BioGRID REST Service
Interaction data in BioGRID can be accessed via the BioGRID REST service. Interactions in various formats can be fetched from the BioGRID REST Service over HTTP, programmatically or in a browser, at http://webservice.thebiogrid.org/interactions/. You can access interactions using both POST and GET operations depending on your application requirements.
To access the BioGRID REST webservice, you will need a unique access key for your application. You can get one by filling out the simple form located here. This key must be included in all queries to the webservice in the form of accesskey=[ACCESSKEY].
The URL http://webservice.thebiogrid.org/interactions/?accesskey=[ACCESSKEY] will retrieve the first 10,000 interactions in BioGRID, ordered by the BioGRID Interaction Id as found in .tab2 files. Single interactions can be retrieved by appending this URL with a Biogrid Interaction ID (e.g. http://webservice.thebiogrid.org/interactions/103?accesskey=[ACCESSKEY]).
The results list returned can be filtered by appending ?parameter1=value1¶meter2=value2 etc. to the URL. A full description of possible parameters is given in the table below.
A formal description of the REST service, in Web Application Description Language (WADL), can be found at http://webservice.thebiogrid.org/application.wadl.
The BioGRID REST service is updated to the latest release of BioGRID on the 2nd of each month and the BioGRID database version being accessed can be determined with the URL: http://webservice.thebiogrid.org/version?accesskey=[ACCESSKEY].
Interactions between genes with GENBANK_DNA_GI 82502895 (TP53) or 158261704 (MDM2), in extendedTab2 format
|start||int||0||0-2147483647||Query results are numbered from 0. Results fetched will start at this value e.g. start = 50 will skip the the first 50 results.|
|max||int||10000||1-10000||Number of results to fetch; this will be ignored if greater than 10,000, i.e. pagination using several requests is required to retrieve more than 10,000 interactions.|
|interSpeciesExcluded||boolean||FALSE||true, false||If ‘true’, interactions with interactors from different species will be excluded.|
|selfInteractionsExcluded||boolean||FALSE||true, false||If ‘true’, interactions with one interactor will be excluded.|
|evidenceList||string||empty||Pipe-separated list of evidence codes from here||Any interaction evidence with its Experimental System in the list will be excluded from the results unless includeEvidence is set to true.|
|includeEvidence||boolean||FALSE||true, false||If set to true, any interaction evidence with its Experimental System in the evidenceList will be included in the result|
|geneList||string||empty||Pipe-separated list of gene names or identifiers.||Interactions between genes in this list will be fetched. This parameter is ignored if one of searchIds, searchNames, searchSynonyms is not ‘true’ and additionalIdentifierTypes is empty.|
|searchIds||boolean||FALSE||true, false||If ‘true’, the interactor ENTREZ_GENE and SYSTEMATIC_NAME (orf) will be examined for a match with the geneList .|
|searchNames||boolean||FALSE||true, false||If ‘true’, the interactor OFFICIAL_SYMBOL will be examined for a match with the geneList.|
|searchSynonyms||boolean||FALSE||true, false||If ‘true’, the interactor SYNONYM will be examined for a match with the geneList.|
|additionalIdentifierTypes||string||empty||Pipe-separated list of identifier types from here||Identifier types on this list are examined for a match with the geneList.|
|excludeGenes||boolean||FALSE||true, false||If ‘true’, interactions containing genes in the geneList will be excluded from the results. Ignored if one of searchIds, searchNames, searchSynonyms is not ‘true’ and additionalIdentifierTypes is empty.|
|includeInteractors||boolean||FALSE||true, false||If ‘true’, in addition to interactions between genes on the geneList, interactions will also be fetched which have only one interactor on the geneList i.e. the geneList’s first order interactors will be included|
|includeInteractorInteractions||boolean||TRUE||true, false||If ‘true’ interactions between the geneList’s first order interactors will be included. Ignored if includeInteractors is ‘false’ or if excludeGenes is set to ‘true’.|
|pubmedList||string||empty string||Pipe-separated list of pubmed IDs||Interactions will be fetched whose Pubmed Id is/ is not in this list, depending on the value of excludePubmeds.|
|excludePubmeds||boolean||FALSE||true, false||If ‘false’, interactions with Pubmed ID in pubmedList will be included in the results; if ‘true’ they will be excluded.|
|htpThreshold||int||2147483647 (maximum 32-bit integer)||0-2147483647||Interactions whose Pubmed ID has more than this number of interactions will be excluded from the results. Ignored if excludePubmeds is ‘false’.|
|throughputTag||string||“any”||“any”,”low”,”high”||If set to 'low or 'high', only interactions with 'Low throughput' or 'High throughput' in the 'throughput' field will be returned. Interactions with both 'Low throughput' and 'High throughput' will be returned by either value.|
|taxId||string||“All”||Any NCBI taxonomy identifier or “All”||Only interactions with at least one interactor with this NCBI taxonomy id will be included in the results.|
|includeHeader||boolean||FALSE||true, false||If ‘true’, the first line of the result will be a BioGRID column header, appropriate for the format parameter (‘count’ format has no header).|
|format||string||“tab2”||“tab1”,”tab2,”extendedTab2”,”count”||‘tab1’ and ‘tab2’ will return data in .tab or .tab2 format respectively. ‘extendedTab2’ will return data in .tab2 file format with extra fields fields for “Source Database Identifiers”, “Number of Interactions per Publication” and “Additional Identifiers”. “Source Database Identifiers” are listed in order corresponding to the values in “Source Databases” e.g if an interaction has BIOGRID|INTACT|MINT in Source_Database, it might have 821622|EBI-1792672|MINT-1999291|
|enableCaching||boolean||false||true, false||If set to true, a header is added to the HTTP response, 'Cache-Control: max-age=86400', which allows repeat queries performed within a day to use a cached copy of the results, allowing faster access to data. WARNING: The BioGRID REST service updates to the new version at 12pm GMT on the 2nd of each month, meaning that you may receive 'old' data for up to a day for previously performed queries - even if http://webservice.thebiogrid.org/resources/version indicates the new version is being used.|
|sourceDatabaseList||string||“BioGRID”||Pipe-separated list of database names, currently including BioGRID, INTACT, MINT, DIP||Only interactions with Source Database on this list will be returned.|
|sourceDatabaseIdList||string||empty||Pipe-separated list of source database identifiers||Interactions with a source database interaction ID in the list will be included in the results. The source database for the identifier must also be selected using sourceDatabaseList.|
These parameters are still available at our old web service location at: sce-bio-c02577.bio.ed.ac.uk:8080/BiogridRestService