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Oncology Diagnosis Representation Proposal #199

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rimusia opened this issue Jul 10, 2018 · 7 comments

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@rimusia
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commented Jul 10, 2018

@rimusia rimusia changed the title OHDSI Oncology Diagnosis Representation Proposal Oncology Diagnosis Representation Proposal Jul 10, 2018

@cgreich

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commented Aug 4, 2018

@rimusia:

this is a very clean proposal. Couple questions:

  1. There is a yellow sentence in the Convention section: Valid Concepts for the value_as_concept field belong to the 'Meas Value' domain. Are you not sure about that one?
  2. We haven't added the various vocabulary modifications. Do folks know?
  3. I know we noodled that a while, but didn't we say we want to use a new EPISODE_OF_CARE table instead CONDITION_ERA? And the condition_era_type_concept_id would also become an episode_type_concept_id.
@vojtechhuser

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commented Aug 7, 2018

in case others look at the same, here is example icdO3 term

http://athena.ohdsi.org/search-terms/terms/44498949

image

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commented Aug 7, 2018

column cancer_modifier_source_concept_id is 33 chars. (I think 32 or so was max for Oracle)

@don-torok

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commented Aug 7, 2018

In the definition of CANCER_MODIFIER – new table

  • Going forward can there be a single column cancer_modifier_datetime? The reason for having both date and datetime columns was for backward compatibility.

  • There should also be a visit_detail_id column.

  • I continue to advocate that for all concept_id's the documentation should describe the range of expected values by providing information about either the expected concept domain or vocabulary.

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commented Aug 7, 2018

If diagnosis modifer is used to represent laterality, analyst will have to account for two ways of getting left lung cancer. Precoordinated and postcoordinated.

See ICD10CM code D02.22

(I hate to muddy this discussion with a related bug but....In fact, current mapping has a bug
It is mapped to non lateral snomed concept
see here: http://athena.ohdsi.org/search-terms/terms/45586077

It should be mapped to (MOROVER - well, there is no good left lung cancer term that captures it well. Only Ca in situ of left LOWER LOBE and UPPER LOBE. Oh, boy....

btw - I am also in favor of not having both date and datetime. Just datetime please (in 21st century.)
+1 also on specifying the expected concept domain (Achilles Heel rules need that)

@mellybelly

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commented Aug 14, 2018

Any reason NCIT was not considered in the proposal?
https://github.com/NCI-Thesaurus/thesaurus-obo-edition
We've been doing some collaborative work with NCI to help with interoperability with basic research and provide robust equivalence mappings to other clinical vocabs.
NCIT is also a standard used for FDA submission etc.
See also: https://medium.com/@MonarchInit/tailoring-the-nci-thesaurus-for-semantic-interoperability-21305ccfe3a6

Maybe worth a look.

@clairblacketer

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commented Nov 15, 2018

closing as this is covered by #216

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