|
|
Attribute: Analysis_Criteria
Attribute details:
| Entity name | Analysis |
| Description | If the criteria to perform an Analysis are described in a Study, they are captured here. E.g. parameters set in an Analysis Tool. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Analysis_Description
Attribute details:
| Entity name | Analysis |
| Description | This field captures a brief description of the Analysis employed in a Study. This information is not always provided in a Study.
Note: specific criteria used during the Analysis should be captured in the 'Analysis_Criteria' field and a general description captured in this field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Analysis_ID
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This is the unique identifer for one Analysis performed within a Study.
This can be used to cross-reference one record in the 'Analysis' table. |
| Primary key | No |
| Refers to | Analysis_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Analysis_ID
Attribute details:
| Entity name | Analysis |
| Description | This is the unique database identifer for one Analysis performed within a Study. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Analysis_Number
Attribute details:
| Entity name | Analysis |
| Description | This is a sequential number assigned to each Analysis employed in a Study. This value is not unique in this table or across the database.
For example, if five Analyses were employed in a Study, each Analysis (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Analysis_Tool
Attribute details:
| Entity name | Analysis |
| Description | This field captures the name of the Analysis Tool employed in a given Analysis.
Examples of Analysis Tools are "Birdsuite", "CNAG", "Genemapper". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Analysis_Tool_Description
Attribute details:
| Entity name | Analysis |
| Description | This is a description of the Analysis Tool that was used in a given Study. This information is not always provided for an Analysis Tool. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Analysis_Tool_Type
Attribute details:
| Entity name | Analysis |
| Description | This field captures whether an Analysis Tool is an Algorithm or a Software Suite. This information is not always provided for a given Analysis Tool in a Study; DGVa and dbVar currently do not capture this information. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Analysis_Tool_Version
Attribute details:
| Entity name | Analysis |
| Description | This is a version number for the Analysis Tool that was used in a given Study. This information is not always provided for an Analysis Tool. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Analysis_Type
Attribute details:
| Entity name | Analysis |
| Description | If this information is provided, the Analysis Type will be captured in this field; this information is not always provided in a Study.
An example of an Analysis Type is "split-read mapping". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: ArrayExpress_Accession_Num
Attribute details:
| Entity name | Platform_Study |
| Description | This field will capture the identifier/accession number that represents a given Platform within the ArrayExpress data repository. This information is not always provided in a Study.
e.g. ArrayExpress accession number, A-AFFY-65 |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Biological_Source
Attribute details:
| Entity name | Sample |
| Description | This field captures a brief description of the Biological Source of a Sample.
For example, the 'Biological_Source' could be "cell line", "blood", "tissue" etc.
Please note how this field relates to the 'Source_Type' field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Calculated_Frequency
Attribute details:
| Entity name | Variant_Type |
| Description | This field will serve as a placeholder in the case that DGV develops a frequency calculation step in the automated DGV-curation pipeline.
This is a frequency that would be calculated during the DGV data curation process. In cases where no 'Reported_Frequency' is available, a Calculated Frequency may be derived from other information that was reported in a Study.
The 'Calculated_Frequency' has an additional descriptor ('Calc_Frequency_Qualifier') to distinguish between the frequency as being "type" (number of Gains or Losses within a Study or Cohort) or "allele" (frequency of the allele in a Variant set). |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Calc_Frequency_Qualifier
Attribute details:
| Entity name | Variant_Type |
| Description | This field will serve as a placeholder in the case that DGV develops a frequency calculation step in the automated DGV-curation pipeline.
The 'Calc_Frequency_Qualifier' is an additional descriptor of 'Calculated_Frequency' to distinguish between the frequency as being either:
"type" = number of Gains or Losses within a Study or Cohort OR
"allele" = frequency of the allele in a Variant set
This is a value that is assigned during the DGV data curation process. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Case_or_Control
Attribute details:
| Entity name | Sample_Study |
| Description | This field will capture whether a Sample is a Case or a Control in a Study. This field will not always be populated.
Note that for the current DGV only Controls, or healthy individuals, are part of the database. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Chromosome
Attribute details:
| Entity name | Coverage |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Chromosome_Length
Attribute details:
| Entity name | Coverage |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | BIGINT |
| Domain | |
Constraints:
Attribute: Chromosome_Number
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the primary Chromosome on which a Translocation Variant has been discovered.
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Chromosome_Number
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the primary Chromosome on which a Variant has been mapped.
The 'Chromosome_B_Number' captures the secondary Chromosome on which a Variant has been discoverd, for example, in the case of a translocation. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Chromosome_Random_Num
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field is to capture coordinates for variants that cannot be mapped on a chromosome but for which we know to what chromosome the variant belongs. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Chromosome_Random_Num
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field is to capture coordinates for variants that cannot be mapped on a chromosome but for which we know to what chromosome the variant belongs. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Cohort_Description
Attribute details:
| Entity name | Cohort |
| Description | This is a short description of the Cohort (within a Study).
For example, the description can include details about what is common among the individuals within the Cohort, such as details about gender, age, etc. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Cohort_ID
Attribute details:
| Entity name | Sample |
| Description | This is the Cohort to which a Sample belongs. This field may not be populated.
A Sample could belong to a commonly referenced Cohort such as HapMap or the Human Genome Diversity Panel. A Sample could also belong to a Cohort within a specific Study. |
| Primary key | No |
| Refers to | Cohort_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Cohort_ID
Attribute details:
| Entity name | Cohort |
| Description | This is the unique identifier for one Cohort that is in the DGV. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Cohort_Name
Attribute details:
| Entity name | Variant |
| Description | This is the Cohort to which a Variant belongs; this information may or may not be provided in a Study. This information is more commonly found in the Sample related tables ('Sample', 'Sample_Xref') but could also be captured here in cases when a Variant is reported with no associated Sample.
Examples of Cohorts are "HapMap" or "Human Genome Diversity Project". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Cohort_Name
Attribute details:
| Entity name | Sample_Xref |
| Description | This is the Cohort to which a Sample belongs; this information may or may not be provided in a Study.
Examples of Cohorts are "HapMap" or "Human Genome Diversity Panel/Project". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Cohort_Name
Attribute details:
| Entity name | Cohort |
| Description | This is the name given to a Cohort within a given Study.
Examples of Cohort Names are: "Human Genome Diversity Panel" or "HapMap". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Comments
Attribute details:
| Entity name | Variant |
| Description | If there is any supplemental information about a Variant that cannot be populated into any of the other fields in the 'Variant' table, that information will go here.
e.g. "does not validate experimentally" may need to be appended to/annotated for a Variant |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Comments
Attribute details:
| Entity name | Variant_Type |
| Description | If further details about the Variant Type are provided, those details could be captured in this field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Copy_Chromosome
Attribute details:
| Entity name | Copy_Number |
| Description | This is the Chromosome on which the Copy of the CNV is found. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Copy_Description
Attribute details:
| Entity name | Copy_Number |
| Description | This is a desription of the structure, or composition of a given Copy of a CNV.
An example of a description is "inverted copy" or "copy with SNP". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Copy_End
Attribute details:
| Entity name | Copy_Number |
| Description | This is the end coordinate for the Copy. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Copy_Number
Attribute details:
| Entity name | Copy_Number |
| Description | This is the sequence number of the Copy in a given CNV.
For example, if a CNV has 5 copies, there will be five records in this table, each representing one of the Copies of that CNV. For the five records in this example , 'Copy_Number' will have the values "1", "2", "3", "4", and "5".
To find the total number of copies in one CNV, perform a query on the 'Variant' table (can use the 'Variant_ID' from this table) and get the 'Copy_Number_Count'. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Copy_Number_Count
Attribute details:
| Entity name | Variant_Type |
| Description | For Variants that are of type "CNV", this field indicates the number of copies of a Variant sequence. If information about each copy of a CNV is available, that information will be captured in the 'Copy_Number' table (1:M relationship with the 'Variant_Type' table).
This information may not be provided in a published dataset. If this information is available, the value in this field willl typically be an absolute copy number state. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Copy_Number_ID
Attribute details:
| Entity name | Copy_Number |
| Description | This uniquely identifies one Copy of a Sample Level Copy Number Variant (CNV) in the DGV. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Copy_Start
Attribute details:
| Entity name | Copy_Number |
| Description | This is the start coordinate for the Copy. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Count
Attribute details:
| Entity name | Variant_Type |
| Description | This is a value related to the Frequency of a Variant. This value is captured during DGVa/dbVar archiving and is described by DGVa/dbVar as: "Number of samples that reported the structural variant". |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Curation_Comments
Attribute details:
| Entity name | Study |
| Description | This field will capture a summary of DGV curation applied to a given Study. This information will be a summary of the DGV Filtering and Merging process.
This information will be made available on the Downloads page of the DGV website under the links to the original data ('Comments' field of the Studies' listing). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Study_File_Prefix |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | 'Y' |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Variant_Analysis |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Merged_Analysis |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Filter |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Sample_Xref |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Dataset_Xref |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Variant_Xref |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Sample_Pooled |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Variant_Mapping |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Copy_Number |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Study |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Platform_Study |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Method_Study |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Reference |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Variant |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Cohort |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Analysis |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Dataset |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Variant_Type |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y".
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Sample_Study |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Current_Record_Flag
Attribute details:
| Entity name | Sample |
| Description | This value in this field indicates whether a given record in this table is Current or not.
If the value in this field is "Y", then this is the current record. If the value in this field is "N", then there is another record in this table that has more recently been added that supersedes the previous record, or the record failed one of the quality checks in the DGV pipeline.
For example, if an error is discovered in a record and that record needs to be "overwritten" with a new, corrected record, there would be two similar, related records in the table, one with a 'Current_Record_Flag'="N" and one with 'Current_Record_Flag'="Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | Y |
Attribute: Cytoband
Attribute details:
| Entity name | Cytoband_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Dataset_Analysis_ID
Attribute details:
| Entity name | Variant_Analysis |
| Description | This uniquely identifies one Dataset that is compared to one Reference within a Study by one Analysis. |
| Primary key | No |
| Refers to | Dataset_Analysis_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_Analysis_ID
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This uniquely identifies one Dataset that is compared to one Reference within a Study by one Analysis. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_Analysis_Number
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This is a sequential number assigned to each Dataset-Analysis employed in a Study. This value is not unique in this table or across the database.
For example, if five Dataset-Analysis were employed in a Study, each Dataset-Analysis (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_Description
Attribute details:
| Entity name | Dataset |
| Description | This field captures a brief description of the Dataset analyzed in a Study. This information is currently not captured by DGVa or dbVar.
For example, if a Study is performing a re-analysis of a Dataset generated in a previous Strudy, such details would be captured in this Description field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Dataset_ID
Attribute details:
| Entity name | Dataset_Xref |
| Description | This is the unique identifer from the 'Dataset' table that represents one Dataset in the DGV.
This can be used to cross-reference one record in the 'Dataset' table. |
| Primary key | No |
| Refers to | Dataset_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_ID
Attribute details:
| Entity name | Reference |
| Description | This field uniquely represents one Dataset that was generated in one Study. |
| Primary key | No |
| Refers to | Dataset_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_ID
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This field uniquely represents one Dataset that was generated in one Study.
This can be used to cross-reference one record in the 'Dataset' table. |
| Primary key | No |
| Refers to | Dataset_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_ID
Attribute details:
| Entity name | Dataset |
| Description | This field uniquely represents one Dataset that was generated in one Study.
A Dataset is the output of examining one or more Samples on a Platform. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_ID
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This is the unique identifier from the 'Dataset' table that describes to which Dataset a given Sample, analyzed by a given Method-Platform, belongs. |
| Primary key | No |
| Refers to | Dataset_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Dataset_Name
Attribute details:
| Entity name | Dataset |
| Description | If a Name has been assigned to a Dataset within a Study, that Name would be captured here. Currently DGVa and dbVar do not capture this information. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Dataset_Number
Attribute details:
| Entity name | Dataset |
| Description | This is a sequential number assigned to each Dataset generated in a Study. This value is not unique in this table or across the database.
For example, if five Datasets were generated in a Study, each Dataset (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Dataset_Xref_ID
Attribute details:
| Entity name | Dataset_Xref |
| Description | This is the unique identifer for one mapping of a Dataset in the DGV to an external identifier. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Description
Attribute details:
| Entity name | Study |
| Description | This field will capture any other descriptors of a Study that need to be stored in the DGV.
For example, if there were special circumnstances under which a Study was performed, or if a special Pre-Publication Agreement exists, this information would be captured here. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: DGVA_Inferred_Flag
Attribute details:
| Entity name | Variant |
| Description | Some Studies do not submit sample-level calls (SSVs) to DGVa or dbVar, but rather only merged calls, or "asserted Variants" (SVs). Thus during accessioning of these Studies, DGVa or dbVar will create what DGVa calls "curated" SSVs to support the submitted SVs; DGV calls these "inferred Variants". A typical scenario in which dbVar or DGVa would created these Inferred Variants is to assign Sample IDs to a Merged Variant (one Inferred Variant per Sample ID).
In order to distinguish between SSVs that are submitted as part of a Study from SSVs that are created by DGVa/dbVar during the accessioning process, DGV has established this flag (DGVA_Inferred_Flag). If an SSV is created by DGVa/dbVar during the accessioning process, this flag will be set to "Y" (yes); if an SSV was submitted as part of a Study's data submission, this flag will be set to "N" (no). These Variants are filtered out in the DGV pipeline. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: DGV_Calculated_Size
Attribute details:
| Entity name | Translocation_Mapping |
| Description | If no Size information was reported with a Variant, the DGV-pipeline may calculate the Size of the Variant using its Start and End coordinates. This calculation is only done if determined appropriate for a given Study.
The Size is calculated as such: 'End' - 'Start' + 1 |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: DGV_Calculated_Size
Attribute details:
| Entity name | Variant_Mapping |
| Description | If no Size information was reported with a Variant, the DGV-Curation process may calculate the Size of the Variant using its Start and End coordinates. This calculation is only done if determined appropriate for a given Study.
The Size is calculated as such: 'End' - 'Start' + 1 |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: DGV_End
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field is for internal use only. This and the 'DGV_Start' field will store start and end coordinates used to determine DGV_Calculated_Size, which will be used for Filter/Merge pipeline. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: DGV_End
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field is for internal use only. This and the 'DGV_Start' field will store start and end coordinates used to determine DGV_Calculated_Size, which will be used for Filter/Merge pipeline. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: DGV_Merged_Flag
Attribute details:
| Entity name | Variant |
| Description | A value of "Y" in this field indicates that this is a Variant that was merged using the DGV-merging criteria (currently 70% reciprocal overlap). If the value in this field is blank or "N", this Variant is not a DGV-merged variant.
If the 'Supporting_Merged_Flag' = "S" and 'DGV_Merged_Flag = "N", this is a Supporting Variant that was reported in a Study. There should be no records in this table with a 'Supporting_Merged_Flag' = "S" and 'DGV_Merged_Flag = "Y". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: DGV_Start
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field is for internal use only. This and the 'DGV_End' field will store start and end coordinates used to determine DGV_Calculated_Size, which will be used for Filter/Merge pipeline. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: DGV_Start
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field is for internal use only. This and the 'DGV_End' field will store start and end coordinates used to determine DGV_Calculated_Size, which will be used for Filter/Merge pipeline. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Display_Name
Attribute details:
| Entity name | Study |
| Description | This is the common name used to refer to a Study. These names are also used by DGVa and dbVar to refer to a Study.
Examples of common names are: "Cooper et al 2008" or "Kidd et al 2008". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: End_A
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Average End Boundary of a Variant. Alternatively, if only one End Coordinate has been provided for a Variant, it will be stored here. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: End_B
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Average End Boundary of a Variant. Alternatively, if only one End Coordinate has been provided for a Variant, it will be stored here. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: End_Random
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the End coordinate that is randomly assigned to a variant that cannot be mapped to a chromosome but for which we know what chromosome the variant belongs. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: End_Random
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the End coordinate that is randomly assigned to a variant that cannot be mapped to a chromosome but for which we know what chromosome the variant belongs. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Estimated_Size
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field captures the Estimated Size of a Variant, if available. The Estimated Size will provide an approximate size, depending on the methods and resolution of the various approaches within a study.
For example, in the case where an insertion is called using a PEM strategy, the ends map to the reference at a distance less than expected by the known fragment insert size (in some studies less than 3 SD from the mean mapping size). Based on the size of the insert library (can't capture insertion larger than clone) and the SD (ability to resolve a small insertion from the inherent variability of insert sizes within that library), a max-min size can be estimated without sequencing the actual insert. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Estimated_Size
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field captures the Estimated Size of a Variant, if available. The Estimated Size will provide an approximate size, depending on the methods and resolution of the various approaches within a study.
For example, in the case where an insertion is called using a PEM strategy, the ends map to the reference at a distance less than expected by the known fragment insert size (in some studies less than 3 SD from the mean mapping size). Based on the size of the insert library (can't capture insertion larger than clone) and the SD (ability to resolve a small insertion from the inherent variability of insert sizes within that library), a max-min size can be estimated without sequencing the actual insert. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Ethnicity
Attribute details:
| Entity name | Sample |
| Description | This field captures the "Ethnicity" of a Sample.
"Ethnicity" is sometimes also referred to as "Population" and refers to the geographic origins of an individual. The use of the term 'Ethnicity' can vary between Studies.
Examples of 'Ethnicity' are: "Asian", "Yoruban", "European", "African" |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Ethnicity
Attribute details:
| Entity name | Variant |
| Description | In the case where a Variant is reported with Ethnicity information but with no corresponding Sample information, Ethnicity will be captured here. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: External_Dataset_ID
Attribute details:
| Entity name | Dataset_Xref |
| Description | A Study may give a Dataset a Name or Identifier-code; this could also be the identifier assigned by an external informaiton system (e.g. DGVa). This field will capture either one of these that has been assigned to a given Dataset. This information is currently not being captured by DGVa or dbVar.
For example, this could be an accession number, e.g. DGVa Dataset accession number, or the Dataset ID assigned in a Study, e.g. "A01". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: External_ID_Source
Attribute details:
| Entity name | Sample_Xref |
| Description | This is the original source system from which the 'External_Sample_ID' comes.
For example, this could be "DGVa" or "dbVar" or "HapMap", or the PubMed ID from a given Study, etc. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: External_ID_Source
Attribute details:
| Entity name | Dataset_Xref |
| Description | This is the original source system from which the 'External_Dataset_ID' comes. This information is currently not being captured by DGVa or dbVar.
For example, this could be "DGVa" or "dbVar", "Smith et al 2009" or a PubMed ID. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: External_ID_Source
Attribute details:
| Entity name | Variant_Xref |
| Description | This is the original source system from which the 'External_Variant_ID' comes.
For example, this could be "DGVa" or "dbVar" or a PubMed ID. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: External_ID_Type
Attribute details:
| Entity name | Sample_Xref |
| Description | This is a further qualifier for an External Sample Identifier, if any has been assigned to an external identifier.
For example, this could say "accession number" or the like. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: External_ID_Type
Attribute details:
| Entity name | Variant_Xref |
| Description | This field will capture additional information about the external identifier, if it is provided in a Study.
For example, DGVa may have a 'Variant Name'/'Submitter ID' and a 'Variant Accession Number'; this field will capture which label has been assigned to the identifier. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: External_Sample_ID
Attribute details:
| Entity name | Sample_Xref |
| Description | This field captures an exernal identifier that is used to describe a Sample that exists in the DGV.
The external identifier could be an accession number, e.g. DGVa Sample accession number, or a Common Cohort Sample ID, e.g. the HamMap Sample ID "NA11994". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: External_Variant_ID
Attribute details:
| Entity name | Variant_Xref |
| Description | This field captures an exernal identifier that is used to describe a Variant that exists in the DGV.
The external identifier could be an accession number, e.g. DGVa 'esv12345', an ID, or a Variant name, or the Variant ID assigned to a Variant within a Study (i.e. the Study's Variant ID). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Family_ID
Attribute details:
| Entity name | Sample |
| Description | This ID will represent a given Family whose data are stored in the DGV. The 'Family_ID' is submitted with a Study and not generated by the database. Thus it is possible that two different Families are assigned the same 'Family_ID', but not likely.
For example, where HapMap Samples are all from the same Family, the same 'Family_ID' will be assigned to each Family member's respective Sample. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Family_Member
Attribute details:
| Entity name | Sample |
| Description | This field will capture which member of a Family is represented by a given Sample.
For example, if a Sample is from the mother in a Family, the value in this field will be "mother", from the father, this value will be "father", etc.. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Family_Type
Attribute details:
| Entity name | Sample |
| Description | This field will describe the type of Family represented by Samples in this table. This field could describe whether a family is a trio, for example.
This field could also capture whether a Family is 'Simplex' or 'Multiplex'. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Father_ID
Attribute details:
| Entity name | Sample |
| Description | If a Sample is part of a Family and Family information is provided, this field would contain the ID of the Father of the individual who provided this Sample
.
This information can be useful when looking at pedigree. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Feature
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Filter_ID
Attribute details:
| Entity name | Filter |
| Description | This is the primary key of the Filter table; it uniquely represents a record in this table. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Filter_Reason
Attribute details:
| Entity name | Filter |
| Description | The value in this field represents the reason for which a record was filtered out during the automated DGV curation process.
For example, if "Variant 123" was filtered out becuase it did not meet the DGV minimum size threshold, the value in this field would be "too small". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Filter_Step
Attribute details:
| Entity name | Filter |
| Description | The value in this field describes the step during the automated DGV curation process on which the record was filtered out.
For example, if the "Variant 123" record was filtered out during step 2 of the curation process, the value in this field would be "2". |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Gender
Attribute details:
| Entity name | Sample |
| Description | This field captures the gender of the Subject who provided the Sample.
The value in this field can be "Male", "Female", "Unknown", or NULL. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Gender
Attribute details:
| Entity name | Variant |
| Description | In the case where a Variant is reported with Gender information but with no corresponding Sample information, Gender will be captured here.
The value in this field can be "Male", "Female", or "Unknown", or NULL. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Gene
Attribute details:
| Entity name | Gene_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Genotype
Attribute details:
| Entity name | Variant_Type |
| Description | This is the genotype of a particular Variant as described for a given individual.
This information may not be provided in a published dataset. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: GEO_Accession_Num
Attribute details:
| Entity name | Platform_Study |
| Description | This field will capture the identifier/accession number that represents a given Platform within the GEO data repository. This information is not always provided in a Study.
e.g. GEO accession number, GPL1352 |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Hold_Until_Publication_Flag
Attribute details:
| Entity name | Study |
| Description | *** this field + its timestamp are only used in the DGVS (staging database for archiving, not for user-access) and not the public version, DGVC - and will infrequently, if at all, be used***
This field will capture whether a Study is to be held until publication.
If a Variant is to be held until publication, this value will be "Y"; if it is not to be held until publication, this value will be either "N" or "NULL".
If the value in this field is "Y", there will also be a timestamp indicating the date/time when the Variant can be published; this will be captured in the 'Publish_Date' field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: ID
Attribute details:
| Entity name | Cytoband_Overlap |
| Description | This is the primary key (PK) for this table; each record in this table will be assigned a unique PK. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: ID
Attribute details:
| Entity name | Gene_Overlap |
| Description | This is the primary key (PK) for this table; each record in this table will be assigned a unique PK. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: ID
Attribute details:
| Entity name | Coverage |
| Description | This is the primary key (PK) for this table; each record in this table will be assigned a unique PK. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: ID
Attribute details:
| Entity name | Feature_Overlap |
| Description | This is the primary key (PK) for this table; each record in this table will be assigned a unique PK. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Individual_Sample_ID
Attribute details:
| Entity name | Sample_Pooled |
| Description | This is the 'Sample_Study_ID' of one of the individual Samples that comprise a Pooled Sample. There will be two or more 'Individual_Sample_IDs' for every 'Pooled_Sample_ID' in this table. |
| Primary key | No |
| Refers to | Sample_Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Inheritance
Attribute details:
| Entity name | Variant |
| Description | This is to indicate whether a Variant is inherited or otherwise.
The value in this field could be for example: "Maternal", "Paternal", "Germline", "De novo", "Somatic", "Not tested", "Tested - inconclusive", "Biparental", or "Uniparental".
This informaiton may not always be provided in a published dataset. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Inner_End_A
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Minimum End Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Inner_End_B
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Minimum End Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Inner_Start_A
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Minimum Start Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Inner_Start_B
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Minimum Start Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Karyotype
Attribute details:
| Entity name | Sample |
| Description | This field will capture the Karyotype of a Sample.
One person can provide one or more Samples and each Sample may have a different Karyotype. For example, an individual with cancerous cells may have one Karyotype from a normal tissue Sample and another Karyotype from a cancer-tissue Sample.
Examples of Karyotypes are: 46, XY; 46, XX, 5p-; 46, XX, del(5)(p15.2) (the first two being normal karyotypes)
It should be noted that DGV currently only presents data for healthy controls so karyotype information will likely not be included for a given Sample. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Landmark
Attribute details:
| Entity name | Variant |
| Description | This field will capture any 'Landmark' that was used to discover a Variant.
Typically the Landmark is a Clone employed to find the location of a Variant on the genome. Thus the most common value in this field will be the Clone Name. E.g. "RP11-420B6"; "AL031643". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Load_Date
Attribute details:
| Entity name | Study_File_Prefix |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | 'now()' |
Attribute: Load_Date
Attribute details:
| Entity name | Variant_Analysis |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Variant_Analysis, etc.
|
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Merged_Analysis |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Sample_Merged_Variant, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Reference_Assembly |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Study, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | 'NOW()' |
Attribute: Load_Date
Attribute details:
| Entity name | Analysis |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given 'Analysis_Study', etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Cytoband_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | 'NOW()' |
Attribute: Load_Date
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given 'Method_Platform_Sample', etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Gene_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | 'NOW()' |
Attribute: Load_Date
Attribute details:
| Entity name | Coverage |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | 'NOW()' |
Attribute: Load_Date
Attribute details:
| Entity name | Dataset |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Dataset, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | 'NOW()' |
Attribute: Load_Date
Attribute details:
| Entity name | Sample |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Sample, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Cohort |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Cohort, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Dataset_Analysis_Reference, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Variant_Mapping, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Variant |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Variant, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Sample_Study |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given 'Sample_Study', etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Filter |
| Description | This is the timestamp that describes when a given record was loaded to this table. This is used for auditing and maintenance purposes. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | 'now()' |
Attribute: Load_Date
Attribute details:
| Entity name | Sample_Xref |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Sample_Xref, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Dataset_Xref |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Dataset_Xref, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Variant_Xref |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Variant_Xref, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Variant_Type |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Variant_Type, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Sample_Pooled |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Sample/Pooled Sample, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Variant_Mapping, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | No |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Reference |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Reference_Dataset, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Copy_Number |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Copy_Number, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Study |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Study, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | 'NOW()' |
Attribute: Load_Date
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Supporting_Merged_Variant, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Platform_Study |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given 'Platform_Study', etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Load_Date
Attribute details:
| Entity name | Method_Study |
| Description | This field captures the load date of a record in this table.
This field can be used for auditing purposes, e.g. to see when a record was loaded to the database/which version of a record existis if there are more than one for a given Method, etc. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | now() |
Attribute: Merged_Analysis_ID
Attribute details:
| Entity name | Merged_Analysis |
| Description | The value in this field uniquely identifies one record in this table. This value represents one relationship between a "Super Analysis" and one of the "Sub Analyses" that comprise the "Super Analysis". |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Merged_ID
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | This field captures the unique identifer of a given Merged Variant in the DGV.
This field cross-references one record in the Variant table. The Variant table stores both Supporting and Merged Variants.
In the case of DGVa and dbVar, this is the "asserted variant", which is comprised of "supporting variants" (those are referenced in the 'Supporting_Variant_ID' field). |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Merging_Criteria
Attribute details:
| Entity name | Variant |
| Description | If a Variant is a Merged Variant, a brief description of the criteria used to merge Supporting Variants to the Merged Variants will be provided here. |
| Primary key | No |
| Refers to | |
| Data type | TEXT |
| Domain | |
Constraints:
Attribute: Method_Description
Attribute details:
| Entity name | Method_Study |
| Description | This field captures a brief description of the Method employed in a Study. This information is not always provided for a given Study. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Method_Name
Attribute details:
| Entity name | Method_Study |
| Description | This is the name of a given Method employed in a Study; e.g. BAC_aCGH; MCD_analysis. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Method_Number
Attribute details:
| Entity name | Method_Study |
| Description | This is a sequential number assigned to each Method empoyed in a Study. This value is not unique in this table or across the database.
For example, if five Methods were generated in a Study, each Method (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Method_Platform_Sample_ID
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This is the unique identifer to repsesent one instance of a Sample that is examined using one Method and one Platform in a given Study. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Method_Study_ID
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This is the unique identifier from the 'Method_Study' table that represents one instance of a Method being employed in one Study.
This can be used to cross-reference one record in the 'Method_Study' table. |
| Primary key | No |
| Refers to | Method_Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Method_Study_ID
Attribute details:
| Entity name | Method_Study |
| Description | This uniquely identifies within the DGV one instance of a Method employed in one Study.
For example, BAC_aCGH may be employed twice in one Study; each instance of this Method being employed in that Study would get its own unique 'Method_Study_ID' |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Method_Type
Attribute details:
| Entity name | Method_Study |
| Description | This field indicates whether a Method employed in a given Study was either a 'Discovery Method' or a 'Validation Method'.
The values in this field are either "Discovery" or "Validation". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Mother_ID
Attribute details:
| Entity name | Sample |
| Description | If a Sample is part of a Family and Family information is provided, this field would contain the ID of the Mother of the individual who provided this Sample.This information can be useful when looking at pedigree. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: NCBI_Tax_ID
Attribute details:
| Entity name | Study |
| Description | This field captures the NCBI Taxonomy ID for the organism being Studied.
For humans, the Taxonomy ID is "9606" so users should expect to always see this value in this field for the DGV. NB A very few Studies loaded to the DGV archival database (DGVS) may also contain data for non-humans; these data are filtered out during the automated DGV-curation pipeline and not presented to users. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Nucleotides_Covered
Attribute details:
| Entity name | Coverage |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | BIGINT |
| Domain | |
Constraints:
Attribute: Number_of_CNVs_Overlapped
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Number_of_Features
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Number_of_Features_Overlapped
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Number_of_Gains
Attribute details:
| Entity name | Variant_Type |
| Description | This value applies only to Merged Variant calls, aka Regions or Events. This refers to the number of individuals that have a copy number gain within a merged CNV event or region. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Number_of_Gains_and_Losses
Attribute details:
| Entity name | Variant_Type |
| Description | This value applies only to Merged Variant calls, aka Regions or Events. This refers to the total number of individuals that have a copy number change within a merged CNV event or region. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Number_of_Losses
Attribute details:
| Entity name | Variant_Type |
| Description | This value applies only to Merged Variant calls, aka Regions or Events. This refers to the number of individuals that have a copy number loss within a merged CNV event or region. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: OneK_Genomes_Project
Attribute details:
| Entity name | Study |
| Description | This is a flag to indicate whether a Study is part of the 1000 Genomes Project.
Multiple "Studies" in the database may actually represent one Study from the 1000 Genomes Project. These Studies generate multiple input files per Study, thus generating multiple Study records in the database. These Studies will have a 1000 Genomes Project flag = "Y". The 'Study_Accession' value can be used to group records in this table (and subsequently on joins to other tables) to see which database Studies are related to one another, thereby representing one 1000 Genomes Project Study. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Original_Method
Attribute details:
| Entity name | Method_Study |
| Description | If data that was generated in a different Study is being re-analyzed/meta-analyzed in a new Study, the 'Primary_Data_Flag' is "N", indicating the data was originally generated in a previous Study. This field captures the Method used in the original Study to first generate the Dataset being analyzed in this Study.
This information is not always provided in a Study (and currently may not be captured by DGVa or dbVar). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Originators_of_Data
Attribute details:
| Entity name | Method_Study |
| Description | The field should capture the original source of the data i.e. the group who ran the samples and generated the dataset.
This field could capture, e.g. the PMID, the primary author of a Study, the Site at which/organization by whom the original Study was performed.
This information is not always provided in a Study (and currently may not be captured by DGVa or dbVar). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Outer_End_A
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Maximum End Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Outer_End_B
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Maximum End Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Outer_Start_A
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Maximum Start Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Outer_Start_B
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Maximum Start Boundary of a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Percent_Coverage
Attribute details:
| Entity name | Coverage |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | DOUBLE PRECISION |
| Domain | |
Constraints:
Attribute: Percent_of_CNVs_Overlapped
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | DOUBLE PRECISION |
| Domain | |
Constraints:
Attribute: Percent_of_Features_Overlapped
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | DOUBLE PRECISION |
| Domain | |
Constraints:
Attribute: Placement_Method
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is a short term used (by DGVa and dbVar) to describe how a Variant was mapped to the genome. The default value is "Genomic" which describes the mapping provided by the Authors of a Study (i.e. the Submitter of the Study's data to dbVar/DGVa).
Other terms include: Artifact, DGV, Clone Registry, Clone ad-hoc, Cytogenetic, Flanking sequences, Remapped auto, Remapped ad-hoc. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Placement_Method
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is a short term used (by DGVa and dbVar) to describe how a Variant was mapped to the genome. The default value is "Genomic" which describes the mapping provided by the Authors of a Study (i.e. the Submitter of the Study's data to dbVar/DGVa).
Other terms include: Artifact, DGV, Clone Registry, Clone ad-hoc, Cytogenetic, Flanking sequences, Remapped auto, Remapped ad-hoc. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Platform_Description
Attribute details:
| Entity name | Platform_Study |
| Description | This is a short description of a given Platform.
Not all Platforms will necessarily have a description for them but if one is available, it will be captured here. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Platform_Name
Attribute details:
| Entity name | Variant |
| Description | If the Platform is known for which a given Variant is associated, this information may be captured here. The value in this field is the name of the Platform used in analyzing a given Sample to discover or validate the Structural Variants described in this table. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Platform_Name
Attribute details:
| Entity name | Platform_Study |
| Description | This is the name used to refer to a Platform.
For example, "Affymetrix GeneChip Human Genome U95Av2 [HG_U95Av2]" |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Platform_Number
Attribute details:
| Entity name | Platform_Study |
| Description | This is a sequential number assigned to each Platform employed in a Study. This value is not unique in this table or across the database.
For example, if five Platforms were employed in a Study, each Platform (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Platform_Study_ID
Attribute details:
| Entity name | Platform_Study |
| Description | This is the database unique identifier that represents one instance of a Platform being employed in one Study. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Platform_Study_ID
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This is the unique identifier from the 'Platform_Study' table that represents one instance of a Platform being employed in one Study.
This can be used to cross-reference one record in the 'Platform_Study' table. |
| Primary key | No |
| Refers to | Platform_Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Platform_Type
Attribute details:
| Entity name | Platform_Study |
| Description | This field captures the Type of a given Platform. This information may not necessarily be provided in a Study.
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Platform_Version
Attribute details:
| Entity name | Platform_Study |
| Description | This describes the version of a given Platform. This information may not necessarily be provided in a Study. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Pooled_Sample_ID
Attribute details:
| Entity name | Sample_Pooled |
| Description | This is the unique identifer of one Pooled Sample within the database. For each 'Pooled_Sample_ID' there will be two or more 'Individual_Sample_IDs'. |
| Primary key | No |
| Refers to | Sample_Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Primary_Author_ID
Attribute details:
| Entity name | Study |
| Description | This is a unique identifier that an Author would use to refer to himself/herself across multiple databases and within Studies. Examples of an 'Author_ID' are "ResearcherID", "OpenID", "Scopus ID" |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Primary_Author_Name
Attribute details:
| Entity name | Study |
| Description | This is the name of the Author whose name appears first on a publication for a given Study. It is noted that there could be multiple authors on a given Study but these are not captured in the DGV. For the full list of authors of a Study, one should refer to the original publication. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Primary_Data_Flag
Attribute details:
| Entity name | Method_Study |
| Description | This field will capture whether the data being analyzed in a given Study is Primary or a Re-Analysis of Primary data that was generated in a different Study. This information is not always provided in a Study (and currently may not be captured by DGVa or dbVar).
The values in this field are, "Y", if the data is Primary data generated by the Study in question, or "N" if the data was generated in a different Study.
If the 'Primary_Data_Flag' is "N", to find the Method employed in the original Study that generated the data, query the 'Original_Method' field in this table. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Principal_Investigator
Attribute details:
| Entity name | Study |
| Description | This field will capture the Principal Investigator of a project if this information is provided for a given Study. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Probe_Count
Attribute details:
| Entity name | Variant |
| Description | This field refers to the number of probes on the array, within the region called as a Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Project_ID
Attribute details:
| Entity name | Study |
| Description | This field may capture a Project Identifier if one has been assigned to a Study, or in the case that the Study is not in PubMed (note this is only in rare cases and these Studies will likely at least have a 'Study_Accession' from either dbVar or DGVa). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Publish_Date
Attribute details:
| Entity name | Study |
| Description | The value in this field will be the date the Study's Author has given us to publish the Study. This field will infrequently, if at all, be used.
If the Author does not provide a specific date, this value will be set to a date far into the future which will be reset when the Author has given the go-ahead to publish the Variant. |
| Primary key | No |
| Refers to | |
| Data type | TIMESTAMP |
| Domain | |
Constraints:
Attribute: PubMed_ID
Attribute details:
| Entity name | Study |
| Description | This is also known as 'PMID' and is the unique indentifer for a citation within PubMed. This identifier can be used to uniquely identify a publication, or Study, across many databases and is seen as a "universal" identifer for a given Study. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Recipient
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field is specific to DGVa and dbVar and is captured here to provide full context of a Variant Mapping. For Variants that span across more than one locus (usually across Chromosomes), the value in this field describes whether that second location is either "known" or "ambiguous". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Recipient
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field is specific to DGVa and dbVar and is captured here to provide full context of a Variant Mapping. For Variants that span across more than one locus (usually across Chromosomes), the value in this field describes whether that second location is either "known" or "ambiguous". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Assembly
Attribute details:
| Entity name | Cytoband_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Assembly
Attribute details:
| Entity name | Gene_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Assembly
Attribute details:
| Entity name | Coverage |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Assembly
Attribute details:
| Entity name | Feature_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Assembly
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Reference Assembly that was used to map a variant's coordinates.
Examples of Reference Assemblies are: GRCh37 (build 37), hg18/Build 36, and hg17/Build 35. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Assembly
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Reference Assembly that was used to map a variant's coordinates.
Examples of Reference Assemblies are: GRCh37 (build 37), hg18/Build 36, and hg17/Build 35. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Reference_Assembly_ID
Attribute details:
| Entity name | Reference_Assembly |
| Description | This is the identifier that uniquely represents a given Reference Assembly in this table. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Reference_Assembly_Name
Attribute details:
| Entity name | Reference_Assembly |
| Description | This is the common name used for a given Reference Assembly; e.g. NCBI36/hg18 |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Description
Attribute details:
| Entity name | Reference |
| Description | This is a brief description of the Reference, if one is available. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_ID
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This uniquely identifies a given Reference against which a Dataset is compared during an Analysis within one Study.
This can be used to cross-reference one record in the 'Reference' table. |
| Primary key | No |
| Refers to | Reference_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Reference_ID
Attribute details:
| Entity name | Reference |
| Description | This uniquely identifies a given Reference against which a Dataset is compared within one Study. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Reference_Number
Attribute details:
| Entity name | Reference |
| Description | This is a sequential number assigned to each Reference employed in a Study. This value is not unique in this table or across the database.
For example, if five References were employed in a Study, each Reference (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Reference_Sample_ID
Attribute details:
| Entity name | Reference |
| Description | If the Reference Type = "Sample", this field will capture the Sample identifier associated to that Sample, if one is provided.
For example, if one HapMap Sample is used as a Reference, the HapMap Sample ID (e.g. NA07019) could be provided in this field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Sequence
Attribute details:
| Entity name | Reference |
| Description | This field captures the specific Sequence name if the Reference Type = "Reference Sequence".
Examples of Sequence names are "HuRef" and "Hg18/Build36". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reference_Type
Attribute details:
| Entity name | Reference |
| Description | This is the type of Reference that could be employed in a Study.
The Reference type could be: "Ref_sequence", "Sampleset", "Sample", "Control_tissue", "Merged", or "Other". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Remap_Status
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field captures a short descriptor of the status of a given Variant Mapping after it has been forward mapped to a newer Reference Assembly. This is a value used by dbVar and DGVa.
Values that could be in this field are: Perfect (perfectly mapped), Deletion (a deletion occured in the remapping), Insertion (an insertin occured in the remapping), No map (the placement did not map). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Remap_Status
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field captures a short descriptor of the status of a given Variant Mapping after it has been forward mapped to a newer Reference Assembly. This is a value used by dbVar and DGVa and may not always be provided in a Study.
Values that could be in this field are: Perfect (perfectly mapped), Deletion (a deletion occured in the remapping), Insertion (an insertin occured in the remapping), No map (the placement did not map). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Reported_Frequency
Attribute details:
| Entity name | Variant_Type |
| Description | This is a value related to the Frequency of a Variant. This value is captured during DGVa/dbVar archiving and is described by DGVa/dbVar as: "Frequency of variant"
This information may not be provided in a published dataset. |
| Primary key | No |
| Refers to | |
| Data type | NUMERIC |
| Domain | |
Constraints:
Attribute: Run_ID
Attribute details:
| Entity name | Filter |
| Description | This identifier uniquely represents one run of the Filtering steps during automated DGV data curation. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_Description
Attribute details:
| Entity name | Sample |
| Description | This field will capture a Description of the Sample when necessary/if available.
For example, a Sample could be "a pool of 10 anonymous male donors". In these cases, a Description of the Sample is important, esp. with regards to representation of Sample/Subject numbers in the DGV (i.e. a pool of 10 anonymous donors translates from one Sample to 10 Subjects). |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Sample_ID
Attribute details:
| Entity name | Sample |
| Description | This is the unique identifier of a given Sample in the DGV. This identifier represents a Sample within the DGV and does not represent the unique identifier of a Sample in other databases.
It is important to note that this identifier is to uniquely identify one Sample in the DGV. Many Studies may examine the same Sample, e.g. a HapMap Sample; this Sample should exist only once in this table but may be cross-referenced several times in the 'Sample_Study' and 'Sample_Xref' tables. we should only load that Sample once to the database |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_ID
Attribute details:
| Entity name | Sample_Study |
| Description | This value uniquely identifies a Sample in the database and will cross-reference one record in the 'Sample' table. |
| Primary key | No |
| Refers to | Sample_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_ID
Attribute details:
| Entity name | Sample_Xref |
| Description | This is the unique identifier that represents one Sample in the DGV. A Sample should be loaded only once to the database and assigned only one Sample ID. This means that there could be one or more records in this table that have the same Sample ID (one for each external identifier assigned to that Sample). |
| Primary key | No |
| Refers to | Sample_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_Merged_Flag
Attribute details:
| Entity name | Variant |
| Description | This field distinguishes whether a Variant is a Supporting Variant or a Merged Variant.
If the Variant is Ssupporting, the value in this field will be "S".
If the Variant is Merged, the value in this field will be "M". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_Number
Attribute details:
| Entity name | Sample_Study |
| Description | This is the number assigned to a Sample within a Study. E.g. if 100 Samples were examined in a Study, those Samples would be assigned a number from 1 to 100. The 'Sample_Number' is meant to label each Sample differently WITHIN a Study and is not a unique identifier across Studies. The 'Sample_ID' and 'Sample_Study_ID' uniquely identify a Sample within the database. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Sample_Pooled_ID
Attribute details:
| Entity name | Sample_Pooled |
| Description | This field uniquely identifies one instance of a mapping between an individual Sample and a Pooled Sample. For each individual Sample that comprises a Pooled Sample in the database, a record will be stored in this table.
For example, if a Pooled Sample is comprised of ten individual Samples, there will be ten records stored in this table, each with the same 'Pooled_Sample_ID' (which can be cross-referenced with a 'Sample_Study_ID' in the 'Sample_Study' table) and ten different 'Sample_Study_ID's (each of which can be cross-referenced with a 'Sample_Study_ID' in the 'Sample_Study' table), each record will have a unique 'Sample_Pooled_ID'. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_Size
Attribute details:
| Entity name | Study |
| Description | This is the number of Samples examined in one Study and will be an integer greater than zero. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Sample_Study_ID
Attribute details:
| Entity name | Sample_Study |
| Description | This is the unique identifer within the DGV of one instance of a Sample being examined in one Study.
One Study may examine one or more Samples. One or more Samples may be examined by one or many Studies. This field is the unique identifer that resolves the many-to-many relationship between these entities (Sample and Study). |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_Study_ID
Attribute details:
| Entity name | Variant |
| Description | This is the unique identifier in the DGV for the Sample in which the Variant was found in a given Study. It is the unique identifier from the 'Sample_Study' table.
This can be used to cross-reference one record in the 'Sample_Study' table. NB this value represents an instance of a Sample as it is analyzed in one Study. The same Sample could be analyzed in different Studies, each instance having a different 'Sample_Study_ID', but the same 'Sample_ID'. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Sample_Study_ID
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This is the unique identifer within the DGV of one instance of a Sample being examined in one Study. |
| Primary key | No |
| Refers to | Sample_Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sample_Xref_ID
Attribute details:
| Entity name | Sample_Xref |
| Description | This is the unique identifer for one mapping of a DGV Sample identifier to an external identifier.
For example, if a Sample has been assigned two external identifiers, there will be two records in this table for that Sample, each having one of the two external identifiers. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Sequence
Attribute details:
| Entity name | Variant |
| Description | The sequence of the variant, if available, is captured in this field. Alternatively, this field may not contain the actual sequence but rather may be a pointer to another table or file where the actual sequence is stored. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Site
Attribute details:
| Entity name | Study |
| Description | This refers to the primary or main Site or Organization at which a Study is performed. This information is not always provided in a Study.
For example, if a 1000 Genomes Study was conducted at multiple sites, the value in this field would be "1000 Genomes: multiple sites". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Size
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field captures the Size of the Variant, if available. The Size is be the number of basepairs contained within the variant. In many cases the size will be equal to the span. For PEM and insertions into the reference, these values may be different, for aCGH etc, they will be the same. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Size
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field captures the Size of the Variant, if available. The Size is be the number of basepairs contained within the variant. In many cases the size will be equal to the span. For PEM and insertions into the reference, these values may be different, for aCGH etc, they will be the same. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Source_System
Attribute details:
| Entity name | Study_File_Prefix |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Reference |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Analysis |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Variant_Analysis |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Variant |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Sample_Xref |
| Description | This field contains an identifier of the data repository in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Merged_Analysis |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Method_Study |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Study |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Dataset |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Sample |
| Description | This field contains an indicator of the data store in which these data were originally archived. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Copy_Number |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Platform_Study |
| Description | This field contains an identifier of the data repository in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | 01.21.10 This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Sample_Pooled |
| Description | This field contains an indicator of the data store in which these data were originally archived. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Dataset_Xref |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Source_System
Attribute details:
| Entity name | Cohort |
| Description | This field contains an indicator of the data store in which these data were originally archived. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Source_System
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Variant_Xref |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Sample_Study |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_System
Attribute details:
| Entity name | Variant_Type |
| Description | This field contains an indicator of the data store in which these data were originally stored. For example:
1) "DGVa" for data originally archived in the Database of Genomic Variants Archive (DGVa) at EBI
2) "dbVar" for data originally archived in dbVar at NCBI
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Source_Type
Attribute details:
| Entity name | Sample |
| Description | This field describes the type of the Sample.
For example, a Sample could be of the Type "Genomic DNA", "RNA", "Clone library", etc.
Please note how this field relates to the 'Biological_Source' field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Span
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field captures the Span of a Variant, if available. The Span is be the distance between the mapped start and mapped end of the variant on the reference assembly.
For example, in a PEM study, the clone end anchors will delineate the start-end of variant, in aCGH, the first/last probe with signal intensity difference will delineate the variant span. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Span
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field captures the Span of a Variant, if available. The Span is be the distance between the mapped start and mapped end of the variant on the reference assembly.
For example, in a PEM study, the clone end anchors will delineate the start-end of variant, in aCGH, the first/last probe with signal intensity difference will delineate the variant span. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Start_A
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Average Start Boundary of a Variant. Alternatively, if only one Start Coordinate has been provided for a Variant, it will be stored here. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Start_B
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Average Start Boundary of a Variant. Alternatively, if only one Start Coordinate has been provided for a Variant, it will be stored here. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Start_Random
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the Start coordinate that is randomly assigned to a variant that cannot be mapped to a chromosome but for which we know what chromosome the variant belongs. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Start_Random
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the Start coordinate that is randomly assigned to a variant that cannot be mapped to a chromosome but for which we know what chromosome the variant belongs. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Study_Accession
Attribute details:
| Entity name | Study |
| Description | The value in this field will be the accession number assigned to a Study by either NCBI-dbVar or EBI-DGVa. This accession number can then be used to cross-reference the Study in either dbVar or DGVa.
If the Study was accessioned in dbVar, this value will be prefixed with "nstd"; e.g. "nstd35"
If the Study was accessioned in DGVa, this value willl be prefixed with "estd"; e.g. "estd1" |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Study_File_Prefix
Attribute details:
| Entity name | Study_File_Prefix |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_File_Prefix_ID
Attribute details:
| Entity name | Study_File_Prefix |
| Description | |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Variant_Type |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Sample_Study |
| Description | This value uniquely identifies a Study in the database and will cross-reference one record in the 'Study' table. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Study_File_Prefix |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Copy_Number |
| Description | This is the unique database identifier that represents one Study in the DGV, from which a given record in this table originated. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Sample_Xref |
| Description | This is the unique database identifier that represents one Study in the DGV, from which a given record in this table originated. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Study_ID
Attribute details:
| Entity name | Variant_Analysis |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Variant_Xref |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Study |
| Description | This is the unique identifier for a given Study within the DGV. This only uniquely identifies a Study in the DGV and not across other (external) databases. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Method_Platform_Sample |
| Description | This is the unique database identifier that represents one Study in the DGV, from which a given record in this table originated. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Merged_Analysis |
| Description | This is the unique database identifier that represents one Study in the DGV, from which a given record in this table originated (or was generated in the case of a join table composed of only database identifiers). |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Sample_Pooled |
| Description | This is the unique database identifier that represents one Study in the DGV, that Study in which the Pooled Samples were analyzed. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Variant |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Study_ID
Attribute details:
| Entity name | Platform_Study |
| Description | This is the unique identifier from the 'Study' table and represents the Study in which an instance of a Platform was employed. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Reference |
| Description | This is the unique database identifier that represents one Study in the DGV, from which a given record in this table originated. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Filter |
| Description | This value represents the Study to which a given record in this table is associated.
For example, if "Variant 123" from "Study 1" was Filtered out because it did not meet the DGV minimum size threshold, the value in this field would be "1". |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Analysis |
| Description | This is the unique identifier from the 'Study' table and represents the Study in which an instance of an Analysis was employed. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Method_Study |
| Description | This is the unique identifier from the 'Study' table and represents the Study in which an instance of a Method was employed. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Study_ID
Attribute details:
| Entity name | Dataset_Xref |
| Description | This is the unique database identifier that represents one Study in the DGV. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Dataset_Analysis |
| Description | This is the unique database identifier that represents one Study in the DGV, from which a given record in this table originated. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Study_ID
Attribute details:
| Entity name | Dataset |
| Description | This is the unique identifier for a Study from the 'Study' table. This refers to the Study in which the Dataset was generated. |
| Primary key | No |
| Refers to | Study_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Study_Mapping
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This field indicates whether this was the original Variant Mapping that was published as part of a Study's dataset or whether the mapping was a result of mitrating the Study-published mapping to another Reference Assembly (e.g. using the LiftOver tool to migrate from Hg17 to Hg18).
If this is the original Variant Mapping as published within a Study, the value in this field is "Y"; if it is not the original Variant Mapping, the value in this field will be "N" or blank. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | Y |
Attribute: Study_Mapping
Attribute details:
| Entity name | Variant_Mapping |
| Description | This field indicates whether this was the original Variant Mapping that was published as part of a Study's dataset or whether the mapping was a result of migrating the Study-published mapping to another Reference Assembly (e.g. using the LiftOver tool to migrate from Hg17 to Hg18).
If this is the original Variant Mapping as published within a Study, the value in this field is "Y"; if it is not the original Variant Mapping, the value in this field will be "N" or blank. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | Y |
Attribute: Subject_ID
Attribute details:
| Entity name | Sample |
| Description | If a Subject identifier of some kind is provided in a Study - as associated to a given Sample, that Subject identifier will be captured here.
Note: one Subject can provide one or more Samples, each of which is captured in the Sample table. Also, in many Studies, the HapMap Sample ID (e.g. "NA19215") is also included as the Subject ID. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Sub_Analysis_ID
Attribute details:
| Entity name | Merged_Analysis |
| Description | This represents the lower-level Analysis that was merged with another Analysis to create a higher-level Analysis, called the "Super Analysis". |
| Primary key | No |
| Refers to | Analysis_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Super_Analysis_ID
Attribute details:
| Entity name | Merged_Analysis |
| Description | This represents the higher-level Analysis that is comprised of two or more lower-level Analyses, called "Sub Analyses". |
| Primary key | No |
| Refers to | Analysis_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Supporting_Merged_Variant_ID
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | 9.10.9 This field represents one instance of a mapping between a Sample Level and a Merged Variant.
For each Merged Variant, there will be as many records in this table as there are Sample Level Variants that comprise the Merged Variant (provided these data are available from a published dataset). |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Supporting_Variant_ID
Attribute details:
| Entity name | Supporting_Merged_Variant |
| Description | This field captures the unique identifer of a given Supporting Variant in the DGV.
This field cross-references one record in the Variant table. The Variant table stores both Supporting and Merged Variants.
In the case of DGVa and dbVar, this is the "supporting variant", which comprises the "asserted variant" (those are referenced in the 'Merged_ID' field). |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Table_ID
Attribute details:
| Entity name | Filter |
| Description | This is the primary key for the record as it is represented in its original table.
For example, if "Variant 123" was filtered out, the value in this field would be "123". This value in conjunction with the 'Table_Name' uniquely represents a record in the database. (I.e. 'table_name.primary_key') |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Table_Name
Attribute details:
| Entity name | Filter |
| Description | This is the table from which the Filtered record originated.
For example, if a record from the 'Variant' table was filtered out, the value in this field would be "Variant". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Total_Reporting
Attribute details:
| Entity name | Variant_Type |
| Description | This is a value related to the Frequency of a Variant. This value is captured during DGVa/dbVar archiving and is described by DGVa/dbVar as: "Number of samples assessed for structural variant". |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Translocation_Mapping_ID
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This uniquely represents one mapping for one Translocation Variant stored in the DGV.
A Translocation Variant may have multiple mappings reported for each part of the Variant. Each part will be represented by this unique identifer. All of the parts comprising one Translocation Variant can be associated in this table by the 'Variant_ID'. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Unmapped_Flag
Attribute details:
| Entity name | Translocation_Mapping |
| Description | A Variant might not map to a given Reference Assembly when that Variant is re-mapped, or migrated, to a newer version of a Reference Assembly (e.g. using the UCSC LiftOver tool to re-map/migrate from Hg17 to Hg18).
For Variants that do not map to a given Reference Assembly, the value in this field will be "Y". If a Variant was successfully mapped to a Reference Assembly, this fileld will be NULL. The current DGV pipeline may not use this field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Unmapped_Flag
Attribute details:
| Entity name | Variant_Mapping |
| Description | A Variant might not map to a given Reference Assembly when that Variant is re-mapped, or migrated, to a newer version of a Reference Assembly (e.g. using the UCSC LiftOver tool to re-map/migrate from Hg17 to Hg18).
For Variants that do not map to a given Reference Assembly, the value in this field will be "Y". If a Variant was successfully mapped to a Reference Assembly, this fileld will be NULL. The current DGV pipeline may not use this field. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Validation_Flag
Attribute details:
| Entity name | Variant |
| Description | This field captures whether a Variant has been Validated or not, and the results of the Validation.
A Variant needs to be 'Discovered' in a Sample before it can be 'Validated'. A Variant is Validated by performing further assays.
-- Flag Values are as follows:
"Y" means that a Validation Method was applied and the Variant was validated
"A" means that a Validation Method was attempted but the Variant was not validated
"N" means that no Validation Method was applied or no Validation information was provided for a given Variant
NB: Multiple Validation Methods can be applied to one Variant; if any of those methods yeilds a positive validation result, the Validation_Flag="Y" |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Validation_Method
Attribute details:
| Entity name | Variant |
| Description | If a Discovered Variant is also Validated, and information about Validation is provided for that Variant, the Validation Method (if available) is captured here.
The list of Validation Methods can be found in the 'Exchange.XSD' file as the controlled list "MethodTypeCV" |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Validation_Platform_Name
Attribute details:
| Entity name | Variant |
| Description | If a Discovered Variant is also Validated, and information about Validation is provided for that Variant, the Validation Platform (if available) is captured here. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Variant_Analysis_ID
Attribute details:
| Entity name | Variant_Analysis |
| Description | This is the unique identifier that represents one record in this table; i.e. one instance of a Dataset-Analysis and associated Variant. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Count
Attribute details:
| Entity name | Study |
| Description | This is the reported number of Variants that were discovered in a given Study. This value is assigned by either DGVa or dbVar.
It is possible that the reported Variant_Count (stored in this table) is different than the actual Variant Count. When performing computations using record counts, it is best to count the actual number of reported Variants as opposed to using this value. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Variant_ID
Attribute details:
| Entity name | Variant |
| Description | This is the unique identifier for a Variant in the DGV. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_ID
Attribute details:
| Entity name | Cytoband_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Variant_ID
Attribute details:
| Entity name | Variant_Xref |
| Description | This is the unique identifer from the 'Variant' table that represents one Variant in the DGV.
This can be used to cross-reference one record in the 'Variant' table. |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_ID
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is the unique identifer for a Variant in the DGV.
The 'Variant_ID' can appear more than once in this table if that Variant has been mapped to more than one reference assembly of the human genome.
This can be used to cross-reference one record in the 'Variant' table. |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_ID
Attribute details:
| Entity name | Variant_Type |
| Description | This is the unique identifer that represents one Variant in the DGV. It is the Variant that is described by the 'Variant_Type'.
This can be used to cross-reference one record in the 'Variant' table. |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_ID
Attribute details:
| Entity name | Translocation_Mapping |
| Description | 9.14.9 This is the unique identifer for a Variant in the DGV.
The 'Variant_ID' can appear more than once in this table if that Variant has been mapped to more than one reference assembly of the human genome.
This can be used to cross-reference one record in the 'Variant' table. |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_ID
Attribute details:
| Entity name | Variant_Analysis |
| Description | This is the unique identifier for a Variant in the DGV. |
| Primary key | No |
| Refers to | Variant_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_ID
Attribute details:
| Entity name | Gene_Overlap |
| Description | |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Variant_Mapping_ID
Attribute details:
| Entity name | Variant_Mapping |
| Description | This uniquely represents one mapping for one Variant stored in the DGV.
This table allows for multiple mappings of one Variant; e.g. to two iterations of the human genome reference assembly |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Number
Attribute details:
| Entity name | Variant |
| Description | This is a sequential number assigned to each Variant discovered or validated in a Study. This value is not unique in this table or across the database.
For example, if five Variants were discovered in a Study, each Variant (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Number
Attribute details:
| Entity name | Translocation_Mapping |
| Description | This is a sequential number assigned to a Variant within a reported Study and is not the database identifier for that Variant (which is the 'Variant.Variant_ID').
For a Translocation Variant, the mapping for each part of the Translocation will be assigned the same Variant Number in the input file. In conjunction with the 'Variant_ID', a user will be able to determine which records/mappings group together to represent one Translocation Variant. |
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Number
Attribute details:
| Entity name | Variant_Mapping |
| Description | This is a sequential number assigned to a Variant within a reported Study and is not the database identifier for that Variant (which is the 'Variant.Variant_ID').
For example, if five Variants were discovered in a Study, each Variant (before being loaded to the database) will be assigned a sequential number from "1" to "5" inclusive. This allows records from the input file to be easily cross-referened in the database, especially for quality checks.
|
| Primary key | No |
| Refers to | |
| Data type | INTEGER |
| Domain | |
Constraints:
Attribute: Variant_Sub_Type
Attribute details:
| Entity name | Variant_Type |
| Description | This field will capture the Variant Sub-Type ascribed to one Variant. Typically a Variant will be assigned only one 'Variant_Sub_Type'.
A Variant could have more than one Type+Sub-Type, e.g. CNV+Duplication and Other+Inversion. If more one Variant Type+Sub-Type is ascribed to a Variant there will be as many records in this table as there are for that number of combinations of Type+Sub-Type assigned to that Variant, each record having the same 'Variant_ID'. |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Variant_Type
Attribute details:
| Entity name | Variant_Type |
| Description | This field will capture the Variant Type ascribed to one Varian. Typically a Variant will only be assigned one Variant Type; i.e. "CNV" or "Other"; a Variant can also be assigned a 'Variant_Sub_Type'; e.g. "Gain" or "Complex".
A Variant could be of more than one Type, e.g. CNV + Other. If more than one Variant Type is ascribed to a Variant, that Variant will have as many records in this table as are Types assigned to that Variant, each record having the same 'Variant_ID'.
|
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Type_Description
Attribute details:
| Entity name | Variant_Type |
| Description | This field provides further information about a Variant Type by way of a short description of the Variant Type.
An example of a Variant Type description for an Insertion is: "Insertion of DNA sequence of known position relative to a reference sequence, detected by sequence/paired-end-mapping technology". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
Attribute: Variant_Type_ID
Attribute details:
| Entity name | Copy_Number |
| Description | This value represents one record from the 'Variant_Type' table and can be used to cross-reference a record in this table to its Variant (via 'Variant_ID') and associated Variant Type. |
| Primary key | No |
| Refers to | Variant_Type_ID |
| Data type | INTEGER |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Type_ID
Attribute details:
| Entity name | Variant_Type |
| Description | This is the unique identifier to represent one instance of a Variant Type in the DGV. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Variant_Xref_ID
Attribute details:
| Entity name | Variant_Xref |
| Description | This is the unique identifer for one mapping of a Variant in the DGV to an external identifier. |
| Primary key | Yes |
| Refers to | |
| Data type | SERIAL |
| Domain | |
Constraints:
| Not null | Yes |
| Check | |
| Default | |
Attribute: Zygosity
Attribute details:
| Entity name | Variant_Type |
| Description | This value is related to the Variant Sub-Type. The allowable values in this field are "Heterozygous", "Homozygous", or "Hemizygous".
For example, if a Variant Type = "CNV" and Sub-Type = "Deletion", the 'Zygosity' could thus be included as either "Heterozygous" or "Homozygous". |
| Primary key | No |
| Refers to | |
| Data type | CHARACTER VARYING |
| Domain | |
Constraints:
|