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ICEES KG meta-KG and Biolink mappings #12
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Hi Kara. What happens here is that we send the specified search term to name resolver and that gives back curies that match. Once we have curies, we get the corresponding biolink categories from node normalizer. I think if we are wanting specific biolink categories, we will either need to update the search term to be something that gives back a curie that has the wanted categories or we need to hard-code the curie and/or biolink categories in the all_features yaml file, or even a mix of both. What are your thoughts? |
Yeah, I understand the process, and I knew that some of the Biolink categories were being dropped when we started leveraging SRI services, but I wasn't really concerned until recently, when a use case arose. Specifically, ICEES KG is returning environmental exposures such as "benzene" in response to the first hop of Path A in the TCDC's workflow (see slide 10 here). This is introducing noise into the final answer set. As such, we would like to filter chemical exposures from the first hop using an |
It's up to you. From my end, I would just need to rerun the precompute script after you update the all_features file. |
To clarify, the all_features YAML files already contain most of the intended Biolink mappings, although I would like to make a few adjustments for consistency. Shouldn't take long. |
Update 11.14.2022: This Node Norm endpoint returns the following output for three test inputs: PUBCHEM.COMPOUND:2083 (albuterol)
MESH:D052638 (particulate matter)
PUBCHEM.COMPOUND:241 (benzene')
If I change the search terms by adding "exposure" for the last two variables above, here's what Node Norm outputs: UMLS:C2136615 (airborne pollutant exposure)
NCIT:C36251 (benzene exposure)
So, Node Norm is now recognizing things like chemical exposures, BUT the mappings to Decision: (1) Add |
Noting that the YAML files contain a number of Biolink mappings that are not supported by Node Norm. For instance:
I mapped "hospitalization" to |
Updated decision / action items [assigned to Kara]:
|
Notes on supplemental Biolink mappings.
|
This issue is to formally report a disconnect between the Biolink mappings that are included in the ICEES API all_features config files and those that support ICEES KG, as reported in the meta-KG. The approach that we've implemented to automate some of the work and leverage SRI services is not picking up certain intended Biolink mappings. For instance,
AvgDailyPM2.5Exposure
should map tobiolink:ChemicalEntity
andbiolink:EnvironmentalExposure
. To provide another example,TotalEDVisits
should map tobiolink:ClinicalIntervention
.The text was updated successfully, but these errors were encountered: