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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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ETL Drug Approvals KP into RTX-KG2.10.2pre #412

Open saramsey opened 2 months ago

saramsey commented 2 months ago

Here are the links to TSV dumps (nodes and edges) for the Drug Approvals KP. URLs provided by @amykglen :

nodes: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.3.tsv edges: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.3.tsv

amykglen commented 1 month ago

just an FYI that a more recent version of the Drug Approvals KP is available (0.3.4 - released three weeks ago) - you can always see the URLs for the latest nodes/edges files here: https://github.com/RTXteam/PloverDB/blob/multiomics/app/config_dakp.json#L2-L3

saramsey commented 6 days ago

doing this development work in branch issue-412 and on EC2 host stevekg2pre.rtx.ai

saramsey commented 6 days ago

Also apparently the extract-clinicaltrialskg.sh script is not properly curl-ing the TSV file from the ISB server; it is set up with a workaround to copy the TSV file from the S3 bucket. I'm going to fix that in this issue as well.