syntax = "proto3";

package ga4ghmetadata;

import "ga4gh-metadata/shared.proto";

// An experimental preparation of a sample.
message Experiment {
  // The experiment ID
  string id = 1;

  // The name of the experiment.
  string name = 2;

  // A description of the experiment.
  string description = 3;

  // The time at which the record of this experiment was last updated.
  // Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
  string updated = 5;

  // The time at which this experiment was performed.
  // Granularity here is variable (e.g. date only).
  // Format: ISO 8601, YYYY-MM-DDTHH:MM:SS (e.g. 2015-02-10T00:03:42)
  string run_time = 6;

  // The molecule examined in this experiment. (e.g. genomics DNA, total RNA)
  string molecule = 7;

  // The experiment technique or strategy applied to the sample.
  // (e.g. whole genome sequencing, RNA-seq, RIP-seq)
  string strategy = 8;

  // The method used to enrich the target. (e.g. immunoprecipitation, size
  // fractionation, MNase digestion)
  string selection = 9;

  // The name of the library used as part of this experiment.
  string library = 10;

  // The configuration of sequenced reads. (e.g. Single or Paired).
  string library_layout = 11;

  // The instrument model used as part of this experiment.
  // This maps to sequencing technology in BAM.
  string instrument_model = 12;

  // The data file generated by the instrument.
  // TODO: This isn't actually a file is it?
  // Should this be `instrumentData` instead?
  string instrument_data_file = 13;

  // Name of the laboratory where this experiment was performed.
  string sequencing_center = 14;

  // The address coded as geolocation object of the laboratory.
  GeoLocation location = 18;

  // The platform unit used as part of this experiment. This is a
  // flowcell-barcode
  // or slide unique identifier.
  string platform_unit = 15;

  // A map of additional experiment information.
  Attributes attributes = 17;
}

// An analysis contains an interpretation of one or several experiments. (e.g.
// SNVs, copy number variations, methylation status) together with information
// about the methodology used.
message Analysis {
  // Formats of id | name | description | accessions are described in the
  // documentation on general attributes and formats.
  string id = 1;

  string name = 2;

  string description = 3;

  // The time at which this record was created, in ISO 8601 format.
  string created = 4;

  // The time at which this record was last updated, in ISO 8601 format.
  string updated = 5;

  // The type of analysis.
  string type = 6;

  // The software run to generate this analysis.
  repeated string software = 7;

  // A map of additional analysis information.
  Attributes attributes = 9;
}