{ "openapi": "3.0.0", "info": { "title": "Neighbors REST API", "version": "2.0", "license": { "name": "Gnu General Public License", "url": "https://www.gnu.org/licenses/gpl.html" }, "description": "The Neighbors REST API gives access to genome sequences via the taxonomy of sequenced life.\nStarting from one or more target organisms, the accessions of their genomes can be looked up.\nIn addition, the genome accessions of the targets' closest relatives, their neighbors, can be looked up.\nSuch pairs of samples of target and neighbor genomes make good starting material for developing diagnostic markers.", "contact": { "url": "https://www.evolbio.mpg.de/16023/group_bioinformatics", "name": "Bernhard Haubold", "email": "haubold@evolbio.mpg.de" } }, "servers": [ { "url": "https://neighbors.evolbio.mpg.de/api/v2" } ], "tags": [ { "name": "Accession", "description": "Endpoints concerning taxon accessions" }, { "name": "Taxon", "description": "Endpoints concerning one or several taxa" }, { "name": "Program", "description": "Endpoints executing programs" }, { "name": "Miscellaneous", "description": "Miscellaneous endpoints" } ], "paths": { "/": { "get": { "summary": "Get services", "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Example": { "value": { "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/{accession_id}", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/ancestors", "action": "GET", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/children", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/parent", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/rank_distribution", "action": "POST", "types": ["text/vnd.graphviz;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/subtree", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/accessions", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/fintac", "action": "POST", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/neighbors", "action": "POST", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } } }, "operationId": "get_services", "parameters": [], "description": "Get a list of the api's services", "tags": ["Miscellaneous"] } }, "/accessions": { "get": { "summary": "Get accession levels", "tags": ["Accession"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "type": "array", "items": { "$ref": "#/components/schemas/Accession" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": [ { "accession": "GCF_000001405.40", "level": "chromosome" }, { "accession": "GCA_000002115.2", "level": "chromosome" } ] }, "Links": { "value": { "data": [ { "accession": "GCF_000001405.40", "level": "chromosome", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/{accession_id}", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "accession": "GCA_000002115.2", "level": "chromosome", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/{accession_id}", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions?accession_ids=GCF_000001405.40,GCA_000002115.2", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/{accession_id}", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "entities", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/{accession_id}", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "Missing required parameter." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_accessions", "parameters": [ { "schema": { "type": "array", "example": ["GCF_000001405.40", "GCA_000002115.2"], "items": { "type": "string" } }, "in": "query", "name": "accession_ids", "description": "IDs of accessions to filter for", "explode": false, "style": "form", "required": true }, { "$ref": "#/components/parameters/offset" }, { "$ref": "#/components/parameters/limit" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ], "description": "Get accessions and their assembly levels filtered by accession IDs" } }, "/accessions/{accession_id}": { "get": { "summary": "Get accession's levels", "tags": ["Accession"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "$ref": "#/components/schemas/Accession" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": { "accession": "GCF_000001405.40", "level": "chromosome" } }, "Links": { "value": { "data": { "accession": "GCF_000001405.40", "level": "chromosome" }, "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/GCF_000001405.40", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "part-of", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "Missing required parameter." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_accession", "parameters": [ { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ], "description": "Get accession and its assembly level" }, "parameters": [ { "schema": { "type": "string", "example": "GCF_000001405.40" }, "name": "accession_id", "in": "path", "required": true, "description": "Accession to look up" } ] }, "/databases": { "get": { "summary": "Get active databases", "tags": ["Miscellaneous"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "string" } }, "examples": { "Example": { "value": ["latest", "2026-07", "2026-06"] } } } } } }, "operationId": "get-databases", "description": "Get active databases", "parameters": [ { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/limit" }, { "$ref": "#/components/parameters/offset" } ] } }, "/taxa": { "get": { "summary": "Get taxa by name", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "type": "array", "items": { "$ref": "#/components/schemas/Taxon" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": [ { "tax_id": 1383439, "parent": 1002697, "name": "Homo sapiens/Mus musculus xenograft" }, { "tax_id": 1573476, "parent": 1002697, "name": "Homo sapiens/Rattus norvegicus xenograft" } ] }, "Links": { "value": { "data": [ { "tax_id": 1383439, "parent": 1002697, "name": "Homo sapiens/Mus musculus xenograft", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/1383439?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 1573476, "parent": 1002697, "name": "Homo sapiens/Rattus norvegicus xenograft", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/1573476?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa?name=homo%20sapiens/&plain_data=false", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/ancestors", "action": "GET", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/children", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/parent", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/rank_distribution", "action": "POST", "types": ["text/vnd.graphviz;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/subtree", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "entities", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa?field_composite=all&name=homo+sapiens%2F&plain_data=false", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa?field_composite=gen_count&name=homo+sapiens%2F&plain_data=false", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa?field_composite=gen_count_rec&name=homo+sapiens%2F&plain_data=false", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa?field_composite=id&name=homo+sapiens%2F&plain_data=false", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa?field_composite=rank&name=homo+sapiens%2F&plain_data=false", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "Missing required parameter." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxa", "parameters": [ { "schema": { "type": "string", "example": "homo sapiens/" }, "in": "query", "name": "name", "description": "Name or pattern of the taxa", "required": true }, { "schema": { "type": "boolean" }, "in": "query", "name": "scientific", "description": "Whether to search in scientific names only" }, { "schema": { "type": "boolean" }, "in": "query", "name": "exact", "description": "Whether to search for exactly that name or use the name as a pattern" }, { "$ref": "#/components/parameters/offset" }, { "$ref": "#/components/parameters/limit" }, { "$ref": "#/components/parameters/field_composite" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ], "description": "Get basic taxon data for taxa with the given name" } }, "/taxa/{taxon_id}": { "parameters": [ { "schema": { "type": "integer", "example": 9606 }, "name": "taxon_id", "in": "path", "required": true, "description": "id of taxon" } ], "get": { "summary": "Get taxon's attributes", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "$ref": "#/components/schemas/Taxon" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": { "tax_id": 9606, "parent": 9605, "name": "Homo sapiens", "common_name": "human" } }, "Links": { "value": { "data": { "tax_id": 9606, "parent": 9605, "name": "Homo sapiens", "common_name": "human" }, "links": [ { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=all", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=gen_count", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=gen_count_rec", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=id", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=rank", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "part-of", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa", "action": "GET", "types": [ "application/json;charset=utf-8", "text/plain;charset=utf-8" ] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "plain_data is not a bool." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxa_taxon_id", "description": "Get information about a specific taxon", "parameters": [ { "$ref": "#/components/parameters/field_composite" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] } }, "/taxa/{taxon_id}/children": { "parameters": [ { "schema": { "type": "integer", "example": 9606 }, "name": "taxon_id", "in": "path", "required": true, "description": "id of taxon" } ], "get": { "summary": "Get taxon's children", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "type": "array", "items": { "$ref": "#/components/schemas/Taxon" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": [ { "tax_id": 741158, "parent": 9606, "name": "Homo sapiens subsp. 'Denisova'", "common_name": "Denisova hominin" }, { "tax_id": 63221, "parent": 9606, "name": "Homo sapiens neanderthalensis", "common_name": "Neandertal" } ] }, "Links": { "value": { "data": [ { "tax-id": 0, "parent": 0, "name": "string", "common_name": "string", "links": [ { "rel": "string", "href": "http://example.com", "action": "string", "types": ["string"] } ] } ], "links": [ { "rel": "string", "href": "http://example.com", "action": "string", "types": ["string"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "plain_data is not a bool." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxa_taxon_id_children", "description": "Get the children of a taxon given its id", "parameters": [ { "$ref": "#/components/parameters/offset" }, { "$ref": "#/components/parameters/limit" }, { "$ref": "#/components/parameters/field_composite" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] } }, "/taxa/{taxon_id}/parent": { "parameters": [ { "schema": { "type": "integer", "example": 9606 }, "name": "taxon_id", "in": "path", "required": true, "description": "id of taxon" } ], "get": { "summary": "Get taxon's parent", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "$ref": "#/components/schemas/Taxon" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": { "tax_id": 9605, "parent": 207598, "name": "Homo" } }, "Links": { "value": { "data": { "tax_id": 9605, "parent": 207598, "name": "Homo" }, "links": [ { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/parent?field_composite=all", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/parent?field_composite=gen_count", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/parent?field_composite=gen_count_rec", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/parent?field_composite=id", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/parent?field_composite=rank", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/parent", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "all ancestors", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}/ancestors", "action": "GET", "types": ["text/plain;charset=utf-8"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "plain is not a bool." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxa_taxon_id_parent", "description": "Get the parent's taxon id of a given taxon", "parameters": [ { "$ref": "#/components/parameters/field_composite" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] } }, "/taxa/{taxon_id}/subtree": { "parameters": [ { "schema": { "type": "integer", "example": 9606 }, "name": "taxon_id", "in": "path", "required": true, "description": "id of taxon" } ], "get": { "summary": "Get subtree of taxon", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "type": "array", "items": { "$ref": "#/components/schemas/Taxon" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": [ { "tax_id": 9606, "parent": 9605, "name": "Homo sapiens", "common_name": "human" }, { "tax_id": 741158, "parent": 9606, "name": "Homo sapiens subsp. 'Denisova'", "common_name": "Denisova hominin" }, { "tax_id": 63221, "parent": 9606, "name": "Homo sapiens neanderthalensis", "common_name": "Neandertal" } ] }, "Links": { "value": { "data": [ { "tax_id": 9606, "parent": 9605, "name": "Homo sapiens", "common_name": "human", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 741158, "parent": 9606, "name": "Homo sapiens subsp. 'Denisova'", "common_name": "Denisova hominin", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/741158?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 63221, "parent": 9606, "name": "Homo sapiens neanderthalensis", "common_name": "Neandertal", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/63221?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/subtree", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "entities", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/subtree?field_composite=all", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/subtree?field_composite=gen_count", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/subtree?field_composite=gen_count_rec", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/subtree?field_composite=id", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606/subtree?field_composite=rank", "action": "GET", "types": [ "application/json;charset=utf-8", "text/vnd.graphviz;charset=utf-8", "text/plain;charset=utf-8" ] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "Taxon id is not an integer." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxa_taxon_id_subtree", "description": "Get the subtree of a taxon including itself", "parameters": [ { "$ref": "#/components/parameters/offset" }, { "$ref": "#/components/parameters/limit" }, { "$ref": "#/components/parameters/field_composite" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] } }, "/taxonomy": { "get": { "summary": "Get taxonomy subservices", "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Example": { "value": { "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/accessions", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/fintac", "action": "POST", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/neighbors", "action": "POST", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } } }, "operationId": "get_taxonomy_enpoints", "parameters": [], "description": "Get subservices of the taxonomy path", "tags": ["Taxon"] }, "parameters": [] }, "/taxonomy/accessions": { "get": { "summary": "Get most recent common ancestor", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "type": "array", "items": { "$ref": "#/components/schemas/TaxonAccessions" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": [ { "tax_id": 278148, "accessions": [ { "accession": "GCF_001618845.1", "level": "complete" } ] }, { "tax_id": 602633, "accessions": [ { "accession": "GCA_003063835.1", "level": "scaffold" } ] }, { "tax_id": 765698, "accessions": [ { "accession": "GCF_000185905.1", "level": "complete" } ] } ] }, "Links": { "value": { "data": [ { "tax_id": 278148, "accessions": [ { "accession": "GCF_001618845.1", "level": "complete", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/GCF_001618845.1", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "taxon", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/278148", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 602633, "accessions": [ { "accession": "GCA_003063835.1", "level": "scaffold", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/GCA_003063835.1", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "taxon", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/GCF_001618845.1", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 765698, "accessions": [ { "accession": "GCF_000185905.1", "level": "complete", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/GCF_000185905.1", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "taxon", "href": "https://neighbors.evolbio.mpg.de/api/v2/accessions/GCA_003063835.1", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/accessions?taxon_ids=278148,602633", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "Missing required parameter." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxonomy_accessions", "description": "Get the recursive accessions for a list of taxa", "parameters": [ { "$ref": "#/components/parameters/field_composite" }, { "schema": { "type": "array", "items": { "type": "integer" }, "example": [278148, 602633] }, "in": "query", "name": "taxon_ids", "style": "form", "explode": false, "required": true, "description": "Ids of taxa for finding accessions" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] }, "parameters": [] }, "/taxonomy/mrca": { "parameters": [], "get": { "summary": "Get most recent common ancestor", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "$ref": "#/components/schemas/Taxon" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": { "tax_id": 9606, "parent": 9605, "name": "Homo sapiens", "common_name": "human" } }, "Links": { "value": { "data": { "tax_id": 9606, "parent": 9605, "name": "Homo sapiens", "common_name": "human", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9606?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, "links": [ { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca?field_composite=all&taxon_ids=9606%2C741158%2C63221", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca?field_composite=gen_count&taxon_ids=9606%2C741158%2C63221", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca?field_composite=gen_count_rec&taxon_ids=9606%2C741158%2C63221", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca?field_composite=id&taxon_ids=9606%2C741158%2C63221", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca?field_composite=rank&taxon_ids=9606%2C741158%2C63221", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca?taxon_ids=9606,741158,63221", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "path", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "Missing required parameter." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxonomy_mrca", "description": "Get the most recent common ancestor of a list of taxa", "parameters": [ { "$ref": "#/components/parameters/field_composite" }, { "schema": { "type": "array", "example": [9606, 741158, 63221], "items": { "type": "integer" } }, "in": "query", "name": "taxon_ids", "style": "form", "explode": false, "required": true, "description": "Ids of taxa for which to find the mrca" }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] } }, "/taxonomy/path": { "parameters": [], "get": { "summary": "Get path connecting two taxa", "tags": ["Taxon"], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "data": { "type": "array", "items": { "$ref": "#/components/schemas/Taxon" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Plain": { "value": [ { "tax_id": 9605, "parent": 207598, "name": "Homo" }, { "tax_id": 207598, "parent": 9604, "name": "Homininae" }, { "tax_id": 9604, "parent": 314295, "name": "Hominidae", "common_name": "great apes" }, { "tax_id": 314295, "parent": 9526, "name": "Hominoidea", "common_name": "apes" }, { "tax_id": 9526, "parent": 314293, "name": "Catarrhini" }, { "tax_id": 314293, "parent": 376913, "name": "Simiiformes" }, { "tax_id": 376913, "parent": 9443, "name": "Haplorrhini" }, { "tax_id": 9443, "parent": 314146, "name": "Primates", "common_name": "primates" }, { "tax_id": 314146, "parent": 1437010, "name": "Euarchontoglires" }, { "tax_id": 1437010, "parent": 9347, "name": "Boreoeutheria" }, { "tax_id": 9347, "parent": 32525, "name": "Eutheria", "common_name": "placentals" }, { "tax_id": 32525, "parent": 40674, "name": "Theria" }, { "tax_id": 40674, "parent": 32524, "name": "Mammalia", "common_name": "mammals" } ] }, "Links": { "value": { "data": [ { "tax_id": 9605, "parent": 207598, "name": "Homo", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9605?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 207598, "parent": 9604, "name": "Homininae", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/207598?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 9604, "parent": 314295, "name": "Hominidae", "common_name": "great apes", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9604?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 314295, "parent": 9526, "name": "Hominoidea", "common_name": "apes", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/314295?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 9526, "parent": 314293, "name": "Catarrhini", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9526?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 314293, "parent": 376913, "name": "Simiiformes", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/314293?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 376913, "parent": 9443, "name": "Haplorrhini", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/376913?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 9443, "parent": 314146, "name": "Primates", "common_name": "primates", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9443?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 314146, "parent": 1437010, "name": "Euarchontoglires", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/314146?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 1437010, "parent": 9347, "name": "Boreoeutheria", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/1437010?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 9347, "parent": 32525, "name": "Eutheria", "common_name": "placentals", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/9347?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 32525, "parent": 40674, "name": "Theria", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/32525?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] }, { "tax_id": 40674, "parent": 32524, "name": "Mammalia", "common_name": "mammals", "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/40674?field_composite=default", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } ], "links": [ { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path?end_id=40674&field_composite=all&start_id=9606", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path?end_id=40674&field_composite=gen_count&start_id=9606", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path?end_id=40674&field_composite=gen_count_rec&start_id=9606", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path?end_id=40674&field_composite=id&start_id=9606", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "more fields", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path?end_id=40674&field_composite=rank&start_id=9606", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path?start_id=9606&end_id=40674", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "entities", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxa/{taxon_id}", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } }, "400": { "description": "Bad Request", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "start id is not an integer." } } } } }, "404": { "description": "Not Found" }, "406": { "description": "Not Acceptable" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_taxonomy_path", "description": "Get the path between a start taxon, that is further from the root and an end taxon that is closer to the root.\nReturns an empty list if no path connects start and end", "parameters": [ { "$ref": "#/components/parameters/offset" }, { "$ref": "#/components/parameters/limit" }, { "$ref": "#/components/parameters/field_composite" }, { "schema": { "type": "integer", "example": 9606 }, "in": "query", "name": "start_id", "description": "Id of start taxon, further from root", "required": true }, { "schema": { "type": "integer", "example": 40674 }, "in": "query", "name": "end_id", "description": "Id of end taxon, closer to root", "required": true }, { "$ref": "#/components/parameters/plain_data" }, { "$ref": "#/components/parameters/db" } ] } }, "/programs": { "get": { "summary": "Get programs subservices", "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "type": "object", "properties": { "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "examples": { "Example": { "value": { "links": [ { "rel": "self", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/accessions", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/fintac", "action": "POST", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/mrca", "action": "GET", "types": ["application/json;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/neighbors", "action": "POST", "types": ["text/plain;charset=utf-8"] }, { "rel": "service", "href": "https://neighbors.evolbio.mpg.de/api/v2/taxonomy/path", "action": "GET", "types": ["application/json;charset=utf-8"] } ] } } } } } } }, "operationId": "get_programs_endpoints", "parameters": [], "description": "Get subservices of the programs path", "tags": ["Program"] }, "parameters": [] }, "/programs/ants": { "get": { "summary": "Execute ants program", "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "# Back ID Name Rank\r\n 31 1 root no rank\r\n 30 131567 cellular organisms cellular root\r\n 29 2759 Eukaryota domain\r\n 28 33154 Opisthokonta clade\r\n 27 33208 Metazoa kingdom\r\n 26 6072 Eumetazoa clade\r\n 25 33213 Bilateria clade\r\n 24 33511 Deuterostomia clade\r\n 23 7711 Chordata phylum\r\n 22 89593 Craniata subphylum\r\n 21 7742 Vertebrata clade\r\n 20 7776 Gnathostomata clade\r\n 19 117570 Teleostomi clade\r\n 18 117571 Euteleostomi clade\r\n 17 8287 Sarcopterygii superclass\r\n 16 1338369 Dipnotetrapodomorpha clade\r\n 15 32523 Tetrapoda clade\r\n 14 32524 Amniota clade\r\n 13 40674 Mammalia class\r\n 12 32525 Theria clade\r\n 11 9347 Eutheria clade\r\n 10 1437010 Boreoeutheria clade\r\n 9 314146 Euarchontoglires superorder\r\n 8 9443 Primates order\r\n 7 376913 Haplorrhini suborder\r\n 6 314293 Simiiformes infraorder\r\n 5 9526 Catarrhini parvorder\r\n 4 314295 Hominoidea superfamily\r\n 3 9604 Hominidae family\r\n 2 207598 Homininae subfamily\r\n 1 9605 Homo genus\r\n 0 9606 Homo sapiens species" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_programs_ants", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["9606"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "$ref": "#/components/parameters/db" } ], "description": "Executes the neighbors program ants remotely", "tags": ["Program"] }, "parameters": [] }, "/programs/dree": { "get": { "summary": "Execute dree program", "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "digraph g {\r\n rankdir=LR\r\n 9592 [label=\"9592\"]\r\n 9592 [label=\"Gorilla\"]\r\n 207598 -> 9592\r\n 9593 [color=\"lightsalmon\",style=filled]\r\n 9593 [label=\"Gorilla gorilla\"]\r\n 9592 -> 9593\r\n 9595 [color=\"lightsalmon\",style=filled]\r\n 9595 [label=\"Gorilla gorilla gorilla\"]\r\n 9593 -> 9595\r\n 9596 [label=\"9596\"]\r\n 9596 [label=\"Pan\"]\r\n 207598 -> 9596\r\n 9597 [color=\"lightsalmon\",style=filled]\r\n 9597 [label=\"Pan paniscus\"]\r\n 9596 -> 9597\r\n 9598 [color=\"lightsalmon\",style=filled]\r\n 9598 [label=\"Pan troglodytes\"]\r\n 9596 -> 9598\r\n 9605 [label=\"9605\"]\r\n 9605 [label=\"Homo\"]\r\n 207598 -> 9605\r\n 9606 [color=\"lightsalmon\",style=filled]\r\n 9606 [label=\"Homo sapiens\"]\r\n 9605 -> 9606\r\n 37012 [color=\"lightsalmon\",style=filled]\r\n 37012 [label=\"Pan troglodytes verus\"]\r\n 9598 -> 37012\r\n 207598 [label=\"207598\"]\r\n 207598 [label=\"Homininae\"]\r\n 499232 [color=\"lightsalmon\",style=filled]\r\n 499232 [label=\"Gorilla beringei\"]\r\n 9592 -> 499232\r\n 1159185 [color=\"lightsalmon\",style=filled]\r\n 1159185 [label=\"Gorilla beringei beringei\"]\r\n 499232 -> 1159185}" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_programs_dree", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["-n", "-g", "207598"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "$ref": "#/components/parameters/db" } ], "description": "Executes the neighbors program dree remotely", "tags": ["Program"] }, "parameters": [] }, "/programs/fintac": { "parameters": [], "post": { "summary": "Execute fintac remotely", "tags": ["Program"], "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "#Clade Targets Neighbors Unknowns Split (%) Parent Dist(Parent)\r\n 5007 22 8 18 98.53 5005 0.000385" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "post-programs-fintac", "description": "Executes the neighbors program fintac remotely", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["-t", "991910_", "-u", "562_"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "schema": { "type": "array", "items": { "type": "string" }, "example": ["eco7k.nwk"] }, "style": "form", "explode": true, "in": "query", "name": "extra", "description": "Names of files. These need to match the filenames of the multipart/form-data exactly" }, { "$ref": "#/components/parameters/db" } ], "requestBody": { "content": { "multipart/form-data": { "schema": { "type": "object", "additionalProperties": {} } } }, "description": "The request body provides the files named in the query parameters. It is essential, that the files' names given in the request body and in the query match." } } }, "/programs/neighbors": { "get": { "summary": "Execute neighbors program", "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "# MRCA(targets): 9606, Homo sapiens\r\n# MRCA(targets+neighbors): 9605, Homo\r\n# Type Taxon-ID Name Genomes\r\nt 9606 Homo sapiens GCA_947361175.1|GCA_963931935.1|GCF_009914755.1\r\ntt 63221 Homo sapiens neanderthalensis -\r\ntt 741158 Homo sapiens subsp. 'Denisova' -\r\nn 1425170 Homo heidelbergensis -\r\nn 2665952 environmental samples -\r\nn 2665953 Homo sapiens environmental sample -\r\nn 2813598 unclassified Homo -\r\nn 2813599 Homo sp. -" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_programs_neighbors", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["-L", "complete", "-t", "9606"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "$ref": "#/components/parameters/db" } ], "description": "Executes the program neighbors remotely", "tags": ["Program"] }, "parameters": [], "post": { "summary": "Execute neighbors remotely with files", "tags": ["Program"], "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "# MRCA(targets): 9606, Homo sapiens\r\n# MRCA(targets+neighbors): 9605, Homo\r\n# Type Taxon-ID Name Genomes\r\nt 9606 Homo sapiens GCA_947361175.1|GCA_963931935.1|GCF_009914755.1\r\ntt 63221 Homo sapiens neanderthalensis -\r\ntt 741158 Homo sapiens subsp. 'Denisova' -\r\nn 1425170 Homo heidelbergensis -\r\nn 2665952 environmental samples -\r\nn 2665953 Homo sapiens environmental sample -\r\nn 2813598 unclassified Homo -\r\nn 2813599 Homo sp. -" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "post-programs-neighbors", "description": "Executes the program neighbors remotely with one or more files of target taxa", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["-L", "complete"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "schema": { "type": "array", "items": { "type": "string" }, "example": ["targets.txt"] }, "style": "form", "explode": false, "in": "query", "name": "extra", "description": "Names of files" }, { "$ref": "#/components/parameters/db" } ], "requestBody": { "content": { "multipart/form-data": { "schema": { "type": "object", "additionalProperties": {} } } }, "description": "The request body provides the files named in the query parameters. It is essential, that the files' names given in the request body and in the query match." } } }, "/programs/ranks": { "get": { "summary": "Execute ranks program", "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "digraph g {\r\n rankdir=LR\r\n 1 [label=\"species\n392350 (97.7%)\"]\r\n 2 [label=\"no rank\n4503 (1.1%)\"]\r\n 3 [label=\"no rank\n17 (< 0.1%)\"]\r\n 4 [label=\"strain\n422 (0.1%)\"]\r\n 5 [label=\"no rank\n2 (< 0.1%)\"]\r\n 6 [label=\"serogroup\n1646 (0.4%)\"]\r\n 7 [label=\"no rank\n15 (< 0.1%)\"]\r\n 8 [label=\"serotype\n6 (< 0.1%)\"]\r\n 9 [label=\"strain\n1 (< 0.1%)\"]\r\n 10 [label=\"strain\n12 (< 0.1%)\"]\r\n 11 [label=\"serotype\n30 (< 0.1%)\"]\r\n 12 [label=\"strain\n1 (< 0.1%)\"]\r\n 13 [label=\"strain\n2438 (0.6%)\"]\r\n 14 [label=\"no rank\n85 (< 0.1%)\"]\r\n 1 -> 2\r\n 2 -> 3\r\n 2 -> 4\r\n 4 -> 5\r\n 1 -> 6\r\n 6 -> 7\r\n 6 -> 8\r\n 8 -> 9\r\n 6 -> 10\r\n 1 -> 11\r\n 11 -> 12\r\n 1 -> 13\r\n 13 -> 14\r\n}" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_programs_ranks", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["562"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "$ref": "#/components/parameters/db" } ], "description": "Executes the neighbors program ranks remotely", "tags": ["Program"] }, "parameters": [], "post": { "summary": "Execute ranks remotely with files", "tags": ["Program"], "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "digraph g {\r\n rankdir=LR\r\n 1 [label=\"species\n392350 (97.7%)\"]\r\n 2 [label=\"no rank\n4503 (1.1%)\"]\r\n 3 [label=\"no rank\n17 (< 0.1%)\"]\r\n 4 [label=\"strain\n422 (0.1%)\"]\r\n 5 [label=\"no rank\n2 (< 0.1%)\"]\r\n 6 [label=\"serogroup\n1646 (0.4%)\"]\r\n 7 [label=\"no rank\n15 (< 0.1%)\"]\r\n 8 [label=\"serotype\n6 (< 0.1%)\"]\r\n 9 [label=\"strain\n1 (< 0.1%)\"]\r\n 10 [label=\"strain\n12 (< 0.1%)\"]\r\n 11 [label=\"serotype\n30 (< 0.1%)\"]\r\n 12 [label=\"strain\n1 (< 0.1%)\"]\r\n 13 [label=\"strain\n2438 (0.6%)\"]\r\n 14 [label=\"no rank\n85 (< 0.1%)\"]\r\n 1 -> 2\r\n 2 -> 3\r\n 2 -> 4\r\n 4 -> 5\r\n 1 -> 6\r\n 6 -> 7\r\n 6 -> 8\r\n 8 -> 9\r\n 6 -> 10\r\n 1 -> 11\r\n 11 -> 12\r\n 1 -> 13\r\n 13 -> 14\r\n}" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "post-programs-ranks", "description": "Executes the neighbors program ranks remotely with one file of genome accessions", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["-g", "myGenomeList.txt", "562"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "$ref": "#/components/parameters/db" } ], "requestBody": { "content": { "multipart/form-data": { "schema": { "type": "object", "additionalProperties": {} } } }, "description": "The request body provides the files named in the query parameters. It is essential, that the files' names given in the request body and in the query match." } } }, "/programs/taxi": { "get": { "summary": "Execute taxi program", "responses": { "200": { "description": "OK", "content": { "text/plain": { "schema": { "type": "string" }, "examples": { "Example": { "value": "# ID Parent Name\r\n 9606 9605 Homo sapiens" } } } } }, "404": { "description": "Not Found" }, "500": { "description": "Internal Server Error" }, "503": { "description": "Service Unavailable" } }, "operationId": "get_programs_taxi", "parameters": [ { "schema": { "type": "array", "items": { "type": "string" }, "example": ["-t", "9606"] }, "style": "form", "explode": true, "in": "query", "name": "options", "description": "Program options" }, { "$ref": "#/components/parameters/db" } ], "description": "Executes the neighbors program taxi remotely", "tags": ["Program"] }, "parameters": [] } }, "components": { "schemas": { "Accession": { "title": "Accession", "type": "object", "properties": { "accession": { "type": "string" }, "level": { "type": "string" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "GenomeCount": { "title": "GenomeCount", "type": "object", "properties": { "level": { "type": "string" }, "count": { "type": "integer" } } }, "Image": { "title": "Image", "type": "object", "properties": { "id": { "type": "integer" }, "url": { "type": "string" }, "attribution": { "type": "string" } } }, "Link": { "title": "Link", "type": "object", "properties": { "rel": { "type": "string" }, "href": { "type": "string", "format": "uri" }, "action": { "type": "string" }, "types": { "type": "array", "items": { "type": "string" } } } }, "Rank": { "title": "Rank", "type": "object", "properties": { "tax_id": { "type": "integer" }, "rank": { "type": "string" } } }, "TaxId": { "title": "TaxId", "type": "object", "properties": { "tax_id": { "type": "integer" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "Taxon": { "title": "Taxon", "type": "object", "properties": { "tax-id": { "type": "integer" }, "parent": { "type": "integer" }, "name": { "type": "string" }, "common_name": { "type": "string" }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "TaxonAccessions": { "title": "TaxonAccessions", "type": "object", "properties": { "tax_id": { "type": "integer" }, "accessions": { "type": "array", "items": { "$ref": "#/components/schemas/Accession" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } }, "TaxonInfo": { "title": "TaxonInfo", "type": "object", "properties": { "tax_id": { "type": "integer" }, "parent": { "type": "integer" }, "is_leaf": { "type": "boolean" }, "name": { "type": "string" }, "common_name": { "type": "string" }, "rank": { "type": "string" }, "raw_genome_counts": { "type": "array", "items": { "$ref": "#/components/schemas/GenomeCount" } }, "rec_genome_counts": { "type": "array", "items": { "$ref": "#/components/schemas/GenomeCount" } }, "images": { "type": "array", "items": { "$ref": "#/components/schemas/Image" } }, "links": { "type": "array", "items": { "$ref": "#/components/schemas/Link" } } } } }, "securitySchemes": {}, "parameters": { "offset": { "name": "offset", "in": "query", "required": false, "schema": { "type": "integer", "default": 0, "example": 0, "minimum": 0 }, "description": "Offset of entries when retrieving lists", "style": "form" }, "limit": { "name": "limit", "in": "query", "required": false, "schema": { "type": "integer", "minimum": -1, "example": 20, "default": -1 }, "description": "Amount of entries per response", "style": "form" }, "field_composite": { "name": "field_composite", "in": "query", "schema": { "type": "string", "default": "default", "enum": ["id", "rank", "all", "default", "gen_count", "gen_count_rec"] }, "description": "Determines fields for the return type" }, "plain_data": { "name": "plain_data", "in": "query", "required": false, "schema": { "type": "boolean" }, "description": "Reduce response to the data property and remove all hyper refereces" }, "db": { "name": "db", "in": "query", "required": false, "schema": { "type": "string", "default": "latest" }, "description": "Defines which database should be queried" } } }, "x-internal": false }