Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  bos
 Type:  enhancement  |  Status:  closed
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:  fixed
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+
Changes (by dconnolly):

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


Comment:

 Reeder's recent update seems to meet all the relevant requirements.

 The only difference from the style of paths from May 18 (comment:43) is
 the initial segment: '\GPC\Laboratory
 Tests\LP31755-9\LP14559-6\LP98185-9\LP14082-9\LP52260-4\'.

 Details (in the style of ticket:78#comment:22):

 ||c_hlevel  ||terms ||path_hash
 ||1 ||1 ||-1697094263
 ||2 ||26||-2809956948
 ||3 ||615   ||1328792910
 ||4 ||5516  ||69848410663
 ||5 ||13742 ||!294847666072
 ||6 ||20088 ||-!214533032734
 ||7 ||14685 ||18805153376
 ||8 ||11652 ||!269089353645
 ||9 ||8258  ||92487708673
 ||10||4332  ||43426607284
 ||11||1055  ||18753800857
 ||12||344   ||-13514181462
 ||13||110   ||9607735669
 ||14||31||-5568709772
 ||15||10||-5365237420
 ||16||7 ||48254689
 ||17||2 ||438915986

 The ontology is available on babel as well as:
- [https://pcornet.imeetcentral.com/c4gpc/file/42713413/ GPC_TERMS.zip]
 file on Central Desktop
  - 23 Oct revision md5sum: `e25453eebc08f9d823de67570a126b5f`

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  bos
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+
Changes (by dconnolly):

 * owner:  Aaron.Meyer => bos


Comment:

 Thanks for the updated flat file and code, Nate.

 Meanwhile, the technique of going straight from UMLS tables is more in
 line with other HERON code, so I worked with Angela a bit on that (#286).
 Unfortunately, the code at KUMC and San Antonio has diverged so much that
 reconciling them is quite a pain.

 Also, the UMLS approach currently ends up with those AUI-based paths with
 loinc codes only at the end. We talked about what it would take to
 reproduce paths such as
 `\i2b2\LOINC\LP31755-9\LP14559-6\LP98185-9\LP14082-9\LP52260-4\`; at the
 time, I wasn't inclined to bother, but I think I have changed my mind:
 AUI-based paths introduce an artificial dependency on UMLS mechanisms;
 there's no reason to rule out the approach that depends only on the flat
 file from the LOINC site.

 Angela, here's hoping you get around to adapting the UTHSCSA_umls branch
 to build this sort of code before I do.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  Aaron.Meyer
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+

Comment (by nateapathy):

 That's correct, and I think appropriate for the scope of this ticket.
 Cerner doesn't map clinical terms to LOINC; those are most often captured
 with SNOMED codes due to LOINC's limited non-lab application among our
 clients. LOINC is almost always limited to lab-only tests, and does not
 extend to other components of the chart. For example, we wouldn't ever see
 age ranges (as we've discussed with GPC-Dev before) coded to LOINC in a
 Cerner database. That mapping is do-able in i2b2, but falls outside the
 scope of what this ticket is looking for.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  Aaron.Meyer
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+

Comment (by campbell):

 Replying to [comment:20 nateapathy]:
 > I've created some [http://goo.gl/h7cTN8 slides] for review and a Google
 Doc for [http://goo.gl/QL6mrW notes] during this Hackathon session. And
 uploaded our [https://pcornet.centraldesktop.com/c4gpc/file/36891223/ JAVA
 transformation code] to the Central Desktop

 Nate
 Nebraska needs to install LOINC 2.50 to bring us up with current LOINC
 codes in CDM V2.  It appears from the csv files you attached that your
 JAVA code only extracts Lab LOINC and ignores Clinical?
 Jim

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  Aaron.Meyer
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+

Comment (by nateapathy):

 I suppose that would be valuable - it's on Central Desktop now
 [https://pcornet.centraldesktop.com/c4gpc/file/40253392/ here]. I also put
 the old LOINC files in an Archive folder within the CMH folder to avoid
 confusion.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  Aaron.Meyer
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+

Comment (by dconnolly):

 How about updated Java code?

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  Aaron.Meyer
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+

Comment (by nateapathy):

 Here's the updated document to include codes in the term paths. The csv
 file is posted on Central Desktop in the CMH folder
 [https://pcornet.centraldesktop.com/c4gpc/file/40238135/ here].

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  Aaron.Meyer
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+
Changes (by dconnolly):

 * owner:  dconnolly => Aaron.Meyer
 * status:  accepted => assigned


Comment:

 Aaron offered to update the paths to include LOINC codes.

 Aaron, the updated Java code is what I'm most interested in, since that's
 how we'd update to new versions of LOINC. I suppose others prefer to just
 get the resulting flat file. So delivering both would be best.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  dconnolly
 Type:  enhancement  |  Status:  accepted
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241, 285 |
-+

Comment (by ngraham):

 One thing we ran in to when implementing at KUMC is that there seem to be
 terms that don't have parents.  I don't know that i2b2 cares (other than I
 think the terms won't show up) but some our ETL code that counts
 patients/facts makes sure that every term has parents.  We filled in the
 missing parents for our production release.

 An example path that I think is an orphan:
 {{{
 \i2b2\Laboratory Tests\Microbiology\Microorganism\Bacteria\Yersinia
 sp\Yersinia pestis\Yersinia pestis Ab\Yersinia pestis Ab | Bld-Ser-Plas\Y
 pestis AbTitr Ser EIA\
 }}}

 I found 63 missing parents using attachment:missing_parents.py run against
 the .dsv from comment:34.  Maybe this isn't something that needs
 addressed, but I wanted to document what we found in case someone else
 runs in to it.

 Also, it seems that the CDT file linked in comment:34 only has 48,943 rows
 rather than the 71,000 noted in comment:34.  Maybe I'm looking at the
 wrong file?
 {{{
 wc -l GPC_LOINC_HIERARCHY.dsv
 48943 GPC_LOINC_HIERARCHY.dsv
 ...
 md5sum ./GPC_LOINC_HIERARCHY.dsv
 9d07adf37a04efe319324a36dcc48e12 *./GPC_LOINC_HIERARCHY.dsv
 }}}

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  dconnolly
 Type:  enhancement  |  Status:  accepted
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  241  |
-+

Comment (by nateapathy):

 I added the raw ontology table in pipe-delimited format to the Central
 Desktop [https://pcornet.centraldesktop.com/c4gpc/file/39991117/ here].

 This is the raw unedited LOINC hierarchy that serves as the base for CMH
 and MU. It is in a pipe-delimited format and should include over 71,000
 rows of LOINC metadata. All C_VISUALATTRIBUTES have been set to "%A" for
 active rather than hidden, and all C_TOTALNUM values have been set to 0.
 Our implementation counts the unique patients for each level of the
 hierarchy (folder and leaf), and adds that number to the C_TOTALNUM field.
 If that number is 0, the C_VISUALATTRIBUTES are changed to "%H" to hide
 the term. This way, we can support queries with terms that have no data in
 our database rather than returning any sort of error.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  dconnolly
 Type:  enhancement  |  Status:  accepted
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by schandaka):

 Adding my experiences from trying to implement this work at KUMC (in
 addition to Dan's comments above).
 - [https://pcornet.centraldesktop.com/c4gpc/file/36891223/ JAVA
 transformation code] is generating null c_fullnames.
 - There are missing trailing '\' in the paths.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  dconnolly
 Type:  enhancement  |  Status:  accepted
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by dconnolly):

 In reviewing work on this at KUMC, I discovered there are no LOINC codes
 in the paths.

 Experience mapping diagnoses to CDM showed that makes life difficult. But
 perhaps relying on `c_basecode` is the cost-effective thing to do at this
 point. I'm still mulling it over.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  dconnolly
 Type:  enhancement  |  Status:  accepted
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

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


Comment:

 KUMC to report experience with Jan 19 design (comment:20)

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by schandaka):

 Replying to [comment:26 dconnolly]:
 > Hubert, is that consistent with HackathonTwo design decisions?

 Dan, I spoke to Hubert. He said that UNMC's design is not consistent with
 HackathonTwo design decissions. As he mentioned in comment:25,
 Drs.Campbell(Jim and Scott) have put together their hierarchy.

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RE: [gpc-informatics] #158: usable view of LOINC lab terms

[Dan Connolly]

Jim and everybody who is interested in a copy...

The ​JAVA transformation 
code<https://pcornet.centraldesktop.com/c4gpc/file/36891223/> on Central 
Desktop was linked from a Jan 19 comment on 
#158<https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20>.

Nate, I'm still interested in clarification on licensing.

--
Dan


From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on 
behalf of Campbell, James R [campb...@unmc.edu]
Sent: Friday, March 27, 2015 11:53 PM
To: ; Apathy Nate
Cc: Campbell, Walter S
Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms

Nate
So, if I understand, you had calculated or developed metadataxml for all the 
entries in the GPC lab metadata? Wow, I did not understand that from Hackathon2 
and we would love to get a copy of your java code to supplement our metadata 
browsing tools. Did you develop a java-based computation of metadataxml from 
the LOINC release record? We have considered that but have not had time.
I thought we might be providing an enhancement to your metadata build but I 
agree entirely that it seems irrelevant.
Jim

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Mar 27, 2015, at 1:11 PM, "GPC Informatics"  wrote:
>
> #158: usable view of LOINC lab terms
> -+
> Reporter: rwaitman | Owner: nateapathy
> Type: enhancement | Status: assigned
> Priority: major | Milestone: data-domains3
> Component: data-stds | Resolution:
> Keywords: | Blocked By:
> Blocking: |
> -+
>
> Comment (by nateapathy):
>
> We reviewed the metadata included in the UNMC LOINC hierarchy and found
> 922 with metadata XML applied. We compared those leaf terms to our current
> hierarchy and found 622 that overlapped with the 71,000+ terms that are in
> our base hierarchy (the majority of which is hidden on Babel). All of our
> metadata XML matched the data you had for yours, only with a few semantic
> differences in naming conventions for tests within the metadata panel.
>
> Since there is not a major material difference between these two sets of
> metadata, I'm inclined to direct the group to the information I shared in
> [https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20
> comment20] on this thread. That comment includes a link to the base
> multiaxial hierarchy from Regenstrief and the Java code we use to
> transform that into our base LOINC hierarchy that was agreed upon as the
> GPC hierarchy during Hackathon II.
>
> Let me know if there are any next steps or additional questions we need to
> answer or clarify before we can close this ticket.
>
> --
> Ticket URL: 
> <http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28>
> gpc-informatics <http://informatics.gpcnetwork.org/>
> Greater Plains Network - Informatics

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[Phillip Reeder]

I'm interested.

Phillip

Sent from my iPhone

> On Mar 31, 2015, at 8:25 AM, Apathy,Nate  wrote:
>
> Hi Jim,
>
> Yes, that's correct. We have a conversion table that holds the necessary 
> conversions from local units to the standard units as dictated by the 
> metadataxml and LOINC. Happy to discuss as well - I'll send another note off 
> this chain to organize that unless it would be valuable to discuss on the Dev 
> call.
>
> The March QA is next on our priority list, and after that we will be able to 
> work on the SNOMED test. I don't anticipate starting on that work until next 
> week at the earliest.
>
> Thanks,
>
> Nate Apathy
> Solution Manager: i2b2 | nate.apa...@cerner.com | 816.201.2785
>
> -Original Message-
> From: Campbell, James R [mailto:campb...@unmc.edu]
> Sent: Monday, March 30, 2015 11:09 PM
> To: Apathy,Nate
> Cc: ; Hickman, Hubert B; Campbell, Walter S; 
> Munns, Michael B
> Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms
>
> Nate
> Yes, I am referring to metadata agreed from H2.  When we rolled out 
> metadataxml, we had to tweak some units but I matched those reported in our 
> i2b2 to UCUM reference and tailored to our lab reports.  Are you saying that 
> you are comparing Regenstrief to local us=nits and compiling a lexicon of 
> conversions into the metadataxml?  I would be interested to discuss by call 
> at your convenience
>
> ETA for SNOMED test load?
> Jim
>
> James R. Campbell MD
> campb...@unmc.edu
> Office: 402-559-7505
> Secretary: 402-559-7299
> Pager: 402-888-1230
>
>> On Mar 30, 2015, at 4:03 PM, "Apathy,Nate"  wrote:
>>
>> Hi Jim,
>>
>> Can you clarify what you mean by the "GPC lab metadata"? Are you referring 
>> to the CMH: LOINC hierarchy on Babel that we decided upon during Hackathon 
>> II? We are working on a project now to normalize our units, as coded LOINC 
>> is a poor predictor of the actual units used in the lab setting for those 
>> tests. We haven't developed a script to build metadataxml; rather we have a 
>> reference table with 27,864 LOINC codes and their associated metadataxml per 
>> the LOINC standard units in the multiaxial hierarchy. We do a lookup on that 
>> table to pull the metadata in to our client lab ontologies, but as you can 
>> probably surmise by now we ran in to a lot of issues initially with 
>> mismatched units that made the metadataxml basically useless unless the 
>> units matched exactly. That is what precipitated the unit normalization 
>> project. There are several upstream data source issues that depend on other 
>> teams and need to take place before that project can be completed, so we are 
>> targeting the creation of 
 t
> hat curated LOINC ontology with standard units by the end of April.
>>
>> Thanks,
>>
>> Nate Apathy
>> Solution Manager: i2b2 | nate.apa...@cerner.com | 816.201.2785
>>
>> -Original Message-
>> From: Campbell, James R [mailto:campb...@unmc.edu]
>> Sent: Friday, March 27, 2015 11:54 PM
>> To: ; Apathy,Nate
>> Cc: Hickman, Hubert B; Campbell, Walter S; Munns, Michael B
>> Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms
>>
>> Nate
>> So, if I understand, you had calculated or developed metadataxml for all the 
>> entries in the GPC lab metadata?  Wow, I did not understand that from 
>> Hackathon2 and we would love to get a copy of your java code to supplement 
>> our metadata browsing tools.  Did you develop a java-based computation of 
>> metadataxml from the LOINC release record?  We have considered that but have 
>> not had time.
>> I thought we might be providing an enhancement to your metadata build but I 
>> agree entirely that it seems irrelevant.
>> Jim
>>
>> James R. Campbell MD
>> campb...@unmc.edu
>> Office: 402-559-7505
>> Secretary: 402-559-7299
>> Pager: 402-888-1230
>>
>>> On Mar 27, 2015, at 1:11 PM, "GPC Informatics"  wrote:
>>>
>>> #158: usable view of LOINC lab terms
>>> -+
>>> Reporter:  rwaitman |   Owner:  nateapathy
>>>   Type:  enhancement  |  Status:  assigned
>>> Priority:  major|   Milestone:  data-domains3
>>> Component:  data-stds|  Resolution:
>>> Keywords:   |  Blocked By:
>>> Blocking:   |
>>> -+
>>>
>>> Comment (by nateapathy):
>>>
>>> We reviewed the met

RE: [gpc-informatics] #158: usable view of LOINC lab terms

[Apathy,Nate]

Hi Jim,

Yes, that's correct. We have a conversion table that holds the necessary 
conversions from local units to the standard units as dictated by the 
metadataxml and LOINC. Happy to discuss as well - I'll send another note off 
this chain to organize that unless it would be valuable to discuss on the Dev 
call.

The March QA is next on our priority list, and after that we will be able to 
work on the SNOMED test. I don't anticipate starting on that work until next 
week at the earliest.

Thanks,

Nate Apathy
Solution Manager: i2b2 | nate.apa...@cerner.com | 816.201.2785

-Original Message-
From: Campbell, James R [mailto:campb...@unmc.edu] 
Sent: Monday, March 30, 2015 11:09 PM
To: Apathy,Nate
Cc: ; Hickman, Hubert B; Campbell, Walter S; Munns, 
Michael B
Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms

Nate
Yes, I am referring to metadata agreed from H2.  When we rolled out 
metadataxml, we had to tweak some units but I matched those reported in our 
i2b2 to UCUM reference and tailored to our lab reports.  Are you saying that 
you are comparing Regenstrief to local us=nits and compiling a lexicon of 
conversions into the metadataxml?  I would be interested to discuss by call at 
your convenience

ETA for SNOMED test load?
Jim  

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Mar 30, 2015, at 4:03 PM, "Apathy,Nate"  wrote:
> 
> Hi Jim,
> 
> Can you clarify what you mean by the "GPC lab metadata"? Are you referring to 
> the CMH: LOINC hierarchy on Babel that we decided upon during Hackathon II? 
> We are working on a project now to normalize our units, as coded LOINC is a 
> poor predictor of the actual units used in the lab setting for those tests. 
> We haven't developed a script to build metadataxml; rather we have a 
> reference table with 27,864 LOINC codes and their associated metadataxml per 
> the LOINC standard units in the multiaxial hierarchy. We do a lookup on that 
> table to pull the metadata in to our client lab ontologies, but as you can 
> probably surmise by now we ran in to a lot of issues initially with 
> mismatched units that made the metadataxml basically useless unless the units 
> matched exactly. That is what precipitated the unit normalization project. 
> There are several upstream data source issues that depend on other teams and 
> need to take place before that project can be completed, so we are targeting 
> the creation of t
 hat curated LOINC ontology with standard units by the end of April.
> 
> Thanks,
> 
> Nate Apathy
> Solution Manager: i2b2 | nate.apa...@cerner.com | 816.201.2785
> 
> -Original Message-
> From: Campbell, James R [mailto:campb...@unmc.edu]
> Sent: Friday, March 27, 2015 11:54 PM
> To: ; Apathy,Nate
> Cc: Hickman, Hubert B; Campbell, Walter S; Munns, Michael B
> Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms
> 
> Nate
> So, if I understand, you had calculated or developed metadataxml for all the 
> entries in the GPC lab metadata?  Wow, I did not understand that from 
> Hackathon2 and we would love to get a copy of your java code to supplement 
> our metadata browsing tools.  Did you develop a java-based computation of 
> metadataxml from the LOINC release record?  We have considered that but have 
> not had time.
> I thought we might be providing an enhancement to your metadata build but I 
> agree entirely that it seems irrelevant.
> Jim
> 
> James R. Campbell MD
> campb...@unmc.edu
> Office: 402-559-7505
> Secretary: 402-559-7299
> Pager: 402-888-1230
> 
>> On Mar 27, 2015, at 1:11 PM, "GPC Informatics"  wrote:
>> 
>> #158: usable view of LOINC lab terms
>> -+
>> Reporter:  rwaitman |   Owner:  nateapathy
>>Type:  enhancement  |  Status:  assigned
>> Priority:  major|   Milestone:  data-domains3
>> Component:  data-stds|  Resolution:
>> Keywords:   |  Blocked By:
>> Blocking:   |
>> -+
>> 
>> Comment (by nateapathy):
>> 
>> We reviewed the metadata included in the UNMC LOINC hierarchy and 
>> found
>> 922 with metadata XML applied. We compared those leaf terms to our 
>> current hierarchy and found 622 that overlapped with the 71,000+ 
>> terms that are in our base hierarchy (the majority of which is hidden 
>> on Babel). All of our metadata XML matched the data you had for 
>> yours, only with a few semantic differences in naming conventions for tests 
>> within the metadata panel.
>> 
>> Since there is not a major material difference betw

Re: [gpc-informatics] #158: usable view of LOINC lab terms

[Campbell, James R]

Nate
Yes, I am referring to metadata agreed from H2.  When we rolled out 
metadataxml, we had to tweak some units but I matched those reported in our 
i2b2 to UCUM reference and tailored to our lab reports.  Are you saying that 
you are comparing Regenstrief to local us=nits and compiling a lexicon of 
conversions into the metadataxml?  I would be interested to discuss by call at 
your convenience

ETA for SNOMED test load?
Jim  

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Mar 30, 2015, at 4:03 PM, "Apathy,Nate"  wrote:
> 
> Hi Jim,
> 
> Can you clarify what you mean by the "GPC lab metadata"? Are you referring to 
> the CMH: LOINC hierarchy on Babel that we decided upon during Hackathon II? 
> We are working on a project now to normalize our units, as coded LOINC is a 
> poor predictor of the actual units used in the lab setting for those tests. 
> We haven't developed a script to build metadataxml; rather we have a 
> reference table with 27,864 LOINC codes and their associated metadataxml per 
> the LOINC standard units in the multiaxial hierarchy. We do a lookup on that 
> table to pull the metadata in to our client lab ontologies, but as you can 
> probably surmise by now we ran in to a lot of issues initially with 
> mismatched units that made the metadataxml basically useless unless the units 
> matched exactly. That is what precipitated the unit normalization project. 
> There are several upstream data source issues that depend on other teams and 
> need to take place before that project can be completed, so we are targeting 
> the creation of t
 hat curated LOINC ontology with standard units by the end of April.
> 
> Thanks,
> 
> Nate Apathy
> Solution Manager: i2b2 | nate.apa...@cerner.com | 816.201.2785
> 
> -Original Message-
> From: Campbell, James R [mailto:campb...@unmc.edu] 
> Sent: Friday, March 27, 2015 11:54 PM
> To: ; Apathy,Nate
> Cc: Hickman, Hubert B; Campbell, Walter S; Munns, Michael B
> Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms
> 
> Nate
> So, if I understand, you had calculated or developed metadataxml for all the 
> entries in the GPC lab metadata?  Wow, I did not understand that from 
> Hackathon2 and we would love to get a copy of your java code to supplement 
> our metadata browsing tools.  Did you develop a java-based computation of 
> metadataxml from the LOINC release record?  We have considered that but have 
> not had time.
> I thought we might be providing an enhancement to your metadata build but I 
> agree entirely that it seems irrelevant.
> Jim
> 
> James R. Campbell MD
> campb...@unmc.edu
> Office: 402-559-7505
> Secretary: 402-559-7299
> Pager: 402-888-1230
> 
>> On Mar 27, 2015, at 1:11 PM, "GPC Informatics"  wrote:
>> 
>> #158: usable view of LOINC lab terms
>> -+
>> Reporter:  rwaitman |   Owner:  nateapathy
>>Type:  enhancement  |  Status:  assigned
>> Priority:  major|   Milestone:  data-domains3
>> Component:  data-stds|  Resolution:
>> Keywords:   |  Blocked By:
>> Blocking:   |
>> -+
>> 
>> Comment (by nateapathy):
>> 
>> We reviewed the metadata included in the UNMC LOINC hierarchy and 
>> found
>> 922 with metadata XML applied. We compared those leaf terms to our 
>> current hierarchy and found 622 that overlapped with the 71,000+ terms 
>> that are in our base hierarchy (the majority of which is hidden on 
>> Babel). All of our metadata XML matched the data you had for yours, 
>> only with a few semantic differences in naming conventions for tests within 
>> the metadata panel.
>> 
>> Since there is not a major material difference between these two sets 
>> of metadata, I'm inclined to direct the group to the information I 
>> shared in
>> [https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20
>> comment20] on this thread. That comment includes a link to the base 
>> multiaxial hierarchy from Regenstrief and the Java code we use to 
>> transform that into our base LOINC hierarchy that was agreed upon as 
>> the GPC hierarchy during Hackathon II.
>> 
>> Let me know if there are any next steps or additional questions we 
>> need to answer or clarify before we can close this ticket.
>> 
>> --
>> Ticket URL: 
>> <http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Netwo

RE: [gpc-informatics] #158: usable view of LOINC lab terms

[Apathy,Nate]

Hi Jim,

Can you clarify what you mean by the "GPC lab metadata"? Are you referring to 
the CMH: LOINC hierarchy on Babel that we decided upon during Hackathon II? We 
are working on a project now to normalize our units, as coded LOINC is a poor 
predictor of the actual units used in the lab setting for those tests. We 
haven't developed a script to build metadataxml; rather we have a reference 
table with 27,864 LOINC codes and their associated metadataxml per the LOINC 
standard units in the multiaxial hierarchy. We do a lookup on that table to 
pull the metadata in to our client lab ontologies, but as you can probably 
surmise by now we ran in to a lot of issues initially with mismatched units 
that made the metadataxml basically useless unless the units matched exactly. 
That is what precipitated the unit normalization project. There are several 
upstream data source issues that depend on other teams and need to take place 
before that project can be completed, so we are targeting the creation of tha
 t curated LOINC ontology with standard units by the end of April.

Thanks,

Nate Apathy
Solution Manager: i2b2 | nate.apa...@cerner.com | 816.201.2785

-Original Message-
From: Campbell, James R [mailto:campb...@unmc.edu] 
Sent: Friday, March 27, 2015 11:54 PM
To: ; Apathy,Nate
Cc: Hickman, Hubert B; Campbell, Walter S; Munns, Michael B
Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms

Nate
So, if I understand, you had calculated or developed metadataxml for all the 
entries in the GPC lab metadata?  Wow, I did not understand that from 
Hackathon2 and we would love to get a copy of your java code to supplement our 
metadata browsing tools.  Did you develop a java-based computation of 
metadataxml from the LOINC release record?  We have considered that but have 
not had time.
I thought we might be providing an enhancement to your metadata build but I 
agree entirely that it seems irrelevant.
Jim

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Mar 27, 2015, at 1:11 PM, "GPC Informatics"  wrote:
>
> #158: usable view of LOINC lab terms
> -+
> Reporter:  rwaitman |   Owner:  nateapathy
> Type:  enhancement  |  Status:  assigned
> Priority:  major|   Milestone:  data-domains3
> Component:  data-stds|  Resolution:
> Keywords:   |  Blocked By:
> Blocking:   |
> -+
>
> Comment (by nateapathy):
>
> We reviewed the metadata included in the UNMC LOINC hierarchy and 
> found
> 922 with metadata XML applied. We compared those leaf terms to our 
> current hierarchy and found 622 that overlapped with the 71,000+ terms 
> that are in our base hierarchy (the majority of which is hidden on 
> Babel). All of our metadata XML matched the data you had for yours, 
> only with a few semantic differences in naming conventions for tests within 
> the metadata panel.
>
> Since there is not a major material difference between these two sets 
> of metadata, I'm inclined to direct the group to the information I 
> shared in
> [https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20
> comment20] on this thread. That comment includes a link to the base 
> multiaxial hierarchy from Regenstrief and the Java code we use to 
> transform that into our base LOINC hierarchy that was agreed upon as 
> the GPC hierarchy during Hackathon II.
>
> Let me know if there are any next steps or additional questions we 
> need to answer or clarify before we can close this ticket.
>
> --
> Ticket URL: 
> <http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28>
> gpc-informatics <http://informatics.gpcnetwork.org/>
> Greater Plains Network - Informatics

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[Campbell, James R]

Nate
So, if I understand, you had calculated or developed metadataxml for all the 
entries in the GPC lab metadata?  Wow, I did not understand that from 
Hackathon2 and we would love to get a copy of your java code to supplement our 
metadata browsing tools.  Did you develop a java-based computation of 
metadataxml from the LOINC release record?  We have considered that but have 
not had time.
I thought we might be providing an enhancement to your metadata build but I 
agree entirely that it seems irrelevant.
Jim

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Mar 27, 2015, at 1:11 PM, "GPC Informatics"  wrote:
>
> #158: usable view of LOINC lab terms
> -+
> Reporter:  rwaitman |   Owner:  nateapathy
> Type:  enhancement  |  Status:  assigned
> Priority:  major|   Milestone:  data-domains3
> Component:  data-stds|  Resolution:
> Keywords:   |  Blocked By:
> Blocking:   |
> -+
>
> Comment (by nateapathy):
>
> We reviewed the metadata included in the UNMC LOINC hierarchy and found
> 922 with metadata XML applied. We compared those leaf terms to our current
> hierarchy and found 622 that overlapped with the 71,000+ terms that are in
> our base hierarchy (the majority of which is hidden on Babel). All of our
> metadata XML matched the data you had for yours, only with a few semantic
> differences in naming conventions for tests within the metadata panel.
>
> Since there is not a major material difference between these two sets of
> metadata, I'm inclined to direct the group to the information I shared in
> [https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20
> comment20] on this thread. That comment includes a link to the base
> multiaxial hierarchy from Regenstrief and the Java code we use to
> transform that into our base LOINC hierarchy that was agreed upon as the
> GPC hierarchy during Hackathon II.
>
> Let me know if there are any next steps or additional questions we need to
> answer or clarify before we can close this ticket.
>
> --
> Ticket URL: 
> 
> gpc-informatics 
> Greater Plains Network - Informatics

The information in this e-mail may be privileged and confidential, intended 
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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by nateapathy):

 We reviewed the metadata included in the UNMC LOINC hierarchy and found
 922 with metadata XML applied. We compared those leaf terms to our current
 hierarchy and found 622 that overlapped with the 71,000+ terms that are in
 our base hierarchy (the majority of which is hidden on Babel). All of our
 metadata XML matched the data you had for yours, only with a few semantic
 differences in naming conventions for tests within the metadata panel.

 Since there is not a major material difference between these two sets of
 metadata, I'm inclined to direct the group to the information I shared in
 [https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20
 comment20] on this thread. That comment includes a link to the base
 multiaxial hierarchy from Regenstrief and the Java code we use to
 transform that into our base LOINC hierarchy that was agreed upon as the
 GPC hierarchy during Hackathon II.

 Let me know if there are any next steps or additional questions we need to
 answer or clarify before we can close this ticket.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by huhickman):

 Attaching CSV per gcc-dev discussion.

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RE: [gpc-informatics] #158: usable view of LOINC lab terms

[Campbell, James R]

UNMC will be deploying GPC standard view in compliance with our network needs 
and to support GPC i2b2 queries. This was the view we agreed as a network to 
accept from Nate Apathy at Hackathon2.   We informed everyone that we were 
developing this for UNMC investigators and can refrain from publishing on Babel 
if Russ directs.

UNMC will be maintaining national reference standards (in i2b2 forma), GPC i2b2 
view, PCORI CDM compliant SQL tables and UNMC pragmatic data views in i2b2 
going forward.
Jim


From: GPC Informatics [d...@madmode.com]
Sent: Tuesday, March 17, 2015 10:53 AM
To: rwait...@kumc.edu; nate.apa...@cerner.com; dconno...@kumc.edu; McClay, 
James C; schand...@kumc.edu; Campbell, James R; Hickman, Hubert B
Cc: tmcma...@kumc.edu; gpc-dev@listserv.kumc.edu; Campbell, Walter S
Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by dconnolly):

 Hubert, is that consistent with HackathonTwo design decisions?

--
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<http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:26>
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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by dconnolly):

 Hubert, is that consistent with HackathonTwo design decisions?

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by huhickman):

 I've uploaded the current version of UNMC_ONE_CHART to babel where folks
 can examine the hierarchy that Drs. Campbell (Jim and Scott) have put
 together.  It does include the latest metadataxml fields.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by nateapathy):

 Thanks Jim - we will definitely be interested in merging that Metadata XML
 as that will speed our build of this during our next cycle. I'll forward
 on to the engineering team for review. One initial question: did you get
 the reference ranges from your own local reference data (that's what it
 sounds like) or from some sort of set of standards from Regenstrief or
 another organization?

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by campbell):

 Nate
 I have uploaded a copy of the metadata build for LOINC lab data that we
 are deploying at UNMC.  Based upon discussion at Hackathon 2, I don't
 expect anyone to be interested in this (although anyone is welcome to use
 it if valuable) but I have split out on the second worksheet the
 METADATAXML that we prepared for 900+ of our lab tests for which we
 verified units of measure and numeric ranges from our data warehouse.  We
 have included normal ranges for only a small set where we thought there
 would be fair uniformity across sites but we have  and
  set for all based on statistical survey of results
 ranges from our fairly voluminous lab history.
 I wonder if it will not be valuable for Cerner to merge the METADATAXML
 into the common GPC lab tests metadata that we agreed to share across the
 network? or have you already created metadataxml for the release?
 Jim

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by campbell):

 * cc: wcampbel@… (added)


Comment:

 Nate
 We are testing out our final

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RE: [gpc-informatics] #158: usable view of LOINC lab terms

[Campbell, James R]

Nate
I would be very surprised if the LOINCParts hierarchy from UMLS is different 
than what Regenstrief released last spring, but I may be wrong.  Looking at the 
CMH Laboratory tests on babel, it appears that what you did was throw out the 
hierarchy elements that did not have data reported at CMH...am I correct?  That 
in itself tends to make the organization more useful for browsing.  I think 
that is a good thing to do since LOINC and SNOMED CT suffer from being so large 
that they are hard to manage.  However for clinical research utility, I think 
that panels need to be supported and I do not see them in the hierarchy you 
have built?

GPC sites that use only the i2b2 query tool have to have a path reference for 
structuring a query but the use of standards reference code (such as a LOINC 
code) in the C_DIMCODE of the metadata has the advantage that you can build as 
many browsable hierarchies as you want; as long as you use the reference 
standard code in C_DIMCODE, the appropriate leaf (LA record) query will always 
execute and retrieve observation facts with the corresponding CONCEPT_CD key.  
Folder (FA record) queries will depend on the path as the i2b2 tool is 
currently deployed but different aggregation query use cases are likely to 
exist and I think we should tailor them to serve our research community.

I share Russ' concern about developing local vocabulary artifacts and I am not 
pushing what we are developing locally for UNMC.  We will be happy to do so if 
that is agreed but everyone will make their own decision there.  Since I 
advocate that a 'standard' LOINC view be available and common to all sites, 
that is what we would use as reference 'paths' to construct i2b2 queries for 
sites that need them.  Speaking with DSSNI last week, we can expect that all 
inbound queries from PCORI will be SQL referring to the CDM and so I do not 
think it is going to be feasible to 'translate' all PCORI queries into i2b2 
formalisms.

I am Looking forward to discussing in San Antonio
Jim

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Monday, January 19, 2015 11:50 AM
To: rwait...@kumc.edu; nate.apa...@cerner.com; dconno...@kumc.edu; McClay, 
James C; schand...@kumc.edu; Campbell, James R
Cc: tmcma...@kumc.edu; gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #158: usable view of LOINC lab terms

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 Jim,
 This is good input and will help with the conversation later this week. I  
have a couple of questions and comments.

 1) We built the CMH hierarchy based on the LOINCPARTS ontology from UMLS,  and 
it is not nearly as flat as the one Nathan Wilson put together, if  that 
hierarchy is currently under the "GPC - Laboratory measurements"
 hierarchy on Babel. I agree, the GPC - Laboratory measurements hierarchy  is 
far too flat, but there are less flat scriptable UMLS-based ontologies.

 2) You are correct, we can extract the equivalent of flowsheet hierarchies  
from Cerner, however those hierarchies will not align across sites since  
different sites inevitably structure the views of their results in  different 
ways, so we have always aligned all of our clients with the  existing hierarchy 
that you see on Babel for CMH - Laboratory Results.
 Since ontology paths must align for the GPC queries to be shared, I worry  
about a hierarchy based on the UNMC lab results view that doesn't concur  with 
other sites' views of the same results. The flip side of that is that  we could 
use the UNMC lab results view as a base, and if we all agree that  that base 
makes most sense structurally, the codes would be the only  things to debate. 
Then, as long as all possible codes had a spot in the  hierarchy somewhere, the 
queries would align based on the paths (rooted in  the UNMC view). The downside 
there is that it is not based on a national  standard hierarchy of any type, so 
it may be harder to repeat at other  sites.

 I think we're well on our way to figuring this out at HackathonTwo -  thanks 
for helping spell out the different options!

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 I've created a Google Doc for [http://goo.gl/QL6mrW notes] during this
 Hackathon session.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 Jim,
 This is good input and will help with the conversation later this week. I
 have a couple of questions and comments.

 1) We built the CMH hierarchy based on the LOINCPARTS ontology from UMLS,
 and it is not nearly as flat as the one Nathan Wilson put together, if
 that hierarchy is currently under the "GPC - Laboratory measurements"
 hierarchy on Babel. I agree, the GPC - Laboratory measurements hierarchy
 is far too flat, but there are less flat scriptable UMLS-based ontologies.

 2) You are correct, we can extract the equivalent of flowsheet hierarchies
 from Cerner, however those hierarchies will not align across sites since
 different sites inevitably structure the views of their results in
 different ways, so we have always aligned all of our clients with the
 existing hierarchy that you see on Babel for CMH - Laboratory Results.
 Since ontology paths must align for the GPC queries to be shared, I worry
 about a hierarchy based on the UNMC lab results view that doesn't concur
 with other sites' views of the same results. The flip side of that is that
 we could use the UNMC lab results view as a base, and if we all agree that
 that base makes most sense structurally, the codes would be the only
 things to debate. Then, as long as all possible codes had a spot in the
 hierarchy somewhere, the queries would align based on the paths (rooted in
 the UNMC view). The downside there is that it is not based on a national
 standard hierarchy of any type, so it may be harder to repeat at other
 sites.

 I think we're well on our way to figuring this out at HackathonTwo -
 thanks for helping spell out the different options!

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by campbell):

 Nate
 I think that Russ' comments are understandable for this metadata view but
 are not achievable with good clinical acceptance using existing UMLS
 publications.  The LOINC views for Lab and Clinical that Nathan Wilson
 prepared are the best that can be done right now with the LOINC Parts
 hierarchy built by regenstrief and it is unmanageable in the i2b2 query
 tool due to its 'flatness'.
 The good news is that deploying the NW LOINC metadata with LOINC codes
 deployed in C_DIMCODE as Nathan has built allows for local pragmatic
 clinical views that can mirror the clinical system (EHR) browsing tool.
 From our Epic results review we have extracted the browsing hierarchy
 mapped to LOINC and are building the metadata from that with C_METADATAXML
 populated so that numeric and code set lab results are appropriately
 viewable in the i2b2 query tool.
 I may or may not have that ready for Thursday but that is the approach
 that UNMC is taking and I suspect that you can probably extract a CERNER
 results review hierarchy of similar utility, can you not?
 I think that such metadata will achieve the greatest clinical/research
 acceptance across our sites since the current LOINC publication does not
 have sufficiently robust ontologic organization to support the browsing
 and decision support use cases that our clinical researchers expect.
 Jim

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  nateapathy
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+
Changes (by dconnolly):

 * cc: bdemeke@… (removed)
 * owner:  bos => nateapathy


Comment:

 Nate has agreed to lead the HackathonTwo session on this.

 Note especially goals from Russ in comment:14:
  - harmonizing with the existing work
  - scriptable from the UMLS
- The bioportal approach in comment:4 presumably is aligned with UMLS
 and meets this "scriptable" goal.
  - doesn't require curation

 p.s. Angela, I'm still interested in your LOINC code. If you have shared
 it, please let me know where.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  bos
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+
Changes (by dconnolly):

 * owner:  budh0007 => bos


Comment:

 2 Dec notes (#12):
   Angela: We’ll share our LOINC code soon.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by schandaka):

 Belay reached out to Supreet and Justin regarding UMN's LOINC hierarchy on
 Babel. Supreet shared their code. Justin gave me the permission to share
 UMN's code [attachment: Update LOINC Ontology.sql] in this ticket.Here is
 Supreet's response to Belay.

 {{{
 Hi Belay,

 The LOINC hierarchy at our site was constructed from the National Library
 of Medicine ( UMLS).

 Some key points related to the lab hierarchy:
 - All the parent levels from MRCONSO where SAB= LNC (LOINC) and TTY =LPN
 (LOINC Parts Name) were  joined to MRHIER.
 - In the MRHIER file the LOINC codes for the leaf nodes i.e. the CXN (The
 context number if the atom has multiple contexts) was filtered on 2.
 - For the LOINC parent folders the CXN was filtered on 1. It also 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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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by rwaitman):

 Scott/Jim: please share.

 Reviewing things with Sravani and Belay.  It seems across our sites, that
 UMN and WISC have the closest ontologies for labs that seem to be built on
 the UMLS and can represent the different ways people might be mapping
 atomic results (epic component_ids) to a loinc term.

 Our goal is to have one consistent way for everyone to organize their
 labs.  Scott/Jim^2: did you review the WISC and UMN approaches or just
 start denovo?  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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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by jmcclay):

 Comments from Scott Campbell at UNMC

 I have created a hierarchical view of the Lab LOINC items for
 approximately 2000 of the 2500 terms used at UNMC.  This also includes
 orderable codes (i.e. batteries) and performable codes (tests/results).
 The hierarchy is based on LOINC class and refined by UNMC departments and
 logical groupings.  Note:  we have generalized the UNMC departments into
 categories that should make sense to most medical centers.

 Jim Campbell is reviewing my categories to ensure that they are in-line
 with a clinician’s perspective.  Based on Jim’s feedback, I will refine
 and issue a testable code set to Hubert.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by dconnolly):

 So it's coming up on 4 weeks since Supreet, Stewart, and company took the
 ball on this. The updates from Nathan from CMH look very promising. Is
 that strategy endorsed by UMN and UNMC as well? i.e. have the three sites
 reached consensus? Does the lab hierarchy from CMH or one of the other
 sites represent the complete proposal? Is it deployed at more than one
 site?

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 Lucky for us, Lori already did some of this in January. Unfortunately, the
 LOINC file is ~460MB so I won't be uploading/attaching it here. Here's the
 link to the site specifically for the Bioportal-to-i2b2 translations:
 http://i2b2.bioontology.org/

 And here's the link to the Bioportal API tool:
 https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 Right - we don't keep that top level of the hierarchy, only below the
 LOINCPARTS section is used.

 And the synonym question is a good one; that answer goes beyond my
 familiarity with Bioportal. Why that would be picked as a "''preferred''
 name" would be even more interesting to know. I'll see if we can pull down
 a raw csv of the export using Lori's API tool and post to this ticket for
 combing through how we might swap those names around in the i2b2
 ontology/metadata tables.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by dconnolly):

 Yes, that's the sort of think I was looking for. But...

 I don't know many clinical researchers who could handle the first choice
 it presents:

  - LOINCCLASSTYPES
  - LOINCPARTS

 Below LOINCPARTS looks OK. And it seems to match CMH's labs on babel. It's
 somewhat similar to the "GPC: Laboratory measurements" area, but where CMH
 has Chemistry (LP31388-9), GPC has Chemistry non challenge tests (7786-9)
 with over 500 children. So yes, the Bioportal ontology looks like a
 worthwhile path to pursue.

 The commonly used potassium code (2823-3) wasn't too hard to find, but the
 label is kinda cryptic: "Potassium:SCnc:Pt:Ser/Plas:Qn". I wonder why they
 didn't choose the synonym "Potassium [Moles/volume] in Serum or Plasma".
 And I wonder if there's a straightforward way to get nicer labels like
 that throughout.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 Try taking a look
 
[http://bioportal.bioontology.org/ontologies/LOINC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FMTHU000999
 here] (by clicking on the "2014AA" you can get a navigable/browsable
 hierarchy) and expand out the LOINCPARTS section to browse. Is that what
 you're looking for?

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by dconnolly):

 Replying to [comment:4 nateapathy]:
 > ... Have other sites used the Bioportal ontology? Or am I missing
 documentation on that investigation for GPC terms? And if not, would that
 be a worthwhile path to pursue?

 I hadn't looked at it closely until now, but "Maximum number of children:
 10329" won't work well in the i2b2 Navigate Terms UI. There are also "No
 views available" so it's not convenient to browse. There is a "Create new
 view" button. Is it straightforward to make a usable view?

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by dconnolly):

 It would be better if we had a (more) objective definition of usable, but
 part of the "reporter" role is judging when things are done. So we can
 expect Russ to judge proposals. My understanding is that the goal is
 something like: it's usable when Russ doesn't feel embarrassed to ask
 researchers to use it.

 Another approach might be: ask a handful of clinical researchers to find
 potassium and a couple others and see how well they do. If they do well, I
 expect that would be compelling evidence that this is done.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+

Comment (by nateapathy):

 In reviewing the lab lead responsibilities, it appears CMH/Cerner is
 responsible for driving this standardization. What is the status of the
 UMN student who was working on a project around this?

 Also, having looked through the documentation on tickets and emails that I
 can find regarding this, I don't see any references to
 http://bioportal.bioontology.org/ontologies/LOINC, which is where we
 derived our LOINC ontology from. They keep versions very up-to-date
 (latest maintained version is from 5/28/14), and the Bioportal site has an
 API that Lori Phillips at Partners has built an "i2b2 ontology builder"
 application on top of. This avoids the issue mentioned above re:
 downloading an Access database from REMLA every time we need to update the
 hierarchy. Have other sites used the Bioportal ontology? Or am I missing
 documentation on that investigation for GPC terms? And if not, would that
 be a worthwhile path to pursue?

 My final question is around the definition of "sufficiently usable" in the
 description of this ticket, which seems opaque to me unless I am missing a
 definition that the group decided upon earlier in the LOINC ontology
 process.

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-domains2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+
Changes (by dconnolly):

 * milestone:   => data-domains2


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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+---
 Reporter:  rwaitman |   Owner:  budh0007
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+---
Changes (by dconnolly):

 * owner:  jdale => budh0007


Comment:

 Supreet @UMN, Scott at UNMC, Stuart took the ball on this in the 30 Sep
 call. (notes: #12)

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Re: [gpc-informatics] #158: usable view of LOINC lab terms

[GPC Informatics]

#158: usable view of LOINC lab terms
-+---
 Reporter:  rwaitman |   Owner:  jdale
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  68   |
-+---
Changes (by dconnolly):

 * owner:  dconnolly => jdale
 * status:  new => assigned


Comment:

 Justin,

 Based on your work so far, Russ nominates UMN to lead on this. Recall:

  - [https://docs.google.com/spreadsheets/d/1
 -uW2hod63gdlNlLAkhleuMvnQG6zNaw2jd-CAhSLqkk/edit#gid=2012749157 leading
 sites by domain]

 We have a student working on a project in this area; he should be in
 touch.

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