taskGNU Health - Tasks: task #13615, Update disease groups

 
 

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task #13615: Update disease groups

Submitted by:  Chris Zimmerman <teffalump>
Submitted on:  Thu 14 May 2015 01:29:33 AM UTC
 
Should Start On:  Thu 14 May 2015 12:00:00 AM UTC Should be Finished on:  Mon 14 Dec 2015 12:00:00 AM UTC
Category:  Epidemiology // OLAP Priority:  * 3 - Low
Status:  In Progress Privacy:  Public
Percent Complete:  90% Assigned to:  teffalump
Open/Closed:  Open Release:  * 2.9.0
Module:  * icd10/reporting
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Mon 07 Dec 2015 03:06:21 AM UTC, comment #8: 

Added a commit for nutritional disorders:

http://hg.savannah.gnu.org/hgweb/health/rev/effc8c594683

The remaining two, SOCIAL and VIOLENCE, are tricky. I need to think more about them, look at research, and ask for advice from clinicians, etc.

On the positive side, the main disease groupings are done. =-)

Chris Zimmerman <teffalump>
Project Member
Sun 22 Nov 2015 05:31:17 PM UTC, comment #7: 

Added codes to the PEDIATRIC group and I fixed the GYNOBS imports, since I realized I committed my non-tested xml. I added a single new disease, too.

The pediatrics list is from two sources:

Pediatric-only codes:
http://www.icd10data.com/ICD10CM/Pediatric_Codes

Common pediatric codes:
http://www.roadto10.org/action-plan/phase-2-train/common-codes-pediatrics/

Both sources are icd10-CM codes, so I simply converted them back into the ICD10 codes. Some of the specificity is lost. For example, infant botulism --> botulism.

Commit: http://hg.savannah.gnu.org/hgweb/health/rev/c3d922cea7fb

Chris Zimmerman <teffalump>
Project Member
Fri 23 Oct 2015 07:20:55 PM UTC, comment #6: 

I spoke with an experienced clinical psychiatrist and professor about useful psychiatric-related disorders to track that were particularly relevant for women. She gave me an informal list of:

- Eating disorders
- Obesity
- Depression
- Sexual/physical abuse
- PTSD
- Anxiety disorders

I will speak with other specialists for disorders in other areas. Hopefully, I can better fill the GYNOBS group with some outside help. Hehe. I'll add the above list soon. =-)

Chris Zimmerman <teffalump>
Project Member
Mon 19 Oct 2015 10:47:21 PM UTC, comment #5: 

Just pushed a commit to add pregnancy related disorders to the GYNOBS pathology. I simply added Categories 15, 16, and 17 of ICD10. Category 17 is congenital issues, so there is an argument not to include them for simple GYNOBS, but seems to fit to me.

For the GYNOBS category, it seems important to add specific issues that are useful and relevant to track separately. Some of these issues affect males and females (e.g., breast cancer), and some are female only (amenorrhoea, vaginal candidiasis, etc), but I'm having trouble defining the criteria for inclusion, and how it would work in practice. For example, we'd have to filter out male diagnoses to generate the reports. I'm generally not familiar with the important disorders to track. Thoughts? I'll do some more research on this topic, too. =-)

http://hg.savannah.gnu.org/hgweb/health/rev/adae8b2861ac

Chris Zimmerman <teffalump>
Project Member
Sat 17 Oct 2015 09:22:19 PM UTC, comment #4: 

Pushed a new commit that adds diseases to the HEART group. I added rheumatic, ischaemic, and other heart problems (like arrhythmias). That is, 'direct' heart problems, not things like hypertension. Can always add more diseases, but there is a VASCULAR catch-all group that subsumes the HEART category.

I renamed the data file in order to simplify the import, so the commit is huge:

http://hg.savannah.gnu.org/hgweb/health/rev/b4c1f1785a10

Chris Zimmerman <teffalump>
Project Member
Wed 30 Sep 2015 03:04:24 PM UTC, comment #3: 

Just pushed a few commits to add diseases to the NOTIFIABLE group. This is another group that should be customized according to local needs. I followed CDC guidelines which recognize certain diseases, for a variety of reasons, as notifiable (although it changes frequently): including novelty, virulence, severity, surveillance (e.g., smallpox), and so on. Add and remove according to each institution's needs!

Commits:

http://hg.savannah.gnu.org/hgweb/health/rev/2c2f8920f1e7
http://hg.savannah.gnu.org/hgweb/health/rev/7b12a675d9fd
http://hg.savannah.gnu.org/hgweb/health/rev/0de60b516b76

PS: I think I may add a category for hospital/clinic-specific infections --- e.g., VISA/VRSA --- which should prove helpful for epidemiological and administration purposes.

Chris Zimmerman <teffalump>
Project Member
Mon 24 Aug 2015 02:47:09 AM UTC, comment #2: 

Thanks Chris !
It looks great, and loaded perfectly into the DB !

True. There are conditions that belong to different groups. Now that you mention it, the conditions that fall into the AUTOIMMUNE groups is a great example for that.

Best,

Luis Falcon <meanmicio>
Project Administrator
Sat 22 Aug 2015 03:22:33 AM UTC, comment #1: 

Just pushed a commit for most of the obvious categories since they are one-to-one mappings from the ICD10 categories. However, I did do a little research on autoimmune disorders, and added reasonably accepted autoimmune diseases to the AUTOIMMUNE group. However, that category is likely to be quite fluid considering research is constantly revealing more.

Commit (Beware! It's huge!):

http://hg.savannah.gnu.org/hgweb/health/rev/4728c08fad57

Chris Zimmerman <teffalump>
Project Member
Thu 14 May 2015 01:29:33 AM UTC, original submission:  

I'm going to do more work connecting diseases with the disease groups (e.g., ALLERGIC). The "top diseases report" is really hampered because only a few diseases are categorized. In general, the icd10 categories fit well with the disease groups, and many diseases will probably only fit one or two obvious groups. However, the multi-group diseases are very important (infectious, notifiable, etc), so there is some tedious work there. Also, I will probably be able to do some cleanup of the icd10 module, adding new diseases, etc.

Chris Zimmerman <teffalump>
Project Member

 

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    Follow 7 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2015-12-07 teffalump Percent Complete80% => 90%
    2015-11-22 teffalump Percent Complete70% => 80%
    2015-10-17 teffalump Percent Complete60% => 70%
    2015-09-30 teffalump Percent Complete50% => 60%
    2015-08-22 teffalump StatusNone => In Progress
    2015-08-22 teffalump Percent Complete0% => 50%
        ReleaseNone => 2.9.0

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