Opened 9 years ago

Closed 8 years ago

Last modified 7 years ago

#766 closed enhancement (fixed)

Query for social history (e.g. tobacco use) in HERON

Reported by: rwaitman Owned by: mhoag
Priority: minor Milestone: heron-council-grove-update
Component: data-repository Keywords: public-web
Cc: dconnolly Blocked By:
Blocking: #1696 Sensitive: no

Description

seems to have lots of goodies regarding tobacco use and other things.

Joe,
Thanks for that pointer. Hadn't looked at that table. We'll see if we can pull that in at a subsequent point and see how it overlaps or exchanges with flowsheet and notes information,

Russ

<Joe.Terdiman@…> 12/15/2011 7:14 PM >>>

Although we do not yet included smoking hx in our i2b2 database or SHRINE, we have looked in our EPIC system at the percentage of patients with smoking hx in the social_hx table vs. free text progress notes. Using NLP on progress notes and an SQL query on the social_hx table in a sample of 1000 patients, we found 20% of patients had a positive hx of smoking from progress notes, but the social_hx table indicated they were either non-smokers or were blank. This ad hoc study clearly demonstrates the ability of NLP to extract significant clinical information from free text reports in the EHR, and the potential for large discrepancies in estimating the prevalence of clinical conditions (smoking in this case) without it.

Joe


Joe Terdiman, MD, PhD
Division of Research
Kaiser Permanente
2000 Broadway
Oakland, CA 94612
(510)891-3814
8-481-3814

Change History (14)

comment:1 Changed 9 years ago by rwaitman

Milestone: heron-clinton-updateheron-bighill-update

Relevant Changelists and Descriptions

ChangelistDateCommitterComment
r19111/4/12MattInitial commit of smoking history concept and ob facts
r19121/4/12MattFix up so that concepts load works
r19141/4/12MattAdded the CSV file to import all of the missing content for the zc_smoking_tob_use table on bmidev
r19221/8/12MattSocial History Additions: quit date, packs per day, years using tobacco, sexual activity, smokeless tobacco usage. Passed basic smoke test after load_all_concepts and heron_load
r19231/8/12MattUpdates from default

comment:2 Changed 9 years ago by dconnolly

Milestone: heron-bighill-updateHERONv.Next

Batch update from file heron-milestone-update.xls

comment:3 Changed 8 years ago by dconnolly

Cc: achoudhary removed
Milestone: HERONv.Nextheron-council-grove-update
Owner: changed from rwaitman to mhoag
Status: newassigned
Type: taskenhancement

comment:4 Changed 8 years ago by mhoag

Status: assignedaccepted

comment:5 Changed 8 years ago by mhoag

Analysis

SOCIAL_HX definitely has a lot of interesting information primarily regarding smoking/drug/alcohol use and sexual activity/birth control usage.

Tobacco

The information regarding tobacco usage ranges from the method of delivery (cigarette/pipe/chew) to the frequency and quantity of usage.

Alcohol

The information regarding Alcohol usage includes whether the patient is a drinker and frequency of usage.

Illicit Drugs

The information regarding Illicit drugs includes whether the patient uses illicit drugs, if they use an IV for delivery, and frequency of usage.

Sexual Activity

The information regarding Sexual Activity includes whether they are sexually active and if they have a male and/or female partner.

Birth Control

The information regarding birth control simply covers whether they utilize one of these 12 means of birth control.

1-Condom
2-Pill
3-Diaphragm
4-IUD
5-Surgical
6-Spermicide
7-Implant
8-Rhythm
9-Injection
10-Sponge
11-Inserts
12-Abstinence

Clearly this is a lot of information that could introduced as different observation facts. I suspect to start (given the early interest in smoking) we could initially mine the relations to the table

52	SMOKING_TOB_USE_C	EPT     19218  INTEGER		No
Stores the patient's usage of smoking tobacco. Data may include, 
Current Everyday Smoker, Current Some Day Smoker, Former Smoker, 
Never Smoker, Unknown If Ever Smoked or Smoker, Current Status Unknown.

which would could provide a nice discrete representation of smoking history (with the parallel addition to the modifier_dimension).

comment:6 Changed 8 years ago by rwaitman

Sensitive: unset

comment:7 Changed 8 years ago by ngraham

Blocking: 1696 added

comment:8 Changed 8 years ago by mhoag

Included Social History

NamePriorityDescriptioni2b2 Usage
Packs Per Day2Packs smoked per dayNumerical (Drop concept into query and select comparison)
Tobacco Used Years2Years of Tobacco UsageNumerical (Drop concept into query and select comparison)
Smoking Quit Date2Date when person quit smokingDate (Use Date Range)
Tobacco User1Description of patients tobacco usageEnumeration (Drop concept enum into query)
Smokeless Tob Use1Description of patients smokeless tobacco usageEnumeration (Drop concept enum into query)
Smokless Quit Date2Date when person quit smokeless TobaccoDate (Use Date Range)
Smoking Tob Use1Description of patients smoking tobacco usageEnumeration (Drop Concept enum into query)


Excluded Social History

NamePriorityDescriptionReason for Exclusion
Cigarettes YN3Type of deliver (cigarettes, pipe, chew, etc.)Priority
IV Drug User3Whether the patient is an IV Drug UserPriority
Condom YN3Type of birth control used (condom, pill, etc.)Priority
Years Education2Years of Education the patient receivedData stored as free text; difficult to generate discrete value
Alcohol Use2Description of the patients alcohol usageReference table is not populated in Clarity
Ill Drug Use2Description of patients illegal drug useReference table is not populated in Clarity

We should probably generate a follow/tracking ticket to decide if we want to include the excluded social history information in future releases.

comment:9 Changed 8 years ago by mhoag

Owner: changed from mhoag to ngraham
Status: acceptedassigned

I did a smoke test to make sure that all of the concepts in the include list showed up in the concept side and returned results as a part of a query. The only item that returned no results was the 'Smokless Quit Date' because there is apparently no test data with that date set.

Sending to Nathan for Code Review.

comment:10 Changed 8 years ago by ngraham

Owner: changed from ngraham to mhoag

Looks good to me! Just a couple of comments:

  • Perhaps consider renaming this ticket to better describe what was done? It says "Evaluate" but in reality you've actually added the new feature.
  • I would suggest adding automated test(s) for this stuff (source:heron_load/test_heron_query.py).
  • Just like 1515#comment:14, you might consider factoring out some of the common path strings in epic_concepts_load.sql.

comment:11 in reply to:  10 Changed 8 years ago by mhoag

Resolution: fixed
Status: assignedclosed

Replying to ngraham:

Looks good to me! Just a couple of comments:

  • Perhaps consider renaming this ticket to better describe what was done? It says "Evaluate" but in reality you've actually added the new feature.

Changed name to represent that the ticket is actually a feature

Added a test

  • Just like 1515#comment:14, you might consider factoring out some of the common path strings in epic_concepts_load.sql.

Shelving this for now as we discussed in person.

Status Change

Resolving as fixed since it has been merged to the default line.

comment:12 Changed 8 years ago by dconnolly

rephrasing the summary to say what enhancement the customer gets, for HeronReleaseNotes
(todo: document this better in TracTickets)

comment:13 Changed 7 years ago by dconnolly

Keywords: public-web added

comment:14 Changed 7 years ago by kcrane2

Approved for public release

Note: See TracTickets for help on using tickets.