acevedol
acevedol
From @dkoslicki via Slack: ``` Question for the RTX-KG2 folks: when you ingest MONDO, is the “rare” tag preserved anywhere? Speaking with the RoboCop team, they use this to identify...
These issues came up when running the KGX validation on kg2-pre ``` Range of slot 'in taxon' (organism taxon) does not line with the domain of its inverse (taxon of)...
The [Translator Implementation Progress Tracker](https://docs.google.com/spreadsheets/d/1LEV3FyXBt3xm4bC5TQkVbrZalrr6OV2LnPtuLj1RVB4/edit#gid=1034097652) says KPs need to provide test data with qualifiers by 9/1. I assume this means test triples, but I need to double check.
Would like to avoid future typos like "ttp://urls..."
https://github.com/RTXteam/RTX/issues/1812 Implement specificity index in KG2 - [x] Add specificity index property to make_node function in `kg2_util.py` - [ ] Calculate node distance from root? - [ ] Calculate distance/...
Check this file on NCATS /NCATSTranslator/testing/blob/main/onehop/test_triples/KP/Expander_Agent/RTX_KG2.json for correctness and bring it up to date. It's supposed to be updated as part of the KG2c process.
There will likely be changes to the requirements for edge merging. Currently `provided_by` is a list type containing a list of KPs that reported the edge. This causes potential issues...
##### 1. Partial Build and load KG2: - [x] Run a dry build using `bash -x ~/kg2-code/build-kg2-snakemake.sh -n` - [x] Check `~/kg2-build/build-kg2-snakemake-n.log` to ensure all expected rules are included -...
`Rule TSV` generates `edges.tsv` and `nodes.tsv` for loading into neo4j, however `kg2_json_to_kgx_tsv.py` also produces a different `edges.tsv` and `nodes.tsv` for loading into KGX. Would it be a better idea to...
I'm currently running `kg2-json_to_kgx_tsv.py` manually when the build is finished running. This should ideally be included in Rule TSV. `Rule TSV` currently generates the TSVs for loading into Neo4j, so...