BioGRID REST Service
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| ====== BioGRID REST Service ====== | ====== 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 | + | 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 HTTPS, programmatically or in a browser, at |
| - | **http://webservice.thebiogrid.org/**. You can access interactions using both POST and GET operations depending on your application requirements. | + | **https://webservice.thebiogrid.org/**. You can access interactions using both POST and GET operations depending on your application requirements. |
| === Get Your Access Key === | === 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 **[[http://webservice.thebiogrid.org|here]]**. This key must be included in all queries to the webservice in the form of accesskey=[ACCESSKEY]. | + | 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 **[[https://webservice.thebiogrid.org|here]]**. This key must be included in all queries to the webservice in the form of accesskey=[ACCESSKEY]. |
| ====== Access Points ======= | ====== Access Points ======= | ||
| - | A formal description of the REST service, in Web Application Description Language (WADL), can be found at **http://webservice.thebiogrid.org/application.wadl**. | + | A formal description of the REST service, in Web Application Description Language (WADL), can be found at **https://webservice.thebiogrid.org/application.wadl**. |
| === /interactions/<INT ID> - Fetching Single Interactions === | === /interactions/<INT ID> - Fetching Single Interactions === | ||
| - | Single interactions can be retrieved by appending this URL with a Biogrid Interaction ID (e.g. **http://webservice.thebiogrid.org/interactions/103?accesskey=[ACCESSKEY]**). | + | Single interactions can be retrieved by appending this URL with a Biogrid Interaction ID (e.g. **https://webservice.thebiogrid.org/interactions/103?accesskey=[ACCESSKEY]**). |
| === /interactions/ - Fetching Multiple Interactions === | === /interactions/ - Fetching Multiple Interactions === | ||
| - | 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 **[[biogrid_tab_version_2.0|.tab2]]** files. Results can be modified and filtered using the options in our REST **[[#list_of_parameters|list of parameters]]**. | + | The URL **https://webservice.thebiogrid.org/interactions/?accesskey=[ACCESSKEY]** will retrieve the first 10,000 interactions in BioGRID, ordered by the BioGRID Interaction Id as found in **[[biogrid_tab_version_2.0|.tab2]]** files. Results can be modified and filtered using the options in our REST **[[#list_of_parameters|list of parameters]]**. |
| === /organisms/ - Fetching Supported Organisms List === | === /organisms/ - Fetching Supported Organisms List === | ||
| - | The URL **http://webservice.thebiogrid.org/organisms/?accesskey=[ACCESSKEY]** will retrieve the list of organism IDs and names supported by the REST taxId option. This call only supports the accessKey and format parameters (can be tab2 or json)(e.g. **http://webservice.thebiogrid.org/organisms/?accesskey=[ACCESSKEY]&format=json**). | + | The URL **https://webservice.thebiogrid.org/organisms/?accesskey=[ACCESSKEY]** will retrieve the list of organism IDs and names supported by the REST taxId option. This call only supports the accessKey and format parameters (can be tab2 or json)(e.g. **https://webservice.thebiogrid.org/organisms/?accesskey=[ACCESSKEY]&format=json**). |
| === /identifiers/ - Fetching Supported Additional Identifier Types === | === /identifiers/ - Fetching Supported Additional Identifier Types === | ||
| - | The URL **http://webservice.thebiogrid.org/identifiers/?accesskey=[ACCESSKEY]** will retrieve the list of identifier type names supported by the REST additionalIdentifierTypes option. This call only supports the accessKey and format parameters (can be tab2 or json)(e.g. **http://webservice.thebiogrid.org/identifiers/?accesskey=[ACCESSKEY]&format=json**). | + | The URL **https://webservice.thebiogrid.org/identifiers/?accesskey=[ACCESSKEY]** will retrieve the list of identifier type names supported by the REST additionalIdentifierTypes option. This call only supports the accessKey and format parameters (can be tab2 or json)(e.g. **https://webservice.thebiogrid.org/identifiers/?accesskey=[ACCESSKEY]&format=json**). |
| === /evidence/ - Fetching Supported Experimental Evidence === | === /evidence/ - Fetching Supported Experimental Evidence === | ||
| - | The URL **http://webservice.thebiogrid.org/evidence/?accesskey=[ACCESSKEY]** will retrieve the list of evidence names supported by the REST evidenceList option. This call only supports the accessKey and format parameters (can be tab2 or json)(e.g. **http://webservice.thebiogrid.org/evidence/?accesskey=[ACCESSKEY]&format=json**). | + | The URL **https://webservice.thebiogrid.org/evidence/?accesskey=[ACCESSKEY]** will retrieve the list of evidence names supported by the REST evidenceList option. This call only supports the accessKey and format parameters (can be tab2 or json)(e.g. **https://webservice.thebiogrid.org/evidence/?accesskey=[ACCESSKEY]&format=json**). |
| === /version/ - Fetching REST Version Number === | === /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: | 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: | ||
| - | **http://webservice.thebiogrid.org/version?accesskey=[ACCESSKEY]**. | + | **https://webservice.thebiogrid.org/version?accesskey=[ACCESSKEY]**. |
| ====== List of Parameters ====== | ====== List of Parameters ====== | ||
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| ^Parameter^Type^Default^Valid Values^Description^ | ^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 **[[http://webservice.thebiogrid.org/|available here]]**. | | + | |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 **[[https://webservice.thebiogrid.org/|available here]]**. | |
| |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.| | |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.| | |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.| | ||
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| |taxId|string|“All”|Pipe-separated list of NCBI taxonomy identifiers or "All". Get full list of supported ids **[[#organisms_-_fetching_supported_organisms_list|here]]**|Only genes from these organisms will be searched with reference to gene identifiers or names. | | |taxId|string|“All”|Pipe-separated list of NCBI taxonomy identifiers or "All". Get full list of supported ids **[[#organisms_-_fetching_supported_organisms_list|here]]**|Only genes from these organisms will be searched with reference to gene identifiers or names. | | ||
| |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).| | |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 **[[http://wiki.thebiogrid.org/doku.php/downloads|file format listing]]**.| | + | |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 **[[https://wiki.thebiogrid.org/doku.php/downloads|file format listing]]**.| |
| |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. | | |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. | | ||
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| === Interactions for human MDM2 gene: === | === Interactions for human MDM2 gene: === | ||
| - | **http://webservice.thebiogrid.org/interactions?searchNames=true&geneList=MDM2&includeInteractors=true&includeInteractorInteractions=false&taxId=9606&accesskey=[ACCESSKEY]** | + | **https://webservice.thebiogrid.org/interactions?searchNames=true&geneList=MDM2&includeInteractors=true&includeInteractorInteractions=false&taxId=9606&accesskey=[ACCESSKEY]** |
| === Interactions for human MDM2 gene and interactions between all interactors of MDM2: === | === Interactions for human MDM2 gene and interactions between all interactors of MDM2: === | ||
| - | **http://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=MDM2&taxId=9606&includeInteractors=true&includeInteractorInteractions=true&accesskey=[ACCESSKEY]** | + | **https://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=MDM2&taxId=9606&includeInteractors=true&includeInteractorInteractions=true&accesskey=[ACCESSKEY]** |
| === First 10 interactions for human MDM2 gene: === | === First 10 interactions for human MDM2 gene: === | ||
| - | **http://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=MDM2&includeInteractors=true&taxId=9606&start=0&max=10&accesskey=[ACCESSKEY]** | + | **https://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=MDM2&includeInteractors=true&taxId=9606&start=0&max=10&accesskey=[ACCESSKEY]** |
| === Interactions between S. cerevisiae CDC27, APC1 and APC2: === | === Interactions between S. cerevisiae CDC27, APC1 and APC2: === | ||
| - | **[[http://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27%7Capc1%7Capc2&taxId=559292&accesskey=[ACCESSKEY]|http://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&taxId=559292&accesskey=[ACCESSKEY]]]** | + | **[[https://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27%7Capc1%7Capc2&taxId=559292&accesskey=[ACCESSKEY]|https://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&taxId=559292&accesskey=[ACCESSKEY]]]** |
| === Interactions from pubmed IDs 18316726 and 17662948: === | === Interactions from pubmed IDs 18316726 and 17662948: === | ||
| - | **[[http://webservice.thebiogrid.org/interactions/?pubmedList=18316726%7C17662948&accesskey=[ACCESSKEY]|http://webservice.thebiogrid.org/interactions/?pubmedList=18316726|17662948&accesskey=[ACCESSKEY]]]** | + | **[[https://webservice.thebiogrid.org/interactions/?pubmedList=18316726%7C17662948&accesskey=[ACCESSKEY]|https://webservice.thebiogrid.org/interactions/?pubmedList=18316726|17662948&accesskey=[ACCESSKEY]]]** |
| === Interactions between CDC27, APC1 and APC2 excluding ‘Affinity Capture-MS’ and ‘Two-hybrid’ data: === | === Interactions between CDC27, APC1 and APC2 excluding ‘Affinity Capture-MS’ and ‘Two-hybrid’ data: === | ||
| - | **[[http://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27%7Capc1%7Capc2&evidenceList=Affinity Capture-MS%7CTwo-hybrid&accesskey=[ACCESSKEY]|http://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&evidenceList=Affinity Capture-MS|Two-hybrid&accesskey=[ACCESSKEY]]]** | + | **[[https://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27%7Capc1%7Capc2&evidenceList=Affinity Capture-MS%7CTwo-hybrid&accesskey=[ACCESSKEY]|https://webservice.thebiogrid.org/interactions/?searchNames=true&geneList=cdc27|apc1|apc2&evidenceList=Affinity Capture-MS|Two-hybrid&accesskey=[ACCESSKEY]]]** |
| === Interactions between genes with REFSEQ IDs NP_001119587 (TP53) or NP_002383 (MDM2), in jsonExtended format === | === Interactions between genes with REFSEQ IDs NP_001119587 (TP53) or NP_002383 (MDM2), in jsonExtended format === | ||
| - | **[[http://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=REFSEQ&geneList=NP_001119587%7CNP_002383&format=jsonExtended&accesskey=[ACCESSKEY]|http://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=REFSEQ&geneList=NP_001119587|NP_002383&format=jsonExtended&accesskey=[ACCESSKEY]]]** | + | **[[https://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=REFSEQ&geneList=NP_001119587%7CNP_002383&format=jsonExtended&accesskey=[ACCESSKEY]|https://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=REFSEQ&geneList=NP_001119587|NP_002383&format=jsonExtended&accesskey=[ACCESSKEY]]]** |
| === Interactions involving Entrez Gene IDs 6783 (SULT1E1), 6820 (SULT2B1), and 55791 (LRIF1) === | === Interactions involving Entrez Gene IDs 6783 (SULT1E1), 6820 (SULT2B1), and 55791 (LRIF1) === | ||
| - | **[[http://webservice.thebiogrid.org/interactions/?geneList=6783%7C6820%7C55791&searchids=true&includeInteractors=true&accessKey=[ACCESSKEY]|http://webservice.thebiogrid.org/interactions/?geneList=6783|6820|55791&searchids=true&includeInteractors=true&accessKey=[ACCESSKEY]]]** | + | **[[https://webservice.thebiogrid.org/interactions/?geneList=6783%7C6820%7C55791&searchids=true&includeInteractors=true&accessKey=[ACCESSKEY]|https://webservice.thebiogrid.org/interactions/?geneList=6783|6820|55791&searchids=true&includeInteractors=true&accessKey=[ACCESSKEY]]]** |
| === Interactions involving SGD IDs S000004354 (STE11) and S000003664 (PBS2) === | === Interactions involving SGD IDs S000004354 (STE11) and S000003664 (PBS2) === | ||
| - | **[[http://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=SGD&geneList=S000004354%7CS000003664&includeInteractors=true&accesskey=[ACCESSKEY]|http://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=SGD&geneList=S000004354|S000003664&includeInteractors=true&accesskey=[ACCESSKEY]]]** | + | **[[https://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=SGD&geneList=S000004354%7CS000003664&includeInteractors=true&accesskey=[ACCESSKEY]|https://webservice.thebiogrid.org/interactions/?additionalIdentifierTypes=SGD&geneList=S000004354|S000003664&includeInteractors=true&accesskey=[ACCESSKEY]]]** |