definition
type: AnnotationProperty

editor note
type: AnnotationProperty

in branch
type: AnnotationProperty

has curation status
type: AnnotationProperty

definition source
type: AnnotationProperty

definition editor
type: AnnotationProperty

alternative term
type: AnnotationProperty

editor preferred term
type: AnnotationProperty

example of usage
type: AnnotationProperty

has measurement unit label
type: ObjectProperty
type: FunctionalProperty
range: measurement unit label
sub property of: has part

is about
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
definition editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting

denotes
type: ObjectProperty
editor note: 2009-08-18 Alan Ruttenberg. changed name to denotes per discussions. Definition still uses specifically denotes. Will fix that in second pass.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The word Boston on a traffic signn in Massachusetts generically denotes the city of Boston
definition: g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
definition editor: person:Alan Ruttenberg
sub property of: is about

is quality measurement of
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
definition editor: Alan Ruttenberg
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
domain: measurement datum
sub property of: is about

has coordinate unit label
type: ObjectProperty
type: FunctionalProperty
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
domain: cartesian spatial coordinate datum
range: length unit
sub property of: has part

is duration of
type: ObjectProperty
definition editor: Person:Alan Ruttenberg
definition: relates a process to a time-measurement-datum that represents the duration of the process
has curation status: metadata complete
sub property of: is about
domain: time measurement datum
range: Process

is quality measured as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
definition: inverse of the relation of is quality measurement of
has curation status: metadata complete
inverse of: is quality measurement of

part of
type: ObjectProperty
editor note: There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: float

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI_0000349
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
editor preferred term: instruction trigger
has curation status: metadata complete

measurement unit label
type: Class
subclass of: label
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
definition editor: PERSON: Melanie Courtot
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
definition editor: PERSON: Alan Ruttenberg
editor preferred term: measurement unit label
has curation status: pending final vetting

objective specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
definition source: OBI_0000217
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor preferred term: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: pending final vetting

narrative object
type: Class
subclass of: information content entity
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000013
definition: A narrative object is an information content entity that is a set of propositions.
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition source: group:OBI
editor preferred term: narrative object
definition editor: person:Chris Stoeckert
has curation status: uncurated

action specification
type: Class
subclass of: directive information entity
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
has curation status: metadata incomplete

label
type: Class
subclass of: information content entity
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
definition editor: GROUP: IAO
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
editor preferred term: label
has curation status: metadata incomplete

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition: Software is a plan specification which is a series of encoded instructions that can be directly executed by a processing unit or transformed in to a form that can be. For programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond to the tokenized version of the text stripped of comments.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
editor preferred term: software
has curation status: metadata complete

journal article
type: Class
subclass of: report
definition source: OBI_0000159
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
definition: a report that is published in a journal
definition source: group:OBI
editor preferred term: journal article
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
has curation status: metadata complete

model number
type: Class
subclass of: symbol
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: Person: Alan Ruttenberg
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
editor preferred term: model number
has curation status: pending final vetting

programming language
type: Class
subclass of: plan specification
definition source: OBI_0000058
definition: A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
example of usage: R, Perl, Java
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: programming language
has curation status: metadata complete

data item
type: Class
subclass of: information content entity
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
editor preferred term: data item
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
alternative term: data
has curation status: pending final vetting

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
definition editor: PERSON: Jonathan Rees
definition: a smallish, word-like datum...
editor preferred term: label

numeral
type: Class
subclass of: symbol
definition: A symbol that denotes a number.
definition editor: PERSON: Jonathan Rees
editor preferred term: numeral

information content entity
type: Class
subclass of: Restriction
  on property: is about
  some values from: Entity
definition source: OBI_0000142
definition editor: PERSON: Chris Stoeckert
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor preferred term: information content entity
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
has curation status: pending final vetting

integer numeral
type: Class
subclass of: numeral
definition editor: PERSON: Jonathan Rees
definition: a numeral that denotes an integer
editor preferred term: integer numeral

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
example of usage: 10 feet. 3 ml.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
definition editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
definition editor: PERSON: Alan Ruttenberg
has curation status: metadata complete

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: RealizableEntity
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
has curation status: metadata incomplete

time trigger
type: Class
subclass of: conditional specification
definition source: OBI_0000331
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
definition: revisit?
editor preferred term: time trigger
has curation status: uncurated

dot plot
type: Class
subclass of: graph
definition source: OBI_0000123
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
example of usage: Dot plot of SSC-H and FSC-H.
editor preferred term: dot plot
definition source: group:OBI
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

graph
type: Class
subclass of: diagram
definition source: OBI_0000240
definition source: group:OBI
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition editor: PERSON: Lawrence Hunter
editor preferred term: graph
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
has curation status: pending final vetting

rule
type: Class
subclass of: conditional specification
definition source: OBI_0500021
editor note: MSI
definition source: PRS
definition editor: PRS
definition: a rule is an executable which guides, defines, restricts actions
example of usage: example to be added
editor preferred term: rule
has curation status: uncurated

contour plot
type: Class
subclass of: graph
definition source: OBI_0000246
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
editor preferred term: contour plot
editor note: generically_dependent_continuants
definition source: group:Flow Cytometry community
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

algorithm
type: Class
subclass of: plan specification
definition source: OBI_0000270
definition: A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: metadata complete

software interpreter
type: Class
subclass of: algorithm
definition source: OBI_0000199
definition: An algorithmy that takes, as input, some digital entity, and takes action driven by the information content of that algorithm
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
example of usage: R program, Perl interpreter, Java virtual machine
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: software interpreter
has curation status: metadata complete

curation status specification
type: Class
equivalent class: Class
  one of: uncurated
  one of: pending final vetting
  one of: ready for release
  one of: metadata incomplete
  one of: metadata complete
  one of: placeholder
  one of: example to be eventually removed
subclass of: data about an ontology part
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
definition editor: PERSON:Bill Bug
definition: 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.
editor preferred term: curation status specification
has curation status: pending final vetting

density plot
type: Class
subclass of: graph
definition source: OBI_0000179
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
example of usage: Density plot of SSC-H and FSC-H.
editor preferred term: density plot
definition source: group:Flow Cytometry community
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

report
type: Class
subclass of: document
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000099
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
definition source: GROUP: OBI
definition editor: PERSON:Chris Stoeckert
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
editor preferred term: report
has curation status: pending final vetting

source code module
type: Class
subclass of: directive information entity
definition source: OBI_0000039
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: source code module
has curation status: uncurated

data format specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
definition source: OBI_0000187
definition editor: PERSON: Alan Ruttenberg
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: metadata incomplete

data set
type: Class
subclass of: data item
definition source: OBI_0000042
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
editor preferred term: data set
definition source: group:OBI
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: metadata complete

image
type: Class
subclass of: figure
definition source: OBI_0000030
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
definition source: group:OBI
editor preferred term: image
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
has curation status: ready for release

data about an ontology part
type: Class
subclass of: data item
definition editor: Person:Alan Ruttenberg
definition: data about an ontology part is a data item about a part of an ontology, for example a term

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
definition editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
editor preferred term: plan specification
has curation status: metadata complete

measurement datum
type: Class
subclass of: data item
editor note: 2/2/2009 is_specified_output of some assay?
definition source: OBI_0000305
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: group:OBI
editor preferred term: measurement datum
definition editor: person:Chris Stoeckert
has curation status: metadata complete

version number
type: Class
subclass of: symbol
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
definition editor: GROUP: IAO
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
editor preferred term: version number
has curation status: uncurated

serial number
type: Class
subclass of: symbol
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
editor preferred term: serial number
has curation status: uncurated

lot number
type: Class
subclass of: symbol
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
alternative term: batch number
editor preferred term: lot number
has curation status: uncurated

setting datum
type: Class
subclass of: data item
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
has curation status: uncurated

conclusion textual entity
type: Class
subclass of: textual entity
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
definition editor: Person:Alan Ruttenberg
editor preferred term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
has curation status: metadata complete

histogram
type: Class
subclass of: graph
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: histogram
has curation status: ready for release

heatmap
type: Class
subclass of: graph
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: heatmap
has curation status: ready for release

Venn diagram
type: Class
subclass of: graph
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: Venn diagram
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram
has curation status: ready for release

survival curve
type: Class
subclass of: graph
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
editor preferred term: survival curve
has curation status: ready for release

dendrogram
type: Class
subclass of: graph
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: dendrogram
has curation status: ready for release

scatter plot
type: Class
subclass of: graph
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
editor preferred term: scatter plot
alternative term: scattergraph
has curation status: ready for release

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
has curation status: ready for release

obsolescence reason specification
type: Class
equivalent class: Class
  one of: other
  one of: terms merged
  one of: term imported
  one of: placeholder removed
  one of: failed exploratory term
  one of: term split
subclass of: data about an ontology part
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition: 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.
editor preferred term: obsolescence reason specification
has curation status: pending final vetting

textual entity
type: Class
subclass of: information content entity
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
editor preferred term: textual entity
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
definition editor: PERSON: Lawrence Hunter
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
alternative term: text

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred term: citation
definition editor: PERSON: Lawrence Hunter
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication
has curation status: pending final vetting

author identification
type: Class
subclass of: textual entity
editor preferred term: author identification
definition: A textual entity intended to identify a particular author
example of usage: L. Hunter
definition editor: PERSON: Lawrence Hunter
has curation status: pending final vetting

institutional identification
type: Class
subclass of: textual entity
editor preferred term: institutional identification
definition: A textual entity intended to identify a particular institution
definition editor: PERSON: Lawrence Hunter
example of usage: University of Colorado Denver School of Medicine
has curation status: pending final vetting

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
editor preferred term: caption
definition: A textual entity that describes a figure
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
definition editor: PERSON: Lawrence Hunter
has curation status: pending final vetting

document title
type: Class
subclass of: textual entity
editor preferred term: document title
definition: A textual entity that names a document
definition editor: PERSON: Lawrence Hunter
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
has curation status: pending final vetting

table
type: Class
subclass of: textual entity
editor preferred term: table
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
definition editor: PERSON: Lawrence Hunter
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting

table of abbreviations
type: Class
subclass of: table
editor preferred term: table of abbreviations
definition: A table where the constituent texts are abbreviations and their expansions
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
definition editor: PERSON: Lawrence Hunter
has curation status: pending final vetting

figure
type: Class
subclass of: information content entity
editor preferred term: figure
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
example of usage: Any picture, diagram or table
definition editor: PERSON: Lawrence Hunter
has curation status: metadata complete

diagram
type: Class
subclass of: figure
editor preferred term: diagram
definition: A figure that expresses one or more propositions
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
definition editor: PERSON: Lawrence Hunter
has curation status: metadata complete

document
type: Class
subclass of: information content entity
editor preferred term: document
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
definition editor: PERSON: Lawrence Hunter
has curation status: metadata complete

publication
type: Class
subclass of: document
editor preferred term: publication
definition: A document that has been accepted by a publisher
example of usage: A journal article or book
definition editor: PERSON: Lawrence Hunter
has curation status: metadata complete

publication about an investigation
type: Class
subclass of: publication
editor preferred term: publication about an investigation
definition: A publication that is about an investigation
example of usage: Most scientific journal articles
definition editor: PERSON: Lawrence Hunter
alternative term: scientific publication
has curation status: metadata complete

patent
type: Class
subclass of: document
editor preferred term: patent
definition: A document that has been accepted by a patent authority
definition editor: PERSON: Lawrence Hunter
example of usage: US Patent 6,449,603
has curation status: metadata complete

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: document
editor preferred term: document part
example of usage: An abstract, introduction, method or results section.
definition editor: PERSON: Lawrence Hunter
definition: an information content entity that is part of a document
has curation status: metadata complete

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred term: abstract
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
definition editor: PERSON: Lawrence Hunter
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
has curation status: metadata complete

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
editor preferred term: introduction to a publication about an investigation
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
definition editor: PERSON: Lawrence Hunter
example of usage: Section labelled 'introduction' of a typical scientific journal article
alternative term: introduction
has curation status: metadata complete

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred term: methods section
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
has curation status: metadata complete

results section
type: Class
subclass of: document part
editor preferred term: results section
definition: A part of a publication about an investigation that is about a study design execution
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'results' in a typical scientific journal article
has curation status: metadata complete

discussion section of a publication about an investigation
type: Class
subclass of: document part
definition editor: PERSON: Lawrence Hunter
editor preferred term: discussion section of a publication about an investigation
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
alternative term: discussion section
has curation status: metadata complete

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: citation
editor preferred term: references section
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
has curation status: metadata complete

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author identification
editor preferred term: author list
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
definition editor: PERSON: Lawrence Hunter
definition: part of a document that enumerates the authors of the document
has curation status: metadata complete

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: institutional identification
editor preferred term: institution list
definition editor: PERSON: Lawrence Hunter
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
definition: part of a document that has parts that are institution identifications associated with the authors of the document
has curation status: metadata complete

author contributions section
type: Class
subclass of: document part
editor preferred term: author contributions section
definition: A part of a publication that is about the specific contributions of each author
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
definition editor: PERSON: Lawrence Hunter
has curation status: metadata complete

acknowledgements section
type: Class
subclass of: document part
editor preferred term: acknowledgements section
definition editor: PERSON: Lawrence Hunter
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
has curation status: metadata complete

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
editor preferred term: footnote
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
definition editor: PERSON: Lawrence Hunter
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
alternative term: endnote
has curation status: metadata complete

supplementary material to a document
type: Class
subclass of: document part
editor preferred term: supplementary material to a document
definition editor: PERSON: Lawrence Hunter
alternative term: appendix
definition: part of a document that is segregated from the rest of the document due to its size
alternative term: supplementary material
has curation status: metadata complete

table of contents
type: Class
subclass of: table
editor preferred term: table of contents
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter
has curation status: pending final vetting

table of figures
type: Class
subclass of: table
editor preferred term: table of figures
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter
has curation status: pending final vetting

running title
type: Class
subclass of: document title
editor preferred term: running title
definition: A shorter version of a document title
definition editor: PERSON: Lawrence Hunter
has curation status: pending final vetting

copyright section
type: Class
subclass of: document part
editor preferred term: copyright section
definition: A document part that describes legal restrictions on making or distributing copies of the document
definition editor: PERSON: Lawrence Hunter
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
has curation status: metadata complete

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: ZeroDimensionalRegion
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
definition editor: Alan Ruttenberg
has curation status: metadata complete

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: ZeroDimensionalRegion
    intersection of: Restriction
      on property: part of
      some values from: OneDimensionalRegion
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: ZeroDimensionalRegion
    intersection of: Restriction
      on property: part of
      some values from: TwoDimensionalRegion
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: ZeroDimensionalRegion
    intersection of: Restriction
      on property: part of
      some values from: ThreeDimensionalRegion
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: length unit
definition: A scalar measurement datum that is the result of measurement of length quality
definition editor: Alan Ruttenberg
has curation status: metadata incomplete

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters
example of usage: 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.

mass measurement datum
type: Class
subclass of: scalar measurement datum
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality
definition editor: Person:Alan Ruttenberg
has curation status: metadata incomplete

hypothesis textual entity
type: Class
subclass of: textual entity
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A textual entity that expresses an assertion that is intended to be tested.
definition editor: Person:Alan Ruttenberg
editor preferred term: hypothesis textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: Process
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measuring a temporal interval
definition editor: Person:Alan Ruttenberg
has curation status: metadata incomplete

study design
type: Class
subclass of: plan specification
definition: A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor preferred term: study design
IAO_0000412: obi.owl

length unit
type: Class
subclass of: measurement unit label
editor preferred term: length unit label
IAO_0000412: UO

mass unit
type: Class
subclass of: measurement unit label
editor preferred term: mass unit label
IAO_0000412: UO

time unit
type: Class
subclass of: measurement unit label
editor preferred term: time unit label
IAO_0000412: UO

example to be eventually removed
type: NamedIndividual
type: curation status specification

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
definition editor: Person:Alan Ruttenberg
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job

metadata complete
type: NamedIndividual
type: curation status specification
definition: 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
type: NamedIndividual
type: curation status specification
definition: 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
type: NamedIndividual
type: curation status specification
definition: 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
type: NamedIndividual
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
definition: 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
type: NamedIndividual
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by OBI to identify main classes.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor note: 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
type: NamedIndividual
type: obsolescence reason specification
editor note: 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
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
editor note: 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
type: NamedIndividual
type: denotator type
editor note: "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.
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg
editor note: 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