MolecularSequence
Semantical type
The FHIR resource type is also used as semantical type of the resource. Include the FHIR resource name MolecularSequence into your applications access filter if you need to use this resource.
Resource owner
If the resource contains a patient which is a Patient or Practitioner that user is the owner of the resource. Otherwise the creator of the resource is the owner.
Default value for “patient”
If a resource with no patient field is send to MIDATA, the backend will set the patient to the current user.
Read
Read a single MolecularSequence by id.
Request:
[GET] /fhir/MolecularSequence/<id>
Read specific version
Read a specific version of a single MolecularSequence by id.
Request:
[GET] /fhir/MolecularSequence/<id>/_history/<version>
Retrieve history
Retrieve all versions of a single resource.
Request:
[GET] /fhir/MolecularSequence/<id>/_history
Search
Search for resources of type MolecularSequence
Request:
[GET] /fhir/MolecularSequence?searchParams
List of supported search parameters:
Supported query parameters:
| Name | Type | Description |
|---|---|---|
| _id | token | The ID of the resource |
| _lastUpdated | date | Only return resources which were last updated as specified by the given range |
| _page | string | |
| chromosome | token | Chromosome number of the reference sequence |
| chromosome-variant-coordinate | composite | 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 | composite | 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 | token | The unique identity for a particular sequence |
| patient | reference | The subject that the observation is about |
| referenceseqid | token | Reference Sequence of the sequence |
| referenceseqid-variant-coordinate | composite | 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 | composite | 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 | token | Amino Acid Sequence/ DNA Sequence / RNA Sequence |
| variant-end | 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 | 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 | 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 | 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. |
Create
Create a new resource of type MolecularSequence.
Request:
[POST] /fhir/MolecularSequence
Update
Updates a resource of type MolecularSequence.
Request:
[PUT] /fhir/MolecularSequence/<id>