Defining Location Constraint

Definition and Information Model

Note

This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

The defining location and its associated relationships that are congruent with member locations.

Information Model

Some DefiningLocationConstraint attributes are inherited from Constraint.

Field	Flags	Type	Limits	Description
type		string	1..1	MUST be “DefiningLocationConstraint”
location		Sequence Location | iriReference	1..1
relations	⋮	MappableConcept	0..m	Defined relationships from which members relate to the defining location.
matchCharacteristic		MappableConcept	1..1	A characteristic of the location that is used to match the defining location to member locations.

Examples

The following are example implementations of DefiningLocationConstraint:

GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3

      {
         "type": "DefiningLocationConstraint",
         "location": {
            "id": "ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
            "description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
            "extensions": [
               {
                  "name": "GRCh38 1-based, inclusive interval",
                  "value": "chr7:5905831-6014161",
                  "description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
               },
               {
                  "name": "GRCh38 0-based, half-open interval",
                  "value": "chr7:5905830-6014161",
                  "description": "Genomic positions 5905830 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
               }
            ],
            "type": "SequenceLocation",
            "digest": "LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
            "sequenceReference": {
               "id": "refseq:NC_000007.14",
               "name": "NC_000007.14",
               "description": "Reference sequence for GRCh38 chromosome 7.",
               "aliases": [
                  "GRCh38:7",
                  "GRCh38:chr7",
                  "ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
               ],
               "type": "SequenceReference",
               "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
               "residueAlphabet": "na"
            },
            "start": [
               null,
               5905830
            ],
            "end": [
               6014161,
               null
            ]
         },
         "relations": [
            {
               "primaryCoding": {
                  "code": "liftover_to",
                  "system": "ga4gh-gks-term:allele-relation"
               }
            }
         ],
         "matchCharacteristic": {
            "primaryCoding": {
               "code": "is_within",
               "system": "ga4gh-gks-term:location-match"
            }
         }
      }

GRCh38 Xp22.31(chrX:6978350-7594949)x3

      {
         "type": "DefiningLocationConstraint",
         "location": {
            "id": "ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
            "description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.",
            "extensions": [
               {
                  "name": "GRCh38 1-based, inclusive interval",
                  "value": "chrX:(6978350\u20136996235)-(7564455\u20137594949)",
                  "description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation."
               },
               {
                  "name": "GRCh38 0-based, half-open interval",
                  "value": "chrX:(6978349\u20136996235)-(7564454\u20137594949)",
                  "description": "Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation."
               }
            ],
            "type": "SequenceLocation",
            "digest": "XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
            "sequenceReference": {
               "id": "refseq:NC_000023.11",
               "name": "NC_000023.11",
               "description": "Reference sequence for GRCh38 chromosome X.",
               "aliases": [
                  "GRCh38:X",
                  "GRCh38:chrX",
                  "ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
               ],
               "type": "SequenceReference",
               "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
            },
            "start": [
               6978350,
               6996235
            ],
            "end": [
               7564455,
               7594949
            ]
         },
         "relations": [
            {
               "primaryCoding": {
                  "code": "liftover_to",
                  "system": "ga4gh-gks-term:allele-relation"
               }
            }
         ],
         "matchCharacteristic": {
            "primaryCoding": {
               "code": "is_within",
               "system": "ga4gh-gks-term:location-match"
            }
         }
      }

BRAF V600

      {
         "type": "DefiningLocationConstraint",
         "location": {
            "id": "ga4gh:SL.1ReS370wzmC9PGTn13XrnG8Ot7UAKYuw",
            "description": "Amino acid position 600 within the BRAF protein (refseq:NP_004324.2), which is the protein product of the MANE Select (GRCh38) coding transcript for BRAF (refseq:NM_004333.6), corresponding to valine in the reference sequence.",
            "type": "SequenceLocation",
            "digest": "1ReS370wzmC9PGTn13XrnG8Ot7UAKYuw",
            "sequenceReference": {
               "id": "refseq:NP_004324.2",
               "name": "NP_004324.2",
               "description": "The protein product of the MANE Select (GRCh38) coding transcript for BRAF (refseq:NM_004333.6), corresponding to the Refseq protein accession NP_004324.2.",
               "aliases": [
                  "ensembl:ENSP00000288602.6",
                  "ga4gh:SQ.cQvw4UsHHRRlogxbWCB8W-mKD4AraM9y"
               ],
               "type": "SequenceReference",
               "refgetAccession": "SQ.cQvw4UsHHRRlogxbWCB8W-mKD4AraM9y",
               "residueAlphabet": "aa"
            },
            "start": 599,
            "end": 600,
            "sequence": "V"
         },
         "relations": [
            {
               "primaryCoding": {
                  "code": "translation_of",
                  "system": "http://www.sequenceontology.org",
                  "iris": [
                     "http://www.sequenceontology.org/browser/current_release/term/translation_of"
                  ]
               }
            }
         ],
         "matchCharacteristic": {
            "primaryCoding": {
               "code": "is_within",
               "system": "ga4gh-gks-term:location-match"
            }
         }

Implementation Guidance