en
$Revision$
has obsolescence reason
in branch
OBI_0000277
example of usage
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example
has curation status
OBI_0000281
definition editor
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Name of editor entering the definition
PERSON:Daniel Schober
definition editor
preferred term
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
preferred term
term replaced by
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
term replaced by
imported from
For external terms/classes, the ontology from which the term was imported
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
alternative term
definition
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
editor note
An administrative note intended for its editor. It will not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
definition source
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
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
data item
information content entity
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
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.
curation status specification
data about an ontology part
Person:Alan Ruttenberg
data about an ontology part is a data item about a part of an ontology, for example a term
obsolescence reason specification
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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.
obsolescence reason specification
failed exploratory term
Person:Alan Ruttenberg
The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
example to be eventually removed
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.
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
ready for release
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."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
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.
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: Alan Ruttenberg
PERSON: Melanie Courtot
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
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 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.
other
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.