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=Integer
numNonFamily=Integer

• 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);
      }
    });

Gene to Query

Takes a focus gene identifier and the number of neighbors as input and passes them to the basic micro-synteny tracks service. Returns the ordered list of genes from the resulting basic track. GCV assumes the returned track's genes are in the order they occur on the focus gene's chromosome.

• URL

  /gene-to-query/

• Method:

  POST

• URL Params

  Required:

None

• Data Params

  query=[family_id, ...]
numNeighbors=Integer

• Success Response:

  • Code: 200
    Content:

  {
    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: "/gene-to-query/",
      dataType: "json",
      data: {
        gene: ["glyma.Glyma.06G088000"],
        numNeighbors: 7
      },
      type : "POST",
      success : function (r) {
        console.log(r);
      }
    });

Macro-Synteny Tracks

Takes a reference chromosome and a set of aligned chromosomes. Returns the synteny blocks of the aligned chromosomes with positions relative to the reference chromosome.

• URL

  /macro-synteny/

• Method:

  POST

• URL Params

  Required:

None

• Data Params

  chromosome=chromosome_id
results=[chromosome_id, ...]

• Success Response:

  • Code: 200
    Content:

  {
    chromosome: String,
    length: Integer,
    tracks: [{
      chromosome: String,
      blocks: [{
        start: Integer,
        stop: Integer,
        orientation: "-" | "+"
      }, ...]
    }, ...]
  }

• Error Response:

  • Code: 404 NOT FOUND

• Sample Call:

    $.ajax({
      url: "/gene-to-query/",
      dataType: "json",
      data: {
        chromosomes: "glyma.Chr06",
        results: ["aradu.Aradu.A08", "cicar.Ca4"]
      },
      type : "POST",
      success : function (r) {
        console.log(r);
      }
    });