RE: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[Campbell, James R]

Dan
Seeing that Jeff is proposing to discuss SCILHS and CDM during the 9/22 call 
(tomorrow), I will plan to speak next week about UNMC deployment since I just 
got back into town last night and I am scrambling to pull the documentation 
together from Hubert's departure.  I will be assembling the ETLs and metadata  
builds that UNMC has deployed for our network and distributing prior to that.

I was surprised when the Data Characterization work showed up on the LEK 
agenda.  I had been told there would be no data standardization activity during 
this round of meetings and had not planned to attend.  Will GPC's CDM build be 
part of that discussion that I heard you assign to Alex or are there other 
issues planned?  What day would those discussions be?
Jim


From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on 
behalf of GPC Informatics [d...@madmode.com]
Sent: Friday, September 18, 2015 2:15 PM
To: dconno...@kumc.edu; nate.apa...@cerner.com; 
verhagen.lau...@mcrf.mfldclin.edu
Cc: jeff.kl...@mgh.harvard.edu; gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as 
i2b2 metadata

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  major  |   Milestone:  data-domains3
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+

Comment (by lv):

 Eric's notes from implementing SCILHS at MCRF:

 \PCORI\DEMOGRAPHIC\HISPANIC\ - This was using Race_CD in
 Patient_Dimension.  We fill race with race, not ethnicity (the Race codes
 were also using this column).  I switch this over to use our local
 basecode and pointed at Concept_Dimension instead.

 \PCORI\ENROLLMENT\ENR_BASIS\*\ - I thought the mappings in this section
 were a little odd…
 Encounter-based: would pull a count of patients that had atleast one fact
 that had a start_date.
 Insurance: would always be 0. (not available for selection in i2b2)
 Geography: was based on having the code LOCATION_CODE:2.  We don’t have
 any location codes, so this would never work (again not available for
 selection in i2b2)
 Algorithmic: would be the same as Encounter-based.

 I switch them to be based on \i2b2\Demographics\Enrollment\ terms
 Encounter-based: Is in one of the two nodes: Face to Face Visit Within One
 Year or Two Encounters or Wellness Within 3 Years (Added two children to
 accomplish)
 Insurance: Is in Insurance
 Geography: Is in Patients Within 50 Miles
 Algorithmic: Is in MCRF Catchment

 \PCORI\ENROLLMENT\ENR_BASIS\ - This had a C_FACTTABLECOLUMN value of
 PATIENT_NUM, since I made the above changes to
 \PCORI\ENROLLMENT\ENR_BASIS\*\, I had to update this to concept_cd. (This
 node is also disable in the hierarchy)

 OTHER NOTES
 I also didn’t do much with modifier’s in the ontology.  I know the
 ‘\PCORI_MOD\CHART\’, which is applied to ‘\PCORI\ENROLLMENT\ENR_BASIS\*\’,
 is all hardcoded to be true or false.  So Yes to chart will always be true
 and all the other modifiers will always be false.  There may be more
 examples of this, but like I said, I didn’t spend much time on modifier’s.

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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  major  |   Milestone:  data-domains3
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+

Comment (by nateapathy):

 We propogated the procedures ontology with ICD9 procedure codes as SCILHS
 indicated. We have a default Cerner i2b2 CPT ontology, but have not had
 any requests or a need to request, so it only exists insofar as the Babel
 ontologies and those on the PCORnet Central Desktop.

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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  major  |   Milestone:  data-domains3
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+

Comment (by lv):

 How did sites that implemented SCILHS handle Procedures? Has anyone
 requested the CPT ontology yet?

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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  medium |   Milestone:
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+

Comment (by lv):

 Is the idea that we'll need CDM v3 compliance earlier than the SCILHS
 timeline (end of the year for v2.1/3), which could provide an opportunity
 to contribute our work?

 Can either KUMC or NateA comment in a general way on the effort required
 to implement the SCILHS work?

 I agree with following one standard rather than creating our own hybrid.
 If the level of granularity is requied, maybe we should advocate for
 including it in their later release?

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Ticket URL: 
http://informatics.gpcnetwork.org/trac/Project/ticket/191#comment:9
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RE: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[Klann, Jeffrey G.]

I've been getting these emails and this is great news that you've found our 
ontology easy to leverage. Let me know if I can be of any help.

FYI, I'd be happy to integrate/accept your improvements into our ontology 
release if they align. What are the improvements? LOINC mappings?

Also fyi, our timeline for CDMv3 is also soon - 10/1 (except for some small 
sections like the trial table). The Google Drive that we've shared with 
collaborators already has CDMv3 ontologies for everything except PRO, Death, 
Trial, and Harvest. (I imagine Dan and co have seen this.) We are using 
modifiers to distinguish Diagnosis from Condition and Prescribed from 
Dispensed, so these are not separate trees.

Thanks!

Jeffrey Klann, PhD
Instructor of Medicine, Harvard Medical School
Assistant in Computer Science, Massachusetts General Hospital
PhD in Research, Partners Healthcare Research Computing
ofc: 617-643-5879
email: jkl...@partners.org

 -Original Message-
 From: GPC Informatics [mailto:d...@madmode.com]
 Sent: Thursday, August 27, 2015 1:00 PM
 To: dconno...@kumc.edu; nate.apa...@cerner.com;
 verhagen.lau...@mcrf.mfldclin.edu
 Cc: gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.
 Subject: Re: [gpc-informatics] #191: represent PCORI CDM 2.x
 terminology as i2b2 metadata
 
 #191: represent PCORI CDM 2.x terminology as i2b2 metadata
 ---+
  Reporter:  dconnolly  |   Owner:  dconnolly
  Type:  problem|  Status:  new
  Priority:  medium |   Milestone:
 Component:  data-stds  |  Resolution:
  Keywords: |  Blocked By:  109
  Blocking:  317|
 ---+
 
 Comment (by nateapathy):
 
  Our implementation effort estimation ended up being much more than the
 actual work effort, which was very reassuring. The SCILHS ontology, due
 to  its limited granularity, is pretty straightforward to implement,
 and  follows best practices for i2b2 design, which makes it easier to
 implement. In terms of mapping our hierarchies and terms to the SCILHS
 ontology hierarchies and terms, that effort which we thought would be
 monumental, was actually not nearly as cumbersome as we thought,
 largely  because we were already fairly well aligned since
 (specifically for
  demographics) Cerner i2b2 uses the standard i2b2 demographic ontology,
 and  the SCILHS ontology sticks fairly closely to that design. Granted,
 the  ease of that transition was due in large part to our local
 standard  following the i2b2 standard pretty tightly, so the degree to
 which on a  site has deviated from the i2b2 standard ontologies will be
 a good proxy  for work effort to align with SCILHS.
 
 --
 Ticket URL:
 http://informatics.gpcnetwork.org/trac/Project/ticket/191#comment:10
 gpc-informatics http://informatics.gpcnetwork.org/
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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  medium |   Milestone:
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+

Comment (by nateapathy):

 Following up on the discussion from 8.11.15 GPC Dev call:

 {{{
 c) how cost effective to switch to SCHILS terms from GPC?
i) Dan : feedback from Cerner folks? (not here today). I’ll try to
 catch up with
them
ii) PR/UTSW: vote to not switch, prefer to maybe map between the two,
 but our
GPC terms cover more granular and we’d lose that if we switch
iii) DC/KUMS: maybe adopt SCHILS terms for things we haven’t settled
 for GPC
yet, e.g. use SCHILS for procedures but not diagnoses
iv) RW/KUMC: obesity  adaptable trials drive timeline (for Sept.) to
 implement new
CDM terms
 }}}

 The most significant improvement that the SCILHS ontology provides is that
 it aligns with best practices for i2b2 design and comes with CDM creation
 scripts using the PCORNET_CD field. The most obvious design improvements
 are how demographics are stored in the database and how modifiers are
 structured. The transition from the Cerner standard i2b2 ontology to the
 SCILHS ontology was relatively straightforward, largely thanks to the use
 of best-practice designs for i2b2. For example, storing patient
 demographic data as observations in the OBSERVATION_FACT table is not a
 standard design practice, and the SCILHS ontology resolves this.

 As for granularity, it can always be added back in later versions, and I
 would like to see us pursue that with SCILHS as a partner rather than
 creating a hybrid which will undoubtedly be more convoluted for the end
 user.

 It also gives us significant ability to leverage other groups' work, and
 decreases the distance between proprietary i2b2 design and something
 moderately resembling a standard, at least across i2b2-using PCORnet
 CDRNs. It would behoove us to tack as closely as possible to any
 repeatable standards emerging from other groups, as it only increases our
 economies of scale. My understanding from comment3 on this ticket is that
 we would be adopting the SCILHS ontology as a group - I did not think the
 decision was still up for debate.

 I also recognize that other groups are focusing on the Obesity terms and
 ADAPTABLE terms. As CMH will not be participating in ADAPTABLE, we've had
 cycles to focus on the SCILHS effort that other teams won't have for some
 time.

--
Ticket URL: 
http://informatics.gpcnetwork.org/trac/Project/ticket/191#comment:7
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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  medium |   Milestone:
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+

Comment (by dconnolly):

 Thanks for the experience report.

 On process...

 Replying to [comment:7 nateapathy]:
  ... My understanding from comment:3 on this ticket is that we would be
 adopting the SCILHS ontology as a group - I did not think the decision was
 still up for debate.

 Well, your experience report aligns with my expectation that adopting
 SCILHS would be cost-effective overall, but where it overlaps with designs
 we have already adopted, for example demographics (#67),
 [wiki:DataRepositoryManagement#design-process due process] involves re-
 opening such tickets and then closing them again.

 I probably should have started to do that by now but I have been reluctant
 on behalf of dev groups (such as KUMC!) that have investment in the
 existing design. (see also
 [https://informatics.kumc.edu/work/wiki/SemanticWeb#TerminologyEvolution
 terminology evolution].)

 This whole SCHILS business really shouldn't be hiding under this CDM 2.x
 ticket at all. I just haven't managed to re-organize tickets properly.
 Here's hoping for time to do so.

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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
 Reporter:  dconnolly  |   Owner:  dconnolly
 Type:  problem|  Status:  new
 Priority:  medium |   Milestone:
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:  109
 Blocking:  317|
---+
Changes (by dconnolly):

 * type:   = problem


Comment:

 I finally got the SCHILS ontology on babel.

 PCORnet Demographics shows up twice, as do the other top level folders
 because I inserted the TABLE_ACCESS rows twice. I hope that's not too much
 of a distraction.

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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
--+
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  design-issue  |  Status:  new
 Priority:  major |   Milestone:  data-domains3
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:  109
 Blocking:|
--+
Changes (by dconnolly):

 * priority:  minor = major
 * milestone:  bariatric-study-data = data-domains3


Comment:

 Replying to [ticket:279#comment:11 nateapathy]:
  Does the SCILHS CDRN CDM ontology and CDM transformation code
 effectively replace the comparable subject areas that are on the GPC_TERMS
 table?

 Since we have been pretty well aligned with SCILHS on goals and high level
 design, I expect the changes to be fairly small, but yes, this may involve
 updates to our design for demographics (#67), vitals (#23), and diagnoses
 (#63) and perhaps enrollment (#229). It should address our outstanding
 issues on procedures (#243).

 As SCILHS addresses CDM v2 and v3, it may impact our design for meds (#78)
 and address labs (#158).

  We are starting this effort and don't want to pursue the GPC_TERMS work
 if we will be adopting the
 
[https://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common+Data+Model+Ontology+Home
 ontologies from SCILHS] instead.

 Feel free to skip to the SCILHS ontology and let us know how it goes, but
 please don't let this stall your work. As I say, I expect the changes are
 small, and if you start work with the current `GPC_TERMS`, migrating
 should be a manageable effort.

 The major benefit to offset the cost of this disruption is filling in gaps
 in our CDM ETL (ticket:240#comment:6), as well as shared development costs
 with SCILHS going forward.

--
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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
--+---
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  design-issue  |  Status:  new
 Priority:  minor |   Milestone:  bariatric-study-data
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:  109
 Blocking:|
--+---

Comment (by dconnolly):

 At the June 23 i2b2 meeting, Jeff Klann presented the
 
[https://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common+Data+Model+Ontology+Home
 SCILHS i2b2 PCORnet Common Data Model Ontology].

 He said they're working on v2 and v3; ETA next couple months.

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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
--+---
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  design-issue  |  Status:  new
 Priority:  minor |   Milestone:  bariatric-study-data
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:  109
 Blocking:|
--+---
Changes (by dconnolly):

 * milestone:  morning-star = bariatric-study-data


Comment:

 prompted by mention of labs in the bariatric study survey (#278) I noticed
 that our i2b2 representation of CDM2 has terms/concepts such as
 RESULT_DATE that belong elsewhere in the i2b2 data model.

 [https://bitbucket.org/gpcnetwork/pcornet-
 dm/commits/4e9d3f0fbde61b15b78e47ce7910469a8a7051d8 4e9d3f0]

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[gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

[GPC Informatics]

#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+--
  Reporter:  dconnolly |  Owner:  dconnolly
  Type:  design-issue  | Status:  new
  Priority:  minor |  Milestone:  morning-star
 Component:  data-stds |   Keywords:
Blocked By:  109   |   Blocking:
---+--
 separating 2.x work out to reduce scope of #109

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