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Semantics for translating the flatfile representation of a BioCyc reaction to columns of the BioWarehouse schema. The left column indicates source data from BioCyc; the right column indicates that data is transferred into the BioWarehouse. One row is added to the Reaction table for each flatfile reaction; rows to other tables are added as indicated. Table.Column indicates a column of a schema table. Attributes followed by [*] may occur multiple times per record. Note that some tables in this figure may not appear in Figure 2 because that figure is an abstraction of the full schema. |
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| BioCyc Attribute |
Warehouse Semantics |
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| LEFT [*] |
A row is added to A row is added to table Reactant. Value should match a Chemical.Name; its WID is stored as Product .WID. If a COEFFICIENT follows immediately, its value is stored as Reactant.Coefficient. Otherwise the value 1 is stored. |
| RIGHT [*] |
A row is added to table product. Value should match a chemical.Name; its WID is stored as product .WID. If a COEFFICIENT follows immediately, its value is stored as Product .Coefficient. Otherwise the value 1 is stored. |
| COEFFICIENT |
Reactant.Coefficient or Product.Coefficient for the immediately preceding LEFT or RIGHT attribute resp. |
| COMMON-NAME |
A row is added to SynonymTable where SynonymTable.Syn is this value and SynonymTable. OtherWID is the WID of this reaction. |
| DELTAG0 |
Reaction.DeltaG |
| EC-NUMBER |
Reaction.ECNumber |
| SPONTANEOUS? |
Reaction.Spontaneous |
| SYNONYMS [*] |
A row is added to SynonymTable where SynonymTable. Syn is this value and SynonymTable.OtherWID is the WID of this reaction |
| UNIQUE-ID |
A row is added to DBID where DBID.XID is this value. and DBID.OtherWID is the WID of this reaction. |
Lee et al. BMC Bioinformatics 2006 7:170 doi:10.1186/1471-2105-7-170 |
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