BioMCP

openapi: 3.0.3 info: contact: email: help@myvariant.info name: Chunlei Wu x-id: https://github.com/newgene x-role: responsible developer description: Documentation of the MyVariant.info genetic variant query web services. Learn more about [MyVariant.info](https://docs.myvariant.info/en/latest/index.html) termsOfService: https://myvariant.info/terms/ title: MyVariant.info API version: "1.0" x-translator: biolink-version: 4.2.2 component: KP infores: infores:myvariant-info team: - Service Provider servers: - description: Encrypted Production server url: https://myvariant.info/v1 x-maturity: production tags: - name: variant - name: query - name: metadata - name: translator - name: biothings paths: /metadata: get: description: Get metadata about the data available from the API responses: "200": description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - metadata /metadata/fields: get: description: Get metadata about the data fields available from the API responses: "200": description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - metadata /query: get: description: MyChem.info chemical query web service. In the output, "total" in the output gives the total number of matching hits, while the actual hits are returned under "hits" field. parameters: - description: Required, passing user query. The detailed query syntax for parameter is explained [here](https://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax). example: rs58991260 in: query name: q required: true schema: type: string - $ref: "#/components/parameters/fields" - $ref: "#/components/parameters/size" - $ref: "#/components/parameters/from" - $ref: "#/components/parameters/fetch_all" - $ref: "#/components/parameters/scroll_id" - $ref: "#/components/parameters/sort" - $ref: "#/components/parameters/facets" - $ref: "#/components/parameters/facet_size" - $ref: "#/components/parameters/callback" - $ref: "#/components/parameters/dotfield" - $ref: "#/components/parameters/email" responses: "200": description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - query post: description: 'Although making simple GET requests above to our variant query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving variant annotation for multiple variants). Fortunately, you can also make batch queries via POST requests when you need to. The "query" field in the returned object indicates the matching query term. If a query term has no match, it will return with a "notfound" field with the value "true".' parameters: - description: "Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted. The request body can also be used to provide these ids." in: query name: q required: false schema: items: type: string type: array - description: 'Optional, specify one or more fields (separated by commas) to search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: _id The request body can also be used to provide this information.' in: query name: scopes required: false schema: type: string - $ref: "#/components/parameters/fields" - $ref: "#/components/parameters/email" - $ref: "#/components/parameters/size" - $ref: "#/components/parameters/from" - $ref: "#/components/parameters/fetch_all" - $ref: "#/components/parameters/scroll_id" requestBody: content: application/json: example: q: - rs58991260 - rs928128624 scopes: - dbsnp.rsid schema: properties: q: description: Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted. items: type: string type: array scopes: description: 'Specify one or more fields (separated by commas) to search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: _id' items: type: string type: array type: object responses: "200": description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - query /variant: post: description: Although making simple GET requests above to our variant query service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving variant annotations for multiple variants). Fortunately, you can also make batch queries via POST requests when you need to. parameters: - description: 'Required. Accepts multiple HGVS variant ids separated by comma, e.g., "ids=chr6:g.152708291G>A,chr7:g.55241707G>T,chr16:g.28883241A>G". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. The request body can also be used to provide these ids.' in: query name: ids required: false schema: type: string - $ref: "#/components/parameters/fields" - $ref: "#/components/parameters/email" - $ref: "#/components/parameters/size" requestBody: content: application/json: example: ids: - chr6:g.152708291G>A - chr7:g.55241707G>T schema: properties: ids: description: Accepts multiple variant ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. items: type: string type: array type: object responses: "200": description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - variant /variant/{id}: get: description: 'By default, this will return the complete variant annotation object in JSON format. See [here](https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#returned-object) for an example and [here](https://docs.myvariant.info/en/latest/doc/data.html#variant-object) for more details. If the input variant ID is not valid, 404 (NOT FOUND) will be returned. Optionally, you can pass a "fields" parameter to return only the annotation you want (by filtering returned object fields). "fields" accepts any attributes (a.k.a fields) available from the object. Multiple attributes should be separated by commas. If an attribute is not available for a specific variant object, it will be ignored. Note that the attribute names are case-sensitive. Just like the variant query service, you can also pass a "callback" parameter to make a JSONP call.' parameters: - description: Retrieve chemical data based on ID - currently the HGVS-based id using genomic location based on hg19 human genome assembly example: chr6:g.152708291G>A in: path name: id required: true schema: type: string - $ref: "#/components/parameters/fields" - $ref: "#/components/parameters/callback" - $ref: "#/components/parameters/email" - $ref: "#/components/parameters/size" responses: "200": description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - variant components: parameters: assembly: in: query name: assembly required: false schema: default: hg19 type: string callback: description: Optional, you can pass a "callback" parameter to make a JSONP call. in: query name: callback required: false schema: type: string dotfield: description: 'Optional, can be used to control the format of the returned object. If "dotfield" is true, the returned data object is returned flattened (no nested objects) using dotfield notation for key names. Default: false.' in: query name: dotfield required: false schema: default: false type: boolean email: description: Optional, if you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you. in: query name: email required: false schema: type: string facet_size: description: Optional, an integer (1 <= facet_size <= 1000) that specifies how many buckets to return in a [faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). in: query name: facet_size required: false schema: default: 10 type: integer facets: description: Optional, a single field or comma-separated fields to return facets, can only be used on non-free text fields. E.g. "facets=chembl.molecule_properties.full_mwt". See [examples of faceted queries here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). in: query name: facets required: false schema: items: type: string type: array fetch_all: description: "Optional, a boolean, which when TRUE, allows fast retrieval of all unsorted query hits. The return object contains a _scroll_id field, which when passed as a parameter to the query endpoint (see the scroll_id parameter), returns the next 1000 query results. Setting fetch_all = TRUE causes the results to be inherently unsorted, therefore the sort parameter is ignored. For more information, see [examples using fetch_all here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). Default: FALSE." in: query name: fetch_all required: false schema: default: false type: boolean fields: description: "Optional, can be a comma-separated list to limit the fields returned\ \ from the object. If \"fields=all\", all available fields will be returned.\ \ Look [here](https://docs.mychem.info/en/latest/doc/data.html#available-fields)\ \ for a list of available fields. \n\nNote that it supports dot notation as\ \ well, e.g., you can pass \"chebi.name\". Default: \"fields=all\". The\ \ parameter \"filter\" is an alias for this parameter." in: query name: fields required: false schema: default: all type: string from: description: "Optional, the number of matching hits to skip, starting from 0. Default: 0. " in: query name: from required: false schema: default: 0 type: integer scroll_id: description: Optional, a string containing the _scroll_id returned from a query request with fetch_all = TRUE. Supplying a valid scroll_id will return the next 1000 unordered results. If the next results are not obtained within 1 minute of the previous set of results, the scroll_id becomes stale, and a new one must be obtained with another query request with fetch_all = TRUE. All other parameters are ignored when the scroll_id parameter is supplied. For more information see [examples using scroll_id here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). in: query name: scroll_id required: false schema: type: string size: description: 'Optional, the maximum number of matching hits to return (with a cap of 1000 at the moment). Default: 10. The combination of "size" and "from" parameters can be used to get paging for a large query.' in: query name: size required: false schema: default: 10 type: integer sort: description: 'Optional, the comma-separated fields to sort on. Prefix with "-" for descending order, otherwise in ascending order. Default: sort by matching scores in descending order.' in: query name: sort required: false schema: items: type: string type: array