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Cellular-Semantics / CL_KG

Building a Cell Ontology Knowledge-Base from data, and LLMs
Apache License 2.0
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Obask refactoring #9

Closed ubyndr closed 3 months ago

ubyndr commented 3 months ago

Resolves #1

Currently we have the following;

Write Makefile that:

reads CSV input - detailing datasets and author_category fields (CSV to be provided by @dosumis) Pulls Anndata file from Census Runs Pandasaurus to generate RDF Run OBASK,

importing all output RDF files from step 1. Ontologies: CL; GO; Uberon

The process is almost fully automated. User need to prepare the file list for their owl files generated via anndata2rdf container and add them to collectdata full_ontologies files.

i.e.

file:///out/local_ontologies/0054013c-290b-437e-b98e-642aa77d6ebc.owl
file:///out/local_ontologies/01afd5b8-21be-4869-a686-1fe94ff6f4d8.owl
file:///out/local_ontologies/06a7ffec-2697-4d6f-96f6-d00a34bedb3d.owl
file:///out/local_ontologies/070d3916-633e-43af-bcc6-30358a327161.owl
file:///out/local_ontologies/0b3d19b3-df06-4265-9803-82f598e59dba.owl
file:///out/local_ontologies/10bb8aaa-ebc6-4026-94ae-a33ac16b5366.owl
file:///out/local_ontologies/1af9835f-469e-452f-a91d-f42af3f91042.owl
file:///out/local_ontologies/1c6e54ca-ef0c-4acc-9891-d3b7d2cd7a0e.ow
github-actions[bot] commented 3 months ago

cl_kb_pipeline/config/dumps/neo4j2owl-config.yaml file passed validation check