acevedol
acevedol
##### 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...
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...
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',...
Recurring issue on `kg290build.rtx.ai` ``` [Wed Feb 21 16:37:57 2024] Error in rule Ontologies_Conversion: jobid: 8 output: /home/ubuntu/kg2-build/kg2-ont-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ont-edges.jsonl log: /home/ubuntu/kg2-build/build-multi-ont-kg.log (check log file(s) for error message) shell: bash -x...
Traceback (most recent call last): File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 1277, in save_pickle) File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 147, in make_kg2 save_pickle) File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 71, in load_ont_fi le_return_ontology_and_metadata ontology = kg2_util.make_ontology_from_local_file(file_name, save_pickle=sav e_pickle)...
Building KG2 often finishes or crashes at odd times when I am unable to check on it for a few hours, leading to unnecessary run time on the instance that...
We need an additional identifier to access records a bit more easily. Let's put a unique numeric identifier on each record.
In `build-multi-ont-kg.log` a bunch of these errors pop up but don't exit. Making note to look into this > 2023-05-18 22:59:42,583 ERROR org.semanticweb.owlapi.util.OWLAnnotationPropertyTransformer - Attempt to transform an axiom to...