Data Dictionary

We describe the logical data model of our database using standard relational database terminology such as table, column, and primary key. The primary key is the collection of columns in a table that uniquely identify a row in that table. Columns tagged with a (PK) symbol are part of the primary key of the table.

Table: VARIANT_TASK

Master list of tasks (categories of variant effect data).

Columns:

CODE (PK) - Unique code for each task
NAME
SOURCE_TYPE
DESCRIPTION

Table: VARIANT_DATA_SOURCE

Master list of sources of data.

Columns:

CODE (PK) - Unique code for each source
NAME
DESCRIPTION

Table: VARIANT_EFFECT_SOURCE

Master list of sources of variant effect score data. Currently all score data originates from a VEP.

Columns:

CODE (PK) - Unique code for each source
NAME
SOURCE_TYPE - Currently, all values are VEP
DESCRIPTION

Table: VARIANT

Master list of variants.

Columns:

GENOME_ASSEMBLY (PK) - Currently, hg38 for all rows.
CHROMOSOME (PK)
POSITION (PK)
REFERENCE_NUCLEOTIDE (PK)
ALTERNATE_NUCLEOTIDE (PK)
PRIOR_GENOME_ASSEMBLY
PRIOR_CHROMOSOME
PRIOR_POSITION
PRIOR_PRIOR_GENOME_ASSEMBLY
PRIOR_PRIOR_CHROMOSOME
PRIOR_PRIOR_POSITION
REFERENCE_AMINO_ACID
ALTERNATE_AMINO_ACID
AMINO_ACID_POSITION
RS_DBSNP
GENE_SYMBOL
ENSEMBL_GENE_ID
ENSEMBL_TRANSCRIPT_ID
ENSEMBL_PROTEIN_ID
ALLELE_FREQUENCY_SOURCE
ALLELE_FREQUENCY

Table: VARIANT_EFFECT_LABEL

Variant labels organized by task.

Columns:

TASK_CODE (PK)
GENOME_ASSEMBLY (PK) - Currently, hg38 for all rows.
CHROMOSOME (PK)
POSITION (PK)
REFERENCE_NUCLEOTIDE (PK)
ALTERNATE_NUCLEOTIDE (PK)
LABEL_SOURCE
RAW_LABEL
BINARY_LABEL

Table: VARIANT_EFFECT_SCORE

Variant effect prediction scores organized by task.

Columns:

TASK_CODE (PK)
GENOME_ASSEMBLY (PK) - Currently, hg38 for all rows.
CHROMOSOME (PK)
POSITION (PK)
REFERENCE_NUCLEOTIDE (PK)
ALTERNATE_NUCLEOTIDE (PK)
SCORE_SOURCE
RAW_SCORE
RANK_SCORE - Normalized score, i.e. value between 0-1

Table: VARIANT_FILTER

Table of system supplied named filters that can be used by the user to restrict the set of variants to be retrieved or to be used in a benchmarking analysis. Filters are defined in terms of a list of genes and/or variants to be included or excluded.

Columns:

CODE (PK) - Unique code for each filter
NAME
INCLUDE_GENES - Y/N, include or exclude genes listed in VARIANT_FILTER_GENE table.
INCLUDE_VARIANTS - Y/N, include or exclude variants listed in VARIANT_FILTER_VARIANT table.

Table: VARIANT_FILTER_GENE

Lists the set of genes to be included or excluded by a filter in the VARIANT_FILTER table.

Columns:

FILTER_CODE (PK) - Refers to a CODE in the variant_filter table.
GENE_SYMBOL (PK)

Table: VARIANT_FILTER_VARIANT

Lists the set of variants to be included or excluded by a filter in the VARIANT_FILTER table.

Columns:

FILTER_CODE (PK) - Refers to a CODE in the variant_filter table.
GENOME_ASSEMBLY (PK)
CHROMOSOME (PK)
POSITION (PK)
REFERENCE_NUCLEOTIDE (PK)
ALTERNATE_NUCLEOTIDE (PK)