Table Index

BioSource


Defines the biological source of an entry in the Protein, NucleicAcid or Gene tables ("the object"), as well as other tables eventually storing experimental data related to e.g., microarray or proteomic experiments. For example, BioSource might be used to specify the organism, organ, and tissue in which gene expression experiments were performed. DEPENDENCIES: 1. As BioSource references Taxon.WID to specify the species, the NCBI taxonomy dataset must have ALREADY been loaded prior to populating BioSource. 2. BioSource stores subtype information in BioSubtype via the BioSourceWIDBioSubtypeWID linking table

Columns

Column MySQL Type Oracle Type Nullable Description
WID BIGINT NUMBER No Warehouse identifier for biological source.
MAGEClass VARCHAR VARCHAR2(100) Yes Discriminator column specifies type of MAGE object this row represents (if needed)
TaxonWID BIGINT NUMBER Yes Warehouse GUID identifying WID of Taxon entry for the species. Always references species level or higher.
Name VARCHAR VARCHAR2(200) Yes Informal name assigned to this source.
Ex. (CMR): 'Escherichia coli K12-MG1655'
Strain VARCHAR VARCHAR2(220) Yes Strain of organism from which object is derived, if applicable. This is a subspecies taxonomic classification not supported by Taxon because it is not a rigorous concept. Strain is defined as a population of homogeneous organisms possessing a set of defined characteristics. In bacteriology, the set of descendants that retains the characteristics of the ancestor. Members of a strain that subsequently differ from the original isolate are regarded as belonging either to a substrain of the original strain, or to a new strain.
Organ VARCHAR VARCHAR2(50) Yes Organ of organism from which object is derived, if applicable.
Organ is defined as any part of the body exercising a specific function, such as
respiration, secretion, or digestion, if applicable.
Organelle VARCHAR VARCHAR2(50) Yes Organelle of organism from which object is derived, if applicable.
Tissue VARCHAR VARCHAR2(100) Yes Tissue of organism from which object is derived, if applicable. Can be used in
conjunction with Organ.
Tissue is defined as a collection of similar cells and the intercellular substances
surrounding them. Multiple tissues can be part of an Organ.
CellType VARCHAR VARCHAR2(50) Yes Cell type of organism from which object is derived, if applicable.
Cell type is defined as the type of an individual cell, e.g., "myoblast". This is a
cellular-level classification.
CellLine VARCHAR VARCHAR2(50) Yes Cell line from which object is derived, if applicable
Cell line usually pertains to an immortalized version of a given cell type
ATCCId VARCHAR VARCHAR2(50) Yes Identifier assigned by ATCC.org to the cell.
Diseased CHAR(1) CHAR(1) Yes 'T' if source is diseased, else 'F'.
Disease VARCHAR VARCHAR2(250) Yes If source was diseased, describes the disease borne by it.
DevelopmentStage VARCHAR VARCHAR2(50) Yes Stage of development associated with the object, if applicable
Sex VARCHAR VARCHAR2(15) Yes Sex of the organism from which object is derived, if applicable Enumerated. Values=Male/Female/Hermaphrodite/Asexual/NULL (NULL here means not provided by dataset)

Enumerated Values:
Male - Sex of organism is male
Female - Sex of organism is female
Hermaphrodite - Sex of organism is hermaphrodite
DoesNotApply - The notion of a sex does not apply to this organism
DataSetWID BIGINT NUMBER No The dataset this entity came from or is associated with

Referenced By

Table Column
FlowCytometrySample BioSourceWID
NucleicAcid BioSourceWID
Pathway BioSourceWID
Experiment BioSourceWID
BioSourceWIDBioSubtypeWID BioSourceWID
BioSourceWIDGeneWID BioSourceWID
BioSourceWIDProteinWID BioSourceWID
ManufactureLIMS BioMaterial
BioEvent BioMaterial_Treatments
BioMaterialMeasurement BioMaterial
BioSourceWIDContactWID BioSourceWID
LabeledExtractWIDCompoundWID LabeledExtractWID
Entry OtherWID
Support OtherWID
RelatedTerm OtherWID
CitationWIDOtherWID OtherWID
CommentTable OtherWID
CrossReference OtherWID
CrossReference CrossWID
Description OtherWID
DBID OtherWID
SynonymTable OtherWID
ToolAdvice OtherWID

Other Constraints

None.

Indexes

Name Columns
BIOSOURCE_NAME Name
BIOSOURCE_STRAIN Strain
BIOSOURCE_ATCC ATCCId
BIOSOURCE_TAXONWID TAXONWID
BIOSOURCE_DATASETWID DATASETWID