Services API

Basic Micro-Synteny Tracks

Takes a set of focus gene identifiers and the number of neighbors to display on either side of each gene. Returns the set of tracks centered about the given focus genes. GCV assumes each returned track's genes are in the order they occur on the track's chromosome.

• URL

  /micro-synteny-basic/

• Method:

  POST

• URL Params

  Required:

None

• Data Params

  genes=[gene_id, ...]
numNeighbors=Number

• Success Response:

  • Code: 200
    Content:

  {
    families: [{
      id : String,
      name : String
    }, ...],
    groups: [{
      chromosome_name: String,
      chromosome_id: String,
      species_name: String,
      species_id: String,
      genes: [{
        id: String,
        name: String,
        fmin: Integer,
        fmax: Integer,
        strand: 0 | -1 | 1,
        family: String
      }]
    }, ...]
  }

• Error Response:

  • Code: 404 NOT FOUND

• Sample Call:

    $.ajax({
      url: "/micro-synteny-basic/",
      dataType: "json",
      data: {
        genes: ["lotja.Lj0g3v0166889", "Ccicar.Ca_05015_gene"],
        numNeighbors: 10
      },
      type : "POST",
      success : function (r) {
        console.log(r);
      }
    });

Search Micro-Synteny Tracks

Takes a query track, that is, an ordered list of gene family identifiers and search parameters: minimum number of matched families and maximum number of non-matched families between any two matched families. Returns all micro-synteny contexts (tracks) in the database that meet the given parameter constraints. GCV assumes each returned track's genes are in the order they occur on the track's chromosome.

• URL

  /micro-synteny-search/

• Method:

  POST

• URL Params

  Required:

None

• Data Params

  query=[family_id, ...]
numMatchedFamilies
numNonFamily

• Success Response:

  • Code: 200
    Content:

  {
    families: [{
      id : String,
      name : String
    }, ...],
    groups: [{
      chromosome_name: String,
      chromosome_id: String,
      species_name: String,
      species_id: String,
      genes: [{
        id: String,
        name: String,
        fmin: Integer,
        fmax: Integer,
        strand: 0 | -1 | 1,
        family: String
      }]
    }, ...]
  }

• Error Response:

  • Code: 404 NOT FOUND

• Sample Call:

    $.ajax({
      url: "/micro-synteny-search/",
      dataType: "json",
      data: {
        query: ["phytozome_10_2.59177331", "phytozome_10_2.59249630", "phytozome_10_2.59166071"],
        numMatchedFamilies: 6,
        numNonFamily: 3
      },
      type : "POST",
      success : function (r) {
        console.log(r);
      }
    });