Opened 4 years ago

Last modified 23 months ago

#2138 accepted design-issue

use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?)

Reported by: dconnolly Owned by: dconnolly
Priority: major Milestone: heron-butternut-update
Component: data-repository Keywords: terminology-evolution technical-debt public-web
Cc: mhoag, ngraham, bzschoche Blocked By:
Blocking: 26, 1844, 3757 Sensitive: no

Description

affects work such as #26, #1843

we have CPT2012 from UMLS loaded; see #1896 for details

Change History (42)

comment:1 Changed 4 years ago by dconnolly

  • Keywords terminology-evolution added

comment:2 Changed 4 years ago by mhoag

  • Milestone changed from heron-crooked-creek-update to heron-solomon-update

comment:3 Changed 4 years ago by ngraham

  • Milestone changed from heron-solomon-update to heron-toronto-update

comment:4 Changed 3 years ago by ngraham

  • Milestone changed from heron-saline-update to heron-verdigris-update
  • Priority changed from minor to major

this blocks GPC:ticket:160. I'd like to talk about scheduling, perhaps in the heron-weekly meeting.

comment:5 Changed 3 years ago by dconnolly

  • Keywords heron-weekly added

comment:6 Changed 3 years ago by ngraham

  • Owner changed from mhoag to dconnolly
  • Status changed from new to assigned

We hope to leverage work by Hubert/GPC work.

comment:7 Changed 3 years ago by ngraham

  • Status changed from assigned to waiting

comment:8 Changed 3 years ago by dconnolly

  • Keywords heron-weekly removed

Batch update from file heron-weekly-8Oct-done.xls

comment:9 Changed 3 years ago by dconnolly

  • Keywords public-web added

comment:10 Changed 3 years ago by dconnolly

  • Milestone changed from heron-verdigris-update to heron-kanopolis-update

postponing tickets other than those identified as Verdigris priorities in today's heron-weekly meeting

comment:11 Changed 3 years ago by ngraham

  • Milestone changed from heron-kanopolis-update to heron-webster-update

in heron-weekly
RW: Let's put this a couple months down the road.
DC: A good chance that this will get fixed by GPC-related work.

comment:12 Changed 3 years ago by dconnolly

  • Milestone changed from heron-webster-update to heron-mcmillan-marsh-update

comment:13 Changed 3 years ago by ngraham

  • Blocking changed from 26, 1844 to 26, 1844, 3310

comment:14 follow-up: Changed 3 years ago by dconnolly

  • Milestone changed from heron-mcmillan-marsh-update to heron-cheyenne-bottoms-update

GPC hasn't made as much progress as I'd hoped back in mid-Jan (comment:11). I just created GPC:ticket:243 to kick off the design discussion.

Meanwhile, I don't see bandwidth to complete this in the current release.

comment:15 in reply to: ↑ 14 Changed 3 years ago by mhoag

  • Blocking changed from 26, 1844, 3310 to 26, 1844

Replying to dconnolly:

GPC hasn't made as much progress as I'd hoped back in mid-Jan (comment:11). I just created GPC:ticket:243 to kick off the design discussion.

Meanwhile, I don't see bandwidth to complete this in the current release.

Based on the above, this ticket should not be blocking "Load Concepts and Prepare for Testing" for milestone:heron-mcmillan-marsh-update.

comment:16 Changed 2 years ago by ngraham

  • Blocking changed from 26, 1844 to 26, 1844, 3395

comment:17 Changed 2 years ago by dconnolly

  • Keywords heron-weekly added

gpc discussion around this is heating up

comment:18 follow-up: Changed 2 years ago by dconnolly

  • Keywords heron-weekly removed
  • Status changed from waiting to assigned

Dan to talk to Russ about bumping one of the other release goals for this, to get us sync'd with GPC discussion.

comment:19 Changed 2 years ago by dconnolly

  • Status changed from assigned to accepted

comment:20 in reply to: ↑ 18 ; follow-up: Changed 2 years ago by ngraham

  • Keywords heron-weekly added

Replying to dconnolly:

Dan to talk to Russ about bumping one of the other release goals for this, to get us sync'd with GPC discussion.

I'm interested to know if we still plan on including this in milestone:heron-cheyenne-bottoms-update release. I suppose we didn't identify it as a high-level goal in milestone summary.

comment:21 in reply to: ↑ 20 Changed 2 years ago by dconnolly

  • Keywords heron-weekly removed
  • Milestone changed from heron-cheyenne-bottoms-update to heron-quivira-update

Replying to ngraham:

Replying to dconnolly:

Dan to talk to Russ about bumping one of the other release goals for this, to get us sync'd with GPC discussion.

I brought it up in the monthly MI meeting on Monday, basically saying "I wish we could do this soon, but we clearly can't due to the clarity 2014 stuff."

I'm interested to know if we still plan on including this in milestone:heron-cheyenne-bottoms-update release.

Nope.

comment:22 Changed 2 years ago by dconnolly

  • Blocking changed from 26, 1844, 3395 to 26, 1844
  • Status changed from accepted to assigned

comment:23 Changed 2 years ago by ngraham

  • Blocking changed from 26, 1844 to 26, 1844, 3470

comment:24 Changed 2 years ago by dconnolly

Angela walked us (Nathan and me) through UTHSCSA's code to get LOINC, CPT, and HCPCS from UMLS

  • heron_staging/umls/UMLS_MMSYS.txt
  • heron_load/umls_lab_concepts.sql

Yes, the "shape" of the lab hierarchy it creates is the same as the shape we're getting via staging with that bit of Java code (#2947).

I wonder what it would take to merge their code... actually using hg merge would probably bring in too much UTHSCSA-specific history, but hg graft might work... there were some conflicts to resolve manually, but we ended up with 66422284a26e on the umls_proc_lab_2138 branch.

Next up: try a test build and see...

comment:25 Changed 2 years ago by dconnolly

comment:26 Changed 2 years ago by dconnolly

  • Blocking changed from 26, 1844, 3470 to 26, 1844, 3468, 3470

This actually impacts staging as well as concept loading.

comment:27 Changed 2 years ago by dconnolly

  • Blocked By set to 1896

comment:28 Changed 2 years ago by dconnolly

  • Blocking changed from 26, 1844, 3468, 3470 to 26, 1844
  • Milestone changed from heron-quivira-update to heron-jamestown-update

heron-weekly:

Grafting the UTHSCSA_umls didn't work out so well (more details in GPC:ticket:286).

Maybe next time?

comment:29 Changed 2 years ago by dconnolly

  • Milestone changed from heron-jamestown-update to heron-calhoun-update

scheduled for delivery in July in HeronProjectTimeline#May2015Planning

I'm not sure what to do next, so I requested a meeting for June 3.

comment:30 Changed 2 years ago by ngraham

  • Blocking changed from 26, 1844 to 26, 1844, 3593

Dan,

I see progress in GPC:ticket:286. Still planning on Calhoun? Adding to critical path for Calhoun for now.

comment:31 Changed 2 years ago by ngraham

  • Blocking changed from 26, 1844, 3593 to 26, 1844
  • Milestone changed from heron-calhoun-update to heron-riverwalk-update

heron-weekly:
DC: Propose to postpone.

comment:32 Changed 2 years ago by dconnolly

  • Status changed from assigned to accepted

I suppose loading the SCILHS CDRN CDM ontology (GPC:ticket:191) would help with this.

comment:33 Changed 2 years ago by mhoag

  • Blocking changed from 26, 1844 to 26, 1844, 3677

comment:34 Changed 2 years ago by ngraham

  • Blocking changed from 26, 1844, 3677 to 26, 1844
  • Milestone changed from heron-riverwalk-update to heron-ray-hubbard-update

heron-weekly:
DC: Making progress, but postpone delivery.

cf. scilhs_cdm_prep job

comment:35 Changed 2 years ago by dconnolly

comment:36 Changed 2 years ago by dconnolly

  • Blocking changed from 26, 1844 to 26, 1844, 3733

comment:37 Changed 2 years ago by dconnolly

  • Keywords heron-weekly added

not sure where this fits...

comment:38 Changed 2 years ago by dconnolly

  • Blocking changed from 26, 1844, 3733 to 26, 1844
  • Milestone changed from heron-ray-hubbard-update to heron-michigan-update

scheduled for Oct (Michigan) in HeronProjectTimeline#August2015Planning

comment:39 Changed 2 years ago by dconnolly

  • Keywords heron-weekly removed

comment:40 Changed 2 years ago by dconnolly

  • Milestone changed from heron-michigan-update to heron-butternut-update

heron-weekly:
DC: I'm overcommitted; bariatric study depends on CDM v3 which depends on this
BZ: study is on hold pending PCORI contracting streamlining
DC: and next month is technical-debt, so... Butternut/Dec?

comment:41 Changed 2 years ago by dconnolly

  • Blocking changed from 26, 1844 to 26, 1844, 3757
  • Cc bzschoche added

comment:42 Changed 23 months ago by tmcmahon

  • Blocked By 1896 deleted
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