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.