Comments (1)
colleenXu
commented on September 28, 2024
During discussion with @tokebe Jackson today, we agreed:
- it doesn't make sense to attach the "edge-attributes list" to every operation - which is what I showed in my rough draft above
- Instead, this is an example of "API-level" information that BTE needs.
So we now propose creating an optional x-bte field for "API-level" information under the info section (same level as x-translator and x-trapi).
My thinking after the discussion today:
A. Previously-discussed "API-level" info that could go into that new x-bte field (as optional fields):
- from the previous post: "fields/edge-attributes whose unique values should be considered for the edge hash to create unique edges". Should be a list of strings.
- batch-query size (exists for multiple pending BioThings here and discussed in #584 (comment). Should be an integer
- request rate-limit (discussed in #556 (comment), see the first point and all its links). Should be an integer, we could set units (likely per-minute?)
B. Here's a rough draft example for the first two kinds of info, using Multiomics Wellness and the field name x-bte-info
click to expand
this is a modified snippet of the Multiomics Wellness KP yaml:
---
info:
x-bte-info:
batch-size: 100
fields-for-unique-edges: ## 2023-05-25: may later change?
- "MeSH:D005260" ## gender female
- "MeSH:D008297" ## gender male
- "UMLS CUI:C0001948" ## alcohol consumption?
- "UMLS CUI:C0005680" ## black population?
- "UMLS CUI:C0043157" ## population white
- "UMLS CUI:C0086409" ## hispanic population?
- "UMLS CUI:C0425379" ## other race?
- "UMLS CUI:C0453995" ## tobacco use and exposure?
- "UMLS CUI:C1515945" ## American Indian or Alaska Native?
- "UMLS CUI:C1519427" ## south asian people?
- "UMLS CUI:C2229974" ## children
- "UMLS CUI:C2698217" ## middle eastern?
- "UMLS CUI:C4316909" ## Marijuana Use?
- "UMLS CUI:C5205795" ## east asian people
- "UMLS CUI:C5418925" ## study age range
## - "NCIT:C61594" ## bonferroni p-value: would maybe work? but Gwênlyn said not needed
x-translator:
infores: "infores:biothings-multiomics-wellness"
component: KP
biolink-version: '3.1.1'
team:
- Multiomics Provider
- Service Provider
version: '1.7'
title: Multiomics Wellness KP API
termsOfService: https://biothings.io/about
contact:
email: [email protected]
name: Gwenlyn Glusman
x-role: responsible developers
x-id: https://github.com/biothings
description: Documentation of the BioThings API for Translator Multiomics Team's Wellness KP.
C. I'm still unclear on whether the "edge hashing" works for all scenarios. See my "side note" at the bottom of the previous post
from biothings_explorer.
Related Issues (20)
- BTE raising odd TypeError, not doing sub-queries for some automated test queries HOT 4
- Recognize MCQ queries and respond with HTTP 501
- Sprint 5: review all x-bte operations with KL/AT "not_provided", change to other terms if possible HOT 3
- Update Tests HOT 11
- Refinement of PFOCR Result-level Enrichment HOT 4
- Issue with logging of results HOT 6
- BTE creating self-edges via subclassing HOT 7
- Use globally-loaded metakg /v1/meta_knowledge_graph endpoint HOT 5
- Improve Redis memory management
- using query_id for creative-mode when input ID isn't the primary one HOT 6
- BTE receiving HTTP 400 from some BioThings APIs
- BTE OTel not properly carrying context between POST and EXEC
- not urgent: ideal KL/AT adjustments
- migrate to Multiomics CTKP, remove other clinicaltrials.gov-based x-bte operations HOT 16
- Pathfinder `dryrun` mode: showing what queries are created from the "template-generation"
- future: Pathfinder scoring HOT 1
- Ongoing Pathfinder improvements
- review translator resources in smartAPI for inclusion in BTE's API list HOT 1
- update "regulates" x-bte operations
- test only: see if Slackbot alerts with this HOT 1
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