en $Revision$ data item named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions A named class expression is a logical expression that is given a name. The name can be used in place of the expression. Alan Ruttenberg named class expression universal A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf Alan Ruttenberg Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. defined class "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal Barry Smith, Werner Ceusters A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor. pending final vetting The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job failed exploratory term Person:Alan Ruttenberg An editor note should explain what were the merged terms and the reason for the merge. terms merged term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. We expect to be able to mine these new reasons and add instances as required. This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. other placeholder removed This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported obsolescence reason specification PERSON: Alan Ruttenberg The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. obsolescence reason specification PERSON: Melanie Courtot The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. OBI_0000266 Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) curation status specification curation status specification GROUP:OBI:<http://purl.obolibrary.org/obo/obi> The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. PERSON:Bill Bug group:OBI Alan Ruttenberg requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. Alan Ruttenberg to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. group:OBI Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. example to be eventually removed metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg core Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Melanie Courtot PERSON: Alan Ruttenberg information content entity In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') is denotator type Alan Ruttenberg is denotator type relates an class defined in an ontology, to the type of it's denotator curator note PERSON:Alan Ruttenberg An administrative note of use for a curator but of no use for a user curator note A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober example of usage GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example has obsolescence reason has obsolescence reason PERSON:Melanie Courtot PERSON:Alan Ruttenberg Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. Person:Alan Ruttenberg Use on obsolete terms, relating the term to another term that can be used as a substitute term replaced by term replaced by Person:Alan Ruttenberg editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term PERSON:Daniel Schober PERSON:Bill Bug PERSON:Melanie Courtot PERSON:Alan Ruttenberg OBI_0000281 has curation status has curation status definition editor GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" expand assertion to expand assertion to Chris Mungall A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from For external terms/classes, the ontology from which the term was imported PERSON:Melanie Courtot PERSON:Alan Ruttenberg imported from GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. PERSON:Daniel Schober definition alternative term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term PERSON:Daniel Schober An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. PERSON:Alan Ruttenberg GROUP:OBO Foundry <http://obofoundry.org/> PERSON:Chris Mungall PERSON:Melanie Courtot The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Bjoern Peters OBO foundry unique label in branch OBI_0000277 An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. in branch GROUP:OBI definition source definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> use boolean value xsd:true to indicate that the property is an antisymmetric property part_of antisymmetric property xsd:true Alan Ruttenberg antisymmetric property antisymmetric property expand expression to expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall first order logic expression first order logic expression PERSON:Alan Ruttenberg GROUP:OBI:<http://purl.obfoundry.org/obo/obi> An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. editor note PERSON:Daniel Schober editor note