LIGAND: Database of Chemical Compounds and Reactions in Biological Pathways
- LIGAND comes from the Bioinformatics Center Institute for Chemical Research at Kyoto University and is described thusly:
- LIGAND is a composite database consisting of the following three
databases:
- COMPOUND - for a collection of chemical compounds that are related to various cellular processes
- REACTION - for a collection of reactions, mostly enzymatic reactions, involving those compounds
- ENZYME - for the Enzyme Nomenclature by IUBMB and IUPAC
- [online; accessed 11/13/02; http://www.genome.ad.jp/ligand/]
CLSD implements schemas for the Compound and Reaction databases within LIGAND.
Schema
REACTION and COMPOUND tables are found under the 'ligand' schema.REACTION tables
| Table | Field | Type | Description |
|---|---|---|---|
| PATHREAC -- Links Pathways to Reactions in that Pathway | PATH_ID | VARCHAR(10) | |
| REAC_ID | VARCHAR(10) | ||
| REACENZY -- Links Reaction to the Enzyme for that Reaction | REAC_ID | VARCHAR(10) | |
| EC_ID | VARCHAR(100) | This field can hold multiple ec_ids, separated by whitespace | |
| REACREAC -- Links Reaction to the Reactants for that Reaction | REAC_ID | VARCHAR(10) | |
| COMP_ID | VARCHAR(10) | Compound identifier | |
| QUANTITY | smallint | Quanitity of the reactant used in the reaction | |
| REACPROD -- Links Reaction to the Products for that Reaction | REAC_ID | VARCHAR(10) | |
| COMP_ID | VARCHAR(10) | Compound identifier | |
| QUANTITY | smallint | Quantity of the given product used in the reaction |
COMPOUND tables
| Table | Field | Type | Description |
|---|---|---|---|
| COMPLINK | COMP_ID | VARCHAR(10) | |
| DB_NAME | VARCHAR(10) | ||
| DB_KEY | VARCHAR(20) | ||
| COMPENZY | COMP_ID | VARCHAR(10) | |
| EC_ID | VARCHAR(10) | ||
| TYPE | VARCHAR(12) | ||
| COMPNAME | COMP_ID | VARCHAR(10) | |
| NAME | VARCHAR(100) | ||
| COMPPATH | COMP_ID | VARCHAR(10) | |
| PATH_ID | VARCHAR(10) | ||
| COMPOUND | COMP_ID | VARCHAR(10) | |
| NAME | VARCHAR(100) | ||
| FORMULA | VARCHAR(50) | ||
| PATHWAY | PATH_ID | VARCHAR(10) | |
| NAME | VARCHAR(100) |
