swagger: '2.0' info: title: OLIDA API description: This API provides machine-readable access to the data stored in the OLIDA database. termsOfService: /about contact: email: olida@ibsquare.com license: name: CC Attribution-NonCommercial 4.0 International License url: https://creativecommons.org/licenses/by-nc/4.0/legalcode version: v1 host: olida.ibsquare.be schemes: - https basePath: / consumes: - application/vnd.api+json produces: - application/vnd.api+json securityDefinitions: Basic: type: basic security: - Basic: [] paths: /api-token/: post: operationId: api-token_create description: '' parameters: - name: data in: body required: true schema: $ref: '#/definitions/AuthToken' responses: '201': description: '' schema: $ref: '#/definitions/AuthToken' consumes: - application/json produces: - application/json tags: - api-token parameters: [] /api/combinations/: get: operationId: api_combinations_list description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: - name: ordering in: query description: Which field to use when ordering the results. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Combination' tags: - api parameters: [] /api/combinations/{combination_id}/: get: operationId: api_combinations_read description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Combination' tags: - api parameters: - name: combination_id in: path description: A unique value identifying this combination. required: true type: string /api/combinations/{combination_id}/relationships/{related_field}: get: operationId: api_combinations_relationships_read description: '' parameters: [] responses: '200': description: '' schema: type: string tags: - api parameters: - name: combination_id in: path description: A unique value identifying this combination. required: true type: string - name: related_field in: path required: true type: string /api/combinations/{combination_pk}/diseases/: get: operationId: api_combinations_diseases_list description: This API endpoint handles listing (/diseases) and retrieval (/diseases//) of genetic diseases that are contained in the database parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Disease' tags: - api parameters: - name: combination_pk in: path required: true type: string /api/combinations/{combination_pk}/diseases/{disease_id}/: get: operationId: api_combinations_diseases_read description: This API endpoint handles listing (/diseases) and retrieval (/diseases//) of genetic diseases that are contained in the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Disease' tags: - api parameters: - name: combination_pk in: path required: true type: string - name: disease_id in: path description: A unique value identifying this disease. required: true type: integer /api/combinations/{combination_pk}/genecombinations/: get: operationId: api_combinations_genecombinations_list description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/GeneCombination' tags: - api parameters: - name: combination_pk in: path required: true type: string /api/combinations/{combination_pk}/genecombinations/{id}/: get: operationId: api_combinations_genecombinations_read description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/GeneCombination' tags: - api parameters: - name: combination_pk in: path required: true type: string - name: id in: path description: A unique integer value identifying this gene combination. required: true type: integer /api/combinations/{combination_pk}/references/: get: operationId: api_combinations_references_list description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Reference' tags: - api parameters: - name: combination_pk in: path required: true type: string /api/combinations/{combination_pk}/references/{id}/: get: operationId: api_combinations_references_read description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Reference' tags: - api parameters: - name: combination_pk in: path required: true type: string - name: id in: path description: A unique integer value identifying this reference. required: true type: integer /api/combinations/{combination_pk}/variants/: get: operationId: api_combinations_variants_list description: This API endpoint handles listing (/variants) and retrieval (/variants//) of genetic variants from the database parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Variant' tags: - api parameters: - name: combination_pk in: path required: true type: string /api/combinations/{combination_pk}/variants/{id}/: get: operationId: api_combinations_variants_read description: This API endpoint handles listing (/variants) and retrieval (/variants//) of genetic variants from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Variant' tags: - api parameters: - name: combination_pk in: path required: true type: string - name: id in: path description: A unique integer value identifying this variant. required: true type: integer /api/diseases/: get: operationId: api_diseases_list description: This API endpoint handles listing (/diseases) and retrieval (/diseases//) of genetic diseases that are contained in the database parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Disease' tags: - api parameters: [] /api/diseases/{disease_id}/: get: operationId: api_diseases_read description: This API endpoint handles listing (/diseases) and retrieval (/diseases//) of genetic diseases that are contained in the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Disease' tags: - api parameters: - name: disease_id in: path description: A unique value identifying this disease. required: true type: integer /api/diseases/{disease_id}/relationships/{related_field}: get: operationId: api_diseases_relationships_read description: '' parameters: [] responses: '200': description: '' schema: type: string tags: - api parameters: - name: disease_id in: path description: A unique value identifying this disease. required: true type: integer - name: related_field in: path required: true type: string /api/diseases/{disease_pk}/combinations/: get: operationId: api_diseases_combinations_list description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: - name: ordering in: query description: Which field to use when ordering the results. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Combination' tags: - api parameters: - name: disease_pk in: path required: true type: string /api/diseases/{disease_pk}/combinations/{combination_id}/: get: operationId: api_diseases_combinations_read description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Combination' tags: - api parameters: - name: combination_id in: path description: A unique value identifying this combination. required: true type: string - name: disease_pk in: path required: true type: string /api/genecombinations/: get: operationId: api_genecombinations_list description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/GeneCombination' tags: - api parameters: [] /api/genecombinations/{genecombination_pk}/combinations/: get: operationId: api_genecombinations_combinations_list description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: - name: ordering in: query description: Which field to use when ordering the results. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Combination' tags: - api parameters: - name: genecombination_pk in: path required: true type: string /api/genecombinations/{genecombination_pk}/combinations/{combination_id}/: get: operationId: api_genecombinations_combinations_read description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Combination' tags: - api parameters: - name: combination_id in: path description: A unique value identifying this combination. required: true type: string - name: genecombination_pk in: path required: true type: string /api/genecombinations/{genecombination_pk}/genes/: get: operationId: api_genecombinations_genes_list description: "This API endpoint handles listing (/genes) and retrieval (/genes//)\ \ of genes that are contained in the database due to their association to\ \ \ngenetic variants that are involved in at least one oligogenic combination\ \ in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Gene' tags: - api parameters: - name: genecombination_pk in: path required: true type: string /api/genecombinations/{genecombination_pk}/genes/{gene_name}/: get: operationId: api_genecombinations_genes_read description: "This API endpoint handles listing (/genes) and retrieval (/genes//)\ \ of genes that are contained in the database due to their association to\ \ \ngenetic variants that are involved in at least one oligogenic combination\ \ in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Gene' tags: - api parameters: - name: gene_name in: path description: A unique value identifying this gene. required: true type: string - name: genecombination_pk in: path required: true type: string /api/genecombinations/{id}/: get: operationId: api_genecombinations_read description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/GeneCombination' tags: - api parameters: - name: id in: path description: A unique integer value identifying this gene combination. required: true type: integer /api/genecombinations/{id}/relationships/{related_field}: get: operationId: api_genecombinations_relationships_read description: '' parameters: [] responses: '200': description: '' schema: type: string tags: - api parameters: - name: id in: path description: A unique integer value identifying this gene combination. required: true type: integer - name: related_field in: path required: true type: string /api/genes/: get: operationId: api_genes_list description: "This API endpoint handles listing (/genes) and retrieval (/genes//)\ \ of genes that are contained in the database due to their association to\ \ \ngenetic variants that are involved in at least one oligogenic combination\ \ in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Gene' tags: - api parameters: [] /api/genes/{gene_name}/: get: operationId: api_genes_read description: "This API endpoint handles listing (/genes) and retrieval (/genes//)\ \ of genes that are contained in the database due to their association to\ \ \ngenetic variants that are involved in at least one oligogenic combination\ \ in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Gene' tags: - api parameters: - name: gene_name in: path description: A unique value identifying this gene. required: true type: string /api/genes/{gene_name}/relationships/{related_field}: get: operationId: api_genes_relationships_read description: '' parameters: [] responses: '200': description: '' schema: type: string tags: - api parameters: - name: gene_name in: path description: A unique value identifying this gene. required: true type: string - name: related_field in: path required: true type: string /api/genes/{gene_pk}/genecombinations/: get: operationId: api_genes_genecombinations_list description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/GeneCombination' tags: - api parameters: - name: gene_pk in: path required: true type: string /api/genes/{gene_pk}/genecombinations/{id}/: get: operationId: api_genes_genecombinations_read description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/GeneCombination' tags: - api parameters: - name: gene_pk in: path required: true type: string - name: id in: path description: A unique integer value identifying this gene combination. required: true type: integer /api/genes/{gene_pk}/variants/: get: operationId: api_genes_variants_list description: This API endpoint handles listing (/variants) and retrieval (/variants//) of genetic variants from the database parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Variant' tags: - api parameters: - name: gene_pk in: path required: true type: string /api/genes/{gene_pk}/variants/{id}/: get: operationId: api_genes_variants_read description: This API endpoint handles listing (/variants) and retrieval (/variants//) of genetic variants from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Variant' tags: - api parameters: - name: gene_pk in: path required: true type: string - name: id in: path description: A unique integer value identifying this variant. required: true type: integer /api/references/: get: operationId: api_references_list description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Reference' tags: - api parameters: [] /api/references/{id}/: get: operationId: api_references_read description: "This API endpoint handles listing (/references) and retrieval\ \ (/references//) of References from the database\nthat support the inclusion\ \ of at least one oligogenic combination in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Reference' tags: - api parameters: - name: id in: path description: A unique integer value identifying this reference. required: true type: integer /api/references/{id}/relationships/{related_field}: get: operationId: api_references_relationships_read description: '' parameters: [] responses: '200': description: '' schema: type: string tags: - api parameters: - name: id in: path description: A unique integer value identifying this reference. required: true type: integer - name: related_field in: path required: true type: string /api/references/{reference_pk}/combinations/: get: operationId: api_references_combinations_list description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: - name: ordering in: query description: Which field to use when ordering the results. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Combination' tags: - api parameters: - name: reference_pk in: path required: true type: string /api/references/{reference_pk}/combinations/{combination_id}/: get: operationId: api_references_combinations_read description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Combination' tags: - api parameters: - name: combination_id in: path description: A unique value identifying this combination. required: true type: string - name: reference_pk in: path required: true type: string /api/variants/: get: operationId: api_variants_list description: This API endpoint handles listing (/variants) and retrieval (/variants//) of genetic variants from the database parameters: - name: filter[search] in: query description: A search term. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Variant' tags: - api parameters: [] /api/variants/{id}/: get: operationId: api_variants_read description: This API endpoint handles listing (/variants) and retrieval (/variants//) of genetic variants from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Variant' tags: - api parameters: - name: id in: path description: A unique integer value identifying this variant. required: true type: integer /api/variants/{id}/relationships/{related_field}: get: operationId: api_variants_relationships_read description: '' parameters: [] responses: '200': description: '' schema: type: string tags: - api parameters: - name: id in: path description: A unique integer value identifying this variant. required: true type: integer - name: related_field in: path required: true type: string /api/variants/{variant_pk}/combinations/: get: operationId: api_variants_combinations_list description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: - name: ordering in: query description: Which field to use when ordering the results. required: false type: string responses: '200': description: '' schema: type: array items: $ref: '#/definitions/Combination' tags: - api parameters: - name: variant_pk in: path required: true type: string /api/variants/{variant_pk}/combinations/{combination_id}/: get: operationId: api_variants_combinations_read description: This API endpoint handles listing (/combinations) and retrieval (/combinations/{combination_pk}/) of oligogenic combinations from the database parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Combination' tags: - api parameters: - name: combination_id in: path description: A unique value identifying this combination. required: true type: string - name: variant_pk in: path required: true type: string /api/variants/{variant_pk}/gene/: get: operationId: api_variants_gene_read description: "This API endpoint handles listing (/genes) and retrieval (/genes//)\ \ of genes that are contained in the database due to their association to\ \ \ngenetic variants that are involved in at least one oligogenic combination\ \ in OLIDA." parameters: [] responses: '200': description: '' schema: $ref: '#/definitions/Gene' tags: - api parameters: - name: variant_pk in: path required: true type: string definitions: AuthToken: required: - username - password type: object properties: username: title: Username type: string minLength: 1 password: title: Password type: string minLength: 1 Combination: type: object properties: url: title: Url type: string format: uri readOnly: true scores: title: Scores type: object additionalProperties: type: string readOnly: true omim_id: title: Omim id type: string readOnly: true oligogenic_effect: title: Oligogenic effect type: string readOnly: true diseases: type: array items: type: string readOnly: true uniqueItems: true variant_set: type: array items: type: integer readOnly: true uniqueItems: true reference_set: type: array items: type: integer readOnly: true uniqueItems: true gene_combination: title: Gene combination type: integer readOnly: true status: title: Status type: string enum: - CU - VA - AD - RM effect_predicted: title: Effect predicted type: boolean ethnicity: title: Ethnicity type: string x-nullable: true lastmodified: title: Lastmodified type: string format: date-time readOnly: true submitter: title: Submitter type: string readOnly: true default: N.A curator: title: Curator type: string readOnly: true default: N.A Disease: required: - disease_name type: object properties: url: title: Url type: string format: uri readOnly: true omim_ids: title: Omim ids type: string readOnly: true combination_set: type: array items: type: string readOnly: true uniqueItems: true status: title: Status type: string enum: - CU - VA - AD - RM disease_name: title: Disease name type: string maxLength: 250 minLength: 1 icd10_category: title: Icd10 category type: string x-nullable: true icd10_specificid: title: Icd10 specificid type: string x-nullable: true lastmodified: title: Lastmodified type: string format: date-time readOnly: true submitter: title: Submitter type: string readOnly: true default: N.A curator: title: Curator type: string readOnly: true default: N.A GeneCombination: type: object properties: url: title: Url type: string format: uri readOnly: true gene_relationship: title: Gene relationship type: string readOnly: true protein_interactions: title: Protein interactions type: string readOnly: true common_pathways: title: Common pathways type: string readOnly: true combination_set: type: array items: type: string readOnly: true uniqueItems: true genes: type: array items: type: integer readOnly: true uniqueItems: true genecomb_metascore: title: Genecomb metascore type: integer maximum: 2147483647 minimum: 0 x-nullable: true lastmodified: title: Lastmodified type: string format: date-time readOnly: true Reference: required: - year - title type: object properties: url: title: Url type: string format: uri readOnly: true combinations: type: array items: type: integer readOnly: true uniqueItems: true status: title: Status type: string enum: - CU - VA - AD - RM pubmed_id: title: Pubmed id type: integer maximum: 2147483647 minimum: 0 x-nullable: true doi: title: Doi type: string x-nullable: true pmc_id: title: Pmc id type: string x-nullable: true abstract: title: Abstract type: string x-nullable: true year: title: Year type: integer maximum: 32767 minimum: 0 pdf: title: Pdf type: string readOnly: true x-nullable: true format: uri comment: title: Comment type: string x-nullable: true uri: title: Uri type: string format: uri maxLength: 200 x-nullable: true bibtex: title: Bibtex type: string readOnly: true x-nullable: true format: uri title: title: Title type: string minLength: 1 lastmodified: title: Lastmodified type: string format: date-time readOnly: true submitter: title: Submitter type: string readOnly: true default: N.A curator: title: Curator type: string readOnly: true default: N.A Variant: required: - submitter type: object properties: id: title: ID type: integer readOnly: true status: title: Status type: string enum: - CU - VA - AD - RM genomic_position_hg19: title: Genomic position hg19 type: integer maximum: 2147483647 minimum: 0 x-nullable: true genomic_position_hg38: title: Genomic position hg38 type: integer maximum: 2147483647 minimum: 0 x-nullable: true chromosome: title: Chromosome type: string maxLength: 2 minLength: 1 x-nullable: true annotation_flag: title: Annotation flag type: string enum: - manually_attributed - manually_corrected - automatically_attributed - automatically_attributed_and_verified - ambiguous_variant - not_found_in_databases - cnv x-nullable: true lastmodified: title: Lastmodified type: string format: date-time readOnly: true submitter: title: Submitter type: integer curator: title: Curator type: integer x-nullable: true polymorphic_ctype: title: Polymorphic ctype type: integer readOnly: true gene_name: title: Gene name type: string x-nullable: true in_combination: type: array items: type: integer readOnly: true uniqueItems: true Gene: type: object properties: url: title: Url type: string format: uri readOnly: true go_molecular_function: title: Go molecular function type: string readOnly: true pathway_id: title: Pathway id type: string readOnly: true essential_gene: title: Essential gene type: string readOnly: true variant_set: type: array items: type: integer readOnly: true uniqueItems: true genecombination_set: type: array items: type: integer readOnly: true uniqueItems: true status: title: Status type: string enum: - CU - VA - AD - RM uniprot_acc: title: Uniprot acc type: string maxLength: 12 x-nullable: true ensembl_id: title: Ensembl id type: string x-nullable: true entrez_id: title: Entrez id type: string x-nullable: true chromosome_number: title: Chromosome number type: string maxLength: 2 minLength: 1 x-nullable: true lastmodified: title: Lastmodified type: string format: date-time readOnly: true submitter: title: Submitter type: string readOnly: true default: N.A curator: title: Curator type: string readOnly: true default: N.A