Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
| # NegBioDB Configuration | |
| # Source of truth for thresholds, paths, and pipeline settings. | |
| # === Inactivity Thresholds === | |
| inactivity_threshold_nm: 10000 # 10 uM in nM; compound inactive if IC50/Ki/Kd > this | |
| positive_pchembl_min: 6.0 # pChEMBL >= 6 for positives (IC50 <= 1 uM) | |
| borderline_exclusion: | |
| lower: 4.5 # Exclude pChEMBL >= 4.5 from negative pool | |
| upper: 6.0 # Matches positive_pchembl_min; effective gap: [4.5, 6.0) | |
| davis_inactive_pkd_threshold: 5.0 # DAVIS: inactive if pKd <= 5 (NOT strictly < 5) | |
| davis_active_pkd_threshold: 7.0 # DAVIS: active if pKd >= 7 (Kd <= 100 nM) | |
| # === ChEMBL ETL Policy === | |
| # Core benchmark should remain conservative by default. | |
| # Optional activity_comment route can be enabled for recall-focused expansion. | |
| chembl_etl: | |
| include_activity_comment: false | |
| inactive_activity_comments: | |
| - "Not Active" | |
| - "Inactive" | |
| - "Not active" | |
| - "inactive" | |
| # === ML Split Configuration === | |
| split_ratios: | |
| train: 0.7 | |
| val: 0.1 | |
| test: 0.2 | |
| random_seed: 42 | |
| # === Processing === | |
| pubchem_chunksize: 100000 # Rows per chunk for streaming PubChem processing | |
| pubchem_etl: | |
| chunksize: 100000 | |
| human_only: true | |
| bindingdb_etl: | |
| chunksize: 100000 | |
| inactive_threshold_nm: 10000 | |
| human_only: true | |
| # === Confidence Tier Ordering (gold = highest) === | |
| confidence_tiers: | |
| - gold | |
| - silver | |
| - bronze | |
| - copper | |
| # === Paths (relative to project root) === | |
| paths: | |
| data_dir: data | |
| exports_dir: exports | |
| migrations_dir: migrations | |
| database: data/negbiodb.db | |
| # === Download URLs === | |
| downloads: | |
| pubchem: | |
| # Legacy keys kept for backward compatibility | |
| url: "https://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/Extras/bioactivities.tsv.gz" | |
| dest: data/pubchem/bioactivities.tsv.gz | |
| min_size_bytes: 1000000000 | |
| # Required files for full PubChem ETL | |
| bioassays_url: "https://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/Extras/bioassays.tsv.gz" | |
| bioassays_dest: data/pubchem/bioassays.tsv.gz | |
| bioassays_min_size_bytes: 10000000 | |
| aid_uniprot_url: "https://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/Extras/Aid2GeneidAccessionUniProt.gz" | |
| aid_uniprot_dest: data/pubchem/Aid2GeneidAccessionUniProt.gz | |
| aid_uniprot_min_size_bytes: 1000000 | |
| sid_cid_smiles_url: "https://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/Extras/Sid2CidSMILES.gz" | |
| sid_cid_smiles_dest: data/pubchem/Sid2CidSMILES.gz | |
| sid_cid_smiles_min_size_bytes: 1000000 | |
| sid_lookup_db: data/pubchem/sid_lookup.sqlite | |
| chembl: | |
| dest_dir: data/chembl | |
| bindingdb: | |
| servlet_url: "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_All_202603_tsv.zip" | |
| file_url: "https://www.bindingdb.org/rwd/bind/downloads/BindingDB_All_202603_tsv.zip" | |
| dest_dir: data/bindingdb | |
| min_size_bytes: 500000000 | |
| davis: | |
| base_url: "https://raw.githubusercontent.com/dingyan20/Davis-Dataset-for-DTA-Prediction/master" | |
| files: | |
| - drugs.csv | |
| - proteins.csv | |
| - drug_protein_affinity.csv | |
| dest_dir: data/davis | |
| min_rows: 25000 | |
| # ============================================================ | |
| # Clinical Trial Failure Domain | |
| # ============================================================ | |
| ct_domain: | |
| # === Paths === | |
| paths: | |
| database: data/negbiodb_ct.db | |
| migrations_dir: migrations_ct | |
| data_dir: data/ct | |
| # === Downloads === | |
| downloads: | |
| aact: | |
| # AACT pipe-delimited snapshot; URL changes monthly — update as needed | |
| # Get latest from: https://aact.ctti-clinicaltrials.org/pipe_files | |
| dest_dir: data/ct/aact | |
| required_disk_gb: 6.0 | |
| # 13 of 46 AACT tables needed for v1 | |
| tables: | |
| - studies | |
| - interventions | |
| - conditions | |
| - outcomes | |
| - outcome_analyses | |
| - outcome_measurements | |
| - designs | |
| - sponsors | |
| - calculated_values | |
| - browse_interventions | |
| - browse_conditions | |
| - drop_withdrawals | |
| - documents | |
| opentargets: | |
| url: "https://huggingface.co/api/datasets/opentargets/clinical_trial_reason_to_stop/parquet/default/train/0000.parquet" | |
| dest: data/ct/opentargets/stop_reasons.parquet | |
| cto: | |
| url: "https://huggingface.co/api/datasets/chufangao/CTO/parquet/human_labels/test/0.parquet" | |
| dest: data/ct/cto/cto_outcomes.parquet | |
| shi_du: | |
| # Figshare: Shi & Du 2024, doi:10.6084/m9.figshare.c.6860254.v1 | |
| efficacy_url: "https://ndownloader.figshare.com/files/42520528" | |
| efficacy_dest: data/ct/shi_du/efficacy_df.csv | |
| safety_url: "https://ndownloader.figshare.com/files/42520534" | |
| safety_dest: data/ct/shi_du/safety_df.csv | |
| # === Failure Classification === | |
| failure_category_precedence: | |
| - safety | |
| - efficacy | |
| - pharmacokinetic | |
| - enrollment | |
| - strategic | |
| - regulatory | |
| - design | |
| - other | |
| # === Drug Name Resolution === | |
| drug_resolution: | |
| fuzzy_threshold: 0.90 | |
| pubchem_rate_limit_per_sec: 5 | |
| pubchem_cache: data/ct/pubchem_name_cache.json | |
| overrides_file: data/ct/drug_name_overrides.csv | |
| # === NLP Classifier === | |
| classifier: | |
| max_features: 10000 | |
| ngram_range: [1, 2] | |
| cv_folds: 5 | |
| # ============================================================ | |
| # Protein-Protein Interaction Negative Domain | |
| # ============================================================ | |
| ppi_domain: | |
| # === Paths === | |
| paths: | |
| database: data/negbiodb_ppi.db | |
| migrations_dir: migrations_ppi | |
| data_dir: data/ppi | |
| # === Downloads === | |
| downloads: | |
| huri: | |
| hi_union_url: "https://www.interactome-atlas.org/data/HI-union.tsv" | |
| # hi_iii_url removed — HI-III-20.tsv returns 404 as of 2026-03 | |
| idmapping_url: "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz" | |
| dest_dir: data/ppi/huri | |
| intact: | |
| url: "https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact_negative.txt" | |
| dest: data/ppi/intact/intact_negative.txt | |
| min_size_bytes: 1000000 | |
| humap: | |
| base_url: "https://humap3.proteincomplexes.org/static/downloads/humap3" | |
| neg_train: ComplexPortal_reduced_20230309.neg_train_ppis.txt | |
| neg_test: ComplexPortal_reduced_20230309.neg_test_ppis.txt | |
| pos_train: ComplexPortal_reduced_20230309.train_ppis.txt | |
| pos_test: ComplexPortal_reduced_20230309.test_ppis.txt | |
| dest_dir: data/ppi/humap | |
| string: | |
| links_url: "https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz" | |
| mapping_url: "https://stringdb-downloads.org/download/mapping_files/uniprot/human.uniprot_2_string.2018.tsv.gz" | |
| dest_dir: data/ppi/string | |
| biogrid: | |
| url: "https://downloads.thebiogrid.org/Download/BioGRID/Latest-Release/BIOGRID-ALL-LATEST.tab3.zip" | |
| dest_dir: data/ppi/biogrid | |
| # === Evidence Type Priority (best first) === | |
| evidence_type_priority: | |
| - experimental_non_interaction | |
| - literature_reported | |
| - ml_predicted_negative | |
| - low_score_negative | |
| - compartment_separated | |
| # === STRING ETL Settings === | |
| string_etl: | |
| min_protein_degree: 5 | |
| max_negative_pairs: 500000 | |
| # === Benchmark Split === | |
| split_ratios: {train: 0.7, val: 0.1, test: 0.2} | |
| random_seed: 42 | |