BioGRID JSON Formatted Downloads

The BioGRID JSON format is a custom BioGRID format that is designed to provide the entirety of our curation efforts in a format that is simple to read in using programmatic means via the simple JavaScript Object Notation format. For more information on working with json, here are some useful guides in a variety of popular programming languages. PHP, Java, Python, Ruby, JavaScript, jQuery, GO, C++, C#

Entry Definitions

The contents of BioGRID JSON output should be as follows. The value in bold is the name of the field accessible via an object or array depending on how you parse the json content.:

  1. BIOGRID_INTERACTION_ID. A unique identifier for each interaction within the BioGRID database.
  2. ENTREZ_GENE_A. The identifier from the Entrez-Gene database that corresponds to Interactor A.
  3. ENTREZ_GENE_B. Same structure as column 2.
  4. BIOGRID_ID_A. The identifier in the BioGRID database that corresponds to Interactor A. 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: to each ID. For example,
  5. BIOGRID_ID_B. Same structure as column 4.
  6. SYSTEMATIC_NAME_A. A plain text systematic name if known for interactor A. Will be a “-” if no name is available.
  7. SYSTEMATIC_NAME_B. Same structure as column 6.
  8. OFFICIAL_SYMBOL_A. A common gene name/official symbol for interactor A. Will be a “-” if no name is available.
  9. OFFICIAL_SYMBOL_B. Same structure as column 8.
  10. SYNONYMS_A. A “|” separated list of alternate identifiers for interactor A. Will be “-” if no aliases are available.
  11. SYNONYMS_B. Same stucture as column 10.
  12. EXPERIMENTAL_SYSTEM. One of the many Experimental Evidence Codes supported by the BioGRID.
  13. EXPERIMENTAL_SYSTEM_TYPE. This will be either “physical” or “genetic” as a classification of the Experimental System Name.
  14. PUBMED_AUTHOR. First author surname of the publication in which the interaction has been shown, optionally followed by additional indicators, e.g. Stephenson A (2005)
  15. PUBMED_ID. Pubmed ID of the publication in which the interaction has been shown.
  16. ORGANISM_A. This is the NCBI Taxonomy ID for Interactor A.
  17. ORGANISM_B. Same structure as 16.
  18. THROUGHPUT. This will be either High Throughput, Low Throughput or Both (separated by “|”).
  19. QUANTITATION. This will be a positive for negative value recorded by the original publication depicting P-Values, Confidence Score, SGA Score, etc. Will be “-” if no score is reported.
  20. MODIFICATION. For any Biochemical Activity experiments, this field will be filled with the associated post translational modification. Will be “-” if no modification is reported.
  21. ONTOLOGY_TERMS. If any ontology terms are recorded, they will be provided here in a separate array. The array is indexed by ontology term ids and contains the relevant annotation to go with each term.
  22. QUALIFICATIONS. If additional plain text information was recorded for an interaction, it will be listed with unique qualifiers separated by “|”. If no qualification is available, this field will contain “-”.
  23. TAGS. If an interaction has been tagged with additional classifications, they will be provided in this column separated by “|”. If no tag information is available, this field will contain “-”.
  24. SOURCEDB. This field will contain the name of the database in which this interaction was provided.

jsonExtended Additional Fields

  1. SOURCEDB_ID. This field will contain the internal ID used for this interaction in the resource(s) specified in the SOURCEDB field.
  2. PUBMED_INTERACTION_COUNT. This field contains the number of interactions available for the publication specified in the PUBMED_ID field.
  3. EXTERNALS_A. This field contains a number of external database ids for interactor A in the format DB_NAME:DB_ID|DB_NAME:DB_ID.
  4. EXTERNALS_B. Same as EXTERNALS_A, but for interactor B.
downloads/biogrid_json.txt · Last modified: 2017/08/08 12:52 (external edit)