Biobank database table description

biobank_database.org

This is a description of the tables found in the Biobank database schema for version 3.10.0.

address

The street address for a center.

aliquoted_specimen

The aliquots / derivatives that are collected by a study.

batch_operation

Used for CSV file import.

This information does not need to be imported.

batch_operation_event_attr

Used for CSV file import of annotations for a study.

This information does not need to be imported.

batch_operation_patient

Used for CSV file import of patients for a study.

This information does not need to be imported.

batch_operation_processing_event

Used for CSV file import of processing events for patient.

This information does not need to be imported.

batch_operation_specimen

Used for CSV file import of specimens for a patient.

This information does not need to be imported.

center

A center can be a storage site or a collection site. A collection site is also referred to as a clinic.

center_comment

Used to record comments left by users for a center.

collection_event

A record of when specimens were collected from a patient.

collection_event_comment

Used to record comments for an individual collection event.

comment

A generic table used for storing comments.

contact

Contact information for an individual that is associated with a study.

container

A physical container. There are two types of containers: top level and non top level:

• A top level container is one that cannot be contained by any others and is usually for freezers.
• A non top level container can be conained by other containers and is usually for a rack or an N sized well plate.

container_comment

Used to record comments for an individual container.

container_labeling_scheme

How the child containers or specimens within a container are labelled.

container_position

Holds the position of this container in its parent container.

container_type

Storage containers share common attributes, these attributes are grouped into and defined in a container type. Some containers hold sub-containers, while others hold specimens.

container_type_comment

Used to record comments for an individual container type.

container_type_container_type

Maintains a relationship between a parent container_type and a child container_type.

container_type_specimen_type

Maintains a relationship between a container type and the specimen types it can hold.

csm_application

A caCORE table.

csm_filter_clause

A caCORE table.

csm_group

A caCORE table.

csm_pg_pe

A caCORE table.

csm_privilege

A caCORE table.

csm_protection_element

A caCORE table.

csm_protection_group

A caCORE table.

csm_role

A caCORE table.

csm_role_privilege

A caCORE table.

csm_user

A caCORE table.

csm_user_group

A caCORE table.

csm_user_group_role_pg

A caCORE table.

csm_user_pe

A caCORE table.

dispatch

Dispatches allow for specimens to be transferred from one center to another.

dispatch_comment

Used to record comments for an individual dispatch.

dispatch_specimen

Contains information of which spcimens were contained in an individual dispatch.

dispatch_specimen_comment

Used to record comments for an individual specimen in a dispatch.

dna

Some specimens are annotated with DNA lab results data. This is the annotation data.

Stanford nor CBSR currently store this type of information.

domain

This table is used to track permission information for individual users or user groups. A domain can apply to sets of centers and studies or ALL centers and / or all studies.

domain_center

When a domain applies to a set of centers, an rows in this table will specify which centers.

domain_study

When a domain applies to a set of studies, an rows in this table will specify which centers.

entity

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

entity_column

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

entity_filter

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

entity_property

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

event_attr

The attribute added to all collection events for a particular study.

Collection events can have user specified annotations. This table is used in conjunction with event_attr_type, global_event_attr, and study_event_attr.

event_attr_type

The type of the annotation. It can be one of:

• number
• text
• date_time
• select_single
• select_mutiple

This table is hard coded and the user cannot modify this table.

Collection events can have user specified annotations. This table is used in conjunction with event_attr, global_event_attr, and study_event_attr.

file_data

Used for CSV file import of specimens for a patient.

This information does not need to be imported.

file_meta_data

Used for CSV file import of specimens for a patient.

This information does not need to be imported.

global_event_attr

This table lists all the possible annotations that can be associated with collection_events for a study.

Collection events can have user specified annotations. This table is used in conjunction with event_attr, event_attr_type, and study_event_attr.

group_user

Used for user permissions. Specifies which users belong to which groups.

hibernate_sequences

This table is not used at the moment.

jasper_template

Used for generating patient labels.

This information does not need to be imported.

log

Tracks the activity of individual users.

This information does not need to be imported.

membership

Used for user permissions. Specifies what the actions a group or user is allowed to perform.

membership_permission

Used for user permissions. Specifies the permissions this membership holds.

membership_role

Used for user permissions. Specifies the roles associated with a membership. See role.

origin_info

The center where a set of specimens originated from.

origin_info_comment

A comment a user can attach to an individual origin_info.

patient

The information stored for an individual participant. No identifying information is stored.

patient_comment

A comment a user can attach to an individual patient.

principal

The principal is the base class for a user and group.

printed_ss_inv_item

Used for printing patient labels.

This information does not need to be imported.

printer_label_template

Used for printing patient labels.

This information does not need to be imported.

processing_event

Information stored when a specimen is processed.

processing_event_comment

A comment a user can attach to an individual processing_event.

property_modifier

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

property_type

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

report

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

report_column

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

report_filter

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

report_filter_value

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

request

Contains information related to a request for specimens for an individual study.

request_specimen

Contains information related to a request for specimens for an individual study.

revision

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

revision_entity_type

This table is used by the Biobank Advanced Reports feature.

This information does not need to be imported.

role

A name given to a set of permissions. A role can then be given to a user group or an individual user.

role_permission

The individual permissions associated with a role.

schema_version

This table is used by the Biobank schema upgrade feature.

This information does not need to be imported.

shipment_info

Storage sites can receive shipments containing specimens from collection sites that do not use the Biobank software. This table stores information about the shipment.

shipping_method

The company or method used to send a shipment to a storage site.

site_study

An association between a center and a study. Only sites associated with a study can store specimens for a study.

source_specimen

Information about the specimens collected at a collection site for a study.

specimen

Information stored for a specimen, aliquot, or derivative.

specimen_comment

A comment a user can attach to an individual specimen.

specimen_position

The position within the container this specimen is stored at.

specimen_type

The type of a specimen.

specimen_type_specimen_type

Used to maintain a hierarchy of specimens to aliquots / derivatives.

study

Defines how specimens are collected and aliquos / derivatives are processed.

study_comment

A comment a user can attach to an individual study.

study_contact

Maintains which contacts are associated with a study.

study_event_attr

This table lists all the collection event annotations currently selected for a study.

Collection events can have user specified annotations. This table is used in conjunction with event_attr, event_attr_type, and global_event_attr.