datamedswagger.json

{
  "swagger": "2.0",
  "info": {
    "description": "",
    "title": "DataMed Web API",
    "version": "1.0.0"
  },
  "host": "datamed.org",
  "basePath": "/webapi",
  "tags": [
    {
      "name": "query",
      "description": "Search datasets from DataMed"

    }

  ],
  "schemes": [
    "https"
  ],
  "paths": {
    "/esearch?searchtype=data": {
      "get": {
        "tags": [
          "query"
        ],
        "summary": "Search datasets from DataMed by query",
        "description": "Get datasets by searching query",
        "produces": [
          "application/xml",
          "application/json"
        ],
        "parameters": [
          {
            "name": "query",
            "in": "query",
            "description": "Search term",
            "required": false,
            "type": "string"
          },
          {
            "name": "offset",
            "in": "query",
            "description": "offset of page number",
            "required": false,
            "type": "number"
          },
          {
            "name": "rowsPerPage",
            "in": "query",
            "description": "rows per page, default is 20, maxmimum is 300",
            "required": false,
            "type": "number"
          }
        ],
        "responses": {
          "200": {
            "description": "successful operation",
            "schema": {
              "type": "array",
              "items": {
                "$ref": "#/definitions/Datasets"
              }
            }
          },
          "400": {
            "description": "Invalid status value"
          }
        }

      }
    },
    "/esearch?searchtype=data&datatypes={datatypes}": {
      "get": {
        "tags": [
          "query"
        ],
        "summary": "Search datasets from DataMed by query for specific datatype",
        "description": "Get datasets by searching query for specific datatype",
        "produces": [
          "application/xml",
          "application/json"
        ],
        "parameters": [
          {
            "name": "query",
            "in": "query",
            "description": "Search term",
            "required": false,
            "type": "string"
          },
          {
            "name": "offset",
            "in": "query",
            "description": "offset of page number",
            "required": false,
            "type": "number"
          },
          {
            "name": "rowsPerPage",
            "in": "query",
            "description": "rows per page, default is 20, maxmimum is 300",
            "required": false,
            "type": "number"
          },
          {
            "name": "datatypes",
            "in": "query",
            "description": "datatypes,multiple datatype values can be provided with comma separated strings",
            "required": false,
            "type": "array",
            "items": {
              "type": "string",
              "enum": [
                "Protein","Phenotype", "Gene Expression",
                "Nucleotide Sequence", "Morphology", "Clinical Trials",
                "Proteomics Data", "Physiological Signals", "Epigenetic Data",
                "Data from Papers", "Omics Data", "Survey Data", "Cell Signaling", "Imaging Data", "Unspecified"

              ]
            }
          }
        ],
        "responses": {
          "200": {
            "description": "successful operation",
            "schema": {
              "type": "array",
              "items": {
                "$ref": "#/definitions/Datasets"
              }
            }
          },
          "400": {
            "description": "Invalid status value"
          }
        }

      }
    },
    "/esearch?searchtype=data&repository={repository}": {
      "get": {
        "tags": [
          "query"
        ],
        "summary": "Search datasets from DataMed by query for specific repository",
        "description": "Get datasets by searching query for specific repository",
        "produces": [
          "application/xml",
          "application/json"
        ],
        "parameters": [
          {
            "name": "query",
            "in": "query",
            "description": "Search term",
            "required": false,
            "type": "string"
          },
          {
            "name": "offset",
            "in": "query",
            "description": "offset of page number",
            "required": false,
            "type": "number"
          },
          {
            "name": "rowsPerPage",
            "in": "query",
            "description": "rows per page, default is 20, maxmimum is 300",
            "required": false,
            "type": "number"
          },
          {
            "name": "repository",
            "in": "query",
            "description": "repository,multiple repository values can be provided with comma separated strings",
            "required": false,
            "type": "array",
            "items":{
              "type":"string",
              "enum":["dbGaP", "PDB", "GEO" , "LINCS", "GEMMA", "ArrayExpress", "SRA", "BioProject", "ClinicalTrials", "Dryad", "cvrg",
                "Dataverse", "NeuroMorpho.Org", "PeptideAtlas", "CTN", "TCIA", "MPD", "NIDDKCR", "openfmri", "NURSA", "PhysioBank", "ProteomeXchange", "YPED", "CIL", "ICPRS",
                "GDC", "BMRB","UniProt:Swiss-Prot", "ClinVar", "Retina", "PDBe:EMDB", "Epigenomics", "nitrcir", "NeuroVault:Atlases", "NeuroVault:Cols", "NeuroVault: NIDM",
                "RGD", "GigaDB", "MorphoBank", "VectorBase", "GND", "PeerJ",
                "Zenodo", "OmicsDI", "SBGrid", "SimTK", "CXIDB", "BILS", "ADA", "UKDA", "Adaptive Biotechnologies", "MITLCP", "UCSF-CTSI", "FDZ-DZA",
                "MBF", "NIMH", "JHUDMS", "CANDI", "LSHTM", "Databrary", "ImmPort",
                "NSGM", "CRCNS", "NSRR","NSD", "LSDB", "GeneNetwork", "Ndar Papers", "Thieme","Figshare","CCDC","Wormbase","GTex","Metabolomics"]

            }
          }
        ],
        "responses": {
          "200": {
            "description": "successful operation",
            "schema": {
              "type": "array",
              "items": {
                "$ref": "#/definitions/Datasets"
              }
            }
          },
          "400": {
            "description": "Invalid status value"
          }
        }

      }
    }



  },

  "definitions": {
    "ApiResponse": {
      "type": "object",
      "properties": {
        "code": {
          "type": "integer",
          "format": "int32"
        },
        "type": {
          "type": "string"
        },
        "message": {
          "type": "string"
        }
      }
    },
    "Datasets": {
      "type": "object",
      "required": [
        "total",
        "offset",
        "rowsPerPage"

      ],
      "properties": {
        "total": {
          "type": "integer",
          "format": "int64"
        },
        "offset": {
          "type": "integer",
          "format": "int64"
        },
        "rowsPerPage": {
          "type": "integer",
          "format": "int64"
        },
        "hits": {
          "$ref": "#/definitions/Hits"
        }


      },
      "xml": {
        "name": "Datasets"
      }
    },
    "Hits": {
      "type": "object",
      "properties": {
        "_index": {
          "type": "string"
        },
        "_type": {
          "type": "string"
        },
        "_id": {
          "type": "string"
        },
        "_score": {
          "type": "number"
        },
        "_source": {
          "type": "string"
        }
      },
      "xml": {
        "name": "Hits"
      }
    }
  }

}