Sample

Bases: NBOBaseClass

Represents the XML element Sample.

This field captures a description of the sample that was imaged in this experiment.

getTypeName()

Returns the class type name.

Returns:

Type	Description
string	The class type name

getXMLName()

Returns the XML element name corresponding to this class.

Returns:

Type	Description
string	The XML element name

getNBOType()

Returns the NBO Type corresponding to this class.

Returns:

Type	Description
int	The NBO Type value

getChildren()

Returns a list of all classes derived from this class.

Returns:

Type	Description
List[NBOBaseClass]	The list of derived classes

getSubElements()

Returns a list of all child elements contained in this class.

Returns:

Type	Description
List[NBOBaseClass]	The list of child classes

fromJsonFile(path)

Populates this object from a JSON file.

Parameters:

Name	Type	Description	Default
path	string	The path to the JSON file	required

fromJsonString(json_string)

Populates this object from a JSON string.

Parameters:

Name	Type	Description	Default
json_string	string	The JSON content as a string	required

fromXmlFile(path)

Populates this object from a XML file.

Parameters:

Name	Type	Description	Default
path	string	The path to the XML file	required

fromXmlString(xml_string)

Populates this object from a XML string.

Parameters:

Name	Type	Description	Default
xml_string	string	The XML content as a string	required

toXmlFile(filename)

Serializes this object to an XML file.

Parameters:

Name	Type	Description	Default
filename	string	The path to the output XML file	required

toXmlString()

Serializes this object to an XML string.

Returns:

Type	Description
string	A string containing the XML representation of this object

setID(value)

Sets the value of the ID attribute.

A unique identifier for this Sample.

Parameters:

Name	Type	Description	Default
value	LSID_Type	The value to set	required

getID()

Returns the value of the ID attribute.

A unique identifier for this Sample.

Returns:

Type	Description
LSID_Type	The value of the attribute

resetID()

Resets the ID attribute to an unset state.

A unique identifier for this Sample.

hasID()

Checks whether the optional ID attribute is present.

A unique identifier for this Sample.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setName(value)

Sets the value of the Name attribute.

A user assigned Name for this Sample.

Parameters:

Name	Type	Description	Default
value	Denomination_Type	The value to set	required

getName()

Returns the value of the Name attribute.

A user assigned Name for this Sample.

Returns:

Type	Description
Denomination_Type	The value of the attribute

resetName()

Resets the Name attribute to an unset state.

A user assigned Name for this Sample.

hasName()

Checks whether the optional Name attribute is present.

A user assigned Name for this Sample.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setBiologicalOrigin(value)

Sets the value of the BiologicalOrigin attribute.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

Parameters:

Name	Type	Description	Default
value	boolean	The value to set	required

getBiologicalOrigin()

Returns the value of the BiologicalOrigin attribute.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

Returns:

Type	Description
boolean	The value of the attribute

setSampleType(value)

Sets the value of the SampleType attribute.

If of Biological Origin, this field records a term that describes the general category of this Sample.

Parameters:

Name	Type	Description	Default
value	SampleType_Type	The value to set	required

getSampleType()

Returns the value of the SampleType attribute.

If of Biological Origin, this field records a term that describes the general category of this Sample.

Returns:

Type	Description
SampleType_Type	The value of the attribute

resetSampleType()

Resets the SampleType attribute to an unset state.

If of Biological Origin, this field records a term that describes the general category of this Sample.

hasSampleType()

Checks whether the optional SampleType attribute is present.

If of Biological Origin, this field records a term that describes the general category of this Sample.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setLiveSample(value)

Sets the value of the LiveSample attribute.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

Parameters:

Name	Type	Description	Default
value	boolean	The value to set	required

getLiveSample()

Returns the value of the LiveSample attribute.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

Returns:

Type	Description
boolean	The value of the attribute

setOrganism(value)

Sets the value of the Organism attribute.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getOrganism()

Returns the value of the Organism attribute.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

Returns:

Type	Description
string	The value of the attribute

setOrganismTermAccession(value)

Sets the value of the OrganismTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getOrganismTermAccession()

Returns the value of the OrganismTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Returns:

Type	Description
string	The value of the attribute

resetOrganismTermAccession()

Resets the OrganismTermAccession attribute to an unset state.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

hasOrganismTermAccession()

Checks whether the optional OrganismTermAccession attribute is present.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setOrganismPart(value)

Sets the value of the OrganismPart attribute.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getOrganismPart()

Returns the value of the OrganismPart attribute.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
string	The value of the attribute

resetOrganismPart()

Resets the OrganismPart attribute to an unset state.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

hasOrganismPart()

Checks whether the optional OrganismPart attribute is present.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setOrganismPartTermAccession(value)

Sets the value of the OrganismPartTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getOrganismPartTermAccession()

Returns the value of the OrganismPartTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
string	The value of the attribute

resetOrganismPartTermAccession()

Resets the OrganismPartTermAccession attribute to an unset state.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

hasOrganismPartTermAccession()

Checks whether the optional OrganismPartTermAccession attribute is present.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setSamplePreparationMethod(value)

Sets the value of the SamplePreparationMethod attribute.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getSamplePreparationMethod()

Returns the value of the SamplePreparationMethod attribute.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
string	The value of the attribute

resetSamplePreparationMethod()

Resets the SamplePreparationMethod attribute to an unset state.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

hasSamplePreparationMethod()

Checks whether the optional SamplePreparationMethod attribute is present.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setSamplePreparationMethodTermAccession(value)

Sets the value of the SamplePreparationMethodTermAccession attribute.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getSamplePreparationMethodTermAccession()

Returns the value of the SamplePreparationMethodTermAccession attribute.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
string	The value of the attribute

resetSamplePreparationMethodTermAccession()

Resets the SamplePreparationMethodTermAccession attribute to an unset state.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

hasSamplePreparationMethodTermAccession()

Checks whether the optional SamplePreparationMethodTermAccession attribute is present.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setMetrologySample(value)

Sets the value of the MetrologySample attribute.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

Parameters:

Name	Type	Description	Default
value	boolean	The value to set	required

getMetrologySample()

Returns the value of the MetrologySample attribute.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

Returns:

Type	Description
boolean	The value of the attribute

setFacingTheObjective(value)

Sets the value of the FacingTheObjective attribute.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

Parameters:

Name	Type	Description	Default
value	FacingTheObjectiveChoice_Type	The value to set	required

getFacingTheObjective()

Returns the value of the FacingTheObjective attribute.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

Returns:

Type	Description
FacingTheObjectiveChoice_Type	The value of the attribute

resetFacingTheObjective()

Resets the FacingTheObjective attribute to an unset state.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

hasFacingTheObjective()

Checks whether the optional FacingTheObjective attribute is present.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setMountingMedium_List(value)

Sets the list of MountingMedium elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[MountingMedium]	The new list of MountingMedium elements	required

getMountingMedium_List()

Returns the list of MountingMedium elements.

No description available in the XSD standard.

Returns:

Type	Description
List[MountingMedium]	The list of MountingMedium elements

addToMountingMedium_List(value)

Adds a new MountingMedium element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	MountingMedium	The element to add	required

clearMountingMedium_List()

Clear the list of MountingMedium.

No description available in the XSD standard.

setCoverGlass_List(value)

Sets the list of CoverGlass elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[CoverGlass]	The new list of CoverGlass elements	required

getCoverGlass_List()

Returns the list of CoverGlass elements.

No description available in the XSD standard.

Returns:

Type	Description
List[CoverGlass]	The list of CoverGlass elements

addToCoverGlass_List(value)

Adds a new CoverGlass element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	CoverGlass	The element to add	required

clearCoverGlass_List()

Clear the list of CoverGlass.

No description available in the XSD standard.

setSampleHolder_List(value)

Sets the list of SampleHolder elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[SampleHolde]	The new list of SampleHolder elements	required

getSampleHolder_List()

Returns the list of SampleHolder elements.

No description available in the XSD standard.

Returns:

Type	Description
List[SampleHolde]	The list of SampleHolder elements

addToSampleHolder_List(value)

Adds a new SampleHolder element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	SampleHolder	The element to add	required

clearSampleHolder_List()

Clear the list of SampleHolder.

No description available in the XSD standard.

setDescription(value)

Sets the value of the Description element.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Description	The value to set	required

getDescription()

Returns the value of the Description element.

No description available in the XSD standard.

Returns:

Type	Description
Description	The value of the element

resetDescription()

Resets the Description element to an unset state.

No description available in the XSD standard.

hasDescription()

Checks whether the optional Description element is present.

No description available in the XSD standard.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setAnnotationRef_List(value)

Sets the list of AnnotationRef elements.

This is a simple multi-line comment or annotation describing this component.

Parameters:

Name	Type	Description	Default
value	List[AnnotationRef]	The new list of AnnotationRef elements	required

getAnnotationRef_List()

Returns the list of AnnotationRef elements.

This is a simple multi-line comment or annotation describing this component.

Returns:

Type	Description
List[AnnotationRef]	The list of AnnotationRef elements

addToAnnotationRef_List(value)

Adds a new AnnotationRef element to this object.

This is a simple multi-line comment or annotation describing this component.

Parameters:

Name	Type	Description	Default
value	AnnotationRef	The element to add	required

clearAnnotationRef_List()

Clear the list of AnnotationRef.

This is a simple multi-line comment or annotation describing this component.