Comments (5)
Update: The dev instance is https://nodenormalization-sri.renci.org
, though there is an alternate instance here: https://nodenormalization-dev.apps.renci.org/1.4
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Noting the SmartAPI registration of NodeNorm: https://smart-api.info/ui/400f7c11028ff36f460af4ea85dc72f5
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And a note @tokebe
I think we are not setting conflate=true
in our queries (a parameter related to gene/protein conflation).
However, right now, it looks like we depend on the default behavior which is to conflate
- compare this w/ no parameter set: https://nodenorm.transltr.io/1.3/get_normalized_nodes?curie=UniProtKB%3AQ08722 UniProtKB ID is a Gene first
- w/ this where
conflate=false
: https://nodenorm.transltr.io/1.3/get_normalized_nodes?curie=UniProtKB%3AQ08722&conflate=false UniProtKB ID is set to Protein
EDIT:
- I'm not sure if we want to set this explicitly or not...
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The dev instances right now have other parameters drug_chemical_conflate
and description
(set to false
by default)
Right now, I'm not sure we need to worry about them. It's not clear if this issue involves using these non-advertised dev instances. And I think those parameters are used by UI auto-complete input and ARS only right now?
But in the future, when these parameters are in the ITRB instances, I think we'll want to use drug_chemical_conflate
aka set it to true
. Since there's been feedback to "merge all results for the same drug together"...
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Related Issues (20)
- update documentation pages
- update source of FDA orphan drug data
- annotate gene-phenotype associations in HPO API
- Find a way to reuse the BTE web app as the landing page for local install
- Record class doesn't handle qualifier value arrays in associations HOT 11
- "explain" query returning server errors HOT 2
- Scoring: broaden use of "knowledge level" and "agent type" into scoring function
- Examples of queries that time out (> 5 mins) HOT 1
- Issues with BioThings BindingDB object fields HOT 5
- BioThings BindingDB: can the relationship be more specific?
- Allow for disabling of cache time limit by setting the limit to 0
- Improve subquery timing HOT 2
- Retry after SRIResolverFailure HOT 1
- Updating / cleaning up translator-api-registry repo
- Update BioThings x-bte annotation to use `post_filter` HOT 5
- tune the use of AEOLUS indications from mychem.info HOT 8
- NodeNorm is sometimes not resolving entities/IDs HOT 1
- CQS work-around to incorporate Multiomics EHR HOT 1
- x-bte operations: replace BioThings `list_filter` with `jmespath` HOT 5
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