BioGRID REST Service
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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://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/ This URL 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://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/103). The results list returned can be filtered by appending ?parameter1=value1& parameter2=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://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/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://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/version .
In addition to BioGRID interaction data, interactions from the IMEx databases IntAct, MINT [2] and DIP have been parsed, mapped to BioGRID evidence codes, according to the mapping in LINK, and included as an option for retrieval in the REST service data. The URL parameter “sourceDatabaseList” has a default value of “BioGRID”, but if set to “BioGRID|MINT|INTACT|DIP” the query will retrieve interactions from all databases. Source database origin can be found in the “Source Databases” column of the retrieved data and the “Source Database Identifiers” column (if the parameter format=extendedTab2 is set) allows mapping back to the interaction in the original database. IMEx interaction files are downloaded from their respective websites and integrated into the REST service to coinicide with each monthly BioGRID release. These additional interactions are only available through the BioGRid REST Service and are not currently present in the BioGRID download files.
Examples
Interactions for human MDM2 gene:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions?searchNames=true&geneList=MDM2&includeInteractors=true&includeInteractorInteractions=false&taxId=9606
Interactions for human MDM2 gene and interactions between all interactors of MDM2:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?searchNames=true&geneList=MDM2&taxId=9606&includeInteractors=true& includeInteractorInteractions=true
First 10 interactions for human MDM2 gene:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?searchNames=true&geneList=MDM2&includeInteractors=true&includeInteractorInteractions=false&taxId=9606&start=0&max=10
Interactions between S. cerevisiae CDC27, APC1 and APC2:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&taxId=4932
Interactions from pubmed IDs 18316726 and 17662948:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?pubmedList=18316726|17662948
Interactions between CDC27, APC1 and APC2 from publications with 50 or less interactions:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&htpThreshold=50&excludePubmeds=true
Interactions between CDC27, APC1 and APC2 excluding ‘Affinity Capture-MS’ and ‘Two-hybrid’ data:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&excludedEvidenceCodes=Affinity Capture-MS|Two-hybrid
Interactions from pubmed ID18316726, excluding those containing HTLF:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?pubmedList=18316726&searchNames=true&geneList=HLTF&excludeGenes=true
Interactions between genes with GENBANK_DNA_GI 82502895 (TP53) or 158261704 (MDM2), in extendedTab2 format with a header:
http://biogrid.bio.ed.ac.uk:8080/BiogridRestService/resources/interactions/?additionalIdentifierTypes=GENBANK_DNA_GI&geneList=82502895|158261704&format=extendedTab2&includeHeader=true
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| start | int | 0 | Any integer | 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 | 0-10000 | 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. |
| excludedEvidenceCodes | string | empty | string | Pipe-separated list of evidence codes from http://wiki.thebiogrid.org/doku.php/experimental_systems. Any interaction evidence with its Experimental System in the list will be excluded from the results. |
| geneList | string | empty | string | Pipe-separated list of gene names or identifiers. Interactions between gene in this list will be fetched. 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 | string | Pipe-separated list of identifier types from http://wiki.thebiogrid.org/doku.php/identifiers Identifier types on this list will be 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’. |
| taxId | string | “All” | Any NCBI taxonomy identifier or “All” | Only interactions 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). |
| 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 interaction ID in the list will be included in the results. |
| 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 |