Amy Glen

Two pairs of 'inverse' predicates have no canonical_predicate specified?

4

**Question:** This question relates to these two pairs of inverse predicates in Biolink 3.0.3: 1. `increases activity of` / `activity increased by` 2. `positively regulates` / `positively regulated by` For...

**Describe the bug** The `neo4j-upload` CLI command fails to successfully upload my KGX-formatted json lines files and complains with the following: ``` [KGX][jsonl_source.py][ parse] WARNING: Parse function cannot resolve the...

Mis-categorization of drug-like nodes as biolink:Procedures

14

There seem to be a number of instances where drug-like nodes are mis-categorized as Procedures in KG2 - here are some examples (from KG2.7.2): 1. Node `LOINC:LA14350-5` is named "Acetaminophen",...

Start naming KG2 TSV tarball with version number (in S3)?

10

Instead of extracting KG2pre data via Neo4j, going forward the KG2c build process is going to ingest `kg2-tsv-for-neo4j.tar.gz` (downloaded from the `rtx-kg2` S3 bucket). Wondering if it would be reasonable...

Edges have a qualified direction of 'decreased' but no qualified predicate

6

About 2,000 edges in KG2.8.2pre have a `qualified_object_direction` of 'decreased', but they have no `qualified_predicate` or `qualified_object_aspect`. This seems like a bug? ``` match (n)-[e]->(m) where e.qualified_predicate is null and...

KEGG disease nodes are categorized as Pathways

7

Andy Crouse reported an issue where very un-pathway-like things are being returned when querying for `biolink:Pathway`s associated with a disease. See this query: https://arax.ncats.io/?r=41416 It looks like the synonym clusters...

More specific categories for Interleukin 2 nodes (from LOINC/UMLS)

1

these three nodes have a category of NamedThing in KG2.8.2pre, which prevents them from being merged with the other nodes representing Interleukin 2 that have Protein/Gene or SmallMolecule categories during...

in today's Relay session on "Similarity Tools, Searches, and Embedding" Chris B. mentioned that the Biolink model includes constraints for predicates as to which subject/object categories are allowed with a...

Make synonymizer/kg2c builds more robust/transparent

1

there are a number of relatively small improvements that would go a long ways to making synonymizer (and kg2c) builds run smoother: - [x] get rid of synonymizer test build?...

KG2c domain_range_exclusion property contains booleans in strings?

4

I noticed today that in the `kg2c_lite.json` file, the `domain_range_exclusion` property on edges appears to be a python boolean in a string - e.g., `"False"` rather than `false`: ``` ubuntu@ip-172-31-52-1:~/plater-plover$...