Atomic Warehouse Model Data Model

Entity

Entity Sequence Variation Detail

Description

A location in the human genome where variations have been identified. A polymorphism such as an SNP, repetitive microsatellite, or other genomic variation.

Attributes
Base Quality Num
Chromosome Num
Chromosome Pos
Cigar String
Dbsnp Link Txt
dbSNP Membership Ind
Effective From Dt
Effective To Dt
Hapmap2 Membership Ind
Hapmap3 Membership Ind
IUPAC Nm
Load Info Sk
Membership 1000 Genomes Ind
Microsatellite Bp End Pos
Microsatellite Bp Start Pos
Original Sequence Txt
Other Variation Kb End Pos
Other Variation Kb Start Pos
Other Variation Type Code Sk
Sequence Type Code Sk
Sequence Variation Sk
SNP Variant Pos
Somatic Mutation Ind
Source Code Sk
Strand Bias
Tenant Sk
Validated Ind
Valid From Ts
Valid To Ts
Variation End Pos
Variation Region Code Sk
Variation Sequence Txt
Variation Start Pos

Relationship
Sequence Variation Detail_Sequence Variation_FK

Primary Key
Sequence Variation Detail PK

Dependencies

Reverse Dependencies

Attribute Details

Base Quality Num

Description	The base quality (RMS - Root Mean Square) of the sequence variation at this position.
Data Type	Standards - Data Domains.ddm/Data Domains/Number Integer [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Chromosome Num

Description	The chromosome where the variant is located.
Data Type	Standards - Data Domains.ddm/Data Domains/Number Integer [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Chromosome Pos

Description	The position of the variant on the chromosome.
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Cigar String

Description	Cigar string describing how to align an alternate allele to the reference allele.
Data Type	Standards - Data Domains.ddm/Data Domains/Alphanumeric [VARCHAR(80)]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Dbsnp Link Txt

Description	A link to dbSNP web URL that contains reference information on the SNP and other variations.
Data Type	Standards - Data Domains.ddm/Data Domains/Text Medium [VARCHAR(255)]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

dbSNP Membership Ind

Description	Indicates the membership of the sequence variation in the database of single nucleotide polymorphisms (SNP).
Data Type	Standards - Data Domains.ddm/Data Domains/Boolean Indicator [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Effective From Dt

Description	Establishes a period where a set of attributes are true according to the business.
Data Type	Standards - Data Domains.ddm/Data Domains/Date [DATE]
Is Part Of PrimaryKey	false
Is Required	true
Is Derived	false
Is Surrogate Key	false

Effective To Dt

Description	Ends a period of effectivity.
Data Type	Standards - Data Domains.ddm/Data Domains/Date [DATE]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Hapmap2 Membership Ind

Description	Indicates the membership of the sequence variation in the Hapmap2 Genome Browser.
Data Type	Standards - Data Domains.ddm/Data Domains/Boolean Indicator [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Hapmap3 Membership Ind

Description	Indicates the membership of the sequence variation in the Hapmap3 Genome Browser.
Data Type	Standards - Data Domains.ddm/Data Domains/Boolean Indicator [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

IUPAC Nm

Description	The International Union of Pure and Applied Chemistry (IUPAC) code for the Single Nucleotide Polymorphism (SNP).
Data Type	Standards - Data Domains.ddm/Data Domains/Name [VARCHAR(30)]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Load Info Sk

Description	The surrogate key of the load information entry describing the details regarding the loading of the row.
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key Large [LONG]
Is Part Of PrimaryKey	false
Is Required	true
Is Derived	false
Is Surrogate Key	false

Membership 1000 Genomes Ind

Description	Indicates the membership in 1000 Genomes Project.
Data Type	Standards - Data Domains.ddm/Data Domains/Boolean Indicator [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Microsatellite Bp End Pos

Description	The ending location for the tandem repeat. bp = base pair(s)—one bp corresponds to approximately 3.4 Å of length along the DNA strand. Base pair (bp): Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs For example, in ACTGTGTGCC, the first occurrence of A is 1991, but the last alphabet of the Tandem repeat [TG] in the nucleotide ends at 1998.
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Microsatellite Bp Start Pos

Description	The starting location for the tandem repeat. bp = base pair(s)—one bp corresponds to approximately 3.4 Å of length along the DNA strand. Base pair (bp): Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs For example: In ACTGTGTGCC, the first occurrence of A is 1991, but the first alphabet of the Tandem repeat [TG] in the nucleotide starts at 1993
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Original Sequence Txt

Description	Original DNA sequence of a gene.
Data Type	Standards - Data Domains.ddm/Data Domains/Text Large [VARCHAR(1024)]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Other Variation Kb End Pos

Description	The location where the variation ends. Unit of length for DNA fragments equal to 1000 nucleotides. kb (= kbp) = kilo base pairs = 1,000 bp
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Other Variation Kb Start Pos

Description	The location where the other variation starts. Unit of length for DNA fragments equal to 1000 nucleotides. kb (= kbp) = kilo base pairs = 1,000 bp
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Other Variation Type Code Sk

Description	Indicates whether it is one of the following: 1) Deletions 2) Insertions 3) Insertions/Deletions 4) Duplications 5) Inversions 6) Translocations
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Sequence Type Code Sk

Description	Indicates whether sequence variation is one of the following: 1 - Single Nucleotide Polymorphism (SNP) 2 - Microsatellite (STR) 3 - Other Variation
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Sequence Variation Sk

Description	The surrogate key for anchor Sequence Variation.
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key Large [LONG]
Is Part Of PrimaryKey	true
Is Required	true
Is Derived	false
Is Surrogate Key	false

SNP Variant Pos

Description	The position of the variant.
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Somatic Mutation Ind

Description	Indicates that the record is a somatic mutation, for cancer genomics.
Data Type	Standards - Data Domains.ddm/Data Domains/Boolean Indicator [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Source Code Sk

Description	The origin of the data identifying the actual load source, vendor, manual key entry, or context of the data in a specific row in the database.
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER]
Is Part Of PrimaryKey	false
Is Required	true
Is Derived	false
Is Surrogate Key	false

Strand Bias

Description	Strand bias at this position.
Data Type	Standards - Data Domains.ddm/Data Domains/Alphanumeric [VARCHAR(80)]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Tenant Sk

Description	The surrogate key of the entry identifying the legal owner of the data.
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER]
Is Part Of PrimaryKey	false
Is Required	true
Is Derived	false
Is Surrogate Key	false

Validated Ind

Description	Indicates that the record has been validated by follow-up experiment.
Data Type	Standards - Data Domains.ddm/Data Domains/Boolean Indicator [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Valid From Ts

Description	Establishes a period where a set of attributes are true in the source system. This would be populated with the transaction timestamp and would be used for the snapshot date.
Data Type	Standards - Data Domains.ddm/Data Domains/Timestamp [TIMESTAMP]
Is Part Of PrimaryKey	true
Is Required	true
Is Derived	false
Is Surrogate Key	false

Valid To Ts

Description	Ends a period of validity.
Data Type	Standards - Data Domains.ddm/Data Domains/Timestamp [TIMESTAMP]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Variation End Pos

Description	The ending position of the variant.
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Variation Region Code Sk

Description	Defines the variant to be in a coding region [Exon] or noncoding region [Intron] of the genome.
Data Type	Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Variation Sequence Txt

Description	Change in the DNA sequence of a gene due to sequence variations/polymorphisms.
Data Type	Standards - Data Domains.ddm/Data Domains/Text Large [VARCHAR(1024)]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Variation Start Pos

Description	The starting position of the variant.
Data Type	Standards - Data Domains.ddm/Data Domains/Position [INTEGER]
Is Part Of PrimaryKey	false
Is Required	false
Is Derived	false
Is Surrogate Key	false

Relationship Details

Sequence Variation Detail_Sequence Variation_FK

Is Identifying Relationship	true
Child Table	Sequence Variation Detail
Child Multiplicity	ZERO_TO_MANY
Child Referential Integrity: On Delete	NONE
Child Referential Integrity: On Insert	NONE
Child Referential Integrity: On Update	NONE
Parent Table	Sequence Variation
Parent Multiplicity	ONE
Parent Referential Integrity: On Delete	NONE
Parent Referential Integrity: On Insert	NONE
Parent Referential Integrity: On Update	NONE

Primary Key Details

Sequence Variation Detail PK

Key Attribute	Sequence Variation Sk
Key Attribute	Valid From Ts

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Atomic Warehouse Model Data Model