RTX-KG2
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RTXteam
Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
See this issue for context: https://github.com/NCATSTranslator/Feedback/issues/422#event-11585511674
My understanding is that result node binding attributes are required: https://github.com/NCATSTranslator/ReasonerAPI/blob/master/TranslatorReasonerAPI.yaml#L665
##### 1. Build and load KG2: - [x] Create new build instance `kg291build.rtx.ai` - [x] Clone the RTX repo from Github `git clone https://github.com/RTXteam/RTX-KG2.git` - [x] Setup the KG2 build...
Tentatively slating this project for Erica in early summer 2024.
From Tyler's post in Architecture today: 
The "treats refactor" requires compliance with a minimum of Biolink 4.1.1
The kg2-versions.md shows that KG2.8.4 uses Biolink version 3.5.2, but the biolink node on the build shows Biolink version 3.1.2 The truth will be on the KG2.8.4 build instance. We...
``` Traceback (most recent call last): File "/home/ubuntu/kg2-code/dgidb_tsv_to_kg_jsonl.py", line 167, in make_kg2_graph(input_file_name, nodes_output, edges_output, test_mode) File "/home/ubuntu/kg2-code/dgidb_tsv_to_kg_jsonl.py", line 83, in make_kg2_graph PMIDs] = fields ValueError: too many values to unpack...
DrugBank has a bunch of extra information on their website; stuff like mechanisms of action:  I'm wondering if: a) this information exists in some downloadable part of DrugBank...
From @sundareswarpullela: Bug found in ARAX Pytest https://github.com/RTXteam/RTX/blob/4c776b4a27d96e1462173abe7963792608d8b879/code/ARAX/test/test_ARAX_expand.py#L247-L257C1 Example: `{'nodes': {'n00': {'ids': ['MONDO:0001280', 'MONDO:0008542', 'MONDO:0005036'], 'categories': ['biolink:DiseaseOrPhenotypicFeature', 'biolink:PhenotypicFeature', 'biolink:Disease'], 'is_set': True, 'constraints': [], 'option_group_id': None}, 'n01': {'ids': None, 'categories': ['biolink:DiseaseOrPhenotypicFeature',...