proposed sequence annotation API

src/main/resources/avro/common.avdl

@@ -409,6 +409,70 @@ record Path {
   array<Segment> segments = [];
 }
 
+/**
+An abstraction for referring to a genomic region, in relation to some already 
+known reference. This will require some significant rework as we move to graph
+coordinates.  
+*/
+// TODO: Add support for paths through the graph.
+record Region {
+  /**
+  The starting point of the region. For the moment the base-pair included in
+  the region, on the 5' end of the oriented region.
+  */
+  Position start;
+
+  /**
+  The length, in base pairs
+  */
+  long length;
+}
+
+/**
+An ontology term describing an attribute. (e.g. the phenotype attribute
+'polydactyly' from HPO)
+*/
+
+record OntologyTerm {
+  /**
+  The source of the onotology term.
+  (e.g. `Ontology for Biomedical Investigation`)
+  */
+  string ontologySource;
+
+  /**
+  The ID defined by the external onotology source.
+  (e.g. `http://purl.obolibrary.org/obo/OBI_0001271`)
+  */
+  string id;
+
+  /** The name of the onotology term. (e.g. `RNA-seq assay`) */
+  union { null, string } name = null;
+}
+
+/**
+Identifier from a public database
+*/
+record ExternalIdentifier {
+  /**
+  The source of the identifier.
+  (e.g. `Ensembl`)
+  */
+  string database;
+
+  /**
+  The ID defined by the external database.
+  (e.g. `ENST00000000000`)
+  */
+  string identifier;
+
+  /**
+  The version of the object or the database
+  (e.g. `78`)
+  */
+  string version;
+}
+
 /**
 An enum for the different types of CIGAR alignment operations that exist.
 Used wherever CIGAR alignments are used. The different enumerated values

src/main/resources/avro/metadata.avdl

@@ -7,28 +7,7 @@ This protocol defines metadata used in the other GA4GH protocols.
 protocol Metadata {
 
 import idl "common.avdl";
-
-/**
-An ontology term describing an attribute. (e.g. the phenotype attribute
-'polydactyly' from HPO)
-*/
-
-record OntologyTerm {
-  /**
-  The source of the onotology term.
-  (e.g. `Ontology for Biomedical Investigation`)
-  */
-  string ontologySource;
-
-  /**
-  The ID defined by the external onotology source.
-  (e.g. `http://purl.obolibrary.org/obo/OBI_0001271`)
-  */
-  string id;
-
-  /** The name of the onotology term. (e.g. `RNA-seq assay`) */
-  union { null, string } name = null;
-}
+import idl "ontologies.avdl";
 
 /**
 An individual (or subject) typically corresponds to an individual

src/main/resources/avro/methods.avdl

@@ -13,6 +13,4 @@ error GAException {
   int errorCode = -1;
 }
 
-
-
 }

src/main/resources/avro/ontologies.avdl

@@ -0,0 +1,26 @@
+@namespace("org.ga4gh.models")
+/**
+Protocol that defines types associated with ontologies.
+*/
+protocol Ontologies {
+  /**
+  An ontology term describing an attribute. (e.g. the phenotype attribute
+  'polydactyly' from HPO)
+  */
+  record OntologyTerm {
+    /**
+    The source of the onotology term.
+    (e.g. `Ontology for Biomedical Investigation`)
+    */
+    string ontologySource;
+
+    /**
+    The ID defined by the external onotology source.
+    (e.g. `http://purl.obolibrary.org/obo/OBI_0001271`)
+    */
+    string id;
+
+    /** The name of the onotology term. (e.g. `RNA-seq assay`) */
+    union { null, string } name = null;
+  }
+}

src/main/resources/avro/sequenceAnnotationmethods.avdl

@@ -0,0 +1,97 @@
+@namespace("org.ga4gh.methods")
+
+protocol SequenceAnnotationMethods {
+
+  import idl "common.avdl";
+  import idl "methods.avdl";
+  import idl "sequenceAnnotations.avdl";
+
+  // FIXME: wiggle methods not defined.
+
+  /******************  /features/search  *********************/
+
+  /**
+  This request maps to the body of `POST /features/search` as JSON.
+  */
+  record SearchFeaturesRequest {
+    /**
+    The annotation sets to search within. Either `featureSetIds` or
+    `parentIds` must be non-empty.
+    */
+    array<string> featureSetIds = [];
+
+    /**
+    Restricts the search to direct children of the given parent `feature`
+    IDs. Either `featureSetIds` or `parentIds` must be non-empty.
+    */
+    array<string> parentIds = [];
+
+    /**
+    If specified, this query matches only annotations which overlap this path.
+    */
+    union { null, org.ga4gh.models.Path } range = null;
+
+    // TODO: Fix this field. Clarify semantics around how OntologyTerm matching works, or
+    // change the Ontology term field on the feature.
+    /**
+    If specified, this query matches only annotations which match one of the
+    provided feature types.
+    */
+    array<org.ga4gh.models.OntologyTerm> features = [];
+
+    /**
+    Specifies the maximum number of results to return in a single page.
+    If unspecified, a system default will be used.
+    */
+    union { null, int } pageSize = null;
+
+    /**
+    The continuation token, which is used to page through large result sets.
+    To get the next page of results, set this parameter to the value of
+    `nextPageToken` from the previous response.
+    */
+    union { null, string } pageToken = null;
+  }
+
+  /** This is the response from `POST /features/search` expressed as JSON. */
+  record SearchFeaturesResponse {
+    /**
+    The list of matching annotations, sorted by start position. Annotations which
+    share a start position are returned in a deterministic order.
+    */
+    array<org.ga4gh.models.Feature> features = [];
+
+    /**
+    The continuation token, which is used to page through large result sets.
+    Provide this value in a subsequent request to return the next page of
+    results. This field will be empty if there aren't any additional results.
+    */
+    union { null, string } nextPageToken = null;
+  }
+
+  /**
+  Gets a list of `Feature` matching the search criteria.
+
+  `POST /features/search` must accept a JSON version of
+  `SearchFeaturesRequest` as the post body and will return a JSON version of
+  `SearchFeaturesResponse`.
+  */
+  SearchFeaturesResponse searchFeatures(
+    /** This request maps to the body of `POST /features/search` as JSON. */
+    SearchFeaturesRequest request) throws GAException;
+
+
+  /****************  /feature/{id}  *******************/
+  /**
+  Gets a `org.ga4gh.models.Feature` by ID.
+  `GET /feature/{id}` will return a JSON version of `Feature`.
+  */
+  org.ga4gh.models.Feature getFeature(
+    /**
+    The ID of the `Feature`.
+    */
+    string id) throws GAException;
+
+}
+
+// TODO: AnnotationSet methods.