Bio-ontology glossary
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ABCD
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TermDefinitionCommentsSynonyms
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This glossary of ontology-related terms originated from student exercises that were part of the 2012 and 2013 NESCent Ontology Summer Courses.
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To make this glossary grow or to suggest improvements or corrections, please write to: segerdel@ohsu.edu
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annotationAn E-Q statement.
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Explanatory information added to a datum or axiom.
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Linking a term to a datum.
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APIApplication programming interface - interface provided by software-systems to interact with other programs.Application Programming Interface
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arborealLiving or existing in a tree or trees.Or having the shape of a tree.
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axiomA premise or starting point of reasoning.
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A statement that is assumed to be true.
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BioPortalA web-based community resource for ontology publication and management.
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boneA rigid structure as part of the endoskeleton of a vertebrate.
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CAROCommon Anatomical Reference Ontology
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childA direct subclass of an upper level class connected by an is_a relationship.
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classesA collection of individuals or instances.
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controlled vocabularyAny closed, prescribed list of terms used for classifying data.
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dbxrefCross reference to an external database.How is this different from xref? Or is there no difference?
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DL queryProvides an interface for querying and searching a classified ontology.DL = description logic
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entityAny distinct thing, a thing, a class or a subclass. A something as opposed to nothing, i.e. cuticle, nail, finger, all are entities.
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An object, a thing; and within OWL a relationship between objects is included as an entity.term
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hexaploidy6N: a condition in which the ploidy level includes 6 copies of chromosomes.
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homologyComparing different organisms, two or more structures are homologous if: 1-They demonstrate the same fundamental organization; 2-They demonstrate the same connexions between neighbor structures; 3-1 and 2 are true regardless of the observable variability of the structures. Then we characterize the structure as a homology shared within the studied group. (Cladistic definition)Good answers, but aren't these "criteria" to recognize homology? It doesn't exactly say what is homology. Also, what about common ancestry? / Very good point, actually homology is a concept that has been very difficult to state. For more information read next paper: "The biological concept of homology (1989)" from Günter Wagner in Annual Review in Ecology and Systematics.
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Shared ancestry
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The same organ or structure in different organisms.But you can actually have two different organs or structures that are homologous like the human arm and the birds wing.
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hyperplasiaEnlargement of a body part due to abnormal increase in cell number.
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IAOInformation Artifact Ontology - an ontology of information entities.Information Artifact Ontology
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instanceAn individual example of a class.
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IRIInternationalized resource identifier - an extension of the URI, which supports Unicode.
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Internationalized resource identifier (URI generalization).
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knowledge representation languageA language used to represent relationships between concepts.
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languageMethod of communication between entities.
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Manchester syntaxOWL syntax that is designed to be easier for non-logicians to read.http://www.w3.org//TR/owl2-primer/
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metadataInformation about data contained in a file: data about data."In a file" seems like too much of a constraint in the definition.data
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microzooplanktonA group of heterotrophic and mixotrophic zooplankton between 20 and 200 µm in length.
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MIREOTA method to integrate parts of one ontology into another.http://obi-ontology.org/page/MIREOTMinimum Information to Reference an External Ontology
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musicMusic *(defined as Music Ontology) provides main concepts and properties for describing music (i.e. artists, albums, tracks, but also performances, arrangements, etc.) on the Semantic Web.http://musicontology.com
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non-lossyWithout losing anything.
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OBOOpen Biomedical Ontologies- an "unbrella organization" where many ontologies convene that use shared vocabularies to be used accress all biological and biomedical domains.Open Biomedical Ontologies
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ontologyFormalized vocabulary + rules.
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OWLA set of formal languages to express semantics for data interoperability.http://en.wikipedia.org/wiki/Web_Ontology_Language
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parent termTerm A is the parent term of B if B has an is-a or subClassOf relationship with A.
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partonomyHeirarchical relationship that associates x and y where x is a part of (or a member of) y
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Hierarchy based on part_of (and/or has_part etc) relationships.
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phototrophyUsing light for energy.
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post-compositionMaking up an anonymous class on the fly while using the ontology.e.g. you ask for "seta:bristles of color:yellow on position:head"
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pre-compositionDefining classes a priori.e.g. you define bristles on wasp heads as a separate entity in the ontology with its own name ("wasp head yellow seta")
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primary labelLabel that appears in the ontology interface - other labels may be included as exact or related synonyms.
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provenanceThe history of attribution of a term or definition.
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PURLA persistent URL that redirects to a currently active URL.The PURL continues to exist as a persistent reference, where the actual underlying location can change.Persistent Uniform Resource Locator
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Persistent uniform resource locator: is an example of a uniform resource locator (URL) or location-based uniform resource identifier (URI) that is used to redirect to the location of the requested web resource: taken from http://en.wikipedia.org/wiki/Persistent_uniform_resource_locator
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RDF/XMLResource Description Framework/Extensible Markup Language
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reasonerSoftware used to infer logical relationships between different terms.inferer
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reasoningReconciling multiple axioms.So is it creating relationships between classes or concepts? More like interpreting the existing relationships. If Axioms are A is_a B and B is_a C, reasoner would determine A is_a C.
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reificationA technique enabling a richer description of a property.
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relationshipMathematically, any linkage between or sharing of data (or absence thereof) within or among sets, be those sets overlapping or discrete.properties
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root termThe only term in an ontology which has no is_a relationship with another term.
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semantic webA set of standards for the interoperation of data (not just documents) on the internet.
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SPARQL queryA query expressed in the SPARQL Protocol and RDF Query Language (SPARQL, yes, really).
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speciesA word referring to a human conceptualization of the basic unit of diversity of life forrms: a group of populations that share morphological, genetic and evolutionary history.
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syntaxFormal rules governing a language.
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tagsClasses annotated onto instances.
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termLabel for an anatomical entity or the descriptor of an anatomical entity.The name/label of any concept? Definition applies to Anatomy Ontologies - if we want a more general definition we can change it.
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transitivityA property of some relations. E.g., the 'is a' relation between sets X, Y, and Z. If X is a Y, and if Y is a Z, then X is a Z.Pretty straightfoward logical property that allows us to get the correct PATH.
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triplestoreA database designed for the storage, and retrieval of subject-predicate-object triples.
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True Path RuleThe pathway from a subClass all the way up to its top level parent(s) must be universally true.
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turtleFabulous animal.Alternate definition: Terse RDF Triple Language - a syntax that can be used for RDFs (applicable to ontologies in OWL).
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UberonIntegrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage.
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upper level ontologyGeneral ontology used to structure more specific ontologies.upper ontology
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An ontology (in the sense used in information science) which describes very general concepts that are the same across all knowledge domains.https://en.wikipedia.org/wiki/Upper_ontology
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URIUniform Resource Identifier - standardized way of naming things.URI schemes describe the type of URI, like URLs: http://www.nescent.org or ISBNs: urn:isbn:978-0-691-15195-3.Uniform Resource Identifier
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URNUniform Resource Name, a type of locator.
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use caseTechnical requirements of the project.
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xrefA cross reference to a term that means exactly the same thing as the entity provided.
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