HDR FHIR API

GET MolecularSequence Resource Bundle

get

/oracle-fhir-server/fhir/MolecularSequence

This endpoint supports the retrieval of MolecularSequence resource list.It returns Bundle of MolecularSequence resource.

Request

Query Parameters

_format(optional): string
_id(optional): string

The ID of the resource
_language(optional): string

The language of the resource
chromosome(optional): string

Chromosome number of the reference sequence
chromosome-variant-coordinate(optional): string

Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
chromosome-window-coordinate(optional): string

Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
identifier(optional): string

The unique identity for a particular sequence
patient(optional): string

The subject that the observation is about
referenceseqid(optional): string

Reference Sequence of the sequence
referenceseqid-variant-coordinate(optional): string

Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
referenceseqid-window-coordinate(optional): string

Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
type(optional): string

Amino Acid Sequence/ DNA Sequence / RNA Sequence
variant-end(optional): number

End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.
variant-start(optional): number

Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.
window-end(optional): number

End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.
window-start(optional): number

Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.

Response

200 Response

Success

Root Schema : schema

Type: array

Show Source

Array of: object MolecularSequence

{
    "type":"array",
    "items":{
        "$ref":"#/definitions/MolecularSequence"
    }
}

Nested Schema : MolecularSequence

Type: object

Show Source

coordinateSystem: number
id: string

Minimum Length: 1
meta: object Account_meta
patient: object Account_coverage
referenceSeq: object MolecularSequence_referenceSeq
repository: array repository

Minimum Number of Items: 1

Unique Items Required: true
resourceType: string

Minimum Length: 1
text: object Account_text
type: string

Minimum Length: 1
variant: array variant

Minimum Number of Items: 1

Unique Items Required: true

{
    "type":"object",
    "required":[
        "coordinateSystem",
        "id",
        "meta",
        "patient",
        "referenceSeq",
        "repository",
        "resourceType",
        "text",
        "type",
        "variant"
    ],
    "properties":{
        "resourceType":{
            "type":"string",
            "minLength":1
        },
        "id":{
            "type":"string",
            "minLength":1
        },
        "text":{
            "$ref":"#/definitions/Account_text"
        },
        "type":{
            "type":"string",
            "minLength":1
        },
        "coordinateSystem":{
            "type":"number"
        },
        "patient":{
            "$ref":"#/definitions/Account_coverage"
        },
        "referenceSeq":{
            "$ref":"#/definitions/MolecularSequence_referenceSeq"
        },
        "variant":{
            "type":"array",
            "uniqueItems":true,
            "items":{
                "$ref":"#/definitions/MolecularSequence_variant"
            },
            "minItems":1
        },
        "repository":{
            "type":"array",
            "uniqueItems":true,
            "items":{
                "$ref":"#/definitions/MolecularSequence_repository"
            },
            "minItems":1
        },
        "meta":{
            "$ref":"#/definitions/Account_meta"
        }
    },
    "description":""
}

Nested Schema : Account_meta

Type: object

Show Source

tag: array tag

Minimum Number of Items: 1

Unique Items Required: true

{
    "required":[
        "tag"
    ],
    "properties":{
        "tag":{
            "type":"array",
            "uniqueItems":true,
            "items":{
                "$ref":"#/definitions/Account_type_coding"
            },
            "minItems":1
        }
    }
}

Nested Schema : Account_coverage

Type: object

Show Source

reference: string

Minimum Length: 1

{
    "required":[
        "reference"
    ],
    "properties":{
        "reference":{
            "type":"string",
            "minLength":1
        }
    }
}

Nested Schema : MolecularSequence_referenceSeq

Type: object

Show Source

referenceSeqId: object Basic_code
strand: string

Minimum Length: 1
windowEnd: number
windowStart: number

{
    "required":[
        "referenceSeqId",
        "strand",
        "windowEnd",
        "windowStart"
    ],
    "properties":{
        "referenceSeqId":{
            "$ref":"#/definitions/Basic_code"
        },
        "strand":{
            "type":"string",
            "minLength":1
        },
        "windowStart":{
            "type":"number"
        },
        "windowEnd":{
            "type":"number"
        }
    }
}

Nested Schema : repository

Type: array

Minimum Number of Items: 1

Unique Items Required: true

Show Source

Array of: object MolecularSequence_repository

{
    "type":"array",
    "uniqueItems":true,
    "items":{
        "$ref":"#/definitions/MolecularSequence_repository"
    },
    "minItems":1
}

Nested Schema : Account_text

Type: object

Show Source

div: string

Minimum Length: 1
status: string

Minimum Length: 1

{
    "required":[
        "div",
        "status"
    ],
    "properties":{
        "status":{
            "type":"string",
            "minLength":1
        },
        "div":{
            "type":"string",
            "minLength":1
        }
    }
}

Nested Schema : variant

Type: array

Minimum Number of Items: 1

Unique Items Required: true

Show Source

Array of: object MolecularSequence_variant

{
    "type":"array",
    "uniqueItems":true,
    "items":{
        "$ref":"#/definitions/MolecularSequence_variant"
    },
    "minItems":1
}

Nested Schema : tag

Type: array

Minimum Number of Items: 1

Unique Items Required: true

Show Source

Array of: object Account_type_coding

{
    "type":"array",
    "uniqueItems":true,
    "items":{
        "$ref":"#/definitions/Account_type_coding"
    },
    "minItems":1
}

Nested Schema : Account_type_coding

Type: object

Show Source

code: string

Minimum Length: 1
display: string

Minimum Length: 1
system: string

Minimum Length: 1

{
    "required":[
        "code",
        "display",
        "system"
    ],
    "properties":{
        "system":{
            "type":"string",
            "minLength":1
        },
        "code":{
            "type":"string",
            "minLength":1
        },
        "display":{
            "type":"string",
            "minLength":1
        }
    }
}

Nested Schema : Basic_code

Type: object

Show Source

coding: array coding

Minimum Number of Items: 1

Unique Items Required: true

{
    "required":[
        "coding"
    ],
    "properties":{
        "coding":{
            "type":"array",
            "uniqueItems":true,
            "items":{
                "$ref":"#/definitions/ActivityDefinition_code"
            },
            "minItems":1
        }
    }
}

Nested Schema : coding

Type: array

Minimum Number of Items: 1

Unique Items Required: true

Show Source

Array of: object ActivityDefinition_code

{
    "type":"array",
    "uniqueItems":true,
    "items":{
        "$ref":"#/definitions/ActivityDefinition_code"
    },
    "minItems":1
}

Nested Schema : ActivityDefinition_code

Type: object

Show Source

code: string

Minimum Length: 1
system: string

Minimum Length: 1

{
    "required":[
        "code",
        "system"
    ],
    "properties":{
        "system":{
            "type":"string",
            "minLength":1
        },
        "code":{
            "type":"string",
            "minLength":1
        }
    }
}

Nested Schema : MolecularSequence_repository

Type: object

Show Source

name: string

Minimum Length: 1
type: string

Minimum Length: 1
url: string

Minimum Length: 1
variantsetId: string

Minimum Length: 1

{
    "required":[
        "name",
        "type",
        "url",
        "variantsetId"
    ],
    "properties":{
        "type":{
            "type":"string",
            "minLength":1
        },
        "url":{
            "type":"string",
            "minLength":1
        },
        "name":{
            "type":"string",
            "minLength":1
        },
        "variantsetId":{
            "type":"string",
            "minLength":1
        }
    }
}

Nested Schema : MolecularSequence_variant

Type: object

Show Source

end: number
observedAllele: string

Minimum Length: 1
referenceAllele: string

Minimum Length: 1
start: number

{
    "required":[
        "end",
        "observedAllele",
        "referenceAllele",
        "start"
    ],
    "properties":{
        "start":{
            "type":"number"
        },
        "end":{
            "type":"number"
        },
        "observedAllele":{
            "type":"string",
            "minLength":1
        },
        "referenceAllele":{
            "type":"string",
            "minLength":1
        }
    }
}