source_ontology	subject_term_type	subject_term_name	relationship_type	predicate_term_name	object_term_type	object_term_name	object_term_definition
OntologyOntology	Root	OntologyOntology			Root	OntologyOntology	An ontology of terms used to defined ontologies
OntologyOntology	Root	OntologyOntology	hasClass		Class	TermType	"The type of the term (e.g., Class, Individual, etc.)"
OntologyOntology	Class	TermType	hasInstance		Individual	Root	
OntologyOntology	Class	TermType	hasInstance		Individual	Class	A class represents a concept and is a set with multiple inheritance and properties.
OntologyOntology	Class	TermType	hasInstance		Individual	Individual	An individual is an instance of one or more classes.
OntologyOntology	Class	TermType	hasInstance		Individual	Datatype	
OntologyOntology	Class	TermType	hasInstance		Individual	DatatypeProperty	A property that relates objects to datatype values.
OntologyOntology	Class	TermType	hasInstance		Individual	ObjectProperty	A property that relates objects to other objects.
OntologyOntology	Class	TermType	hasInstance		Individual	TransitiveProperty	A property that is transitive. A TransitiveProperty is a subclass of ObjectProperty.
OntologyOntology	Class	TermType	hasInstance		Individual	UnambiguousProperty	A property that an instance y can only be the value of a Property P for a single instance x.
OntologyOntology	Class	TermType	hasInstance		Individual	UniqueProperty	A property that can only have one (unique) value y for each instance x.
OntologyOntology	Class	TermType	hasInstance		Individual	UNKNOWN	UNKNOWN TERM TYPE
OntologyOntology	Root	OntologyOntology	hasClass		Class	RelationshipType	"The type of relationship between terms (e.g., subClassOf, instanceOf, etc.)"
OntologyOntology	Class	RelationshipType	hasInstance		Individual	hasClass	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	hasInstance	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	hasThing	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	hasDatatype	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	subClassOf	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	oneOf	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	instanceOf	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	intersectionOf	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	unionOf	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	complementOf	
OntologyOntology	Class	RelationshipType	hasInstance		Individual	domain	

SBEAMSOntology	Root	SBEAMSOntology			Root	SBEAMSOntology	The ontology developed for use with SBEAMS
SBEAMSOntology	Root	SBEAMSOntology	hasClass		Class	SBEAMSCore	"Core functionality of SBEAMS including user, project, and permission management and much more.  Individual modules designed for a specific biological datatype are built on top of the core."
SBEAMSOntology	Class	SBEAMSOntology	hasClass		Class	ProteomicsModule	SBEAMS Module designed for LC-MS/MS proteomics data searched with SEQUEST
SBEAMSOntology	Class	SBEAMSOntology	hasClass		Class	ImmunostainModule	"SBEAMS module designed for storage and analysis of immunohistochemistry, in situ hybridization, and other gene expression localization experiments"
SBEAMSOntology	Class	ImmunostainModule	hasClass		Class	Specimen	Whole or part of an individual which is the primary biosource for subsequent processing
SBEAMSOntology	Class	Specimen	hasClass		Class	SurgicalProcedure	Method by which the specimen is obtained
SBEAMSOntology	Class	SurgicalProcedure	hasInstance		Individual	Radical prostatectomy	Complete surgical removal of the prostate and seminal vesicles performed for patients with clinically localized prostate cancer. 
SBEAMSOntology	Class	SurgicalProcedure	hasInstance		Individual	Cystoprostatectomy	"Complete removal of the bladder, prostate, and seminal vesicles. This is most commonly performed for patients with invasive bladder cancer, however, occasionally is performed for patients with advanced prostate cancer. "
SBEAMSOntology	Class	Specimen	hasClass		Class	ClinicalDiagnosis	Provides the rationale for the surgical procedure
SBEAMSOntology	Class	ClinicalDiagnosis	hasInstance		Individual	Adenocarcinoma	Carcinoma arising from glandular epithelial cells such as within the prostate.
SBEAMSOntology	Class	ClinicalDiagnosis	hasInstance		Individual	Transitional cell carcinoma	"Carcinoma arising from transitional epithelium which lines the bladder, ureters, urethra, and the collecting system of the kidneys. "

SBEAMSOntology	Class	Specimen	hasClass		Class	Sex	Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
SBEAMSOntology	Class	Sex	hasInstance		Individual	male	individual whose sex organs contain only male gametes
SBEAMSOntology	Class	Sex	hasInstance		Individual	female	"of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes."
SBEAMSOntology	Class	Sex	hasInstance		Individual	hermaphrodite	an organism with both male and female sexual organs in one individual
SBEAMSOntology	Class	Sex	hasInstance		Individual	mixed_sex	"A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites."
SBEAMSOntology	Class	Sex	hasInstance		Individual	F-	mating type indicating the absence of F plasmid in a bacterial cell
SBEAMSOntology	Class	Sex	hasInstance		Individual	Hfr	def?
SBEAMSOntology	Class	Sex	hasInstance		Individual	F+	mating type indicating the presence of F plasmid in a bacterial cell
SBEAMSOntology	Class	Sex	hasInstance		Individual	mating_type_a	Mating type of S. cerevisiae.
SBEAMSOntology	Class	Sex	hasInstance		Individual	mating_type_alpha	Mating type of S. cerevisiae.
SBEAMSOntology	Class	Sex	hasInstance		Individual	unknown_sex	organism(s) whose sex is unknown

SBEAMSOntology	Class	ImmunostainModule	hasClass		Class	Assay	One imaged location on an Assay
SBEAMSOntology	Class	Assay	hasClass		Class	AssayType	"Type of image that is provided (e.g., White light, single channel, composite, etc.)"
SBEAMSOntology	Class	AssayType	hasInstance		Individual	Immunohistochemistry	Assay that detects antigen proteins via antibodies linked to detectable markers
SBEAMSOntology	Class	AssayType	hasInstance		Individual	In situ hybridization	Assay that detects mRNA presence via probes linked to detectable markers
SBEAMSOntology	Class	AssayType	hasInstance		Individual	GFP	Assay that detects the expression of a gene by observing the presence of the Green Fluorescent Protein which is being expressed by virtue of its DNA having been inserted into the DNA of the gene 

SBEAMSOntology	Class	Assay	hasClass		Class	AssayChannel	A wavelength band of detection of one or more components in the image
SBEAMSOntology	Class	AssayChannel	hasClass		Class	AssayUnitExpression	Quantified expression level for a StructuralUnit within an Assay
SBEAMSOntology	Class	AssayUnitExpression	hasClass		Class	PercentType	Type of total population of which the specified percent is a fraction of
SBEAMSOntology	Class	PercentType	hasInstance		Individual	PercentOfTotal	The value is expressed as the percentage of the total population which is visible or well known
SBEAMSOntology	Class	PercentType	hasInstance		Individual	PercentOfVisible	The value is expressed as the percentage of the visible population which is likely or know to be less than the true total population

SBEAMSOntology	Class	AssayUnitExpression	hasClass		Class	ExpressionPattern	A qualitative morphological description of the expression
SBEAMSOntology	Class	ExpressionPattern	hasInstance		Individual	graded	
SBEAMSOntology	Class	ExpressionPattern	hasInstance		Individual	homogenous	
SBEAMSOntology	Class	ExpressionPattern	hasInstance		Individual	regionally restricted	
SBEAMSOntology	Class	ExpressionPattern	hasInstance		Individual	single cells	
SBEAMSOntology	Class	ExpressionPattern	hasInstance		Individual	spotted	


SBEAMSOntology	Class	AssayChannel	hasClass		Class	AssayImage	One imaged location on an Assay
SBEAMSOntology	Class	AssayImage	hasClass		Class	AssayImageType	"Type of image that is provided (e.g., White light, single channel, composite, etc.)"
SBEAMSOntology	Class	AssayImageType	hasInstance		Individual	White light	Unfiltered transmitted or reflected light image of the assay
SBEAMSOntology	Class	AssayImageType	hasInstance		Individual	Single channel	Narrow wavelength filtered light imaging one component of the assay
SBEAMSOntology	Class	AssayImageType	hasInstance		Individual	Composite	Computer-generated composite image combining two or more images of other type











STOP							


MISFISHIEOntology							

MO	Root	MGEDOntology					
MO	Class	MGEDCoreOntology	subClassOf			MGEDOntology	An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
MO	Class	MGEDExtendedOntology	subClassOf			MGEDOntology	Location for those classes that are not in the Core ontology as they do are not containable in MAGE. It is not yet structured to work with the Core ontology
MO	Class	Scale	subClassOf			MGEDOntology	"The scale (linear, log10, ln, etc) used to represent the value."
MO	Class	URI	subClassOf			MGEDOntology	Uniform Resource Identifier
MO	Class	DataType	subClassOf			MGEDOntology	"Primitive data types found in computing languages such as float, boolean, etc."
MO	Individual	log_base_2	instanceOf			Scale	"The values presented are logarithm, base 2."
MO	Individual	log_base_e	instanceOf			Scale	"The values presented are logarithm, base e."
MO	Individual	log_base_10	instanceOf			Scale	"The values presented are logarithm, base 10."
MO	Individual	linear_scale	instanceOf			Scale	"The scale is a standard base 10, non logarithmic scale."
MO	Individual	unscaled	instanceOf			Scale	The values are unordered and have no scale.
MO	Individual	positive_float	instanceOf			DataType	
MO	Individual	discrete	instanceOf			DataType	
MO	Individual	negative_integer	instanceOf			DataType	
MO	Individual	list_of_integer	instanceOf			DataType	
MO	Class	DescriptionPackage	subClassOf			MGEDCoreOntology	MAGE package for description of annotations and references to annotations.
MO	Class	PublicationType	subClassOf			DescriptionPackage	"Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.)."
MO	Class	OntologyEntry	subClassOf			DescriptionPackage	External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
MO	Class	DatabaseEntryType	subClassOf			DescriptionPackage	Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
MO	Class	Database	subClassOf			DescriptionPackage	Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
MO	Class	BibliographicReference	subClassOf			DescriptionPackage	"A bibliographic reference is a published citation in a journal, book, other format e.g. web resource"

MO	Class	Protocol	hasClass	has_citation	Class	BibliographicReference	"A bibliographic reference is a published citation in a journal, book, other format e.g. web resource"
MO	Class	Protocol	subClassOf			ProtocolPackage	The MAGE package for protocols.
MO	Class	Transformation	hasClass	has_protocol	Class	Protocol	Documentation of the set of steps taken in a procedure.
MO	Class	Water	hasClass	has_treatment	Class	Protocol	Documentation of the set of steps taken in a procedure.
MO	Class	Preservation	hasClass	has_protocol	Class	Protocol	Documentation of the set of steps taken in a procedure.
MO	Class	Treatment	hasClass	has_protocol	Class	Protocol	Documentation of the set of steps taken in a procedure.
MO	Class	Protocol	hasClass	has_type	Class	ProtocolType	A controlled set of terms to provide a descriptor for the type of protocol.
MO	Class	Protocol	hasClass	has_hardware	Class	Hardware	The machine or instrument used.
MO	Class	Protocol	hasClass	has_software	Class	Software	The software application used.
MO	Class	Protocol	hasClass	has_URI	Class	URI	Uniform Resource Identifier
MO	Class	Protocol	hasThing	text		thing	
MO	Class	Protocol	hasDatatype	title		string	
MO	Class	Protocol	hasDatatype	description		string	

MO	Class	BioSequence	subClassOf		Class	BioSequencePackage	MAGE package for biological sequences (biosequence).
MO	Class	BioSequence	hasClass	has_type	Class	PolymerType	"Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence."
MO	Class	BioSequence	hasClass	has_type	Class	BioSequenceType	"Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g BAC, cDNA clone), or  computational (e.g unigene cluster, consensus)"
MO	Class	BioSequence	hasClass	has_species	Class	Organism	The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
