olukotunjosh/cdcl-data

CDCL research data

This repository contains the fixed data snapshots used by the CDCL GO/PPI and TREC Clinical Trials experiments. Paths are preserved relative to the CDCL code repository root so a downloaded snapshot can be copied into a code checkout. These are research datasets, not clinical decision-support resources.

Contents

• dataset/go_ppi/: STRING v12.0 human protein files, the GO ontology (go-basic.obo, release 2026-07-26), human GO annotations (goa_human.gaf.gz, generated 2026-05-21), and independent HuRI/Lit-BM data.
• preprocess/go_ppi/, preprocess/go_ppi_splits/, and preprocess/go_ppi_lc/: converted protein/pair views, GO indexes, the fixed protein-disjoint splits and negative pools, and learning-curve fractions.
• trec-clinical-trials/raw/: the five-part April 27, 2021 ClinicalTrials.gov corpus snapshot distributed for the TREC Clinical Trials track, 2021/2022 topics and relevance judgments, and the 2021 MeSH descriptor file ontology/desc2021.gz.
• preprocess/trec_ct/, preprocess/trec_ct_splits/, preprocess/trec_ct_lc/, and preprocess/trec_ct_budget/: converted records, fixed splits, negative pools, learning-curve fractions, and budget arms.
• embedding_cache/: reusable text-embedding caches and the 2021 MeSH index. These are accelerators; the raw ontology and dataset files are the sources.

The TREC patient topics are synthetic case descriptions, not real EHRs. Maintain the published train/validation/test boundaries when running experiments.

Source attribution and reuse

This repository combines materials with different terms; no single license applies to every file.

• Gene Ontology Consortium ontology and annotations: CC BY 4.0. Cite the consortium and the specific GO release used here. See https://geneontology.org/docs/go-citation-policy/ .
• STRING Consortium v12.0 download files: CC BY 4.0; credit STRING and note that these are human-filtered files. See https://string-db.org/cgi/access?footer_active_subpage=licensing .
• TREC Clinical Trials track topics, judgments, and the April 27, 2021 ClinicalTrials.gov snapshot: credit TREC/NIST and ClinicalTrials.gov. See https://www.trec-cds.org/2021.html and https://www.trec-cds.org/2022.html .
• MeSH 2021 descriptors: National Library of Medicine data. This is the 2021 version, not current MeSH. Credit NLM; do not imply NLM endorsement. Redistribution conditions: https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html .

For reproducibility, keep the dated ontology/corpus snapshots rather than silently replacing them with newer downloads. The included split manifests record counts, seeds, and source hashes.