BioMCP

// Copyright 2024 Google LLC.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

syntax = "proto3";

package google.gdm.gdmscience.alphagenome.v1main;

import "dna_model.proto";
import "tensor.proto";

option go_package = "google.golang.org/genproto/googleapis/gdm/gdmscience/alphagenome/v1main;alphagenome";
option java_multiple_files = true;
option java_outer_classname = "DnaModelServiceProto";
option java_package = "com.google.gdm.gdmscience.alphagenome.v1main";

// Service for making predictions with DNA models.
service DnaModelService {
  // Makes a prediction for DNA sequence.
  rpc PredictSequence(stream PredictSequenceRequest)
      returns (stream PredictSequenceResponse) {}

  // Make prediction for a single genomic interval.
  rpc PredictInterval(stream PredictIntervalRequest)
      returns (stream PredictIntervalResponse) {}

  // Make variant effect predictions for a genomic interval.
  rpc PredictVariant(stream PredictVariantRequest)
      returns (stream PredictVariantResponse) {}

  // Score a genomic interval.
  rpc ScoreInterval(stream ScoreIntervalRequest)
      returns (stream ScoreIntervalResponse) {}

  // Score a variant for a genomic interval.
  rpc ScoreVariant(stream ScoreVariantRequest)
      returns (stream ScoreVariantResponse) {}

  // Score ISM variant effect predictions for a genomic interval.
  rpc ScoreIsmVariant(stream ScoreIsmVariantRequest)
      returns (stream ScoreIsmVariantResponse) {}

  // Get metadata for the model.
  rpc GetMetadata(MetadataRequest) returns (stream MetadataResponse) {}
}

// Request message for predicting a sequence.
message PredictSequenceRequest {
  // DNA sequence to make prediction for. Must only contain characters "ACGTN".
  string sequence = 1;

  // Organism to use for the prediction.
  Organism organism = 2;

  // Ontology terms to generate predictions for. If empty returns all
  // ontologies.
  repeated OntologyTerm ontology_terms = 3;

  // Output types to generate predictions for.
  repeated OutputType requested_outputs = 4;

  // Model version to use.
  string model_version = 5;
}

// Response message for predicting a sequence.
message PredictSequenceResponse {
  // The payload for the response.
  oneof payload {
    // Output for a single output type.
    Output output = 1;

    // Tensor chunk related to the last output message received. It is an error
    // to receive a tensor chunk without a previous output message.
    TensorChunk tensor_chunk = 2;
  }
}

// Request message for predicting an interval.
message PredictIntervalRequest {
  // DNA interval to make prediction for.
  Interval interval = 1;

  // Organism to use for the prediction.
  Organism organism = 2;

  // Output types to generate predictions for.
  repeated OutputType requested_outputs = 3;

  // Ontology terms to generate predictions for. If empty returns all
  // ontologies.
  repeated OntologyTerm ontology_terms = 4;

  // Model version to use.
  string model_version = 5;
}

// Response message for predicting an interval.
message PredictIntervalResponse {
  // The payload for the response.
  oneof payload {
    // Output for a single output type.
    Output output = 1;

    // Tensor chunk related to the last output message received. It is an error
    // to receive a tensor chunk without a previous output message.
    TensorChunk tensor_chunk = 2;
  }
}

// Request message for predicting a variant.
message PredictVariantRequest {
  // DNA interval to make prediction for.
  Interval interval = 1;

  // DNA variant to make prediction for.
  Variant variant = 2;

  // Organism to use for the prediction.
  Organism organism = 3;

  // Output types to generate predictions for.
  repeated OutputType requested_outputs = 4;

  // Ontology terms to generate predictions for. If empty returns all
  // ontologies.
  repeated OntologyTerm ontology_terms = 5;

  // Model version to use.
  string model_version = 6;
}

// Response message for predicting a variant.
message PredictVariantResponse {
  // The payload for the response.
  oneof payload {
    // Reference output for a single output type.
    Output reference_output = 1;

    // Alternate output for a single output type.
    Output alternate_output = 2;

    // Tensor chunk related to the last reference or alternate output message
    // received. It is an error to receive a tensor chunk without a previous
    // reference or alternate output message.
    TensorChunk tensor_chunk = 3;
  }
}

// Request message for scoring an interval.
message ScoreIntervalRequest {
  // DNA interval to make prediction for.
  Interval interval = 1;

  // Organism to use for the prediction.
  Organism organism = 2;

  // Interval scorers to use for the prediction.
  repeated IntervalScorer interval_scorers = 3;

  // Model version to use.
  string model_version = 4;
}

// Response message for scoring an interval.
message ScoreIntervalResponse {
  // The payload for the response.
  oneof payload {
    // Score interval output.
    ScoreIntervalOutput output = 1;

    // Tensor chunk related to the last score interval output message received.
    // It is an error to receice a tensor chunk without a previous output
    // message.
    TensorChunk tensor_chunk = 2;
  }
}

// Request message for scoring a variant.
message ScoreVariantRequest {
  // DNA interval to make prediction for.
  Interval interval = 1;

  // DNA variant to make prediction for.
  Variant variant = 2;

  // Organism to use for the prediction.
  Organism organism = 3;

  // Variant scorers to use for the prediction.
  repeated VariantScorer variant_scorers = 4;

  // Model version to use.
  string model_version = 5;
}

// Response message for scoring a variant.
message ScoreVariantResponse {
  // The payload for the response.
  oneof payload {
    // Score variant output.
    ScoreVariantOutput output = 1;

    // Tensor chunk related to the last score variant output message received.
    // It is an error to receive a tensor chunk without a previous output
    // message.
    TensorChunk tensor_chunk = 2;
  }
}

// Request message for scoring an in-silico mutagenesis (ISM) interval.
message ScoreIsmVariantRequest {
  // DNA interval to make the prediction for.
  Interval interval = 1;

  // ISM interval to make the prediction for.
  Interval ism_interval = 2;

  // Organism to use for the prediction.
  Organism organism = 3;

  // Variant scorers to use for the prediction.
  repeated VariantScorer variant_scorers = 4;

  // Optional variant applied to the reference interval. If provided, the
  // alternate allele is used for in-silico mutagenesis, otherwise the
  // unaltered reference sequence is used.
  optional Variant interval_variant = 6;

  // Model version to use.
  string model_version = 5;
}

// Response message for scoring an in-silico mutagenesis (ISM) interval.
message ScoreIsmVariantResponse {
  // The payload for the response.
  oneof payload {
    // Score variant output.
    ScoreVariantOutput output = 1;

    // Tensor chunk related to the last score variant output message received.
    // It is an error to receive a tensor chunk without a previous output
    // message.
    TensorChunk tensor_chunk = 2;
  }
}

// Request message for getting metadata for an organism.
message MetadataRequest {
  // The organism we should return metadata for.
  Organism organism = 1;
}

// Response message for getting metadata for an organism.
message MetadataResponse {
  // The metadata for each output type.
  repeated OutputMetadata output_metadata = 1;
}