Open karafecho opened 3 years ago
The ICEES+ Exposures Provider considers LOINC codes + flags (standardized to "high", "low", "normal") to provide meaning/interpretation. LOINC codes are rolled up such that any LOINC code related to, say, ALT is treated the same, with the flags providing the interpretation. The service itself exposes LOINC IDs, SNOMED IDs, UMLS IDs, etc., which is less than ideal, as the mappings are loose and not very informative.
We are considering mappings to HPO (e.g., LOINC2HPO) to support TRAPI queries related to phenotypes (not lab results), but we are interested in hearing how others are treating labs.
Also, we're linking labs to Biolink as biolink:PhenotypicFeature. I'm pretty sure that other clinical KPs are, too, but I'd like to confirm that.
It seems like annotating these labs with HPO (and/or other non-LOINC things) would be very helpful with integrating into Translator.
But, as I guess most folks know, HPO and LOINC id's are not equivalent, even where there is a mapping. It's something more like LOINC + as specific result = HPO.
It seems like that kind of mapping should be done once somewhere, maybe exposed as a KP or part of a KP?
Yes, and we (Exposures Provider) are conceptualizing the implementation as LOINC + flag = HPO.
Lab tests and their results are currently not available in COHD, but we have a similar plan to what Kara already mentioned. We've made some efforts into applying LOINC2HPO (with help from OMOP2OBO for applying the LOINC2HPO mappings to our OMOP database), but we've had limited success so far in terms of 1) the number of phenotypes we're finding per patient (much lower than what the UNC folks saw in their publication) and 2) accuracy of the resulting HPO concepts.
Good to know, Casey.
The initial LOINC2HPO mappings were developed using lab data from UNC's asthma cohort, so I'm not surprised by (1), but (2) is concerning.
Summary from 03.12.21 meeting, with a few additional thoughts:
clinical finding: is_a: phenotypic feature description: >- this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations. slot_usage: has attribute: range: clinical attribute id_prefixes:
Also see meeting notes for additional details.
General note, consider tackling this complex problem in steps over time, while addressing other high-yield priorities.
Specific issues include the following.
Ways to address issues.
A few quick thoughts, @jh111 :
Thanks!
This issue is intended to initiate a discussion regarding the treatment of clinical laboratory measurements within the context of Translator.