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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| openapi: 3.0.3 | ||
| openapi: 3.1.0 | ||
| info: | ||
| title: viguno | ||
| description: Phenotype/disease for VarFish | ||
|
|
@@ -7,7 +7,7 @@ info: | |
| email: [email protected] | ||
| license: | ||
| name: Apache-2.0 | ||
| version: 0.2.1 | ||
| version: 0.3.2 | ||
| paths: | ||
| /hpo/genes: | ||
| get: | ||
|
|
@@ -21,23 +21,25 @@ paths: | |
| description: The gene ID to search for. | ||
| required: false | ||
| schema: | ||
| type: string | ||
| nullable: true | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - name: gene_symbol | ||
| in: query | ||
| description: The gene symbol to search for. | ||
| required: false | ||
| schema: | ||
| type: string | ||
| nullable: true | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - name: match_ | ||
| in: query | ||
| description: The match mode. | ||
| required: false | ||
| schema: | ||
| allOf: | ||
| oneOf: | ||
| - type: 'null' | ||
| - $ref: '#/components/schemas/Match' | ||
| nullable: true | ||
| - name: max_results | ||
| in: query | ||
| description: Maximal number of results to return. | ||
|
|
@@ -70,30 +72,33 @@ paths: | |
| description: The OMIM ID to search for. | ||
| required: false | ||
| schema: | ||
| type: string | ||
| nullable: true | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - name: name | ||
| in: query | ||
| description: The disease name to search for. | ||
| required: false | ||
| schema: | ||
| type: string | ||
| nullable: true | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - name: match_ | ||
| in: query | ||
| description: The match mode, default is `Match::Exact`. | ||
| required: false | ||
| schema: | ||
| allOf: | ||
| oneOf: | ||
| - type: 'null' | ||
| - $ref: '#/components/schemas/Match' | ||
| nullable: true | ||
| - name: ignore_case | ||
| in: query | ||
| description: Whether case is insentivie, default is `false`. | ||
| required: false | ||
| schema: | ||
| type: boolean | ||
| nullable: true | ||
| type: | ||
| - boolean | ||
| - 'null' | ||
| - name: max_results | ||
| in: query | ||
| description: Maximal number of results to return. | ||
|
|
@@ -118,8 +123,9 @@ paths: | |
| get: | ||
| tags: | ||
| - hpo_sim::term_gene | ||
| summary: Query for similarity between a set of terms to each entry in a | ||
| description: list of genes. | ||
| summary: |- | ||
| Query for similarity between a set of terms to each entry in a | ||
| list of genes. | ||
| operationId: hpo_sim_term_gene | ||
| parameters: | ||
| - name: terms | ||
|
|
@@ -135,19 +141,21 @@ paths: | |
| description: The set of ids for genes to use as "database". | ||
| required: false | ||
| schema: | ||
| type: array | ||
| type: | ||
| - array | ||
| - 'null' | ||
| items: | ||
| type: string | ||
| nullable: true | ||
| - name: gene_symbols | ||
| in: query | ||
| description: The set of symbols for genes to use as "database". | ||
| required: false | ||
| schema: | ||
| type: array | ||
| type: | ||
| - array | ||
| - 'null' | ||
| items: | ||
| type: string | ||
| nullable: true | ||
| responses: | ||
| '200': | ||
| description: The query was successful. | ||
|
|
@@ -225,15 +233,17 @@ paths: | |
| description: The term ID to search for. | ||
| required: false | ||
| schema: | ||
| type: string | ||
| nullable: true | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - name: name | ||
| in: query | ||
| description: The term name to search for. | ||
| required: false | ||
| schema: | ||
| type: string | ||
| nullable: true | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - name: max_results | ||
| in: query | ||
| description: Maximal number of results to return. | ||
|
|
@@ -253,9 +263,29 @@ paths: | |
| content: | ||
| application/json: | ||
| schema: | ||
| $ref: '#/components/schemas/Result' | ||
| $ref: '#/components/schemas/Result_' | ||
| components: | ||
| schemas: | ||
| Gene: | ||
| type: object | ||
| description: Struct for storing gene information in the result. | ||
| required: | ||
| - entrez_id | ||
| - gene_symbol | ||
| properties: | ||
| entrez_id: | ||
| type: integer | ||
| format: int32 | ||
| description: The NCBI gene ID. | ||
| minimum: 0 | ||
| gene_symbol: | ||
| type: string | ||
| description: The gene symbol. | ||
| hgnc_id: | ||
| type: | ||
| - string | ||
| - 'null' | ||
| description: The HGNC ID. | ||
| HpoTerm: | ||
| type: object | ||
| description: Struct for loading an HPO term from JSON. | ||
|
|
@@ -266,9 +296,10 @@ components: | |
| type: string | ||
| description: The term ID. | ||
| term_name: | ||
| type: string | ||
| type: | ||
| - string | ||
| - 'null' | ||
| description: The term name (optional). | ||
| nullable: true | ||
| IcBasedOn: | ||
| type: string | ||
| description: |- | ||
|
|
@@ -290,36 +321,21 @@ components: | |
| Query: | ||
| type: object | ||
| title: HpoSimTermGeneQuery | ||
| description: |- | ||
| Parameters for `handle`. | ||
| This allows to compute differences between | ||
| - `terms` -- set of terms to use as query | ||
| - `gene_ids` -- set of ids for genes to use as "database", can be NCBI\ | ||
| gene ID or HGNC gene ID. | ||
| - `gene_symbols` -- set of symbols for genes to use as | ||
| "database" | ||
| description: The performed query. | ||
| required: | ||
| - terms | ||
| - genes | ||
| properties: | ||
| terms: | ||
| type: array | ||
| items: | ||
| type: string | ||
| description: Set of terms to use as query. | ||
| gene_ids: | ||
| $ref: '#/components/schemas/HpoTerm' | ||
| description: The query HPO terms. | ||
| genes: | ||
| type: array | ||
| items: | ||
| type: string | ||
| description: The set of ids for genes to use as "database". | ||
| nullable: true | ||
| gene_symbols: | ||
| type: array | ||
| items: | ||
| type: string | ||
| description: The set of symbols for genes to use as "database". | ||
| nullable: true | ||
| $ref: '#/components/schemas/Gene' | ||
| description: The gene list to score. | ||
| ResponseQuery: | ||
| type: object | ||
| title: HpoSimTermTermQuery | ||
|
|
@@ -343,47 +359,55 @@ components: | |
| description: The second set of HPO terms to compute similarity for. | ||
| ic_base: | ||
| $ref: '#/components/schemas/IcBasedOn' | ||
| description: What should information content be based on. | ||
| similarity: | ||
| $ref: '#/components/schemas/SimilarityMethod' | ||
| description: The similarity method to use. | ||
| combiner: | ||
| $ref: '#/components/schemas/ScoreCombiner' | ||
| description: The score combiner. | ||
| Result: | ||
| type: object | ||
| title: HpoSimTermTermResult | ||
| description: Result container. | ||
| title: HpoSimTermGeneResult | ||
| description: Result container data structure. | ||
| required: | ||
| - version | ||
| - query | ||
| - result | ||
| properties: | ||
| version: | ||
| $ref: '#/components/schemas/Version' | ||
| description: Version information. | ||
| query: | ||
| $ref: '#/components/schemas/ResponseQuery' | ||
| $ref: '#/components/schemas/Query' | ||
| description: The original query records. | ||
| result: | ||
| type: array | ||
| items: | ||
| $ref: '#/components/schemas/ResultEntry' | ||
| description: The resulting records for the scored genes. | ||
| ResultEntry: | ||
| type: object | ||
| title: HpoSimTermTermResultEntry | ||
| description: Result entry for `handle`. | ||
| title: HpoSimTermGeneResultEntry | ||
| description: Store score for a record with information on individual terms. | ||
| required: | ||
| - lhs | ||
| - rhs | ||
| - score | ||
| - gene_symbol | ||
| - raw_score | ||
| properties: | ||
| lhs: | ||
| type: string | ||
| description: The lhs entry. | ||
| rhs: | ||
| gene_symbol: | ||
| type: string | ||
| description: The rhs entry. | ||
| score: | ||
| description: The gene symbol. | ||
| raw_score: | ||
| type: number | ||
| format: float | ||
| description: The similarity score. | ||
| description: The raw Phenomizer score. | ||
| terms: | ||
| type: | ||
| - array | ||
| - 'null' | ||
| items: | ||
| $ref: '#/components/schemas/TermDetails' | ||
| description: Details on individual terms. | ||
| ResultGene: | ||
| type: object | ||
| description: Representation of a gene. | ||
|
|
@@ -400,9 +424,10 @@ components: | |
| type: string | ||
| description: The description. | ||
| hgnc_id: | ||
| type: string | ||
| type: | ||
| - string | ||
| - 'null' | ||
| description: The HGNC ID. | ||
| nullable: true | ||
| ResultHpoTerm: | ||
| type: object | ||
| description: Representation of an HPO term. | ||
|
|
@@ -427,8 +452,10 @@ components: | |
| properties: | ||
| version: | ||
| $ref: '#/components/schemas/Version' | ||
| description: Version information. | ||
| query: | ||
| $ref: '#/components/schemas/Query' | ||
| description: The original query records. | ||
| result: | ||
| type: array | ||
| items: | ||
|
|
@@ -470,11 +497,13 @@ components: | |
| - score | ||
| properties: | ||
| term_query: | ||
| allOf: | ||
| oneOf: | ||
| - type: 'null' | ||
| - $ref: '#/components/schemas/HpoTerm' | ||
| nullable: true | ||
| description: The query HPO term. | ||
| term_gene: | ||
| $ref: '#/components/schemas/HpoTerm' | ||
| description: The gene's HPO term. | ||
| score: | ||
| type: number | ||
| format: float | ||
|
|
||