bioDBnet: Web Services: REST Web Services

Documentation using bioDBnet through REST web services

All the main functions of bioDBnet can be accessed through REST API calls. Each of the calls can be used to return results in the default XML format or in the JSON format.
All the bioDBnet REST calls can be accessed from https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi using different arguments. Below is an explanation of the services offered and required arguments. The argument 'method' is optional in all calls but is highly recommended as it's a good validation method for ensuring that the correct bioDBnet function is being called.

getInputs: Gets all the input nodes in bioDBnet.

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getinputs

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getinputs


getOutputsForInput: Gets all the possible output nodes for a given input node (All outputs accessible by following single or multiple edges in the bioDBnet graph).

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getoutputsforinput&input=genesymbol

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getoutputsforinput&input=genesymbol


getDirectOutptsForInput: Gets all the direct output nodes for a given input node (Outputs reachable by single edge connection in the bioDBnet graph).

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getdirectoutputsforinput&input=genesymbol&directOutput=1

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getdirectoutputsforinput&input=genesymbol&directOutput=1


getPathways: REST call for getting all available pathways in bioDBnet.

REST call for getting all pathways from all databases.
XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=1&taxonId=9606

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getpathways&pathways=1&taxonId=9606


REST call for getting all pathways from specific databases.
XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=ncipid,kegg&taxonId=9606

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getpathways&pathways=ncipid,kegg&taxonId=9606


db2db: The web service operation offering the functionality of db2db.

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row

Argument 'format': The format argument can be used with REST calls for db2db, dbReport, dbWalk, dbFind and dbOrtho. The argument can take either 'row' or 'col' as values to return results formatted as rows or formatted as columns respectively. Not specifying the format argument returns the default format where all inp ut parameters and results are returned in the REST response.

Example db2db calls with and without the format argument
DEFAULT: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606
ROW: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row
COL: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=col


dbReport: The web service operation offering the functionality of dbReport. Due to the nature of the web services the dbReport results are returned in the same format as db2db. The only difference between the db2db and dbReport services are that db2db returns results only for the requested output types while dbReport returns results for all possible outputs.

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbreport&input=geneid&inputValues=1,3&taxonId=9606&format=row

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbreport&input=geneid&inputValues=1,3&taxonId=9606&format=row


dbWalk: The web service operation offering the functionality of dbWalk
.

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbwalk&inputValues=A1BG,MYC&dbPath=genesymbol-%3Egeneid-%3Eaffyid&taxonId=9606&format=row

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbwalk&inputValues=A1BG,MYC&dbPath=genesymbol-%3Egeneid-%3Eaffyid&taxonId=9606&format=row


dbFind: The web service operation offering the functionality of dbFind.

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbfind&inputValues=A1BG,MYC,1,3&output=geneid&taxonId=9606&format=row

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbfind&inputValues=A1BG,MYC,1,3&output=geneid&taxonId=9606&format=row


dbOrtho: The web service operation offering the functionality of dbOrtho.

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbortho&input=geneid&inputValues=1,3&inputTaxon=9606&outputTaxon=10090&output=genesymbol&format=row

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbortho&input=geneid&inputValues=1,3&inputTaxon=9606&outputTaxon=10090&output=genesymbol&format=row


dbAnnot: The web service operation offering the functionality of dbAnnot. Available annotations are Genes, Drugs, Diseases, GO Terms, Pathways and Protein Interactors

XML: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row

JSON: https://fsabcl-bdb01p.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row