genotype_phenotype_service

************* /phenotypeassociationsets/search **************** ************* /phenotypes/search **************** ************* /featurephenotypeassociations/search ****************

SearchPhenotypeAssociationSets(request)

Parameters:request – SearchPhenotypeAssociationSetsRequest Return type:SearchPhenotypeAssociationSetsResponse Throws:GAException

Gets a list of association sets accessible through the API. POST /phenotypeassociationsets/search must accept a JSON version of SearchPhenotypeAssociationSetsRequest as the post body and will return a JSON version of SearchPhenotypeAssociationSetsResponse.

SearchPhenotype(request)

Parameters:request – SearchPhenotypesRequest Return type:SearchPhenotypesResponse Throws:GAException

Gets a list of phenotypes accessible through the API. POST /phenotypes/search must accept a JSON version of SearchPhenotypesRequest as the post body and will return a JSON version of SearchPhenotypeAssociationSetsResponse.

SearchPhenotypeAssociations(request)

Parameters:request – SearchGenotypePhenotypeRequest Return type:SearchGenotypePhenotypeResponse Throws:GAException

Gets a list of genotype-phenotype assoications accessible through the API. POST /featurephenotypeassociations/search must accept a JSON version of SearchPhenotypesRequest as the post body and will return a JSON version of SearchPhenotypeAssociationSetsResponse.

message SearchPhenotypeAssociationSetsRequest

Fields:

• dataset_id (string) – The Dataset to search. Mandatory
• page_size (long) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
• page_token (string) – 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.

This request maps to the body of POST /phenotypeassociationsets/search as JSON.

message SearchPhenotypeAssociationSetsResponse

Fields:

• phenotype_association_sets (list of PhenotypeAssociationSet) – The list of matching phenotype association sets.
• next_page_token (string) – 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.

This is the response from POST /phenotypeassociationsets/search expressed as JSON.

message OntologyTermQuery

Fields:

• terms (list of OntologyTerm) –

One or more ontology terms can be queried together.

message ExternalIdentifierQuery

Fields:

• ids (list of ExternalIdentifier) –

One or more ids can be queried together. Generally used for instances of a particular class of object (e.g. a specific gene or SNP).

message EvidenceQuery

Fields:

• evidenceType (OntologyTerm) – ECO or OBI is recommended
• description (string) – The system may support regex. https://www.w3.org/TR/xpath-functions/#regex-syntax
• external_identifiers (list of ExternalIdentifier) – Only match Evidence messages that have any of these external identifiers

Evidence for the phenotype association.

message SearchPhenotypesRequest

Fields:

• phenotype_association_set_id (string) – The PhenotypeAssociationSet to search. Mandatory
• id (string) – Phenotype ID TODO remove if a get-by-phenotype ID endpoint is added
• description (string) – The system may support regex. https://www.w3.org/TR/xpath-functions/#regex-syntax
• type (OntologyTerm) – Only return results that match this type
• qualifiers (list of OntologyTerm) – terms should be OR’d together. e.g. (severe OR abnormal)
• age_of_onset (OntologyTerm) – Only return results that match this age of onset
• page_size (long) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
• page_token (string) – 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 next_page_token from the previous response.

message SearchPhenotypesResponse

Fields:

• phenotypes (list of PhenotypeInstance) – The list of matching PhenotypeInstances.
• next_page_token (string) – 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.

This is the response from POST /phenotypes/search expressed as JSON.

message SearchGenotypePhenotypeRequest

Fields:

• phenotype_association_set_id (string) – The PhenotypeAssociationSet to search. Mandatory
• feature_ids (string) – At least one feature_id or phenotype_id must be provided.
• phenotype_ids (string) – Phenotype IDs
• evidence (list of EvidenceQuery) – evidence
• page_size (long) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
• page_token (string) – 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.

This request maps to the body of POST /featurephenotypeassociations/search as JSON.

The goal here is to allow users to query using one or more of Genotype, Phenotype, Environment, and Evidence.

A query using one of the above items is to mean, by default, that the remainder of the query is as a “wildcard”, such that all matches to just that query term would come back. Combinations of the above are to act like AND rather than OR.

The “genotype” part of the query methods can be one or more genomic features. Associations can be made at many levels of granularity (from whole genotypes down to individual SNVs), but users may use these methods with partial or inexact information. Therefore, the query methods must be able to support query of some or all of the associated features. Furthermore, use of the relationships between genomic features means that when querying for a gene, any variants to that gene are also returned. For example, a query with BRCA2 would mean that in addition to any direct associations to the BRCA2, all associations to sequence variants of BRCA2 would also be returned. Similarly, queries with OntologyTerms should perform the subclass closure.

Each query can be made against a string, an array of external identifers (such as for gene or SNP ids), ontology term ids, or full feature/phenotype/evidence objects.

message SearchGenotypePhenotypeResponse

Fields:

• associations (list of FeaturePhenotypeAssociation) – The list of matching FeaturePhenotypeAssociation.
• next_page_token (string) – 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.

This is the response from POST /genotypephenotype/search expressed as JSON.