BioGRID REST Service
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biogridrest [2015/04/26 18:39] biogridadmin [Access Points] |
biogridrest [2015/05/01 20:48] biogridadmin [List of Parameters] |
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| |interSpeciesExcluded|boolean|FALSE|true, false|If ‘true’, interactions with interactors from different species will be excluded.| | |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.| | |selfInteractionsExcluded|boolean|FALSE|true, false|If ‘true’, interactions with one interactor will be excluded.| | ||
| - | |evidenceList|string|empty|Pipe-separated list of evidence codes from **[[#fetching_supported_experimental_evidence|here]]**|Any interaction evidence with its Experimental System in the list will be excluded from the results unless includeEvidence is set to true.| | + | |evidenceList|string|empty|Pipe-separated list of evidence codes from **[[#evidence_-_fetching_supported_experimental_evidence|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| | |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.| | |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.| | ||
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| |searchSynonyms|boolean|FALSE|true, false|If ‘true’, the interactor SYNONYM 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.| | ||
| |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.| | |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 **[[#fetching_supported_additional_identifier_types|here]]**|Identifier types on this list are examined for a match with the geneList. Some identifier types search multiple types simultaneously. UNIPROT or UNIPROTKB will search SWISS-PROT/TREMBL/UNIPROT-ACCESSION/UNIPROT-ISOFORM. REFSEQ will search REFSEQ-RNA-GI, REFSEQ-RNA-ACCESSION, REFSEQ-PROTEIN-GI, REFSEQ-PROTEIN-ACCESSION-VERSIONED, REFSEQ-PROTEIN-ACCESSION, REFSEQ-LEGACY. WORMBASE will search WORMBASE and WORMBASE-OLD. ENSEMBL will search ENSEMBL, ENSEMBL GENE, ENSEMBL PROTEIN, ENSEMBL RNA.| | + | |additionalIdentifierTypes|string|empty|Pipe-separated list of identifier types from **[[#identifiers_-_fetching_supported_additional_identifier_types|here]]**|Identifier types on this list are examined for a match with the geneList. Some identifier types search multiple types simultaneously. UNIPROT or UNIPROTKB will search SWISS-PROT/TREMBL/UNIPROT-ACCESSION/UNIPROT-ISOFORM. REFSEQ will search REFSEQ-RNA-GI, REFSEQ-RNA-ACCESSION, REFSEQ-PROTEIN-GI, REFSEQ-PROTEIN-ACCESSION-VERSIONED, REFSEQ-PROTEIN-ACCESSION, REFSEQ-LEGACY. WORMBASE will search WORMBASE and WORMBASE-OLD. ENSEMBL will search ENSEMBL, ENSEMBL GENE, ENSEMBL PROTEIN, ENSEMBL RNA.| |
| |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.| | |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| | |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| | ||
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| |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’.| | |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.| | |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 **[[#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 **[[http://wiki.thebiogrid.org/doku.php/downloads|file format listing]]**.| | ||