cbizon

**Is your feature request related to a problem? Please describe.** In biolink 2.x, there are mappings for RO:0002213 to etc. positively regulates. But that is now a deprecated predcate, replaces...

2 changes: 1. replaces trainer.is_world_master() with trainer.is_world_process_zero() allowing newer version of Transformer library 2. Writes the entire label to the label rather than just the first character

FMA identifiers don't resolve

1

There are many mappings from biolink predicates to FMA terms. They mostly look like readable identifiers. ``` FMA:connected_to FMA:continuous_with FMA:homonym_of ``` Using the expansion in biolink_model_prefix_map.json, these get expanded to...

Bug? "has allergenic trigger" subproperty of "causes or contributes to condition"

9

From ontobee:  but if "shrimp allergy" "has allergenic trigger" "shrimp" then this implies: "shrimp allergy" "causes or contributes to condition" "shrimp" "has autoimmune trigger" is also a subproperty of...

Error in get_descendents with curies

3

v. 1.1.2 If I lookup descendents of `noncoding RNA product` it works: ``` tk.get_descendants("noncoding RNA product") ['noncoding RNA product', 'microRNA', 'siRNA'] ``` But if I use the curie form (which...

liver diseases subtypes of liver? Chemical returned as phenotype

2

https://arax.ncats.io/?r=06f9907b-bc1b-45e5-a21b-e71bc6d7869c This query is (?DiseaseOrPhenotypicFeature)-[related_to]->(Liver). The results look good, but many also contain an edge like (Hepatitis)-[subclass of]->liver, which I don't think makes sense. Also, acetylcarnitine is returned as a...

Glucose returned as a gene.

5

Running this query against KGX2 (what genes are downregulated by Gefitanib?) ```{ "edges": { "e00": { "predicates": ["biolink:entity_negatively_regulates_entity"], "object": "n1", "subject": "n0" } }, "nodes": { "n0": { "categories": [...

Protein returned as a chemical

3

This query asks what chemical entity interacts with a particular gene: ``` {"query_graph": { "nodes": { "$source": { "categories": [ "biolink:ChemicalEntity" ] }, "$target": { "ids": [ "NCBIGene:23162" ], "categories":...

Unexpected use of qualifiers

1

While reviewing some ARAGORN creative mode queries, I ran across this edge: ``` { "subject": "PUBCHEM.COMPOUND:5917", "object": "MONDO:0005027", "predicate": "biolink:regulates", "qualifiers": [ { "qualifier_type_id": "biolink:object_direction_qualifier", "qualifier_value": "increased" }, { "qualifier_type_id":...

Trouble linking aeolus compounds

3

If I do a simple query q=siltuximab, I get 5 results, with these identifiers and keys: ``` 57894-421 ['_id', '_score', 'ndc'] 57894-420 ['_id', '_score', 'ndc'] CHEMBL1743070 ['_id', '_score', 'chembl', 'drugcentral']...