Open joeflack4 opened 1 year ago
@Sigfried This isn't related to TermHub but Stephanie doesn't have any code for this yet, and it uses enclave_wrangelr
, so just making an issue here.
@stephanieshong FYI, I created this issue for Nico to respond to.
@matentzn Here you are!
mapping_justification
currently allowes these values, but it is extensible and can take any input. (Make pr here).semapv:UnspecifiedMatching
(highly discouraged) or make a comment on https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/1@matentzn - ok. Thank you. I will give you some example of one to many map that you can comment on. @joeflack4 - there should a input parameter of value sets that specifies what to map which list source code and code system. Where should I grab the input from? input - list of source code /code system pair to map input - target code system for the output output- map in SSSOM format.
@matentzn Awesome answers, thanks. I spoke with @stephanieshong and got her what she needs. She was asking about how to construct the curie_map
for the most part.
mapping_justification
values somewhere in my notes. Eventually we'll need to update the documentation w/ these.sempav:UnspecifiedMatching
. I do have some thoughts about it, which I will share in that other issue.@matentzn I added a new question (4): What CURIE to use for OMOP?
For now I randomly picked https://www.ohdsi.org/data-standardization/the-common-data-model/ , but I know that this is wrong. I don't know if there is any URL pattern for pulling up pages that show information about OMOP codes.
What CURIE to use for OMOP?
In all my projects we use OMOP: https://athena.ohdsi.org/search-terms/terms/
All codes resolve there.
Thank you.
@matentzn - thank you I will use athena link to resolve in the curie map. I am just making a note for myself here:
- equals_string: semapv:LexicalMatching
- equals_string: semapv:LogicalReasoning
- equals_string: semapv:CompositeMatching
- equals_string: semapv:UnspecifiedMatching
- equals_string: semapv:SemanticSimilarityThresholdMatching
- equals_string: semapv:LexicalSimilarityThresholdMatching
- equals_string: semapv:MappingChaining
- equals_string: semapv:MappingReview
- equals_string: semapv:ManualMappingCuration
@Sigfried Just FYI TIMS woulda been the better place to put this issue, but w/ the discussion here so far, too late to move it. I'll make a mirror issue and link it.
@joeflack4 - did you remove the sssom_map branch?
@joeflack4 Stephanie is asking me where the sssom_mapping branch and files went. I didn't know. I had her add them to the develop branch: 077da0c808a754204ce483a4b31b2d087d2cde1d
@joeflack4 - checked in my sample files under the sample_mapping_files directory
Hey @stephanieshong, I know we talked about this on Teams. Yeah, I'm not sure; I don't remember us creating that branch.
I think @Sigfried and I have not yet decided where mapping content should go. Maybe we need a new git submodule
? Or we could move them into termhub-csets
, if we want to use that submodule for mapping content as well.
For now I agree they are fine there. Could always just add these to a standalone repo as well.
Yes, I created the branch from my machine. But I think I created from the sub-directory and then later removed the .git so i think it got lost. all I need to check-in was the sample SSSOM mapping file for Nico to review.
@joeflack4 - I will create a branch from the main and use that branch for the SSSOM mapping files. This has nothing to do with TermHub for now. Unless you want to use it to map the terminologies from the TermHub which is related. (ICD10CM to SNOMED CT)
A ---[narrowMatch]-->B means that B is narrower than A. So for most part we would be using [boardMatch]
Overview
Stephanie is doing some mapping work, I think for N3C (I'm not sure the exact nature of it). There is a desire create SSSOM for these mappings. After creating the SSSOM files, we'll convert to FHIR ConceptMap and load onto the TIMS server.
Tasks
Questions
mapping_justification
: What is the valid range? Is there an enumeration of permissible values somewhere?mapping_justification
: We know that OMOP has mapped to various terminologies using automation. However, we don't know how it was done. Doessemapv:lexicalMatch
have an abstract parent classsemapv:match
that we could use? Or is there something insemapv
(or elsewhere) for 'unspecified algorithm'?mapping_justification
, if we don't know the details for "use mapping_tool, mapping_tool_version, confidence , match_string, subject_preprocessing, object_preprocessing,", should we leave these fields out? Or should we include them and leave them blank or populate them with some 'unknown' value or null value?Additional information
Slack Conversation
Related
https://github.com/HOT-Ecosystem/hapi-fhir-jpaserver-starter/issues/59 https://github.com/jhu-bids/TermHub/issues/145