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83c84e4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 | # 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) |
|