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: infores: "infores:myvariant-info" component: KP team: - Service Provider biolink-version: "4.2.2" 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: "/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: ## these are provided in the docs https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html - name: id description: >- Retrieve chemical data based on ID - currently the HGVS-based id using genomic location based on hg19 human genome assembly in: path required: true example: "chr6:g.152708291G>A" schema: type: string - "$ref": "#/components/parameters/fields" - "$ref": "#/components/parameters/callback" - "$ref": "#/components/parameters/email" ## this is useful even when it's not noted in the docs - "$ref": "#/components/parameters/size" ## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now ## assembly is unique to MyVariant # - "$ref": "#/components/parameters/assembly" # - "$ref": "#/components/parameters/raw" # - "$ref": "#/components/parameters/rawquery" # - "$ref": "#/components/parameters/dotfield" # - "$ref": "#/components/parameters/_sorted" # - "$ref": "#/components/parameters/always_list" # - "$ref": "#/components/parameters/allow_null" # - "$ref": "#/components/parameters/format" responses: '200': ## description from https://docs.myvariant.info/en/latest/doc/response_status_codes.html description: A 200 status code indicates a successful query, and is accompanied by the query response payload. ## commenting out schemas and other status codes for now # content: # application/json: # schema: # $ref: '#/components/schemas/Chem' # '404': # description: A response indicating an unknown chemical ID tags: - variant "/variant": post: description: >- Although making simple GET requests above to our variant query service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving variant annotations for multiple variants). Fortunately, you can also make batch queries via POST requests when you need to. parameters: ## these are provided in the docs https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html - name: ids description: >- Required. Accepts multiple HGVS variant ids separated by comma, e.g., "ids=chr6:g.152708291G>A,chr7:g.55241707G>T,chr16:g.28883241A>G". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. The request body can also be used to provide these ids. in: query ## setting to false since putting this info in the request body seems to work as well required: false schema: type: string - "$ref": "#/components/parameters/fields" - "$ref": "#/components/parameters/email" ## this is useful even when it's not noted in the docs - "$ref": "#/components/parameters/size" ## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now ## assembly is unique to MyVariant # - "$ref": "#/components/parameters/assembly" # - "$ref": "#/components/parameters/raw" # - "$ref": "#/components/parameters/rawquery" # - "$ref": "#/components/parameters/dotfield" # - "$ref": "#/components/parameters/_sorted" # - "$ref": "#/components/parameters/always_list" # - "$ref": "#/components/parameters/allow_null" # - "$ref": "#/components/parameters/format" requestBody: content: application/json: example: ids: - "chr6:g.152708291G>A" - "chr7:g.55241707G>T" schema: type: object 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. type: array items: type: string responses: '200': description: A 200 status code indicates a successful query, and is accompanied by the query response payload. tags: - variant "/metadata": get: description: Get metadata about the data available from the API ## these are noted in the hhttps://myvariant.info/v1/spec endpoint; commenting out for now # parameters: # - "$ref": "#/components/parameters/format" # - "$ref": "#/components/parameters/raw" 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 ## these are noted in the hhttps://myvariant.info/v1/spec endpoint; commenting out for now # parameters: # - "$ref": "#/components/parameters/format" # - "$ref": "#/components/parameters/raw" # - "$ref": "#/components/parameters/search" # - "$ref": "#/components/parameters/prefix" 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: - name: q ## description partially from https://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax 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). in: query required: true example: "rs58991260" 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" - "$ref": "#/components/parameters/email" ## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now ## assembly is unique to MyVariant # - "$ref": "#/components/parameters/assembly" # - "$ref": "#/components/parameters/aggs" # - "$ref": "#/components/parameters/userquery" # - "$ref": "#/components/parameters/explain" # - "$ref": "#/components/parameters/raw" # - "$ref": "#/components/parameters/rawquery" # - "$ref": "#/components/parameters/_sorted" # - "$ref": "#/components/parameters/always_list" # - "$ref": "#/components/parameters/allow_null" # - "$ref": "#/components/parameters/format" responses: '200': description: A 200 status code indicates a successful query, and is accompanied by the query response payload. ## commenting out schemas and other status codes for now # content: # application/json: # schema: # "$ref": "#/components/schemas/QueryResult" # '400': # content: # application/json: # schema: # "$ref": "#/components/schemas/ErrorResult" # description: A response indicating an improperly formatted query # description: Make queries and return matching gene hits. Supports JSONP and CORS # as well. tags: - query post: description: >- Although making simple GET requests above to our variant query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving variant annotation for multiple variants). Fortunately, you can also make batch queries via POST requests when you need to. The "query" field in the returned object indicates the matching query term. If a query term has no match, it will return with a "notfound" field with the value "true". parameters: ## these are provided in the docs https://docs.myvariant.info/en/latest/doc/variant_query_service.html#id2 - name: q description: >- Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted. The request body can also be used to provide these ids. in: query ## setting to false since putting this info in the request body seems to work as well required: false schema: type: array items: type: string - name: scopes description: >- Optional, specify one or more fields (separated by commas) to search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: _id The request body can also be used to provide this information. in: query ## setting to false since putting this info in the request body seems to work as well required: false schema: type: string - "$ref": "#/components/parameters/fields" - "$ref": "#/components/parameters/email" ## this is useful even when it's not noted in the docs - "$ref": "#/components/parameters/size" - "$ref": "#/components/parameters/from" - "$ref": "#/components/parameters/fetch_all" - "$ref": "#/components/parameters/scroll_id" ## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now ## assembly is unique to MyVariant ## others haven't been written down here: with_total, analyzer # - "$ref": "#/components/parameters/assembly" # - "$ref": "#/components/parameters/sort" # - "$ref": "#/components/parameters/raw" # - "$ref": "#/components/parameters/rawquery" # - "$ref": "#/components/parameters/dotfield" # - "$ref": "#/components/parameters/_sorted" # - "$ref": "#/components/parameters/always_list" # - "$ref": "#/components/parameters/allow_null" # - "$ref": "#/components/parameters/format" requestBody: content: application/json: example: q: - "rs58991260" - "rs928128624" scopes: - "dbsnp.rsid" schema: type: object 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. type: array items: type: string 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 type: array items: type: string responses: '200': description: A 200 status code indicates a successful query, and is accompanied by the query response payload. ## commenting out schemas and other status codes for now # content: # application/json: # schema: # "$ref": "#/components/schemas/QueryPOSTResult" # '400': # content: # application/json: # schema: # "$ref": "#/components/schemas/ErrorResult" # description: A response indicating an improperly formatted query # description: Make batch gene queries and return matching gene hits tags: - query ## 32 operations (16 sets) x-bte-kgs-operations: - "$ref": "#/components/x-bte-kgs-operations/civic-geneDisease" - "$ref": "#/components/x-bte-kgs-operations/civic-geneDisease-rev" - "$ref": "#/components/x-bte-kgs-operations/civic-variantDisease" - "$ref": "#/components/x-bte-kgs-operations/civic-variantDisease-rev" - "$ref": "#/components/x-bte-kgs-operations/dbsnp-variantGene" - "$ref": "#/components/x-bte-kgs-operations/dbsnp-variantGene-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variantGene" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variantGene-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseOMIM" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseORPHANET" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseMONDO" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseMESH" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-phenoHP" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseOMIM-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseORPHANET-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseMONDO-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-diseaseMESH-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-gene-phenoHP-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseOMIM" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseORPHANET" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseMONDO" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseMESH" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-phenoHP" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseOMIM-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseORPHANET-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseMONDO-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-diseaseMESH-rev" - "$ref": "#/components/x-bte-kgs-operations/clinvar-variant-phenoHP-rev" components: parameters: ## assembly is specific to MyVariant assembly: name: assembly in: query required: false schema: type: string default: hg19 callback: name: callback description: >- Optional, you can pass a "callback" parameter to make a JSONP call. in: query required: false schema: type: string dotfield: name: 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 required: false schema: type: boolean default: false email: name: 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 required: false schema: type: string facet_size: name: 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 required: false schema: type: integer default: 10 facets: name: 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 required: false schema: type: array items: type: string fetch_all: name: 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 required: false schema: type: boolean default: false fields: name: 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. Note 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 required: false schema: type: string default: all from: name: from description: >- Optional, the number of matching hits to skip, starting from 0. Default: 0. in: query required: false schema: type: integer default: 0 scroll_id: name: 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 required: false schema: type: string size: name: 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 required: false schema: type: integer default: 10 sort: name: 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 required: false schema: type: array items: type: string ## these are noted in the https://mychem.info/v1/spec endpoint; commenting out for now # _sorted: # name: _sorted # in: query # required: false # schema: # type: boolean # default: true # aggs: # name: aggs # in: query # required: false # schema: # type: array # items: # type: string # allow_null: # name: allow_null # in: query # required: false # schema: # type: array # items: # type: string # always_list: # name: always_list # in: query # required: false # schema: # type: array # items: # type: string # explain: # name: explain # in: query # required: false # schema: # type: boolean # format: # name: format # description: 'controls output format of server response, currently supports: # "json", "jsonld", "html". Type: string. Default: json.' # in: query # required: false # schema: # type: string # default: json # prefix: # name: prefix # in: query # required: false # schema: # type: string # raw: # name: raw # in: query # required: false # schema: # type: boolean # rawquery: # name: rawquery # in: query # required: false # schema: # type: boolean # search: # name: search # in: query # required: false # schema: # type: string # userquery: # name: userquery # in: query # required: false # schema: # type: string ## commenting out schemas and other status codes for now # schemas: # Chem: # properties: # _id: # type: string # required: # - _id # type: object # ErrorResult: # properties: # message: # type: string # success: # type: boolean # type: object # QueryPOSTResult: # items: # allOf: # - "$ref": "#/components/schemas/Chem" # - properties: # _score: # format: float # type: number # query: # type: string # type: object # type: array # QueryResult: # properties: # hits: # items: # "$ref": "#/components/schemas/Chem" # type: array # max_score: # format: float # type: number # took: # type: integer # total: # type: integer # type: object # int64_or_array: # oneOf: # - items: # format: int64 # type: integer # type: array # - format: int64 # type: integer # string_or_array: # oneOf: # - items: # type: string # type: array # - type: string x-bte-response-mapping: civic-geneDisease: DOID: civic.evidence_items.disease.doid ref_pmid: civic.evidence_items.source.pubmed ## no prefix ref_clinicaltrials: civic.evidence_items.source.clinical_trials.nct_id ## no prefix (ID starts with "NCT") ## commenting out because data-processing / biolink-modeling issues # ## categorical var / relation # civic_clinical_significance: civic.evidence_items.clinical_significance # ## free text # civic_description: civic.evidence_items.description # ## context: drugs involved # civic_drug_interaction: civic.evidence_items.drug_interaction_type # civic_drugs_involved: civic.evidence_items.drugs.name # ## categorical vars # civic_evidence_direction: civic.evidence_items.evidence_direction # civic_evidence_level: civic.evidence_items.evidence_level # civic_evidence_type: civic.evidence_items.evidence_type # ## context: variant involved, could use "biolink:sequence_variant_qualifier" # ## but then ID-namespace would be unclear (this ID doesn't have a prefix) # civic_variant_id: civic.evidence_items.variant_id # ## context: variant involved was Somatic, unknown... # civic_variant_origin: civic.evidence_items.variant_origin civic-geneOnly: NCBIGene: civic.entrez_id civic-variantDisease: DOID: civic.evidence_items.disease.doid ## variant name input_name: _id ref_pmid: civic.evidence_items.source.pubmed ## no prefix ref_clinicaltrials: civic.evidence_items.source.clinical_trials.nct_id ## no prefix (ID starts with "NCT") ## commenting out because data-processing / biolink-modeling issues # ## categorical var / relation # civic_clinical_significance: civic.evidence_items.clinical_significance # ## free text # civic_description: civic.evidence_items.description # ## context: gene involved # civic_variant_in_gene: civic.entrez_name # ## context: drugs involved # civic_drug_interaction: civic.evidence_items.drug_interaction_type # civic_drugs_involved: civic.evidence_items.drugs.name # ## categorical vars # civic_evidence_direction: civic.evidence_items.evidence_direction # civic_evidence_level: civic.evidence_items.evidence_level # civic_evidence_type: civic.evidence_items.evidence_type # ## context: variant involved was Somatic, unknown... # civic_variant_origin: civic.evidence_items.variant_origin dbsnp-rsid: DBSNP: dbsnp.rsid ## no prefix output_name: _id ## variant name dbsnp-gene: NCBIGene: dbsnp.gene.geneid ## no prefix input_name: _id ## variant name clinvar-rsid: DBSNP: clinvar.rsid ## no prefix output_name: _id ## variant name clinvar-diseaseOMIM: OMIM: clinvar.rcv.conditions.identifiers.omim ## no prefix input_name: clinvar.gene.symbol ## Node Norm doesn't recognize all NCBIGene IDs ## commenting out because data-processing / biolink-modeling issues # ## edge attributes # clinvar_clinical_significance: clinvar.rcv.clinical_significance ## similar to relation # variant_rsid: dbsnp.rsid ## no prefix # clinvar_submission_last_evaluated: clinvar.rcv.last_evaluated ## gives a date yyyy-mm-dd # clinvar_num_submitters: clinvar.rcv.number_submitters # clinvar_variant_origin: clinvar.rcv.origin # clinvar_review_status: clinvar.rcv.review_status clinvar-diseaseORPHANET: ORPHANET: clinvar.rcv.conditions.identifiers.orphanet ## no prefix input_name: clinvar.gene.symbol clinvar-diseaseMONDO: MONDO: clinvar.rcv.conditions.identifiers.mondo ## HAS PREFIX (MONDO) input_name: clinvar.gene.symbol clinvar-diseaseMESH: MESH: clinvar.rcv.conditions.identifiers.mesh ## no prefix input_name: clinvar.gene.symbol clinvar-phenoHP: HP: clinvar.rcv.conditions.identifiers.human_phenotype_ontology ## HAS PREFIX input_name: clinvar.gene.symbol clinvar-gene-variant-start: NCBIGene: clinvar.gene.id ## no prefix input_name: _id ## variant name clinvar-variantDiseaseOMIM: OMIM: clinvar.rcv.conditions.identifiers.omim ## no prefix input_name: _id ## variant name ## commenting out because data-processing / biolink-modeling issues # ## edge attributes # clinvar_clinical_significance: clinvar.rcv.clinical_significance ## similar to relation # clinvar_variant_in_gene: clinvar.gene.symbol ## context: gene # clinvar_submission_last_evaluated: clinvar.rcv.last_evaluated ## gives a date yyyy-mm-dd # clinvar_num_submitters: clinvar.rcv.number_submitters # clinvar_variant_origin: clinvar.rcv.origin # clinvar_review_status: clinvar.rcv.review_status clinvar-variantDiseaseORPHANET: ORPHANET: clinvar.rcv.conditions.identifiers.orphanet ## no prefix input_name: _id ## variant name clinvar-variantDiseaseMONDO: MONDO: clinvar.rcv.conditions.identifiers.mondo ## HAS PREFIX input_name: _id ## variant name clinvar-variantDiseaseMESH: MESH: clinvar.rcv.conditions.identifiers.mesh ## no prefix input_name: _id ## variant name clinvar-variantPhenoHP: HP: clinvar.rcv.conditions.identifiers.human_phenotype_ontology ## HAS PREFIX input_name: _id ## variant name clinvar-gene: NCBIGene: clinvar.gene.id ## no prefix output_name: clinvar.gene.symbol ## Node Norm doesn't recognize all NCBIGene IDs ## not included: ## - cgi: only 323 records, doesn't have IDs for disease, gene, or drug ID... ## - cosmic: only seems to connect variants to tissue they were found in, but no IDs for the tissue... ## - dbnsfp.clinvar: overlap with clinvar section? ## missing indexing for omim, orphanet IDs have ORPHA000 format... ## - dbnsfp.ensembl.geneid: very repetitive for some reason... ## - dbnsfp.gtex.tissue: string, no IDs... ## - docm: Chunlei said not to annotate this data. It's a very old tool doing variant impact prediction ## - grasp.publication.phenotype: looks like curation of publications for variants / phenotypes. string, no IDs... ## - gwassnps.trait: looks like curation of publications for variants / phenotypes. string, no IDs... x-bte-kgs-operations: ## CIVIC: ## knowledge_level / agent_type: appears to be heavily manually-curated ## see https://www.nature.com/articles/ng.3774 (and website https://civicdb.org/) ## data seems to be connecting variant-disease, sometimes with a drug (although that drug may not have an ID) ## having a drug means looking at drug response (given the disease...) ## However, the civic variant IDs don't seem to be easily mapped... ## The variants are mapped to their genes: 2648 records total, all have entrez_id field... ## - not including ## - civic assertions (only 30 variant records https://myvariant.info/v1/query?q=_exists_:%22civic.assertions%22) ## - civic evidence_items.phenotypes: 598 records, some seem to repeat the disease info ## - civic variant_groups: 129 records, not clear how to structure / what the relationship is ## civic data currently not in hg38: ## https://myvariant.info/v1/metadata/fields?assembly=hg38 ## https://docs.myvariant.info/en/latest/doc/data.html?highlight=hg19#data-sources civic-geneDisease: - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: civic.entrez_id outputs: - id: DOID semantic: Disease ## out of 2648 civic records, most (2610) have the doid disease field...only some have dbsnp.rsid... parameters: ## most fields below are categorical variables ## description is free text, Disease ID has prefix (DOID), variant ID is CIVIC (no prefix) ## only some records have drug information, and only some drugs have NCIT IDs ## commenting out because data-processing / biolink-modeling issues # fields: civic.evidence_items fields: >- civic.evidence_items.disease.doid, civic.evidence_items.source.pubmed, civic.evidence_items.source.clinical_trials.nct_id size: 1000 ## note size limit; added just in case assembly: hg19 predicate: affects source: "infores:civic" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/civic-geneDisease" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22 testExamples: - qInput: "NCBIGene:1956" ## EGFR oneOutput: "DOID:3910" ## Lung Adenocarcinoma aka MONDO:0005061 civic-geneDisease-rev: - supportBatch: true useTemplating: true inputs: - id: DOID semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## HAS PREFIX scopes: civic.evidence_items.disease.doid outputs: - id: NCBIGene semantic: Gene parameters: fields: civic.entrez_id ## no prefix size: 1000 assembly: hg19 predicate: affected_by source: "infores:civic" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/civic-geneOnly" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22 testExamples: - qInput: "DOID:9256" ## Colorectal Cancer aka MONDO:0005575 oneOutput: "NCBIGene:5290" ## PIK3CA civic-variantDisease: ## out of 2648 civic records, only some (653) have the doid disease field... - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: DOID semantic: Disease parameters: ## most fields below are categorical variables ## description is free text, Disease ID has prefix (DOID), variant ID is CIVIC (no prefix) ## only some records have drug information, and only some drugs have NCIT IDs ## using entrez gene name for now (human-readable) rather than id ## commenting out because data-processing / biolink-modeling issues # fields: >- # civic.evidence_items, # civic.entrez_name, # _id fields: >- civic.evidence_items.disease.doid, _id, civic.evidence_items.source.pubmed, civic.evidence_items.source.clinical_trials.nct_id size: 1000 ## note size limit; added just in case assembly: hg19 predicate: affects source: "infores:civic" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/civic-variantDisease" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22%20AND%20_exists_:%22dbsnp.rsid%22 testExamples: - qInput: "DBSNP:rs121913521" ## chr4:g.55593613T>G in KIT oneOutput: "DOID:9253" ## Gastrointestinal Stromal Tumor aka MONDO:0011719 civic-variantDisease-rev: - supportBatch: true useTemplating: true inputs: - id: DOID semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## HAS PREFIX scopes: civic.evidence_items.disease.doid outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 ## note size limit; added just in case assembly: hg19 predicate: affected_by source: "infores:civic" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22%20AND%20_exists_:%22dbsnp.rsid%22 testExamples: - qInput: "DOID:2671" ## Transitional Cell Carcinoma aka MONDO:0006474 oneOutput: "DBSNP:rs1057519803" ## chr12:g.56481922G>A in ERBB3 dbsnp-variantGene: ## knowledge_level / agent_type: gene assignments seem to happen in automated build process ## https://www.ncbi.nlm.nih.gov/books/NBK21088/#_ch5_ch5_s4_ ## note: there may be redundant results in the response ## there are 741 million records for hg38 - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: NCBIGene semantic: Gene parameters: fields: dbsnp.gene.geneid,_id ## no prefix size: 1000 assembly: hg38 predicate: is_sequence_variant_of source: "infores:dbsnp" knowledge_level: knowledge_assertion agent_type: automated_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-gene" ## https://myvariant.info/v1/query?q=_exists_:%22dbsnp.rsid%22%20AND%20_exists_:%22dbsnp.gene.geneid%22&fields=dbsnp&assembly=hg38 testExamples: - qInput: "DBSNP:rs770112667" ## chr10:g.14218676G>A (diff for hg19) oneOutput: "NCBIGene:55691" ## FRMD4A dbsnp-variantGene-rev: - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.gene.geneid outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 assembly: hg38 predicate: has_sequence_variant source: "infores:dbsnp" knowledge_level: knowledge_assertion agent_type: automated_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" ## https://myvariant.info/v1/query?q=_exists_:%22dbsnp.rsid%22%20AND%20_exists_:%22dbsnp.gene.geneid%22 testExamples: - qInput: "NCBIGene:102724392" ## LINC02197 oneOutput: "DBSNP:rs188861200" ## chr5:g.71414410C>T (diff for hg19) ## CLINVAR ## knowledge_level / agent_type: data going in seems to be manually-curated ## https://www.ncbi.nlm.nih.gov/clinvar/docs/datasources/ clinvar-variantGene: ## possibly redundant, with all hg38 clinvar data already covered by hg38 dbsnp.rsid <-> gene... ## > 822k records for hg38 - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rsid outputs: - id: NCBIGene semantic: Gene parameters: fields: clinvar.gene.id,_id ## no prefix size: 1000 assembly: hg38 predicate: is_sequence_variant_of source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene-variant-start" testExamples: - qInput: "DBSNP:rs794727661" ## chrX:g.32343175_32343176dup (diff for hg19) oneOutput: "NCBIGene:1756" ## DMD clinvar-variantGene-rev: - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.gene.id outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: clinvar.rsid,_id ## no prefix size: 1000 assembly: hg38 predicate: has_sequence_variant source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-rsid" testExamples: - qInput: "NCBIGene:9231" ## DLG5 oneOutput: "DBSNP:rs200237878" ## chr10:g.77811216G>A ## clinvar disease ID info: ## - some conditions have no IDs, some have multiple IDs (not all have OMIM). ## - omim: 987390 (no prefix) ## - orphanet: 826717 (no prefix) ## - human_phenotype_ontology: 141752 ## - efo: 5236, has EFO_000 format (not ID or CURIE) ## - medgen: 2162595, but I don't think SRI ID resolver supports this... ## - not indexed yet: mesh, mondo clinvar-gene-diseaseOMIM: ## 986988 records for hg38 ## (987068 - 986988 = 80 records have the omim field but lack the gene field) - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.gene.id outputs: - id: OMIM semantic: Disease parameters: ## most should have dbsnp.rsid ID (see above) ## commenting out because data-processing / biolink-modeling issues # fields: >- # clinvar.rcv.conditions.identifiers.omim, # clinvar.rcv.clinical_significance, # dbsnp.rsid, # clinvar.rcv.last_evaluated, # clinvar.rcv.number_submitters, # clinvar.rcv.origin, # clinvar.rcv.review_status fields: clinvar.rcv.conditions.identifiers.omim,clinvar.gene.symbol size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to ## clinical significance is like a relation: ## Uncertain significance, Pathogenic, Likely pathogenic, other source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseOMIM" testExamples: - qInput: "NCBIGene:55806" ## HR oneOutput: "OMIM:209500" ## Atrichia with papular lesions (APL) aka MONDO:0008847 clinvar-gene-diseaseORPHANET: ## see original operation clinvar-gene-diseaseOMIM notes ## 826439 records for hg38 ## (826456 - 826439 = 17 records have the orphanet field but lack the gene field) - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.gene.id outputs: - id: ORPHANET semantic: Disease parameters: fields: clinvar.rcv.conditions.identifiers.orphanet,clinvar.gene.symbol size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseORPHANET" testExamples: - qInput: "NCBIGene:106099062" ## LOC106099062 oneOutput: "ORPHANET:848" ## beta Thalassemia (BTHAL) aka MONDO:0019402 clinvar-gene-diseaseMONDO: ## see original operation clinvar-gene-diseaseOMIM notes ## 1133095 records ## (1133285 - 1133095 = 190 records have the MONDO field but lack the gene field) - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.gene.id outputs: - id: MONDO semantic: Disease parameters: fields: clinvar.rcv.conditions.identifiers.mondo,clinvar.gene.symbol size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseMONDO" ## https://myvariant.info/v1/query?q=_exists_:clinvar.rcv.conditions.identifiers.mondo%20AND%20NOT%20(_exists_:clinvar.rcv.conditions.identifiers.mesh%20OR%20_exists_:clinvar.rcv.conditions.identifiers.omim%20%20OR%20_exists_:clinvar.rcv.conditions.identifiers.orphanet)%20AND%20_exists_:clinvar.gene%20AND%20clinvar.rcv.clinical_significance:Pathogenic&fields=clinvar,dbsnp.rsid testExamples: - qInput: "NCBIGene:3897" ## L1CAM oneOutput: "MONDO:0017140" ## L1 syndrome clinvar-gene-diseaseMESH: ## see original operation clinvar-gene-diseaseOMIM notes ## 558108 records for hg38 ## (558199 - 558108 = 91 records have the MESH field but lack the gene field) - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.gene.id outputs: - id: MESH semantic: Disease parameters: fields: clinvar.rcv.conditions.identifiers.mesh,clinvar.gene.symbol size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseMESH" testExamples: - qInput: "NCBIGene:4359" ## MPZ oneOutput: "MESH:D030342" ## Inborn genetic diseases, aka MONDO:0003847 hereditary disease clinvar-gene-phenoHP: ## see original operation clinvar-gene-diseaseOMIM notes ## 141412 records ## (141595 - 141412 = 183 records have the hp field but lack the gene field) - supportBatch: true useTemplating: true inputs: - id: NCBIGene semantic: Gene requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.gene.id outputs: - id: HP semantic: PhenotypicFeature parameters: fields: clinvar.rcv.conditions.identifiers.human_phenotype_ontology,clinvar.gene.symbol size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-phenoHP" testExamples: - qInput: "NCBIGene:5314" ## PKHD1 oneOutput: "HP:0004719" ## Hyperechogenic kidneys clinvar-gene-diseaseOMIM-rev: - supportBatch: true useTemplating: true inputs: - id: OMIM semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rcv.conditions.identifiers.omim outputs: - id: NCBIGene semantic: Gene parameters: fields: clinvar.gene.id,clinvar.gene.symbol size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" testExamples: - qInput: "OMIM:615592" ## Immunodeficiency 15 (IMD15B) oneOutput: "NCBIGene:3551" ## IKBKB clinvar-gene-diseaseORPHANET-rev: - supportBatch: true useTemplating: true inputs: - id: ORPHANET semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rcv.conditions.identifiers.orphanet outputs: - id: NCBIGene semantic: Gene parameters: fields: clinvar.gene.id,clinvar.gene.symbol size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" testExamples: - qInput: "ORPHANET:827" ## Stargardt disease (FFM) oneOutput: "NCBIGene:5961" ## PRPH2 clinvar-gene-diseaseMONDO-rev: - supportBatch: true useTemplating: true inputs: - id: MONDO semantic: Disease requestBody: body: q: "{{ queryInputs | replPrefix('MONDO') }}" ## HAS PREFIX scopes: clinvar.rcv.conditions.identifiers.mondo outputs: - id: NCBIGene semantic: Gene parameters: fields: clinvar.gene.id,clinvar.gene.symbol size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" testExamples: - qInput: "MONDO:0001464" ## Sigmoid colon cancer oneOutput: "NCBIGene:4436" ## MSH2 clinvar-gene-diseaseMESH-rev: - supportBatch: true useTemplating: true inputs: - id: MESH semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rcv.conditions.identifiers.mesh outputs: - id: NCBIGene semantic: Gene parameters: fields: clinvar.gene.id,clinvar.gene.symbol size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" testExamples: - qInput: "MESH:D003123" ## Hereditary nonpolyposis colorectal neoplasms / Lynch syndrome oneOutput: "NCBIGene:4292" ## MLH1 clinvar-gene-phenoHP-rev: - supportBatch: true useTemplating: true inputs: - id: HP semantic: PhenotypicFeature requestBody: body: q: "{{ queryInputs | replPrefix('HP') }}" ## HAS PREFIX scopes: clinvar.rcv.conditions.identifiers.human_phenotype_ontology outputs: - id: NCBIGene semantic: Gene parameters: fields: clinvar.gene.id,clinvar.gene.symbol size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" testExamples: - qInput: "HP:0000105" ## Enlarged kidney oneOutput: "NCBIGene:5314" ## PKHD1 clinvar-variant-diseaseOMIM: ## using dbsnp.rsid rather than clinvar.rsid field, because more records have dbsnp.rsid... ## 858244 records ## (987068 total, so >86% of records have dbsnp.rsid field) - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: OMIM semantic: Disease parameters: ## using gene symbol rather than gene.id so it's human-readable ## commenting out because data-processing / biolink-modeling issues # fields: >- # clinvar.rcv.conditions.identifiers.omim, # _id, # clinvar.rcv.clinical_significance, # clinvar.gene.symbol, # clinvar.rcv.last_evaluated, # clinvar.rcv.number_submitters, # clinvar.rcv.origin, # clinvar.rcv.review_status fields: clinvar.rcv.conditions.identifiers.omim,_id size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to ## clinical significance is like a relation: ## Uncertain significance, Pathogenic, Likely pathogenic, other source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseOMIM" ## https://myvariant.info/v1/query?q=_exists_:%22clinvar.rcv.conditions.identifiers.omim%22%20AND%20_exists_:%22dbsnp.rsid%22 testExamples: - qInput: "DBSNP:rs1193171808" ## chr8:g.42314329A>G oneOutput: "OMIM:615592" ## MONDO:0014267 / severe combined immunodeficiency due to IKK2 deficiency clinvar-variant-diseaseORPHANET: ## see original operation clinvar-variant-diseaseOMIM notes ## 719970 records ## (826456 total, so >87% of records have dbsnp.rsid field) - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: ORPHANET semantic: Disease parameters: fields: clinvar.rcv.conditions.identifiers.orphanet,_id size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseORPHANET" testExamples: - qInput: "DBSNP:rs1554270834" ## chr6:g.42722069_42722076del oneOutput: "ORPHANET:827" ## Stargardt disease (FFM) / MONDO:0019353 clinvar-variant-diseaseMONDO: ## see original operation clinvar-variant-diseaseOMIM notes ## 973693 records ## (1133285 total, so >85% of records have dbsnp.rsid field) - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: MONDO semantic: Disease parameters: fields: clinvar.rcv.conditions.identifiers.mondo,_id size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseMONDO" testExamples: - qInput: "DBSNP:rs1860418734" ## chr10:g.87952157T>G oneOutput: "MONDO:0017623" ## PTEN hamartoma tumor syndrome (PHTS) clinvar-variant-diseaseMESH: ## see original operation clinvar-variant-diseaseOMIM notes ## 472287 records ## (558199 total, so >84% of records have dbsnp.rsid field) - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: MESH semantic: Disease parameters: fields: clinvar.rcv.conditions.identifiers.mesh,_id size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseMESH" testExamples: - qInput: "DBSNP:rs1554897280" ## chr10:g.87925558G>A oneOutput: "MESH:D009386" ## MONDO:0015356 / Hereditary cancer-predisposing syndrome / hereditary neoplastic syndrome clinvar-variant-phenoHP: ## see original operation clinvar-variant-diseaseOMIM notes ## 125085 records ## (141595 total, so >88% of records have dbsnp.rsid field) - supportBatch: true useTemplating: true inputs: - id: DBSNP semantic: SequenceVariant requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: dbsnp.rsid outputs: - id: HP semantic: PhenotypicFeature parameters: fields: clinvar.rcv.conditions.identifiers.human_phenotype_ontology,_id size: 1000 ## note size limit; added just in case assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantPhenoHP" testExamples: - qInput: "DBSNP:rs367947846" ## chr11:g.47346298G>T oneOutput: "HP:0001638" ## Cardiomyopathy (CMYO) / MONDO:0004994 clinvar-variant-diseaseOMIM-rev: - supportBatch: true useTemplating: true inputs: - id: OMIM semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rcv.conditions.identifiers.omim outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" testExamples: - qInput: "OMIM:602629" ## Torsion dystonia 6 (DYT6) oneOutput: "DBSNP:rs1480200060" ## chr8:g.42837127T>C clinvar-variant-diseaseORPHANET-rev: - supportBatch: true useTemplating: true inputs: - id: ORPHANET semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rcv.conditions.identifiers.orphanet outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" testExamples: - qInput: "ORPHANET:848" ## beta Thalassemia (BTHAL) oneOutput: "DBSNP:rs33956879" ## chr11:g.5226928A>C clinvar-variant-diseaseMONDO-rev: - supportBatch: true useTemplating: true inputs: - id: MONDO semantic: Disease requestBody: body: q: "{{ queryInputs | replPrefix('MONDO') }}" ## HAS PREFIX scopes: clinvar.rcv.conditions.identifiers.mondo outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" testExamples: - qInput: "MONDO:0016268" ## Papillary carcinoma of the corpus uteri oneOutput: "DBSNP:rs398123231" ## chr2:g.47804948C>G clinvar-variant-diseaseMESH-rev: - supportBatch: true useTemplating: true inputs: - id: MESH semantic: Disease requestBody: body: q: "{{ queryInputs }}" ## no prefix scopes: clinvar.rcv.conditions.identifiers.mesh outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" testExamples: - qInput: "MESH:D003123" ## Hereditary nonpolyposis colorectal neoplasms / Lynch syndrome oneOutput: "DBSNP:rs398123231" ## chr2:g.47804948C>A clinvar-variant-phenoHP-rev: - supportBatch: true useTemplating: true inputs: - id: HP semantic: PhenotypicFeature requestBody: body: q: "{{ queryInputs | replPrefix('HP') }}" ## HAS PREFIX scopes: clinvar.rcv.conditions.identifiers.human_phenotype_ontology outputs: - id: DBSNP semantic: SequenceVariant parameters: fields: dbsnp.rsid,_id size: 1000 ## note size limit assembly: hg38 predicate: related_to source: "infores:clinvar" knowledge_level: knowledge_assertion agent_type: manual_agent response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" testExamples: - qInput: "HP:0011040" ## Abnormal intrahepatic bile duct morphology oneOutput: "DBSNP:rs727504096" ## chr6:g.52079920G>A