org.biopax.paxtools.model.level3

Interface BioSource

All Superinterfaces:

BioPAXElement, Cloneable, Level3Element, Named, Serializable, UtilityClass, XReferrable

All Known Implementing Classes:

BioSourceImpl

public interface BioSource
extends UtilityClass, Named

Definition: The biological source of an entity (e.g. protein, RNA or DNA). Some entities are considered source-neutral (e.g. small molecules), and the biological source of others can be deduced from their constituentss (e.g. complex, pathway). Examples: HeLa cells, human, and mouse liver tissue.

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
CellVocabulary	getCellType() A cell type, e.g.
TissueVocabulary	getTissue() An external controlled vocabulary of tissue types.
void	setCellType(CellVocabulary cellType) A cell type, e.g.
void	setTissue(TissueVocabulary tissue) An external controlled vocabulary of tissue types.

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getUri, isEquivalent

Method Detail

getCellType

CellVocabulary getCellType()

A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.

Returns:

cell type if this biosource is a cell line or a specific tissue. Null otherwise.

setCellType

void setCellType(CellVocabulary cellType)

A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.

Parameters:

cellType - if this biosource is a cell line or a specific tissue. Null for n/a.

getTissue

TissueVocabulary getTissue()

An external controlled vocabulary of tissue types. A reference to the BRENDA

Returns:

An external controlled vocabulary of tissue types.

setTissue

void setTissue(TissueVocabulary tissue)

An external controlled vocabulary of tissue types. A reference to the BRENDA

Parameters:

tissue - An external controlled vocabulary of tissue types.