6: Fasting glucose
 [398797 facts; 150656 patients])

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+-
 Reporter:  mish  |   Owner:  dconnolly
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290
 Blocking:|
--+-
Changes (by dconnolly):

 * cc: jvanschyndle@… (added)
 * owner:  mish => dconnolly
 * status:  new => assigned


Comment:

 We've got some code:

 [https://bitbucket.org/jvanschyndle/gpc-2015-q2-qa-
 files/commits/4d7def85af3604448c0aac7dff5bbdeecfcc1948 4d7def8]

 Who wants to try it out?

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+-
 Reporter:  mish  |   Owner:  mish
 Type:  problem   |  Status:  new
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290
 Blocking:|
--+-

Comment (by mish):

 First draft of QA code covering:
 * Modify the code to allow for easier substitution of local paths.
 * Review of performance on Oracle systems (specifically KUMC)

 should be available on Bit Bucket at the end of this week.

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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+-
 Reporter:  mish  |   Owner:  mish
 Type:  problem   |  Status:  new
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  259, 281, 285, 290
 Blocking:|
--+-
Changes (by dconnolly):

 * blockedby:  285 => 259, 281, 285, 290


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Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results

[GPC Informatics]

#291: Gather 2015 2nd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  mish
 Type:  problem   |  Status:  new
 Priority:  major |   Milestone:  data-quality-q2
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  285
 Blocking:|
--+--
Changes (by dconnolly):

 * cc: gpc-dev (removed)
 * cc: gpc-dev@… (added)
 * milestone:   => data-quality-q2


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