BioGRID REST Service
Differences
This shows you the differences between two versions of the page.
| - | Both sides previous revision Previous revision Next revision |
| - | biogridrest [2015/04/26 17:46] biogridadmin [Examples] |
|---|---|
| + | Previous revision |
| + | biogridrest [2020/09/13 17:02] (current) biogridadmin [BioGRID REST Service] |
| @@ Line -1,32 +1,33 @@ | |
| ====== 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 | |
| ** | |
| === Get Your Access Key === | |
| 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 **[[ | |
| === Code Examples === | |
| For example code (written in Python) demonstrating basic usage of the REST Service, please visit our [[https://github.com/BioGRID/BIOGRID-REST-EXAMPLES|github repository]]. | |
| ====== Access Points ======= | |
| A formal description of the REST service, in Web Application Description Language (WADL), can be found at ** | |
| === /interactions/<INT ID> - Fetching Single Interactions === | |
| Single interactions can be retrieved by appending this URL with a Biogrid Interaction ID (e.g. ** | |
| === /interactions/ - Fetching Multiple Interactions === | |
| The URL ** | |
| === /organisms/ - Fetching Supported Organisms List === | |
| The URL ** | |
| === /identifiers/ - Fetching Supported Additional Identifier Types === | |
| The URL ** | |
| === /evidence/ - Fetching Supported Experimental Evidence === | |
| The URL ** | |
| === /version/ - Fetching REST Version Number === | |
| The BioGRID REST service is updated to the latest release of BioGRID on the 4th of each month and the BioGRID database version being accessed can be determined with the URL: | |
| ** | |
| ====== List of Parameters ====== | |
| @@ Line -36,10 +37,10 @@ | |
| ^Parameter^Type^Default^Valid Values^Description^ | |
| |accessKey|string|NONE|Only 32 character Alphanumeric strings|All rest access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly **[[ | |
| |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. Ignored if using "count" in the format parameter.| | |
| |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. Ignored if using "count" in the format parameter.| | |
| |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 **[[# | |
| |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.| | |
| @@ Line -48,5 +49,5 @@ | |
| |searchSynonyms|boolean|FALSE|true, false|If ‘true’, the interactor SYNONYM will be examined for a match with the geneList.| | |
| |searchBiogridIds|boolean|FALSE|true, false|If ‘true’, the entries in 'GENELIST' will be compared to BIOGRID internal IDS which are provided in all Tab2 formatted files.| | |
| |additionalIdentifierTypes|string|empty|Pipe-separated list of identifier types from **[[# | |
| |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|TRUE|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| | |
| @@ Line -56,7 +57,7 @@ | |
| |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”|Pipe-separated list of NCBI taxonomy identifiers or "All". Get full list of supported ids **[[# | |
| |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”, "json", "jsonExtended"|‘tab1’ and ‘tab2’ will return data in .tab or .tab2 format respectively. 'json' will return data in json a json formatted object. ‘extendedTab2’ and 'jsonExtended' will return data in .tab2 and json file formats respectively with extra fields for "Source Database Identifiers", "Number of Interactions per Publication" and "Additional Identifiers". For more information on file formats, visit our **[[ | |
| |translate|boolean|FALSE|true,false|If 'true', the rest service will show a small snippet above your results detailing how your input parameters were translated for use in returning your data. This is helpful in troubleshooting why you may or may not be getting back the results expected. For example, if you enter a typo for a field such as "searchNamez", no result will be translated, and thus this parameter will be ignored. | | |
| @@ Line -71,35 +72,35 @@ | |
| === Interactions for human MDM2 gene: === | |
| ** | |
| === Interactions for human MDM2 gene and interactions between all interactors of MDM2: === | |
| ** | |
| === First 10 interactions for human MDM2 gene: === | |
| ** | |
| === Interactions between S. cerevisiae CDC27, APC1 and APC2: === | |
| **[[ | |
| === Interactions from pubmed IDs 18316726 and 17662948: === | |
| **[[ | |
| === Interactions between CDC27, APC1 and APC2 excluding ‘Affinity Capture-MS’ and ‘Two-hybrid’ data: === | |
| **[[ | |
| === Interactions between genes with REFSEQ IDs NP_001119587 (TP53) or NP_002383 (MDM2), in jsonExtended format === | |
| **[[ | |
| === Interactions involving Entrez Gene IDs 6783 (SULT1E1), 6820 (SULT2B1), and 55791 (LRIF1) === | |
| **[[ | |
| === Interactions involving SGD IDs S000004354 (STE11) and S000003664 (PBS2) === | |
| **[[ | |