BioGRID CHEMTAB Formatted Downloads
BioGRID CHEMTAB Formatted Downloads
The BioGRID CHEMTAB format is a custom BioGRID format that is designed to provide the entirety of our chemical interaction curation efforts in a format that is simple to read in Microsoft Excel or to script into Bioinformatics applications. All Columns are separated by tabulations.
How to Detect a BioGRID CHEMTAB file
BioGRID CHEMTAB files are denoted by the extension .chemtab.txt or .chemtab.zip
Header Definitions
The first line of a BioGRID CHEMTAB file is the heading line and starts with a hash (#). This line is purely for informational purposes and gives a brief description of the content contained in each column. If you are scripting the use of this file, you can simply ignore it.
Column Definitions
The column contents of BioGRID CHEMTAB files should be as follows:
- BioGRID Chemical Interaction ID. A unique identifier for each interaction within the BioGRID database.
- BioGRID ID for Gene Interactor. The identifier in the BioGRID database that corresponds to the interacting gene. These identifiers are best used for creating links to the BioGRID from your own websites or applications. To link to a page within our site, simply append the URL: http://www.thebiogrid.org/ID/ to each ID. For example, http://www.thebiogrid.org/31623/.
- Entrez Gene ID for Gene Interactor. The identifier from the Entrez-Gene database that corresponds to the interacting gene. If no Entrez Gene ID is available, this will be a “-”.
- Systematic name for Gene Interactor. A plain text systematic name if known for the interacting gene. Will be a “-” if no name is available.
- Official symbol for Gene Interactor. A common gene name/official symbol for the interacting gene. Will be a “-” if no name is available.
- Synonyms/Aliases for Gene Interactor. A “|” separated list of alternate identifiers for the interacting gene. Will be “-” if no aliases are available.
- Organism ID for Gene Interactor. An NCBI taxonomy ID for the interacting gene.
- Organism Name for Gene Interactor. The official name of the organism for the interacting gene.
- Action. Chemical action for this interaction.
- Interaction Type. Methods such as target, enzyme, carrier, transporter, etc.
- First author surname of the publication in which the interaction has been shown, optionally followed by additional indicators, e.g. Stephenson A (2005)
- Pubmed ID of the publication in which the interaction has been shown.
- BioGRID Publication ID. This is the internal BioGRID reference id for this publication. Useful for linking to BioGRID publication pages, such as: http://thebiogrid.org/101382/publication/
- BioGRID Chemical ID. The internal BioGRID identifier for the interacting chemical.
- Chemical Name. Common name for the Chemical.
- Chemical Synonyms. A “|” separated list of synonyms for this chemical. Will be “-” if non-exist.
- Chemical Brands. A “|” separated list of brand names for this chemical. Will be “-” if non-exist.
- Molecular Formula. A molecular formula for this chemical, will be “-” if unknown.
- Chemical Type. Will be “-” if unknown.
- Chemical ATC Codes. A “|” separated list of ATC codes for the chemical. Will be “-” if unknown.
- Chemical CAS Number. Will be “-” if unknown.
- Curated By. Name of the database interaction was curated by.
- Method. The method used to create the chemical interaction. Will be “-” if not applicable.
- Method Description. A description of the method used to create the chemical interaction. Will be “-” if not applicable.
- Related BioGRID Gene ID. A BioGRID Gene ID for any gene related to this interaction. Will be “-” if not applicable.
- Related Entrez Gene ID. An Entrez Gene ID for any gene related to this interaction. Will be “-” if not applicable.
- Related Systematic Name. A Systematic Name for any gene related to this interaction. Will be “-” if not applicable.
- Related Official Symbol. An official symbol for any gene related to this interaction. Will be “-” if not applicable.
- Related Synonyms. A set of synonymns for any gene related to this interaction. Multipes will be “|” separated. Will be “-” if not applicable.
- Related Organism ID. An NCBI organism ID for any gene related to this interaction. Will be “-” if not applicable.
- Related Organism. An Organism name for any gene related to this interaction. Will be “-” if not applicable.
- Related Type. The type of relationship for any gene related to this interaction (example: target, recruited e3 ligase etc.). Will be “-” if not applicable.
- Notes. A set of curator notes about this interaction. Multiple notes will be separated by “|” when required. Will be “-” if not applicable.
All columns are mandatory so columns with no values are filled with “-“