Reaction db creator

Typing name : TASK.gws_biota.ReactionDBCreator

Brick : gws_biota

Download the online files from expasy and rhea databases, and use them to load the “biota_reaction” table from the BIOTA database.

Base class

Input

link to compound

Resource that holds a text

Optional

Text

link to taxonomy

Resource that holds a text

Optional

Text

link to enzyme

Resource that holds a text

Optional

Text

Output

Text

Resource that holds a text

Optional

Text

Configuration

rhea_direction_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea-directions.tsv

rhea2ecocyc_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea2ecocyc.tsv

rhea2metacyc_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea2metacyc.tsv

rhea2macie_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea2macie.tsv

rhea2kegg_reaction_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea2kegg%5Freaction.tsv

rhea2ec_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea2ec.tsv

rhea2reactome_file

Optional

Type : string

Default value : https://ftp.expasy.org/databases/rhea/tsv/rhea2reactome.tsv

rhea_reactions_file

Optional

Type : string

Default value : https://www.rhea-db.org/rhea/?query=uniprot:*&columns=rhea-id,equation,chebi-id,ec&format=tsv

Input

Output

Configuration

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