File configuration

The configuration file is used to control how information is extracted from a file and how this information is put into the tsv files. For each file a row in the CSV file is required with the following columns:

generation_type (required)
Controls how the generator extracts information from the file. There is a limited number of Generation Types available.

file_url (required)
URL to the actual CSV file.

bco_url (optional)
URL to the BCO JSON file.

local_id (required)
Local ID to be used for the CFDE metadata.

persistent_id (required)
Persistent ID to be used for the CFDE metadata.

creation_time (required)
Time the file was created.

file_format (optional)
An EDAM CV term ID identifying the digital format of this file. (e.g., format:3752 ).

data_type (optional)
An EDAM CV term ID identifying the type of information stored in this file (e.g. RNA sequence reads).

mime_type (required)
MIME type of this file.

protein (optional)
Column definition that defines how to get the UniProtKB accession number.

gene (optional)
Column definition that defines how to get the Ensembl gene ID.

glycan (optional)
Column definition that defines how to get the GlyTouCan accession.

disease (optional)
Column definition that defines how to get the DOID of the disease.

anatomy (optional)
Column definition that defines how to get the UBERON ID for the anatomical term.

species (optional)
Column definition that defines how to get the NCBI taxonomy ID.