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Systems Genomics and Bioinformatics Unit · Laboratory of Systems Biology · National Institute of Allergy and Infectious Diseases
OMics Compendia Commons (OMiCC)

RESTful APIs

The OMiCC system also proivdes RESTful API access to its internal data, such as GEO studies, samples, platforms, sample groups, CGPs and projects. The current available APIs are described below.

Authentication

Before you make the request to the OMiCC resource through RESTful APIs, you need to acquire a token through authentication on your own OMiCC account. You can use the following URL to get the token:
                
                    https://omicc.niaid.nih.gov/api/login
                
            
  • Method: POST
  • Input (in JSON format): {"username": "YOUR_ACCOUNT", "password": "YOUR_PASSWORD"}
  • Output (in JSON format): {"username":"YOUR_ACCOUNT","roles":["ROLE_USER"],"token_type":"Bearer","access_token":"TOKEN_STRING"}

In the following API calls, please add Authorization: Bearer TOKEN_STRING in the request header.

The following URL can be used to get the list of GEO Studies in OMiCC.
                                
                                    https://omicc.niaid.nih.gov/api/studies
                                
                            
  • Method: GET
  • Input: None
  • Output: A JSON data string. For example:
    [{"contact":"Catherine Klapperich,Catherine Klapperich,Jie Song,Carolyn Bertozzi","hasLocalData":false,"hasSharedData":false,"lastUpdateDate":"2013-08-29T04:00:00Z","meshTerms":null,"onPlatform":[{"_link":"/platforms/6996"}],"overallDesign":"","pubmedId":"","releaseDate":"2004-01-28T05:00:00Z","sampleCount":10,"samples":[{"_link":"/samples/GSM15794"},{"_link":"/samples/GSM15785"},{"_link":"/samples/GSM15786"},{"_link":"/samples/GSM15795"},{"_link":"/samples/GSM15791"},{"_link":"/samples/GSM15792"},{"_link":"/samples/GSM15790"},{"_link":"/samples/GSM15788"},{"_link":"/samples/GSM15789"},{"_link":"/samples/GSM15787"}],"seriesType":"Expression profiling by array","studyId":"GSE1000","summary":"Amino acid conjugated surfaces and controls at 6 and 32 hours\nKeywords: other","superseriesOf":"","supplementaryLinks":"","supplementaryTypes":"","title":"Osteosarcoma TE85 cell tissue culture study"}]
                                        
Please be aware the response header has the following entries:
X-hedtech-totalCount: 26644
X-hedtech-pageOffset: 1
X-hedtech-pageMaxSize: 1
                            

The value for X-hedtech-totalCount is the total number of studies in OMiCC. With the information, you can develop the call with pagination by adding the following query string ...?max=MAX_VALUE&offset=OFFSET_VALUE

To get the specific GEO study data, please use the following url:

                                
                                    https://omicc.niaid.nih.gov/api/studies/studyId
                                
                            

where the "studyId" is like GSE10000

The following URL can be used to get the list of GEO Platforms in OMiCC.
                                
                                        https://omicc.niaid.nih.gov/api/platforms
                                
                                
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of GEO Platforms in OMiCC. Please refer to GEO Studies section for more details

To get the specific GEO platform data, please use the following url:

                                    
                                        https://omicc.niaid.nih.gov/api/platforms/platformId
                                    
                                

where the "platformId" is like GPL1

The following URL can be used to get the list of GEO Samples in OMiCC.
                                    
                                        https://omicc.niaid.nih.gov/api/samples
                                    
                                    
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of GEO Samples in OMiCC. Please refer to GEO Studies section for more details

To get the specific GEO sample data, please use the following url:

                                        
                                            https://omicc.niaid.nih.gov/api/samples/sampleId
                                        
                                    

where the "sampleId" is like GSE40736

The following URL can be used to get the list of public Sample Groups in OMiCC.
                                            
                                            https://omicc.niaid.nih.gov/api/publicSampleGroups
                                            
                                        
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of public Sample Groups in OMiCC. Please refer to GEO Studies section for more details

To get the specific public Sample Group data, please use the following url:

                                            
                                                https://omicc.niaid.nih.gov/api/publicSampleGroups/groupId
                                            
                                        
The following URL can be used to get the list of your own Sample Groups in OMiCC.
                                                
                                                    https://omicc.niaid.nih.gov/api/sampleGroups
                                                
                                            
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of your own Sample Groups in OMiCC. Please refer to GEO Studies section for more details

To get the specific Sample Group data, please use the following url:

                                                
                                                    https://omicc.niaid.nih.gov/api/sampleGroups/groupId
                                                
                                            
The following URL can be used to get the list of public CGPs in OMiCC.
                                                    
                                                        https://omicc.niaid.nih.gov/api/publicCGPs
                                                    
                                                
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of public CGPs in OMiCC. Please refer to GEO Studies section for more details

To get the specific pubilc CGP data, please use the following url:

                                                    
                                                        https://omicc.niaid.nih.gov/api/publicCGPs/cgpId
                                                    
                                                
The following URL can be used to get the list of your own CGPs in OMiCC.
                                                        
                                                            https://omicc.niaid.nih.gov/api/CGPs
                                                        
                                                    
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of your own CGPs in OMiCC. Please refer to GEO Studies section for more details

To get the specific CGP data, please use the following url:

                                                        
                                                            https://omicc.niaid.nih.gov/api/CGPs/cgpId
                                                        
                                                    
The following URL can be used to get the list of your own compendia in OMiCC.
                                                            
                                                                https://omicc.niaid.nih.gov/api/projects
                                                            
                                                        
  • Method: GET
  • Input: None
  • Output: A JSON data string.
The response header has the data entries for the total count of your own compendia in OMiCC. Please refer to GEO Studies section for more details

To get the specific compendium data, please use the following url:

                                                            
                                                                https://omicc.niaid.nih.gov/api/projects/projectId
                                                            
                                                        

where the projectId is the compendium ID