common

This file defines common types used in other parts of the schema. There are no directly associated methods.
enum Strand
Symbols:STRAND_UNSPECIFIED|NEG_STRAND|POS_STRAND

Indicates the associated DNA strand for some data item.

  • STRAND_UNSPECIFIED: If no strand data is available.
  • NEG_STRAND: The negative (-) strand.
  • POS_STRAND: The postive (+) strand.
enum NullValue
Symbols:NULL_VALUE
  • NULL_VALUE: Null value.
message GAException
Fields:
  • error_code (integer) – Numerical error code
  • message (string) – The error message.

When returning an HTTP error response, a server may also return a JSON formatted GAException to better describe the error.

message Position
Fields:
  • reference_name (string) – The name of the Reference on which the Position is located.
  • position (long) – The 0-based offset from the start of the forward strand for that Reference. Genomic positions are non-negative integers less than Reference length.
  • strand (Strand) – Strand the position is associated with.

A Position is an unoriented base in some Reference. A Position is represented by a Reference name, and a base number on that Reference (0-based).

message ExternalIdentifier
Fields:
  • database (string) – The source of the identifier, e.g. Ensembl.
  • identifier (string) – The ID defined by the external database, e.g. ENST00000000000.
  • version (string) – The version of the object or the database, e.g. 78.

Identifier from a public database

message Experiment
Fields:
  • id (string) – The experiment ID
  • name (string) – The name of the experiment.
  • description (string) – A description of the experiment.
  • message_create_time (string) – The time at which this message was created. Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
  • message_update_time (string) – The time at which this message was last updated. Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
  • run_time (string) – 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)
  • molecule (string) – The molecule examined in this experiment. (e.g. genomics DNA, total RNA)
  • strategy (string) – The experiment technique or strategy applied to the sample. (e.g. whole genome sequencing, RNA-seq, RIP-seq)
  • selection (string) – The method used to enrich the target. (e.g. immunoprecipitation, size fractionation, MNase digestion)
  • library (string) – The name of the library used as part of this experiment.
  • library_layout (string) – The configuration of sequenced reads. (e.g. Single or Paired).
  • instrument_model (string) – The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
  • instrument_data_file (string) – The data file generated by the instrument. TODO: This isn’t actually a file is it? Should this be instrumentData instead?
  • sequencing_center (string) – The sequencing center used as part of this experiment.
  • platform_unit (string) – The platform unit used as part of this experiment. This is a flowcell-barcode or slide unique identifier.
  • attributes (Attributes) – A map of additional experiment information.

An experimental preparation of a sample.

message Analysis
Fields:
  • id (string) – Formats of id | name | description | accessions are described in the documentation on general attributes and formats.
  • name (string) –
  • description (string) –
  • created (string) – The time at which this record was created, in ISO 8601 format.
  • updated (string) – The time at which this record was last updated, in ISO 8601 format.
  • type (string) – The type of analysis.
  • software (string) – The software run to generate this analysis.
  • attributes (Attributes) – A map of additional analysis information.

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 OntologyTerm
Fields:
  • term_id (string) – Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema’s id in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation.
  • term (string) – Ontology term - the label of the ontology term the termId is pointing to.

An ontology term describing an attribute. (e.g. the phenotype attribute ‘polydactyly’ from HPO)

message Program
Fields:
  • command_line (string) – The command line used to run this program.
  • id (string) – The user specified ID of the program.
  • name (string) – The name of the program.
  • prev_program_id (string) – The ID of the program run before this one.
  • version (string) – The version of the program run.

A Program describes software used in data processing or analysis.

message AttributeValue
Fields:

Type defining a collection of attributes associated with various protocol records. Each attribute is a name that maps to an array of one or more values. Values are chosen from both internal protobuf types and GA4GH. Values should be split into array elements instead of using a separator syntax that needs to parsed.

message AttributeValueList
Fields:
message Attributes
Fields: