Source Concepts for Local Variables

[ericaVoss]

TYPE	NOTES
ITEM	How should local source codes be managed? Should I assign my own CONCEPT_IDs? How have others handled this?
FORUM POST	http://forums.ohdsi.org/t/themis-question-what-do-people-put-in-the-source-value-fields/4092/
SOLUTION	There are three approaches to handle source codes that are not in the OMOP Vocabulary (in order of complexity): 1. Leveraging the SOURCE_TO_CONCEPT_MAP: In the OMOP Vocabulary there is an empty table called the SOURCE_TO_CONCEPT_MAP. It is a simple table structure that allows you to establish mapping(s) for each source code with a standard concept in the OMOP Vocabulary (TARGET_CONCEPT_ID). This work can be facilitated by the OHDSI tool USAGI which does text similarity between your source code descriptions and the OMOP Vocabulary and exports mappings in a SOURCE_TO_CONCEPT_MAP table structure. Example SOURCE_TO_CONCEPT_MAP files can be found here. These generated SOURCE_TO_CONCEPT_MAP files are then loaded into the OMOP Vocabulary's empty SOURCE_TO_CONCEPT_MAP prior to processing the native data into the CDM so that the CDM builder can use them in a build. 2. Adding CONCEPT.CONCEPT_IDs: When an source code is not supported by the OMOP Vocabulary, one can create a new records in the CONCEPT table, however the CONCEPT_IDs should start >2000000000 so that it is easy to tell between the OMOP Vocabulary concepts and the site specific concepts. Once those concepts exist CONCEPT_RELATIONSHIPS can be generated to assign them to a standard terminologies, USAGI can facilitate this process as well. 3. Work with ODYSSEUS Data Services to add to OMOP Vocabulary: The OMOP Vocabulary is an evolving thing and new vocabularies can be added, however working with the ODYSSEUS team is the best way to manage performing this task.
NEXT STEPS	Add this description with the CDM WG to the FAQ section.

[PRijnbeek]

We agree with the proposal and are testing out option 2 on our data at the moment

[cgreich]

@ericaVoss:

Can we shift your point 1 all the way down to point 3, and type it in font size = 6 or so? :)

[ericaVoss]

[clairblacketer]

#teamSTCM

[alondhe]

My vote is for number 3, but in the interim, I'd go with number 1 (or, #teamSTCM). Number 2 should be in size 3 AND white font.

[PRijnbeek]

:) @alondhe if this is about preference we all want number 3 sure.

Number 2 just let’s me use all the tools and methods. I could run Achilles on my local coding system that is not yet in the vocab etc. Number 1 advantage for ETL step i see as well but does not allow me to use the tools.

Disadvantage of number 2 could be that others touch the vocabulary and may introduce errors.