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://biodbnet-abcc.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.
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).
getDirectOutptsForInput: Gets all the direct output nodes for a given input node (Outputs reachable by single edge connection in the bioDBnet graph).
getPathways: REST call for getting all available pathways in bioDBnet.
db2db: The web service operation offering the functionality of db2db.
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.
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.
dbWalk: The web service operation offering the functionality of dbWalk
.
dbFind: The web service operation offering the functionality of dbFind.
dbOrtho: The web service operation offering the functionality of dbOrtho.
dbAnnot: The web service operation offering the functionality of dbAnnot. Available annotations are Genes, Drugs, Diseases, GO Terms, Pathways and Protein Interactors
All the bioDBnet REST calls can be accessed from https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getinputs
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getinputs
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getoutputsforinput&input=genesymbol
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getoutputsforinput&input=genesymbol
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getdirectoutputsforinput&input=genesymbol&directOutput=1
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getdirectoutputsforinput&input=genesymbol&directOutput=1
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=1&taxonId=9606
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getpathways&pathways=1&taxonId=9606
REST call for getting all pathways from specific databases.
XML: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=ncipid,kegg&taxonId=9606
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getpathways&pathways=ncipid,kegg&taxonId=9606
XML: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=1&taxonId=9606
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getpathways&pathways=1&taxonId=9606
REST call for getting all pathways from specific databases.
XML: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=ncipid,kegg&taxonId=9606
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606
ROW: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row
COL: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=col
DEFAULT: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606
ROW: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row
COL: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbreport&input=geneid&inputValues=1,3&taxonId=9606&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbreport&input=geneid&inputValues=1,3&taxonId=9606&format=row
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbwalk&inputValues=A1BG,MYC&dbPath=genesymbol-%3Egeneid-%3Eaffyid&taxonId=9606&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbwalk&inputValues=A1BG,MYC&dbPath=genesymbol-%3Egeneid-%3Eaffyid&taxonId=9606&format=row
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbfind&inputValues=A1BG,MYC,1,3&output=geneid&taxonId=9606&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbfind&inputValues=A1BG,MYC,1,3&output=geneid&taxonId=9606&format=row
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbortho&input=geneid&inputValues=1,3&inputTaxon=9606&outputTaxon=10090&output=genesymbol&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbortho&input=geneid&inputValues=1,3&inputTaxon=9606&outputTaxon=10090&output=genesymbol&format=row
JSON: https://biodbnet-abcc.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://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row
JSON: https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row
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