Table 1

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.

BioCyc Attribute

Warehouse Semantics


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

Open Data