{"openapi": "3.1.0", "info": {"title": "MGnify API", "version": "2.0.0", "description": "**The API for [MGnify](https://www.ebi.ac.uk/metagenomics), EBI\u2019s platform for the submission, analysis, discovery and comparison of metagenomic-derived datasets.**\n\n## Endpoints\nAPI endpoints (URLs) are available for all data types stored in MGnify.\nIn general, there are list endpoints (ending `/`) and detail endpoints (ending `/<accession>`) for individually accessioned data.\nWhere a data type is not accessioned, alternative natural identifiers are used (like a short `slug` for Super Studies).\nCommonly used relationships are available as nested list endpoints, like `studies/{accession}/samples` for the samples belonging to a study.\n\n## Data format\nThe API returns JSON responses.\nList endpoints return data in the format `{count: 10, items: [{...}, ...]}` (unless specified otherwise).\nDetail endpoints return a single object `{...}`.\n\n## Data availability\nMost data are public, available without authentication.\nPrivate data is available only to authenticated users, and the authentication is based on Webin credentials from ENA.\nTo use these, a JWT token must be obtained for the Webin credentials, using the `/auth` endpoints.\n", "contact": {"name": "MGnify Support", "url": "https://www.ebi.ac.uk/about/contact/support/metagenomics"}, "termsOfService": "https://www.ebi.ac.uk/about/terms-of-use"}, "paths": {"/metagenomics/api/v2/analyses/{accession}": {"get": {"operationId": "get_mgnify_analysis", "summary": "Get MGnify analysis by accession", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/MGnifyAnalysisDetail"}}}, "links": {"GetStudyForAnalysis": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/study_accession"}, "description": "The study_accession is an identifier that can be used to access the Study detail"}}}}, "description": "MGnify analyses are accessioned with an MYGA-prefixed identifier and correspond to an individual Run or Assembly analysed by a Pipeline.", "tags": ["Analyses"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/analyses/": {"get": {"operationId": "list_mgnify_analyses", "summary": "List all analyses (MGYAs) available from MGnify", "parameters": [{"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyAnalysisDetail_"}}}}}, "description": "Each analysis is the result of a Pipeline execution on a reads dataset (either a raw read-run, or an assembly).", "tags": ["Analyses"]}}, "/metagenomics/api/v2/analyses/{accession}/annotations": {"get": {"operationId": "analysis_get_mgnify_analysis_with_annotations_d52a8e0a", "summary": "Get MGnify analysis by accession, with annotations and downloadable files", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/MGnifyAnalysisWithAnnotations"}}}}}, "description": "MGnify analyses have annotations (taxonomic and functional assignments), and downloadable files (outputs from the pipeline execution).", "tags": ["Analyses"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/analyses/{accession}/annotations/{annotation_type}": {"get": {"operationId": "analysis_get_mgnify_analysis_with_annotations_of_type_4ac98f9b", "summary": "Get a named set of annotations for a MGnify analysis by accession.", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "path", "name": "annotation_type", "schema": {"enum": ["taxonomies__ssu", "taxonomies__lsu", "taxonomies__its_one_db", "taxonomies__unite", "taxonomies__pr2", "taxonomies__dada2_pr2", "taxonomies__dada2_silva", "pfams"], "title": "MGnifyFunctionalAnalysisAnnotationType", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyAnalysisTypedAnnotation_"}}}}}, "description": "List the annotations of a given type for a MGnify analysis referred to by its accession.", "tags": ["Analyses"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/publications/{pubmed_id}": {"get": {"operationId": "get_mgnify_publication", "summary": "Get the detail of a single publication", "parameters": [{"in": "path", "name": "pubmed_id", "schema": {"title": "Pubmed Id", "type": "integer"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/MGnifyPublicationDetail"}}}}}, "description": "Get detailed information about a publication, including associated studies.", "tags": ["Publications"]}}, "/metagenomics/api/v2/publications/{pubmed_id}/annotations": {"get": {"operationId": "get_mgnify_publication_annotations", "summary": "Get any full-text annotations associated with the publication", "parameters": [{"in": "path", "name": "pubmed_id", "schema": {"title": "Pubmed Id", "type": "integer"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/PublicationAnnotations"}}}}}, "description": "Full-text annotations are retrieved from Europe PMC, text mined for relevant metagenomic metadata terms", "tags": ["Publications"]}}, "/metagenomics/api/v2/publications/": {"get": {"operationId": "list_mgnify_publications", "summary": "List all publications", "parameters": [{"in": "query", "name": "order", "schema": {"anyOf": [{"enum": ["published_year", "-published_year", ""], "type": "string"}, {"type": "null"}], "title": "Order"}, "required": false}, {"in": "query", "name": "published_after", "schema": {"anyOf": [{"type": "integer"}, {"type": "null"}], "description": "Filter by minimum publication year", "q": "published_year__gte", "title": "Published After"}, "required": false, "description": "Filter by minimum publication year"}, {"in": "query", "name": "published_before", "schema": {"anyOf": [{"type": "integer"}, {"type": "null"}], "description": "Filter by maximum publication year", "q": "published_year__lte", "title": "Published Before"}, "required": false, "description": "Filter by maximum publication year"}, {"in": "query", "name": "title", "schema": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Search within publication titles", "q": "title__icontains", "title": "Title"}, "required": false, "description": "Search within publication titles"}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyPublication_"}}}}}, "description": "List all publications in the MGnify database.", "tags": ["Publications"]}}, "/metagenomics/api/v2/samples/{accession}": {"get": {"operationId": "get_mgnify_sample", "summary": "Get the detail of a single sample analysed by MGnify", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/MGnifySampleDetail"}}}, "links": {"GetStudyFromSampleStudiesList": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/studies/0/accession"}, "description": "The accession is an identifier that can be used to access the Study detail"}}}}, "description": "MGnify samples inherit directly from samples (or BioSamples) in ENA.", "tags": ["Samples"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/samples/": {"get": {"operationId": "list_mgnify_samples", "summary": "List all samples analysed by MGnify", "parameters": [{"in": "query", "name": "biome_lineage", "schema": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "The lineage to match, including all descendant biomes", "title": "Biome Lineage"}, "required": false, "description": "The lineage to match, including all descendant biomes"}, {"in": "query", "name": "search", "schema": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Search within sample titles and accessions", "q": ["sample_title__icontains", "ena_accessions__icontains"], "title": "Search"}, "required": false, "description": "Search within sample titles and accessions"}, {"in": "query", "name": "order", "schema": {"anyOf": [{"enum": ["sample_title", "-sample_title", "updated_at", "-updated_at", ""], "type": "string"}, {"type": "null"}], "title": "Order"}, "required": false}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifySample_"}}}}}, "description": "MGnify samples inherit directly from samples (or BioSamples) in ENA.", "tags": ["Samples"]}}, "/metagenomics/api/v2/samples/{accession}/runs/": {"get": {"operationId": "list_sample_runs", "summary": "List ENA Runs associated with this sample", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_AnalysedRun_"}}}, "links": {"GetRunFromSampleItemsList": {"operationId": "get_analysed_run", "parameters": {"accession": "$response.body#/items/0/accession"}, "description": "The accession is an identifier that can be used to access the Run detail"}}}}, "description": "Samples may be associated with one or more ENA runs. ENA runs 'Hold raw read files and sequencing methods'", "tags": ["Samples", "Runs"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/studies/{accession}": {"get": {"operationId": "get_mgnify_study", "summary": "Get the detail of a single study analysed by MGnify", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/MGnifyStudyDetail"}}}}}, "description": "MGnify studies inherit directly from studies (or projects) in ENA.", "tags": ["Studies"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/studies/": {"get": {"operationId": "list_mgnify_studies", "summary": "List all studies analysed by MGnify", "parameters": [{"in": "query", "name": "order", "schema": {"anyOf": [{"enum": ["accession", "-accession", "updated_at", "-updated_at", ""], "type": "string"}, {"type": "null"}], "title": "Order"}, "required": false}, {"in": "query", "name": "biome_lineage", "schema": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "The lineage to match, including all descendant biomes", "title": "Biome Lineage"}, "required": false, "description": "The lineage to match, including all descendant biomes"}, {"in": "query", "name": "has_analyses_from_pipeline", "schema": {"anyOf": [{"$ref": "#/components/schemas/PipelineVersions"}, {"type": "null"}], "description": "If set, will only show studies with analyses from the specified MGnify pipeline version"}, "required": false, "description": "If set, will only show studies with analyses from the specified MGnify pipeline version"}, {"in": "query", "name": "search", "schema": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Search within study titles and accessions", "q": ["title__icontains", "accession", "ena_accessions__icontains"], "title": "Search"}, "required": false, "description": "Search within study titles and accessions"}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyStudy_"}}}}}, "description": "MGnify studies inherit directly from studies (or projects) in ENA.", "tags": ["Studies"]}}, "/metagenomics/api/v2/studies/{accession}/analyses/": {"get": {"operationId": "list_mgnify_study_analyses", "summary": "List MGnify Analyses associated with this Study", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyAnalysis_"}}}, "links": {"GetAnalysisFromStudyItemsList": {"operationId": "get_mgnify_analysis", "parameters": {"accession": "$response.body#/items/0/accession"}, "description": "The accession is an identifier that can be used to access the Analysis detail"}}}}, "description": "MGnify analyses correspond to an individual Run or Assembly within this study,analysed by a MGnify Pipelione. ", "tags": ["Studies", "Analyses"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/studies/{accession}/publications/": {"get": {"operationId": "list_mgnify_study_publications", "summary": "List Publications associated with this Study", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyPublication_"}}}, "links": {"GetPublicationFromStudyItemsList": {"operationId": "get_mgnify_publication", "parameters": {"pubmed_id": "$response.body#/items/0/pubmed_id"}, "description": "The pubmed_id is an identifier that can be used to access the Publication detail"}}}}, "description": "List all publications associated with this study.", "tags": ["Studies", "Publications"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/studies/{accession}/samples/": {"get": {"operationId": "list_mgnify_study_samples", "summary": "List Samples associated with this Study", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifySampleWithMetadata_"}}}, "links": {"GetSampleFromStudyItemsList": {"operationId": "get_mgnify_sample", "parameters": {"accession": "$response.body#/items/0/accession"}, "description": "The accession is an identifier that can be used to access the Sample detail"}}}}, "description": "List all samples associated with this study.", "tags": ["Studies", "Samples"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/super-studies/{slug}": {"get": {"operationId": "get_super_study", "summary": "Get the detail of a single Super Study", "parameters": [{"in": "path", "name": "slug", "schema": {"title": "Slug", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/SuperStudyDetail"}}}, "links": {"GetStudyFromSuperStudyFlagshipStudiesList": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/flagship_studies/0/accession"}, "description": "The accession is an identifier that can be used to access the Study detail"}, "GetStudyFromSuperStudyRelatedStudiesList": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/related_studies/0/accession"}, "description": "The accession is an identifier that can be used to access the Study detail"}, "GetGenomeCatalogueFromSuperStudyGenomeCataloguesList": {"operationId": "get_genome_catalogue", "parameters": {"catalogue_id": "$response.body#/genome_catalogues/0/catalogue_id"}, "description": "The catalogue_id is an identifier that can be used to access the Genome Catalogue detail"}}}}, "description": "A Super Study is a collection of MGnify Studies all related to a single large initiative. They may also reference Genome Catalogues that were assembled from the Studies or as part of the Super Study initiative.", "tags": ["Studies"]}}, "/metagenomics/api/v2/super-studies/": {"get": {"operationId": "list_super_studies", "summary": "List all Super Studies", "parameters": [{"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_SuperStudy_"}}}, "links": {"GetSuperStudyFromSuperStudyItemsList": {"operationId": "get_super_study", "parameters": {"slug": "$response.body#/items/0/slug"}, "description": "The slug is an identifier that can be used to access the Super Study detail"}}}}, "description": "Super Studies are collections of MGnify Studies associated with major initiatives.", "tags": ["Studies"]}}, "/metagenomics/api/v2/genomes/{accession}": {"get": {"operationId": "get_mgnify_genome", "summary": "Get the detail of a single MGnify Genome", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/GenomeDetail"}}}, "links": {"GetCatalogueForGenome": {"operationId": "get_genome_catalogue", "parameters": {"accession": "$response.body#/catalogue_id"}, "description": "The catalogue_id is an identifier that can be used to access the Catalogue detail"}}}}, "description": "MGnify Genomes are either isolates, or MAGs derived from binned metagenomes.", "tags": ["Genomes"]}}, "/metagenomics/api/v2/genomes/{accession}/annotations": {"get": {"operationId": "get_genome_annotations", "summary": "Get the annotations for a single MGnify Genome", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/GenomeWithAnnotations"}}}}}, "description": "Annotations are taxonomic and functional assignments for the genome.", "tags": ["Genomes"]}}, "/metagenomics/api/v2/genomes/": {"get": {"operationId": "list_mgnify_genomes", "summary": "List all genomes across MGnify Genome catalogues", "parameters": [{"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_GenomeList_"}}}}}, "description": "MGnify Genomes are either isolates, or MAGs derived from binned metagenomes.", "tags": ["Genomes"]}}, "/metagenomics/api/v2/genomes/catalogues/": {"get": {"operationId": "list_genome_catalogues", "summary": "List all genome catalogues", "parameters": [{"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_GenomeCatalogueList_"}}}}}, "description": "MGnify Genomes Catalogues are biome-specific collections of isolate and MAG genomes.", "tags": ["Genomes"]}}, "/metagenomics/api/v2/genomes/catalogues/{catalogue_id}": {"get": {"operationId": "get_genome_catalogue", "summary": "Get genome catalogue by ID", "parameters": [{"in": "path", "name": "catalogue_id", "schema": {"title": "Catalogue Id", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/GenomeCatalogueDetail"}}}}}, "tags": ["Genomes"]}}, "/metagenomics/api/v2/genomes/catalogues/{catalogue_id}/genomes/": {"get": {"operationId": "get_genome_catalogue_genomes", "summary": "Get genomes within the genome catalogue", "parameters": [{"in": "path", "name": "catalogue_id", "schema": {"title": "Catalogue Id", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_GenomeList_"}}}}}, "tags": ["Genomes"]}}, "/metagenomics/api/v2/assemblies/": {"get": {"operationId": "list_assemblies", "summary": "List all assemblies available in MGnify", "parameters": [{"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_Assembly_"}}}}}, "description": "Each assembly represents a collection of contigs generated by assembling sequencing reads from an MGnify or run ", "tags": ["Assemblies"]}}, "/metagenomics/api/v2/assemblies/{accession}": {"get": {"operationId": "get_assembly", "summary": "Get assembly by accession", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/AssemblyDetail"}}}, "links": {"GetStudyForAssembly": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/reads_study_accession"}, "description": "The reads_study_accession is an identifier that can be used to access the Study detail"}, "GetStudyForAnalysis": {"operationId": "get_mgnify_sample", "parameters": {"accession": "$response.body#/study_accession"}, "description": "The study_accession is an identifier that can be used to access the Study detail"}, "GetGenomelinksForAssembly": {"operationId": "list_genome_links_for_assembly", "parameters": {"accession": "$request.path.accession"}, "description": "Genome/MAG links for this assembly"}, "GetAdditionalcontainedgenomesForAssembly": {"operationId": "list_additional_contained_genomes_for_assembly", "parameters": {"accession": "$request.path.accession"}, "description": "Additional contained genomes discovered for this assembly"}}}}, "description": "Get detailed information about a specific assembly. ", "tags": ["Assemblies"]}}, "/metagenomics/api/v2/assemblies/{accession}/genome-links": {"get": {"operationId": "list_genome_links_for_assembly", "summary": "List genome/MAG links for an assembly", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_GenomeAssemblyLinkSchema_"}}}}}, "description": "Return genome links (e.g. MAG associations) for a specific assembly.\nAccessible at `/assemblies/{accession}/genome-links`.", "tags": ["Assemblies", "Genomes"]}}, "/metagenomics/api/v2/assemblies/{accession}/additional-contained-genomes": {"get": {"operationId": "list_additional_contained_genomes_for_assembly", "summary": "List additional contained genomes for an assembly", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_AdditionalContainedGenomeSchema_"}}}}}, "description": "Return additional contained genomes (and their metrics) discovered for this assembly.\nAccessible at `/assemblies/{accession}/additional-contained-genomes`.", "tags": ["Assemblies", "Genomes"]}}, "/metagenomics/api/v2/assemblies/{accession}/analyses": {"get": {"operationId": "list_analyses_for_assembly", "summary": "List analyses for an assembly", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyAnalysis_"}}}}}, "description": "Return MGnify analyses (MGYAs) that were generated from this assembly.\nAccessible at `/assemblies/{accession}/analyses`.", "tags": ["Assemblies", "Analyses"]}}, "/metagenomics/api/v2/biomes/": {"get": {"operationId": "list_mgnify_biomes", "summary": "List all biomes", "parameters": [{"in": "query", "name": "biome_lineage", "schema": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "The lineage to match, including all descendant biomes", "title": "Biome Lineage"}, "required": false, "description": "The lineage to match, including all descendant biomes"}, {"in": "query", "name": "max_depth", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "description": "Maximum depth of the biome lineage to include, e.g. `root` is 1 and `root:Host-Associated:Human` is level 3", "q": "path__depth__lte", "title": "Max Depth"}, "required": false, "description": "Maximum depth of the biome lineage to include, e.g. `root` is 1 and `root:Host-Associated:Human` is level 3"}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_Biome_"}}}}}, "description": "List all biomes in the MGnify database.", "tags": ["Miscellaneous"]}}, "/metagenomics/api/v2/my-data/studies/": {"get": {"operationId": "list_private_mgnify_studies", "summary": "List all private studies available from MGnify", "parameters": [{"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyStudy_"}}}}}, "tags": ["Private Data"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}]}}, "/metagenomics/api/v2/runs/": {"get": {"operationId": "list_analysed_runs", "summary": "List all analysed runs", "parameters": [{"in": "query", "name": "has_experiment_type", "schema": {"anyOf": [{"$ref": "#/components/schemas/ExperimentTypes"}, {"type": "null"}], "description": "If set, will only show runs with the specified experiment type"}, "required": false, "description": "If set, will only show runs with the specified experiment type"}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_AnalysedRun_"}}}, "links": {"GetRunForRun": {"operationId": "get_analysed_run", "parameters": {"accession": "$response.body#/accession"}, "description": "The accession is an identifier that can be used to access the Run detail"}, "GetSampleForRun": {"operationId": "get_mgnify_sample", "parameters": {"accession": "$response.body#/sample_accession"}, "description": "The sample_accession is an identifier that can be used to access the Sample detail"}, "GetStudyForRun": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/study_accession"}, "description": "The study_accession is an identifier that can be used to access the Study detail"}}}}, "description": "List all analysed runs in the MGnify database.", "tags": ["Runs"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/runs/{accession}": {"get": {"operationId": "get_analysed_run", "summary": "Get the detail of a single analysed run", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/AnalysedRunDetail"}}}, "links": {"GetSampleForRun": {"operationId": "get_mgnify_sample", "parameters": {"accession": "$response.body#/sample_accession"}, "description": "The sample_accession is an identifier that can be used to access the Sample detail"}, "GetStudyForRun": {"operationId": "get_mgnify_study", "parameters": {"accession": "$response.body#/study_accession"}, "description": "The study_accession is an identifier that can be used to access the Study detail"}, "GetAnalysesForRun": {"operationId": "list_runs_analyses", "parameters": {"accession": "$request.path.accession"}, "description": "Analyses performed on this run"}, "GetAssembliesForRun": {"operationId": "list_runs_assemblies", "parameters": {"accession": "$request.path.accession"}, "description": "Assemblies generated from or including this run"}}}}, "description": "Get the detail of a single analysed run in the MGnify database.", "tags": ["Runs"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/runs/{accession}/analyses/": {"get": {"operationId": "list_runs_analyses", "summary": "List MGnify Analyses associated with this Run", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_MGnifyAnalysis_"}}}, "links": {"GetAnalysisFromRunItemsList": {"operationId": "get_mgnify_analysis", "parameters": {"accession": "$response.body#/items/0/accession"}, "description": "The accession is an identifier that can be used to access the Analysis detail"}}}}, "description": "MGnify analyses correspond to an individual Run or Assembly", "tags": ["Runs", "Analyses"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/runs/{accession}/assemblies/": {"get": {"operationId": "list_runs_assemblies", "summary": "List Assemblies associated with this Run", "parameters": [{"in": "path", "name": "accession", "schema": {"title": "Accession", "type": "string"}, "required": true}, {"in": "query", "name": "page", "schema": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "required": false}, {"in": "query", "name": "page_size", "schema": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}, "required": false}], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/NinjaPaginationResponseSchema_AssemblyDetail_"}}}, "links": {"GetAssemblyFromRunItemsList": {"operationId": "get_assembly", "parameters": {"accession": "$response.body#/items/0/accession"}, "description": "The accession is an identifier that can be used to access the Assembly detail"}}}}, "description": "Assemblies generated from or including this run", "tags": ["Runs", "Assemblies"], "security": [{"WebinJWTAuth": []}, {"SessionAuthSuperUser": []}, {"NoAuth": []}]}}, "/metagenomics/api/v2/auth/sliding": {"post": {"operationId": "token_obtain_sliding", "summary": "Obtain an authentication token using Webin credentials.", "parameters": [], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/WebinTokenResponse"}}}}}, "description": "Obtain an authentication JWT token using Webin credentials. This token is sliding, i.e. it can be used both to access private data endpoints and to refresh itself after expiry.", "tags": ["Authentication"], "requestBody": {"content": {"application/json": {"schema": {"$ref": "#/components/schemas/WebinTokenRequest"}}}, "required": true}}}, "/metagenomics/api/v2/auth/sliding/refresh": {"post": {"operationId": "token_refresh_sliding", "summary": "Refresh an authentication token to increase its validity duration.", "parameters": [], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/WebinTokenResponse"}}}}}, "description": "If a token's expiry has passed, but its (longer) refresh expiry remains valid, this endpoint can be used to fetch a replacement token without logging in again. ", "tags": ["Authentication"], "requestBody": {"content": {"application/json": {"schema": {"$ref": "#/components/schemas/WebinTokenRefreshRequest"}}}, "required": true}}}, "/metagenomics/api/v2/auth/verify": {"post": {"operationId": "token_verify", "summary": "Verify Token", "parameters": [], "responses": {"200": {"description": "OK", "content": {"application/json": {"schema": {"$ref": "#/components/schemas/Schema"}}}}}, "tags": ["Authentication"], "requestBody": {"content": {"application/json": {"schema": {"$ref": "#/components/schemas/TokenVerifyInputSchema"}}}, "required": true}}}}, "components": {"schemas": {"AnalysedRun": {"properties": {"experiment_type": {"description": "Experiment type refers to the type of sequencing data that was analysed, e.g. amplicon reads or a metagenome assembly", "examples": ["Metatranscriptomic", "Metagenomic", "Amplicon", "Assembly", "Hybrid assembly", "Long-read assembly", "Metabarcoding", "Unknown"], "title": "Experiment Type", "type": "string"}, "accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["ERR0000001"], "title": "Accession"}, "sample_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "ENA accession of the sample associated with this run", "examples": ["ERS000001", "SAMEA000000001"], "title": "Sample Accession"}, "study_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "ENA accession of the study associated with this run", "examples": ["SRP135937", "PRJNA438545"], "title": "Study Accession"}, "instrument_model": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["Illumina HiSeq 2000"], "title": "Instrument Model"}, "instrument_platform": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["Illumina"], "title": "Instrument Platform"}}, "required": ["experiment_type", "instrument_model", "instrument_platform"], "title": "AnalysedRun", "type": "object"}, "Assembly": {"properties": {"accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["ERZ000001"], "title": "Accession"}, "updated_at": {"format": "date-time", "title": "Updated At", "type": "string"}}, "required": ["updated_at"], "title": "Assembly", "type": "object"}, "Biome": {"properties": {"biome_name": {"examples": ["Engineered", "Mammals"], "title": "Biome Name", "type": "string"}, "lineage": {"examples": ["root:Engineered", "root:Host-associated:Mammals"], "title": "Lineage", "type": "string"}}, "required": ["biome_name"], "title": "Biome", "type": "object"}, "DownloadFileIndexFile": {"description": "An index file (e.g., a .fai for a FASTA file of .gzi for a bgzip file) of a DownloadFile.", "properties": {"index_type": {"enum": ["fai", "gzi", "csi"], "title": "Index Type", "type": "string"}, "path": {"anyOf": [{"type": "string"}, {"format": "path", "type": "string"}], "title": "Path"}}, "required": ["index_type", "path"], "title": "DownloadFileIndexFile", "type": "object"}, "DownloadFileType": {"enum": ["fasta", "tsv", "biom", "csv", "json", "svg", "tree", "html", "gff", "other"], "title": "DownloadFileType", "type": "string"}, "DownloadType": {"enum": ["Coding Sequences", "Sequence data", "Quality control", "Functional analysis", "Taxonomic analysis", "Statistics", "non-coding RNAs", "Genome analysis", "Analysis RO Crate", "Other"], "title": "DownloadType", "type": "string"}, "MGnifyAnalysisDetail": {"properties": {"experiment_type": {"description": "Experiment type refers to the type of sequencing data that was analysed, e.g. amplicon reads or a metagenome assembly", "examples": ["Metatranscriptomic", "Metagenomic", "Amplicon", "Assembly", "Hybrid assembly", "Long-read assembly", "Metabarcoding", "Unknown"], "title": "Experiment Type", "type": "string"}, "study_accession": {"examples": ["MGYS000000001"], "title": "Study Accession", "type": "string"}, "accession": {"examples": ["MGYA000000001"], "title": "Accession", "type": "string"}, "run": {"anyOf": [{"$ref": "#/components/schemas/AnalysedRun"}, {"type": "null"}]}, "sample": {"anyOf": [{"$ref": "#/components/schemas/MGnifySample"}, {"type": "null"}]}, "assembly": {"anyOf": [{"$ref": "#/components/schemas/Assembly"}, {"type": "null"}]}, "pipeline_version": {"anyOf": [{"$ref": "#/components/schemas/PipelineVersions"}, {"type": "null"}]}, "downloads": {"items": {"$ref": "#/components/schemas/MGnifyAnalysisDownloadFile"}, "title": "Downloads", "type": "array"}, "read_run": {"anyOf": [{"items": {"$ref": "#/components/schemas/AnalysedRun"}, "type": "array"}, {"type": "null"}], "description": "Metadata associated with the original read run(s) this analysis is based on, whether or not those reads were assembled.", "title": "Read Run"}, "quality_control_summary": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "examples": [{"after_filtering": {"total_bases": 700000}, "before_filtering": {"total_bases": 1000000}}], "title": "Quality Control Summary"}, "results_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Directory path where analysis results are stored", "examples": ["http://example.org/data/analyses/MGYA00000001/results"], "title": "Results Dir"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "description": "Additional metadata associated with the analysis", "examples": [{"marker_gene_summary": {"ssu": {"total_read_count": 11}}}], "title": "Metadata"}}, "required": ["experiment_type", "study_accession", "accession", "run", "sample", "assembly", "pipeline_version", "read_run", "quality_control_summary"], "title": "MGnifyAnalysisDetail", "type": "object"}, "MGnifyAnalysisDownloadFile": {"properties": {"file_type": {"$ref": "#/components/schemas/DownloadFileType", "description": "File type of the downloadable file, e.g. its file extension"}, "download_type": {"$ref": "#/components/schemas/DownloadType", "description": "Category of the download"}, "download_group": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Group identifier for the download", "examples": ["taxonomies.closed_reference.ssu"], "title": "Download Group"}, "short_description": {"description": "Brief description of the file", "examples": ["Tax. assignments"], "title": "Short Description", "type": "string"}, "long_description": {"description": "Detailed description of the file", "examples": ["A table of taxonomic assignments"], "title": "Long Description", "type": "string"}, "path": {"title": "Path", "type": "string"}, "alias": {"examples": ["SILVA-SSU.tsv"], "title": "Alias", "type": "string"}, "file_size_bytes": {"anyOf": [{"type": "integer"}, {"type": "null"}], "examples": [1024], "title": "File Size Bytes"}, "index_file": {"anyOf": [{"$ref": "#/components/schemas/DownloadFileIndexFile"}, {"items": {"$ref": "#/components/schemas/DownloadFileIndexFile"}, "type": "array"}, {"type": "null"}], "title": "Index File"}, "parent_identifier": {"anyOf": [{"type": "integer"}, {"type": "string"}], "title": "Parent Identifier"}, "parent_is_private": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "title": "Parent Is Private"}, "parent_results_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Parent Results Dir"}, "index_files": {"anyOf": [{"items": {"$ref": "#/components/schemas/MGnifyDownloadFileIndexFile"}, "type": "array"}, {"type": "null"}], "examples": [[{"index_type": "gzi", "url": "https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_results/annotations.tsv.gz.gzi"}]], "title": "Index Files"}, "url": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_results/annotations.tsv.gz"], "title": "Url"}}, "required": ["file_type", "download_type", "short_description", "long_description", "path", "alias", "parent_identifier"], "title": "MGnifyAnalysisDownloadFile", "type": "object"}, "MGnifyDownloadFileIndexFile": {"properties": {"index_type": {"enum": ["fai", "gzi", "csi"], "title": "Index Type", "type": "string"}, "path": {"title": "Path", "type": "string"}, "url": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Full URL of the index file.", "examples": ["https://www.ebi.ac.uk/metagenomics/path/to/annotations.tsv.gz.gzi"], "title": "Url"}}, "required": ["index_type", "path"], "title": "MGnifyDownloadFileIndexFile", "type": "object"}, "MGnifySample": {"properties": {"accession": {"examples": ["ERS000001", "SAMEA000000001"], "title": "Accession", "type": "string"}, "ena_accessions": {"examples": [["ERS000001", "SAMEA000000001"], ["ERS000002"]], "items": {"type": "string"}, "title": "Ena Accessions", "type": "array"}, "sample_title": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["space suit expedition sample", "Patient 3 stool"], "title": "Sample Title"}, "biome": {"anyOf": [{"$ref": "#/components/schemas/Biome"}, {"type": "null"}]}, "updated_at": {"format": "date-time", "title": "Updated At", "type": "string"}}, "required": ["accession", "ena_accessions", "sample_title", "biome", "updated_at"], "title": "MGnifySample", "type": "object"}, "PipelineVersions": {"enum": ["V1", "V2", "V3", "V4", "V4.1", "V5", "V6", "V6.1"], "title": "PipelineVersions", "type": "string"}, "Input": {"properties": {"page": {"default": 1, "minimum": 1, "title": "Page", "type": "integer"}, "page_size": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "title": "Page Size"}}, "title": "Input", "type": "object"}, "NinjaPaginationResponseSchema_MGnifyAnalysisDetail_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/MGnifyAnalysisDetail"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[MGnifyAnalysisDetail]", "type": "object"}, "MGnifyAnalysisTypedAnnotation": {"properties": {"count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "title": "Count"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Description"}, "organism": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Organism"}}, "title": "MGnifyAnalysisTypedAnnotation", "type": "object"}, "MGnifyAnalysisWithAnnotations": {"properties": {"experiment_type": {"description": "Experiment type refers to the type of sequencing data that was analysed, e.g. amplicon reads or a metagenome assembly", "examples": ["Metatranscriptomic", "Metagenomic", "Amplicon", "Assembly", "Hybrid assembly", "Long-read assembly", "Metabarcoding", "Unknown"], "title": "Experiment Type", "type": "string"}, "study_accession": {"examples": ["MGYS000000001"], "title": "Study Accession", "type": "string"}, "accession": {"examples": ["MGYA000000001"], "title": "Accession", "type": "string"}, "run": {"anyOf": [{"$ref": "#/components/schemas/AnalysedRun"}, {"type": "null"}]}, "sample": {"anyOf": [{"$ref": "#/components/schemas/MGnifySample"}, {"type": "null"}]}, "assembly": {"anyOf": [{"$ref": "#/components/schemas/Assembly"}, {"type": "null"}]}, "pipeline_version": {"anyOf": [{"$ref": "#/components/schemas/PipelineVersions"}, {"type": "null"}]}, "downloads": {"items": {"$ref": "#/components/schemas/MGnifyAnalysisDownloadFile"}, "title": "Downloads", "type": "array"}, "read_run": {"anyOf": [{"items": {"$ref": "#/components/schemas/AnalysedRun"}, "type": "array"}, {"type": "null"}], "description": "Metadata associated with the original read run(s) this analysis is based on, whether or not those reads were assembled.", "title": "Read Run"}, "quality_control_summary": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "examples": [{"after_filtering": {"total_bases": 700000}, "before_filtering": {"total_bases": 1000000}}], "title": "Quality Control Summary"}, "results_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Directory path where analysis results are stored", "examples": ["http://example.org/data/analyses/MGYA00000001/results"], "title": "Results Dir"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "description": "Additional metadata associated with the analysis", "examples": [{"marker_gene_summary": {"ssu": {"total_read_count": 11}}}], "title": "Metadata"}, "annotations": {"additionalProperties": {"anyOf": [{"items": {"$ref": "#/components/schemas/MGnifyAnalysisTypedAnnotation"}, "type": "array"}, {"additionalProperties": {"anyOf": [{"items": {"$ref": "#/components/schemas/MGnifyAnalysisTypedAnnotation"}, "type": "array"}, {"type": "null"}]}, "type": "object"}]}, "examples": [{"pfams": [{"count": 1, "description": "PFAM1", "organism": null}], "taxonomics": {"lsu": [{"count": 1, "description": null, "organism": "Bacteria"}]}}], "title": "Annotations", "type": "object"}}, "required": ["experiment_type", "study_accession", "accession", "run", "sample", "assembly", "pipeline_version", "read_run", "quality_control_summary", "annotations"], "title": "MGnifyAnalysisWithAnnotations", "type": "object"}, "MGnifyFunctionalAnalysisAnnotationType": {"enum": ["taxonomies__ssu", "taxonomies__lsu", "taxonomies__its_one_db", "taxonomies__unite", "taxonomies__pr2", "taxonomies__dada2_pr2", "taxonomies__dada2_silva", "pfams"], "title": "MGnifyFunctionalAnalysisAnnotationType", "type": "string"}, "NinjaPaginationResponseSchema_MGnifyAnalysisTypedAnnotation_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/MGnifyAnalysisTypedAnnotation"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[MGnifyAnalysisTypedAnnotation]", "type": "object"}, "MGnifyPublicationDetail": {"properties": {"pubmed_id": {"examples": [12345678], "title": "Pubmed Id", "type": "integer"}, "title": {"examples": ["The Origin of Species"], "title": "Title", "type": "string"}, "published_year": {"anyOf": [{"type": "integer"}, {"type": "null"}], "examples": [1859], "title": "Published Year"}, "metadata": {"additionalProperties": true, "examples": [{"authors": "Darwin C", "doi": "10.1017/CBO9780511694295"}], "title": "Metadata", "type": "object"}, "studies": {"items": {"$ref": "#/components/schemas/MGnifyStudy"}, "title": "Studies", "type": "array"}}, "required": ["title", "metadata", "studies"], "title": "MGnifyPublicationDetail", "type": "object"}, "MGnifyStudy": {"properties": {"accession": {"examples": ["MGYS00000001"], "title": "Accession", "type": "string"}, "ena_accessions": {"examples": [["SRP135937", "PRJNA438545"]], "items": {"type": "string"}, "title": "Ena Accessions", "type": "array"}, "title": {"examples": ["ISS Metagenomes"], "title": "Title", "type": "string"}, "biome": {"anyOf": [{"$ref": "#/components/schemas/Biome"}, {"type": "null"}]}, "updated_at": {"examples": ["1998-11-20T09:40:00+03:00"], "format": "date-time", "title": "Updated At", "type": "string"}}, "required": ["accession", "ena_accessions", "title", "biome", "updated_at"], "title": 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"examples": ["The Atlantic Ocean and its ecosystem services"], "title": "Description"}, "logo_url": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["https://example.com/logo.png"], "title": "Logo Url"}}, "required": ["slug", "title"], "title": "SuperStudy", "type": "object"}, "GenomeCatalogueBase": {"properties": {"catalogue_id": {"examples": ["marine-v1-0"], "title": "Catalogue Id", "type": "string"}, "version": {"examples": ["v1.0"], "title": "Version", "type": "string"}, "name": {"examples": ["Marine"], "title": "Name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Description"}, "protein_catalogue_name": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Protein Catalogue Name"}, "protein_catalogue_description": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Protein Catalogue Description"}, "updated_at": {"format": "date-time", "title": "Updated At", "type": "string"}, "result_directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Result Directory"}, "genome_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "title": "Genome Count"}, "unclustered_genome_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "description": "Total number of genomes in the catalogue, including non-cluster-representatives not available via this API.", "title": "Unclustered Genome Count"}, "ftp_url": {"title": "Ftp Url", "type": "string"}, "pipeline_version_tag": {"examples": ["v2.5"], "title": "Pipeline Version Tag", "type": "string"}, "catalogue_biome_label": {"examples": ["Marine"], "title": "Catalogue Biome Label", "type": "string"}, "catalogue_type": {"enum": ["prokaryotes", "eukaryotes", "viruses"], "title": "Catalogue Type", "type": "string"}, "other_stats": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "examples": [{"Total proteins": "12,345,678"}], "title": "Other Stats"}, "biome": {"anyOf": [{"$ref": "#/components/schemas/Biome"}, {"type": "null"}]}}, "required": ["catalogue_id", "version", "name", "description", "protein_catalogue_description", "updated_at", "result_directory", "unclustered_genome_count", "ftp_url", "pipeline_version_tag", "catalogue_biome_label", "catalogue_type", "other_stats"], "title": "GenomeCatalogueBase", "type": "object"}, "GenomeDetail": {"properties": {"accession": {"examples": ["MGYG000000001"], "title": "Accession", "type": "string"}, "ena_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ena Genome Accession"}, "ena_sample_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ena Sample Accession"}, "ncbi_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ncbi Genome Accession"}, "img_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Img Genome Accession"}, "patric_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Patric Genome Accession"}, "length": {"title": "Length", "type": "integer"}, "num_contigs": {"title": "Num Contigs", "type": "integer"}, "n_50": {"title": "N 50", "type": "integer"}, "gc_content": {"title": "Gc Content", "type": "number"}, "type": {"$ref": "#/components/schemas/GenomeType"}, "completeness": {"title": "Completeness", "type": "number"}, "contamination": {"title": "Contamination", "type": "number"}, "catalogue_id": {"title": "Catalogue Id", "type": "string"}, "geographic_origin": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Geographic Origin"}, "geographic_range": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": [], "title": "Geographic Range"}, "biome": {"anyOf": [{"$ref": "#/components/schemas/Biome"}, {"type": "null"}]}, "downloads": {"items": {"$ref": "#/components/schemas/MGnifyGenomeDownloadFile"}, "title": "Downloads", "type": "array"}, "catalogue": {"anyOf": [{"$ref": "#/components/schemas/GenomeCatalogueBase"}, {"type": "null"}]}}, "required": ["accession", "ena_genome_accession", "ena_sample_accession", "ncbi_genome_accession", "img_genome_accession", "patric_genome_accession", "length", "num_contigs", "n_50", "gc_content", "type", "completeness", "contamination", "catalogue_id", "geographic_origin", "downloads"], "title": "GenomeDetail", "type": "object"}, "GenomeType": {"enum": ["MAG", "Isolate"], "title": "GenomeType", "type": "string"}, "MGnifyGenomeDownloadFile": {"properties": {"file_type": {"$ref": "#/components/schemas/DownloadFileType", "description": "File type of the downloadable file, e.g. its file extension"}, "download_type": {"$ref": "#/components/schemas/DownloadType", "description": "Category of the download"}, "download_group": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Group identifier for the download", "examples": ["taxonomies.closed_reference.ssu"], "title": "Download Group"}, "short_description": {"description": "Brief description of the file", "examples": ["Tax. assignments"], "title": "Short Description", "type": "string"}, "long_description": {"description": "Detailed description of the file", "examples": ["A table of taxonomic assignments"], "title": "Long Description", "type": "string"}, "path": {"title": "Path", "type": "string"}, "alias": {"examples": ["SILVA-SSU.tsv"], "title": "Alias", "type": "string"}, "file_size_bytes": {"anyOf": [{"type": "integer"}, {"type": "null"}], "examples": [1024], "title": "File Size Bytes"}, "index_file": {"anyOf": [{"$ref": "#/components/schemas/DownloadFileIndexFile"}, {"items": {"$ref": "#/components/schemas/DownloadFileIndexFile"}, "type": "array"}, {"type": "null"}], "title": "Index File"}, "parent_identifier": {"anyOf": [{"type": "integer"}, {"type": "string"}], "title": "Parent Identifier"}, "url": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Url"}}, "required": ["file_type", "download_type", "short_description", "long_description", "path", "alias", "parent_identifier"], "title": "MGnifyGenomeDownloadFile", "type": "object"}, "GenomeWithAnnotations": {"properties": {"accession": {"title": "Accession", "type": "string"}, "annotations": {"additionalProperties": true, "title": "Annotations", "type": "object"}}, "required": ["accession", "annotations"], "title": "GenomeWithAnnotations", "type": "object"}, "GenomeList": {"properties": {"accession": {"examples": ["MGYG000000001"], "title": "Accession", "type": "string"}, "ena_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ena Genome Accession"}, "ena_sample_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ena Sample Accession"}, "ncbi_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ncbi Genome Accession"}, "img_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Img Genome Accession"}, "patric_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Patric Genome Accession"}, "length": {"title": "Length", "type": "integer"}, "num_contigs": {"title": "Num Contigs", "type": "integer"}, "n_50": {"title": "N 50", "type": "integer"}, "gc_content": {"title": "Gc Content", "type": "number"}, "type": {"$ref": "#/components/schemas/GenomeType"}, "completeness": {"title": "Completeness", "type": "number"}, "contamination": {"title": "Contamination", "type": "number"}, "catalogue_id": {"title": "Catalogue Id", "type": "string"}, "geographic_origin": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Geographic Origin"}, "geographic_range": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": [], "title": "Geographic Range"}, "biome": {"anyOf": [{"$ref": "#/components/schemas/Biome"}, {"type": "null"}]}}, "required": ["accession", "ena_genome_accession", "ena_sample_accession", "ncbi_genome_accession", "img_genome_accession", "patric_genome_accession", "length", "num_contigs", "n_50", "gc_content", "type", "completeness", "contamination", "catalogue_id", "geographic_origin"], "title": "GenomeList", "type": "object"}, "NinjaPaginationResponseSchema_GenomeList_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/GenomeList"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[GenomeList]", "type": "object"}, "NinjaPaginationResponseSchema_GenomeCatalogueList_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/GenomeCatalogueList"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[GenomeCatalogueList]", "type": "object"}, "GenomeCatalogueDetail": {"properties": {"catalogue_id": {"examples": ["marine-v1-0"], "title": "Catalogue Id", "type": "string"}, "version": {"examples": ["v1.0"], "title": "Version", "type": "string"}, "name": {"examples": ["Marine"], "title": "Name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Description"}, "protein_catalogue_name": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Protein Catalogue Name"}, "protein_catalogue_description": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Protein Catalogue Description"}, "updated_at": {"format": "date-time", "title": "Updated At", "type": "string"}, "result_directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Result Directory"}, "genome_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "title": "Genome Count"}, "unclustered_genome_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "description": "Total number of genomes in the catalogue, including non-cluster-representatives not available via this API.", "title": "Unclustered Genome Count"}, "ftp_url": {"title": "Ftp Url", "type": "string"}, "pipeline_version_tag": {"examples": ["v2.5"], "title": "Pipeline Version Tag", "type": "string"}, "catalogue_biome_label": {"examples": ["Marine"], "title": "Catalogue Biome Label", "type": "string"}, "catalogue_type": {"enum": ["prokaryotes", "eukaryotes", "viruses"], "title": "Catalogue Type", "type": "string"}, "other_stats": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "examples": [{"Total proteins": "12,345,678"}], "title": "Other Stats"}, "biome": {"anyOf": [{"$ref": "#/components/schemas/Biome"}, {"type": "null"}]}}, "required": ["catalogue_id", "version", "name", "description", "protein_catalogue_description", "updated_at", "result_directory", "unclustered_genome_count", "ftp_url", "pipeline_version_tag", "catalogue_biome_label", "catalogue_type", "other_stats"], "title": "GenomeCatalogueDetail", "type": "object"}, "NinjaPaginationResponseSchema_Assembly_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/Assembly"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[Assembly]", "type": "object"}, "AssemblyDetail": {"properties": {"accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["ERZ000001"], "title": "Accession"}, "updated_at": {"format": "date-time", "title": "Updated At", "type": "string"}, "run_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Run Accession"}, "sample_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Sample Accession"}, "reads_study_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Reads Study Accession"}, "assembly_study_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Assembly Study Accession"}, "assembler_name": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Assembler Name"}, "assembler_version": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Assembler Version"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "description": "Additional metadata associated with the assembly", "examples": [{"coverage": 30, "coverage_depth": 100, "n_contigs": 1000}], "title": "Metadata"}, "status": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "description": "Status information for the assembly", "examples": [{"assembly_completed": true, "assembly_uploaded": true}], "title": "Status"}}, "required": ["updated_at"], "title": "AssemblyDetail", "type": "object"}, "GenomeAssemblyLinkSchema": {"properties": {"genome": {"$ref": "#/components/schemas/GenomeSchema"}, "species_rep": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Deposition database accession for species representative", "examples": ["GCA_123456789"], "title": "Species Rep"}, "mag_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Deposition database for MAG", "examples": ["MGYG000000001"], "title": "Mag Accession"}, "updated_at": {"anyOf": [{"format": "date-time", "type": "string"}, {"type": "null"}], "title": "Updated At"}}, "required": ["genome", "updated_at"], "title": "GenomeAssemblyLinkSchema", "type": "object"}, "GenomeSchema": {"description": "Simple schema for a Genome model.", "properties": {"accession": {"examples": ["MGYG000000001"], "title": "Accession", "type": "string"}, "catalogue_id": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Catalogue Id"}, "taxon_lineage": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Taxon Lineage"}, "catalogue_version": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "Version of the genome catalogue", "title": "Catalogue Version"}, "ena_genome_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Ena Genome Accession"}}, "required": ["accession", "catalogue_id", "taxon_lineage", "ena_genome_accession"], "title": "GenomeSchema", "type": "object"}, "NinjaPaginationResponseSchema_GenomeAssemblyLinkSchema_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/GenomeAssemblyLinkSchema"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[GenomeAssemblyLinkSchema]", "type": "object"}, "AdditionalContainedGenomeSchema": {"properties": {"genome": {"$ref": "#/components/schemas/GenomeSchema"}, "run_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "ENA accession of the run that produced this assembly", "examples": ["ERR0000001", "SRR0000001"], "title": "Run Accession"}, "containment": {"anyOf": [{"type": "number"}, {"type": "null"}], "description": "Containment score for the genome within the assembly", "examples": [0.65, 1.0], "title": "Containment"}, "cani": {"anyOf": [{"type": "number"}, {"type": "null"}], "description": "Containment Average Nucleotide Identity (cANI)", "examples": [0.97, 1.0], "title": "Cani"}, "updated_at": {"anyOf": [{"format": "date-time", "type": "string"}, {"type": "null"}], "title": "Updated At"}}, "required": ["genome", "updated_at"], "title": "AdditionalContainedGenomeSchema", "type": "object"}, "NinjaPaginationResponseSchema_AdditionalContainedGenomeSchema_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/AdditionalContainedGenomeSchema"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[AdditionalContainedGenomeSchema]", "type": "object"}, "BiomeListFilters": {"properties": {"biome_lineage": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "The lineage to match, including all descendant biomes", "title": "Biome Lineage"}, "max_depth": {"anyOf": [{"minimum": 1, "type": "integer"}, {"type": "null"}], "description": "Maximum depth of the biome lineage to include, e.g. `root` is 1 and `root:Host-Associated:Human` is level 3", "q": "path__depth__lte", "title": "Max Depth"}}, "title": "BiomeListFilters", "type": "object"}, "NinjaPaginationResponseSchema_Biome_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/Biome"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[Biome]", "type": "object"}, "ExperimentTypes": {"enum": ["METAT", "METAG", "AMPLI", "ASSEM", "HYASS", "LRASS", "METAB", "UNKNO"], "title": "ExperimentTypes", "type": "string"}, "RunListFilters": {"properties": {"has_experiment_type": {"anyOf": [{"$ref": "#/components/schemas/ExperimentTypes"}, {"type": "null"}], "description": "If set, will only show runs with the specified experiment type"}}, "title": "RunListFilters", "type": "object"}, "AnalysedRunDetail": {"properties": {"experiment_type": {"description": "Experiment type refers to the type of sequencing data that was analysed, e.g. amplicon reads or a metagenome assembly", "examples": ["Metatranscriptomic", "Metagenomic", "Amplicon", "Assembly", "Hybrid assembly", "Long-read assembly", "Metabarcoding", "Unknown"], "title": "Experiment Type", "type": "string"}, "accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["ERR0000001"], "title": "Accession"}, "sample_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "ENA accession of the sample associated with this run", "examples": ["ERS000001", "SAMEA000000001"], "title": "Sample Accession"}, "study_accession": {"anyOf": [{"type": "string"}, {"type": "null"}], "description": "ENA accession of the study associated with this run", "examples": ["SRP135937", "PRJNA438545"], "title": "Study Accession"}, "instrument_model": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["Illumina HiSeq 2000"], "title": "Instrument Model"}, "instrument_platform": {"anyOf": [{"type": "string"}, {"type": "null"}], "examples": ["Illumina"], "title": "Instrument Platform"}, "sample": {"anyOf": [{"$ref": "#/components/schemas/MGnifySample"}, {"type": "null"}]}, "study": {"anyOf": [{"$ref": "#/components/schemas/MGnifyStudy"}, {"type": "null"}]}}, "required": ["experiment_type", "instrument_model", "instrument_platform", "sample", "study"], "title": "AnalysedRunDetail", "type": "object"}, "NinjaPaginationResponseSchema_AssemblyDetail_": {"properties": {"count": {"title": "Count", "type": "integer"}, "items": {"items": {"$ref": "#/components/schemas/AssemblyDetail"}, "title": "Items", "type": "array"}}, "required": ["count", "items"], "title": "NinjaPaginationResponseSchema[AssemblyDetail]", "type": "object"}, "WebinTokenResponse": {"properties": {"token": {"title": "Token", "type": "string"}, "token_type": {"default": "sliding", "title": "Token Type", "type": "string"}}, "required": ["token"], "title": "WebinTokenResponse", "type": "object"}, "WebinTokenRequest": {"properties": {"username": {"title": "Username", "type": "string"}, "password": {"title": "Password", "type": "string"}}, "required": ["username", "password"], "title": "WebinTokenRequest", "type": "object"}, "WebinTokenRefreshRequest": {"properties": {"token": {"title": "Token", "type": "string"}}, "required": ["token"], "title": "WebinTokenRefreshRequest", "type": "object"}, "Schema": {"properties": {}, "title": "Schema", "type": "object"}, "TokenVerifyInputSchema": {"properties": {"token": {"title": "Token", "type": "string"}}, "required": ["token"], "title": "TokenVerifyInputSchema", "type": "object"}}, "securitySchemes": {"WebinJWTAuth": {"type": "http", "scheme": "bearer"}, "SessionAuthSuperUser": {"type": "apiKey", "in": "cookie", "name": "sessionid"}, "NoAuth": {"type": "none"}}}, "servers": [], "externalDocs": {"description": "MGnify documentation", "url": "https://docs.mgnify.org/"}, "tags": [{"name": "Studies", "description": "\nMGnify studies are based on ENA studies/projects, and are collections of samples, runs, assemblies,\nand analyses associated with a certain set of experiments.\n"}, {"name": "Samples", "description": "\nMGnify samples are based on ENA/BioSamples samples, and represent individual biological samples.\n"}, {"name": "Runs", "description": "\nSequencing runs are based on ENA run accessions, and represent individual sequencing runs of a sample.\n"}, {"name": "Assemblies", "description": "\nMGnify assemblies are equivalent to metagenome assemblies in ENA: the (meta)genome assembly of\none or more sequencing runs.\n"}, {"name": "Analyses", "description": "\nMGnify analyses are runs of a standard pipeline on an individual sequencing run or assembly.\nThey can include collections of taxonomic and functional annotations.\n"}, {"name": "Publications", "description": "\nPublications (e.g. journal articles) may describe or analyse the content of MGnify Studies\nor their corresponding datasets in ENA.\n"}, {"name": "Genomes", "description": "\nMGnify Genomes are annotated draft genomes based on either isolates, or metagenome-assembled genomes (MAGs).\nThey are arranged in biome-specific catalogues.\n"}, {"name": "Private Data", "description": "\nMGnify supports private data, inheriting ENA's data privacy model and public release times.\nAuthentication is required to view private data owned by a Webin account.\n"}, {"name": "Miscellaneous", "description": "\nOther miscellaneous endpoints in support of the API.\n"}, {"name": "Authentication", "description": "\nA Token can be obtained using an ENA Webin username and password,\nto access the Private Data endpoints.\n"}]}