en 2009-11-06 This file is based on checkout of our SVN repository revision $Revision: 2489 $ data item 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. A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal Alan Ruttenberg named class expression 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 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 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final vetting obsolescence reason specification PERSON: Alan Ruttenberg This is to be used when the original term has been replaced by a term imported from an other ontology.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 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. placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged 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 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 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 example to be eventually removed placeholder This isn't a class that OBI will keep - it's a placeholder for edits that are underway. The class name should start with an underscore 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. uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. Class has undergone final review, is ready for use, and will be included in the next OBI 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 incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. 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 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 OBI to identify main classes. PERSON: Melanie Courtot PERSON: Alan Ruttenberg information content entity imported from GROUP:OBI:<http://purl.obolibrary.org/obo/obi> For external terms/classes, the ontology from which the term was imported imported from In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') is denotator type Alan Ruttenberg relates an class defined in an ontology, to the type of it's denotator 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 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 OBI_0000281 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition The official OBI 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) in branch OBI_0000277 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 An administrative note of use for a curator but of no use for a user curator note PERSON:Alan Ruttenberg curator note