Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
---+--
 Reporter:  rwaitman   |   Owner:  ngraham
 Type:  enhancement|  Status:  closed
 Priority:  major  |   Milestone:  drn-basic-query
Component:  data-sharing   |  Resolution:  fixed
 Keywords: |  Blocked By:  89
 Blocking:  145, 146, 191  |
---+--

Comment (by dconnolly):

 In the i2b2 wiki, I recently discovered:

  -
 
[https://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common+Data+Model+Ontology+Home
 SCILHS i2b2 PCORnet Common Data Model Ontology Home]

   What does the ontology cover?

   Demographics: Similar to the i2b2demodata, with a more granular age tree
 to support pediatric age queries.
   Diagnoses: Includes ICD-10 2014AA and ICD-9 2014AA, generated by Lori
 Phillips from ontologies on BioPortal.
   Procedures: Includes ICD-9 2014AA, Partners’ RPDR CMS-DRG tree, Beth
 Israel’s MS-DRG tree (version unknown), and Nathan Wilson’s HCPCS tree
   Encounters: Includes PCORnet-specific additions, and a tree of 3-digit
 zip codes derived from the i2b2 demo data
   Enrollment: To allow sites to specify which patients have "complete
 longitudinal data" for selected date ranges.
   Vitals: A simple vitals implementation including height, weight, and
 blood pressure.

 Here's hoping for time to upload i2b2_PCORNET_CDM_v152.zip into babel.

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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
---+--
 Reporter:  rwaitman   |   Owner:  ngraham
 Type:  enhancement|  Status:  assigned
 Priority:  major  |   Milestone:  drn-basic-query
Component:  data-sharing   |  Resolution:
 Keywords: |  Blocked By:  89, 182
 Blocking:  145, 146, 191  |
---+--

Comment (by dconnolly):

 Replying to [comment:10 dconnolly]:
 > Next up: fill in the terminology stubs such as ICD9 using Jeff's work
 and/or other work based on UMLS.

 for current approach, see `Augment the PCORI terms with GPC sub-trees
 (ICD9 from UMLS, etc)` in [https://bitbucket.org/gpcnetwork/gpc-pcornet-
 cdm/src/tip/pcori_to_gpc.sql pcori_to_gpc.sql] (developed as part of
 #145).

--
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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
---+--
 Reporter:  rwaitman   |   Owner:  ngraham
 Type:  enhancement|  Status:  closed
 Priority:  major  |   Milestone:  drn-basic-query
Component:  data-sharing   |  Resolution:  fixed
 Keywords: |  Blocked By:  89
 Blocking:  145, 146, 191  |
---+--
Changes (by dconnolly):

 * status:  assigned => closed
 * resolution:   => fixed
 * blockedby:  89, 182 => 89


Comment:

 Finally found time to address the c_columndatatype='T' issue (in
 070e087801db/pcornet-dm) and update babel (using 2fec4738bb8d/pcornet-dm,
 which is the same, modulo graft across branches).

 As a consequence, babel reflects work on CDM 2.x. I hope that doesn't
 introduce much confusion. Our target for milestone:drn-basic-query remains
 CDM 1.x.

--
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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
---+--
 Reporter:  rwaitman   |   Owner:  ngraham
 Type:  enhancement|  Status:  assigned
 Priority:  major  |   Milestone:  drn-basic-query
Component:  data-sharing   |  Resolution:
 Keywords: |  Blocked By:  89, 182
 Blocking:  145, 146, 191  |
---+--
Changes (by dconnolly):

 * owner:  dconnolly => ngraham
 * status:  accepted => assigned


Comment:

 Nathan, I found this while going 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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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  accepted
 Priority:  major |   Milestone:  data-domains2
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89, 182
 Blocking:  145, 146  |
--+

Comment (by dconnolly):

 I managed to scrape the CDM 2.x spec today

 [https://bitbucket.org/DanC/pcornet-
 dm/commits/b14948170b242fa5c6e9c9d9b1b834ed8022ac33 b14948170b24/pcornet-
 dm]

 It's not quite in the form that I need for generating i2b2 metadata, so I
 haven't merged this `cdm2x` branch.

--
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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  accepted
 Priority:  major |   Milestone:  data-domains2
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89, 182
 Blocking:  145, 146  |
--+
Changes (by dconnolly):

 * blockedby:  89 => 89, 182


Comment:

 Hubert, it looks like the new LOINC codes (#182) impact the representation
 of CDM in i2b2.

 I wonder how we'll integrate this with the [https://bitbucket.org/DanC
 /pcornet-dm pcornet-dm scripts] that generate our CDM metadata. Do you
 plan to update the scripts?

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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  accepted
 Priority:  major |   Milestone:  data-domains2
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89
 Blocking:  145, 146  |
--+
Changes (by dconnolly):

 * status:  assigned => accepted


Comment:

 started looking at v2.0...

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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  assigned
 Priority:  major |   Milestone:  data-domains2
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89
 Blocking:  145, 146  |
--+

Comment (by dconnolly):

 Here's hoping for time to update [https://bitbucket.org/DanC/pcornet-dm
 pcornet-dm] w.r.t. v2.0. Bonus points to anyone who beats me to it:

  - [http://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000638.html PCORnet
 CDM v2.0 - Draft for Review and Feedback]

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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  assigned
 Priority:  major |   Milestone:  data-domains2
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89
 Blocking:  145, 146  |
--+
Changes (by dconnolly):

 * owner:  ngraham => dconnolly


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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+---
 Reporter:  rwaitman  |   Owner:  ngraham
 Type:  enhancement   |  Status:  assigned
 Priority:  major |   Milestone:  initial-data-domains
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89
 Blocking:  145, 146  |
--+---
Changes (by dconnolly):

 * owner:  dconnolly => ngraham
 * status:  accepted => assigned


Comment:

 Nathan and I started loading the SCILHS stuff (Version 1.4 - 8/19/14) in
 hopes of double-checking that we're in sync, but we didn't finish.

 Nathan, over to you; let me know when you've done the next bit.

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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[Klann, Jeffrey G.]

Dan, if you want to do some verification on your side, all the terms that
originally came from your code have sourcesystem_cd=³PCORNET_CDM². I do
wonder if something in the vitals ontology changed to get the hierarchy we
wanted, so it is worth a look.
 
Jeff Klann


On 9/8/14, 7:36 PM, "GPC Informatics"  wrote:

>#109: represent PCORI CDM terminology as i2b2 metadata
>--+---
> Reporter:  rwaitman  |   Owner:  dconnolly
> Type:  enhancement   |  Status:  accepted
> Priority:  major |   Milestone:  initial-data-domains
>Component:  data-sharing  |  Resolution:
> Keywords:|  Blocked By:  89
> Blocking:  145, 146  |
>--+---
>
>Comment (by dconnolly):
>
> Russ forwarded me an update from Jeff Klann Monday, September 08, 2014
> 2:49 PM. I haven't managed to take a close look, though he says:
>
> > It is based on Dan¹s code to generate the core ontology, and I¹ve been
> careful not to change the paths (C_FULLNAME). So any transform that uses
> the path names will work at SCILHS also.
>
>--
>Ticket URL: 
>
>gpc-informatics 
>Greater Plains Network - Informatics



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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+---
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  accepted
 Priority:  major |   Milestone:  initial-data-domains
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89
 Blocking:  145, 146  |
--+---

Comment (by dconnolly):

 Russ forwarded me an update from Jeff Klann Monday, September 08, 2014
 2:49 PM. I haven't managed to take a close look, though he says:

 > It is based on Dan’s code to generate the core ontology, and I’ve been
 careful not to change the paths (C_FULLNAME). So any transform that uses
 the path names will work at SCILHS also.

--
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Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata (was: mapping to PCORI CDM (aka mini-sentinel data model))

[GPC Informatics]

#109: represent PCORI CDM terminology as i2b2 metadata
--+---
 Reporter:  rwaitman  |   Owner:  dconnolly
 Type:  enhancement   |  Status:  accepted
 Priority:  major |   Milestone:  initial-data-domains
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  89
 Blocking:  145, 146  |
--+---
Changes (by dconnolly):

 * cc: mhoag, ngraham, campbell, hhickman (removed)
 * cc: gpc-dev@… (added)
 * blocking:  145 => 145, 146


Comment:

 reducing scope of this ticket; see #145, #146 for other parts.

 "approximate a popmednet query by an i2b2 query" should probably be its
 own ticket too, but until we have an example query (#143) it's hardly
 worth the bother.

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