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| # Data Schema — DDI Checker | |
| 27 normalised tables produced by `parser/run_all.py` from the DrugBank XML. | |
| --- | |
| ## Key Statistics | |
| | | Full (step1) | Approved-only (step3) | | |
| |---|---|---| | |
| | Drugs | 19,842 | **4,795** | | |
| | DDI pairs (directed) | 2,911,156 | — | | |
| | DDI pairs (undirected) | 1,455,878 | **824,249** | | |
| | Products | 475,225 | 473,660 | | |
| | Polypeptides | 5,394 | 3,439 | | |
| | Interactants (BE-IDs) | 5,449 | 3,458 | | |
| | Pathways | 48,627 | 48,622 | | |
| | References | 43,553 | 35,721 | | |
| | Drug-protein links | 34,931 | 20,700 | | |
| --- | |
| ## FK Convention | |
| Every `drugbank_id` column is a FK to `drugs.drugbank_id` unless noted. | |
| --- | |
| ## Tables | |
| ### 1. `drugs` | |
| One row per drug. Scalar fields + inlined ClassyFire classification. | |
| | Column | Description | | |
| |---|---| | |
| | **drugbank_id** | PK — primary DrugBank ID (e.g. DB00001) | | |
| | name | Drug name | | |
| | drug_type | `small molecule` or `biotech` | | |
| | description | Full drug description | | |
| | cas_number | CAS Registry Number | | |
| | unii | FDA Unique Ingredient Identifier | | |
| | average_mass / monoisotopic_mass | Molecular masses (float) | | |
| | state | `solid` / `liquid` / `gas` | | |
| | indication | Therapeutic indications | | |
| | pharmacodynamics | Pharmacodynamics description | | |
| | mechanism_of_action | Mechanism of action | | |
| | toxicity | Toxicity and overdose information | | |
| | metabolism | Metabolic pathway description | | |
| | absorption / half_life / protein_binding | PK parameters | | |
| | route_of_elimination / volume_of_distribution / clearance | PK parameters | | |
| | classification_description | ClassyFire description | | |
| | classification_direct_parent / kingdom / superclass / class / subclass | ClassyFire hierarchy | | |
| | created_date / updated_date | Record timestamps | | |
| ### 2. `drug_ids` | |
| | Column | Description | | |
| |---|---| | |
| | drugbank_id | FK → drugs | | |
| | legacy_id | ID value (DB#####, BIOD#####, BTD#####, APRD#####, EXPT#####, NUTR#####) | | |
| | is_primary | `True` for the canonical PK used in `drugs` | | |
| ### 3. `drug_attributes` | |
| Catch-all for 9 multi-valued list fields. Filter by `attr_type`. | |
| | attr_type | value | value2 | value3 | | |
| |---|---|---|---| | |
| | `group` | `approved` / `withdrawn` / `experimental` / `investigational` / `illicit` / `nutraceutical` / `vet_approved` | — | — | | |
| | `synonym` | synonym text | language code | coder | | |
| | `affected_organism` | organism name | — | — | | |
| | `food_interaction` | description | — | — | | |
| | `sequence` | FASTA string | format | — | | |
| | `ahfs_code` | AHFS code | — | — | | |
| | `pdb_entry` | PDB ID | — | — | | |
| | `classification_alt_parent` | ClassyFire alt parent | — | — | | |
| | `classification_substituent` | ClassyFire substituent | — | — | | |
| ### 4. `drug_properties` | |
| | Column | Description | | |
| |---|---| | |
| | drugbank_id | FK → drugs | | |
| | property_class | `calculated` (ChemAxon/ALOGPS) or `experimental` | | |
| | kind | Property name (logP, SMILES, Melting Point, Water Solubility, IUPAC Name, …) | | |
| | value | Property value | | |
| | source | Source tool (ChemAxon, ALOGPS, …) | | |
| ### 5. `external_identifiers` | |
| | Column | Description | | |
| |---|---| | |
| | entity_type | `drug` / `polypeptide` / `salt` / `drug_link` | | |
| | entity_id | PK of the entity | | |
| | resource | Database name (ChEBI, ChEMBL, PubChem, KEGG, BindingDB, PharmGKB, ZINC, RxCUI, HGNC, …) | | |
| | identifier | ID value or URL | | |
| ### 6. `references` + 7. `reference_associations` | |
| Globally deduplicated bibliography. Dedup keys: articles → pubmed_id; textbooks → isbn+citation; links → url; attachments → title+url. | |
| ### 8. `salts`, 9. `products`, 10. `drug_commercial_entities`, 11. `mixtures`, 12. `prices` | |
| Standard commercial/formulation tables. | |
| ### 13. `categories` + 14. `drug_categories` | |
| Normalized MeSH pharmacological categories. | |
| ### 15. `dosages`, 16. `atc_codes`, 17. `patents` | |
| `atc_codes` has full 4-level hierarchy: `l1_code/l1_name` … `l4_code/l4_name`. | |
| ### 18. `drug_interactions` | |
| Core edge table (directed). Both A→B and B→A stored. Use `drug_interactions_dedup.csv` for undirected edges. | |
| | Column | Description | | |
| |---|---| | |
| | drugbank_id | Source drug FK | | |
| | interacting_drugbank_id | Target drug FK | | |
| | description | Interaction description text | | |
| ### 19. `drug_snp_data`, 20. `pathways`, 21. `pathway_members`, 22. `reactions` | |
| Pharmacogenomics (SNP), SMPDB pathways, metabolic reactions. | |
| ### 23. `interactants` + 24. `drug_interactants` | |
| Binding entities (targets, enzymes, carriers, transporters). | |
| | Column | Description | | |
| |---|---| | |
| | interactant_id | BE-ID (e.g. BE0000048) | | |
| | role | `target` / `enzyme` / `carrier` / `transporter` | | |
| | known_action | `yes` / `no` / `unknown` | | |
| | actions | Pipe-delimited (e.g. `inhibitor\|substrate`) | | |
| | inhibition_strength / induction_strength | Enzyme-only | | |
| ### 25. `polypeptides`, 26. `interactant_polypeptides`, 27. `polypeptide_attributes` | |
| UniProt protein records, globally deduplicated. Attributes: synonyms, Pfam domains, GO classifiers. | |
| --- | |
| ## `drug_interactions_dedup.csv` | |
| Undirected DDI pairs with integer PK. Present in `step2_dedup/` and `step3_approved/`. | |
| | Column | Description | | |
| |---|---| | |
| | **interaction_id** | PK — auto-increment integer (1-based) | | |
| | drugbank_id_a | Drug A (lexicographically smaller ID) | | |
| | drugbank_id_b | Drug B (lexicographically larger ID) | | |
| | description | Merged description (both directions joined with ` \| ` if they differ) | | |