Closed colleenXu closed 1 year ago
From today's group meeting:
What's checked off is done, don't need to think about it unless bugs arise JC is working on provenance (3), some aux-graph/results stuff that isn't subclassing (4), and directing Rohan on qualifiers (2)
Qualifiers: poll isn't complete, but we can move forward with "MetaEdge has union of qualifier sets" -> means we can work on the first two issues in that section
CX: I think we want to support sources ingest from Multiomics/Text-Mining ASAP (specific part of provenance work). Since their APIs will provide this info soon (BioThings API parser updates discussed in Translator #bte channel)
And a note regarding PFOCR "augmentation" work: https://github.com/biothings/biothings_explorer/issues/538 and https://github.com/biothings/biothings_explorer/issues/420...
Unclear how results-refactoring (4) affects this work...
@tokebe Here's some possible test-queries for node-expansion. Let me know if you need more.
[UPDATED 2023-05-22 1:00PM Pacific]
@tokebe also just in case, here's the infores IDs for each ontology in node-expansion right now
They aren't always the same as the ID-prefix :P
GO -> infores:go
DOID -> infores:disease-ontology
MONDO -> infores:mondo
CHEBI -> infores:chebi
HP -> infores:hpo
UMLS -> infores:umls
With subclassing done, we're at a point where this issue is basically remaining for tracking any last-minute bugfixing, and waiting to close when TRAPI 1.4 is deployed to Prod.
In today's meeting, the main way we'll know that we've implemented everything for TRAPI 1.4 is if we pass TRAPI 1.4 validation in the ARAX UI (https://github.com/biothings/biothings_explorer/issues/587#issuecomment-1611893691).
However, I'd also like to check:
Regarding what else is needed to deploy TRAPI 1.4 to Prod (all instances on TRAPI 1.4)...
TRAPI spec 1.4.2 reviewed and updates made to SmartAPI yamls https://github.com/biothings/biothings_explorer/issues/594#issuecomment-1629687393, no other changes needed. Related to my earlier comment https://github.com/biothings/biothings_explorer/issues/613#issuecomment-1611996930
Closing this -- the last few stragglers are more separate from this major push, now.
[WILL BE UPDATED AS WE DISCUSS; last updated 2022-05-22]
This is an overview of what the TRAPI 1.4 topics are, what their github issues are, and their statuses.
General topics
Consensus reached within our team:
1. Async endpoints - done, but see note
Note: not advertised yet (since we haven't updated SmartAPI yamls for our tools -> which is in section 5 Misc)
2. qualifiers in
/meta_knowledge_graph
- doneLess important:
/meta_knowledge_graph
response (phase 3)Note: Assuming that "qualifier-set" merging is required. Based on TRAPI/Translator group (Slack poll) on whether to do "qualifier-set merging" (our questions and references)
3. provenance refactor - done, but see notes
Notes:
4. aux-graph / result.analyses refactor - ongoing, on node-expansion/subclassing
Decision was made to implement TRAPI 1.4 "without" node-expansion/subclassing first, and then work on this part last.
First round, these issues WITHOUT node-expansion/subclassing work:
Second round, these issues with node-expansion/subclassing work:
5. Misc - ongoing, only the SmartAPI yaml part is critical
May be important to have the yaml to advertise the TRAPI 1.4 instances, and then the rest aren't as critical?
Less important:
Related but much less important