BioGRID ORCS REST Service
BioGRID ORCS REST Service
CRISPR Screen Data in BioGRID ORCS can be accessed via the BioGRID ORCS REST service. Data in various formats can be fetched from the BioGRID ORCS REST Service over HTTPS, programmatically or in a browser, at https://orcsws.thebiogrid.org/. You can access interactions using both POST and GET operations depending on your application requirements.
Get Your Access Key
To access the BioGRID ORCS 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].
Code Examples
For example code (written in Python) demonstrating basic usage of the REST Service, please visit our github repository.
/organisms/ - Fetching Supported Organisms List
The URL https://orcsws.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 tab or json)(e.g. https://orcsws.thebiogrid.org/organisms/?accesskey=[ACCESSKEY]&format=json).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab format). |
/vocabs/ - Fetching a List of Controlled Vocabulary Categories
The URL https://orcsws.thebiogrid.org/vocabs/?accesskey=[ACCESSKEY] will retrieve all the controlled vocabulary categories used by BioGRID ORCS. This call only supports the accessKey and format parameters (can be tab or json)(e.g. https://orcsws.thebiogrid.org/vocabs/?accesskey=[ACCESSKEY]&format=json).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab format). |
/vocab/<VOCAB CATEGORY ID> - Fetch all terms in a single controlled vocabulary category
Single sets of controlled vocabulary terms can be retrieved by appending this URL with a controlled vocabulary term category id (provided by the endpoint listed above. (e.g. https://orcsws.thebiogrid.org/vocab/5?accesskey=[ACCESSKEY]).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab format). |
/screens/ - Fetch a list of screens
The URL https://orcsws.thebiogrid.org/screens/?accesskey=[ACCESSKEY] will retrieve the list of screens filtered by applied parameters. This call supports a wide number of parameters (listed below). (e.g https://orcsws.thebiogrid.org/screens/?accesskey=[ACCESSKEY]&format=json).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab 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 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 results. |
| screenType | string | empty | Pipe-separated list of screen type vocab terms (https://orcsws.thebiogrid.org/vocab/2?accesskey=[ACCESSKEY]) (only if required). | Enter screen types you want to search for, invalid screen types will be ignored. (eg. screenType=negative selection) |
| throughput | string | empty | Pipe-separated list of throughput vocab terms from (https://orcsws.thebiogrid.org/vocab/1?accesskey=[ACCESSKEY]) (only if required) | Enter throughput terms you want to search for, invalid throughput terms will be ignored. (eg. throughput=high throughput|low throughput ) |
| experimentalSetup | string | empty | Pipe-separated list of experimental setup vocabulary terms from https://orcsws.thebiogrid.org/vocab/3?accesskey=[ACCESSKEY] | Enter experimental setup terms you want to search for, invalid terms will be ignored. (eg. experimentalSetup=toxin exposure ) |
| conditionName | string | empty | Pipe-separated list of condition name vocabulary terms from https://orcsws.thebiogrid.org/vocab/4?accesskey=[ACCESSKEY] | Enter condition name terms you want to search for, invalid terms will be ignored. (eg. conditionName=ricin|insulin ) |
| libraryName | string | empty | Pipe-separated list of library name vocabulary terms from https://orcsws.thebiogrid.org/vocab/5?accesskey=[ACCESSKEY] | Enter Library terms you want to search for, invalid terms will be ignored. (eg. libraryName=gecko|gecko v2 ) |
| libraryType | string | empty | Pipe-separated list of Library Type vocabulary terms from https://orcsws.thebiogrid.org/vocab/6?accesskey=[ACCESSKEY] | Enter Library Type terms you want to search for, invalid terms will be ignored. (eg. libraryType=crispra ) |
| libraryMethodology | string | empty | Pipe-separated list of Library Methodology vocabulary terms from https://orcsws.thebiogrid.org/vocab/7?accesskey=[ACCESSKEY] | Enter Library Methodology terms you want to search for, invalid terms will be ignored. (eg. libraryMethodology=knockout|inhibition ) |
| screenFormat | string | empty | Pipe-separated list of screen format vocabulary terms from https://orcsws.thebiogrid.org/vocab/8?accesskey=[ACCESSKEY] | Enter screen format terms you want to search for, invalid terms will be ignored. (eg. screenFormat=array ) |
| enzyme | string | empty | Pipe-separated list of enzyme vocabulary terms from https://orcsws.thebiogrid.org/vocab/9?accesskey=[ACCESSKEY] | Enter enzyme terms you want to search for, invalid terms will be ignored. (eg. enzyme=cas9|suncas9 ) |
| cellLine | string | empty | Pipe-separated list of cell line vocabulary terms from https://orcsws.thebiogrid.org/vocab/10?accesskey=[ACCESSKEY] | Enter cell line terms you want to search for, invalid terms will be ignored. (eg. cellLine=hela|ramos cell ) |
| cellType | string | empty | Pipe-separated list of cell line vocabulary terms from https://orcsws.thebiogrid.org/vocab/11?accesskey=[ACCESSKEY] | Enter cell type terms you want to search for, invalid terms will be ignored. (eg. cellType=lymphoma cell line ) |
| phenotype | string | empty | Pipe-separated list of phenotype vocabulary terms from https://orcsws.thebiogrid.org/vocab/12?accesskey=[ACCESSKEY] | Enter phenotype terms you want to search for, invalid terms will be ignored. (eg. phenotype=viability|toxin resistance ) |
| statisticalAnalysis | string | empty | Pipe-separated list of statistical analysis vocabulary terms from https://orcsws.thebiogrid.org/vocab/15?accesskey=[ACCESSKEY] | Enter statistical analysis terms you want to search for, invalid terms will be ignored. (eg. statisticalAnalysis=bagel|castle|ranks ) |
| organismID | string | empty | Pipe-separated list of organism IDs from https://orcsws.thebiogrid.org/organisms/?accesskey=[ACCESSKEY] | Enter organisms ids you want to search for, invalid organism ids will be ignored. (eg. organismID=9606|10090 ) |
| pubmedID | string | empty | Pipe-separated list of pubmed IDs | Enter pubmed ids to search for, if they exist in our database. (eg. pubmedID=27869803|26627737 ) |
| screenID | string | empty | Pipe-separated list of screen IDs | Enter screen ids to search retrieve, if they exist in our database. (eg. screenID=172|12 ) |
/screen/<SCREEN ID> - Fetch all score results in a single screen
Fetches a set of proteins and associated score values for a single screen as specified by the <SCREEN ID>. (e.g. https://orcsws.thebiogrid.org/screen/1?accesskey=[ACCESSKEY]).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab format). |
| hit | string | “all” | “yes”,“no”,“all” | ‘yes’ will return only scores considered significant, 'no' will return only scores considered insignificant, 'all' will return both significant and insignificant results. If no significance is determined for the screen, this option will be ignored. |
| score[X]Min | string | empty | float | This will set the lower bound for scores in the score.X column where X is an integer between 1 and 5. If no value is specified for a particular column, all results are returned. If there is no score.X value, this option is ignored. (eg. score1Min=-0.995 will limit results to those with score.1 value greater than or equal to -0.995) (eg. score2Min=0.23&score4Min=-5.6) |
| score[X]Max | string | empty | float | This will set the upper bound for scores in the score.X column where X is an integer between 1 and 5. If no value is specified, all results are returned. If there is no score.X value, this option is ignored. (eg. score3Max=2.75 will limit results to those with score.3 value less than or equal to 2.75) (eg. score2Max=0.56&score5Max=2.881) |
| idType | string | empty | Pipe-separated list of the terms 'gene','unknown','ambiguous' for different identifier types. | Enter which types of identifiers you want to see, or do not include this parameter to see all identifier types. (eg. idType=ambiguous|gene) |
| geneID | string | empty | Pipe-separated list of gene ids to search for. | Enter gene ids you want to search for, these are the identifiers in the IDENTIFIER_ID column. Note: This does not search ambiguous or unknown types. (eg. geneid=66050|66056|66044) |
| name | string | empty | Pipe-separated list of official symbols to search for. | Enter official symbol you want to search for, these are the identifiers in the OFFICIAL_SYMBOL column. Note: This does not search ambiguous or unknown types. (eg. name=dtd1|sult1e1) |
/gene/<GENE ID> - Fetch all score results for multiple screens for a single gene
Fetches a set of screen scores across all screens involving the single gene represented by <GENE ID>. (e.g. https://orcsws.thebiogrid.org/gene/1?accesskey=[ACCESSKEY]).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab format). |
| hit | string | “all” | “yes”,“no”,“all” | ‘yes’ will return only scores considered significant, 'no' will return only scores considered insignificant, 'all' will return both significant and insignificant results. If no significance is determined for the screen, this option will be ignored. |
| score[X]Min | string | empty | float | This will set the lower bound for scores in the score.X column where X is an integer between 1 and 5. If no value is specified for a particular column, all results are returned. If there is no score.X value, this option is ignored. (eg. score1Min=-0.995 will limit results to those with score.1 value greater than or equal to -0.995) (eg. score2Min=0.23&score4Min=-5.6) |
| score[X]Max | string | empty | float | This will set the upper bound for scores in the score.X column where X is an integer between 1 and 5. If no value is specified, all results are returned. If there is no score.X value, this option is ignored. (eg. score3Max=2.75 will limit results to those with score.3 value less than or equal to 2.75) (eg. score2Max=0.56&score5Max=2.881) |
/genes/ - Fetch all score results for multiple screens for a single gene
Fetches a set of screen scores across all screens involving the single gene represented by <GENE ID>. (e.g. https://orcsws.thebiogrid.org/genes/?geneid=1021&name=SULT1E1&accesskey=[ACCESSKEY]).
Valid Params
| Parameter | Type | Default | Valid Values | Description |
|---|---|---|---|---|
| accessKey | string | NONE | Only 32 character Alphanumeric strings | All webservice access must supply a valid accessKey to prevent spamming of the service. Access Keys are free and openly available here. |
| format | string | “tab” | “tab”,“json” | ‘tab’ will return data in tab delimited text format. 'json' will return data in a javascript object notation formatted string. |
| header | string | “no” | “yes”,“no” | ‘yes’ will return data with a header attached (only applies to tab format). |
| hit | string | “all” | “yes”,“no”,“all” | ‘yes’ will return only scores considered significant, 'no' will return only scores considered insignificant, 'all' will return both significant and insignificant results. If no significance is determined for the screen, this option will be ignored. |
| score[X]Min | string | empty | float | This will set the lower bound for scores in the score.X column where X is an integer between 1 and 5. If no value is specified for a particular column, all results are returned. If there is no score.X value, this option is ignored. (eg. score1Min=-0.995 will limit results to those with score.1 value greater than or equal to -0.995) (eg. score2Min=0.23&score4Min=-5.6) |
| score[X]Max | string | empty | float | This will set the upper bound for scores in the score.X column where X is an integer between 1 and 5. If no value is specified, all results are returned. If there is no score.X value, this option is ignored. (eg. score3Max=2.75 will limit results to those with score.3 value less than or equal to 2.75) (eg. score2Max=0.56&score5Max=2.881) |
| geneID | string | empty | Pipe-separated list of gene ids to search for. (this or name MUST be filled in) | Enter gene ids you want to search for, these are the identifiers in the IDENTIFIER_ID column. Note: This does not search ambiguous or unknown types. (eg. geneid=66050|66056|66044) |
| name | string | empty | Pipe-separated list of official symbols to search for. (this or geneID MUST be filled in) | Enter official symbol you want to search for, these are the identifiers in the OFFICIAL_SYMBOL column. Note: This does not search ambiguous or unknown types. (eg. name=dtd1|sult1e1) |
| organismID | string | empty | Pipe-separated list of organism IDs from https://orcsws.thebiogrid.org/organisms/?accesskey=[ACCESSKEY] | Enter organisms ids you want to search for, invalid organism ids will be ignored. (eg. organismID=9606|10090 ) |
Examples
Screens with Cell Line of HELA and CRISPR Methodology of Knockout:
Screens with Phenotype of Viability or Toxin Resistance and Statistical Analysis Method of Castle, Bagel, or Mageck with header enabled in Human:
https://orcsws.thebiogrid.org/screens/?phenotype=viability%7Ctoxin resistance&statisticalAnalysis=castle%7Cbagel%7Cmageck&header=yes&format=tab&organismID=9606&accesskey=[ACCESSKEY|https://orcsws.thebiogrid.org/screens/?phenotype=viability|toxin resistance&statisticalAnalysis=castle|bagel|mageck&header=yes&format=tab&organismID=9606&accesskey=[ACCESSKEY]]]
All scores for Genes 1021 and 1022 flagged as HITS in json format
https://orcsws.thebiogrid.org/genes/?geneid=1021%7C1022&format=json&hit=yes&accesskey=[ACCESSKEY|https://orcsws.thebiogrid.org/genes/?geneid=1021|1022&format=json&hit=yes&accesskey=[ACCESSKEY]]]
All significant scores for Gene 1021 in json format
https://orcsws.thebiogrid.org/gene/1021?format=json&hit=yes&accesskey=[ACCESSKEY|https://orcsws.thebiogrid.org/gene/1021?format=json&hit=yes&accesskey=[ACCESSKEY]]]
All scores for Screen 178 in tab format with a header and where the scores in Score.1 are both >= 0.9 and <= 0.98
https://orcsws.thebiogrid.org/screen/178?format=tab&header=yes&score1min=0.9&score1max=0.98&accesskey=[ACCESSKEY|https://orcsws.thebiogrid.org/screen/178?format=tab&header=yes&score1min=0.9&score1max=0.98&accesskey=[ACCESSKEY]]]