iao-main.owl
type: Ontology
default language: en
version info: 2009-11-06
version IRI: iao-main.owl
comment: This file is based on checkout of our SVN repository revision $Revision: 2489 $
imports: ro.owl
imports: protege-dc.owl
comment: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/
imports: ontology-metadata.owl
imports: http://www.ifomis.org/bfo/1.1

graph
type: Class
definition editor: person:Allyson Lister
editor preferred term: graph
definition editor: person:Alan Ruttenberg
subclass of: diagram
definition editor: PERSON: Lawrence Hunter
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.
has curation status: IAO_0000125
definition source: OBI_0000240

diagram
type: Class
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
definition: A figure that expresses one or more propositions
subclass of: figure
definition editor: PERSON: Lawrence Hunter
has curation status: IAO_0000120
editor preferred term: diagram

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

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

contour plot
type: Class
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
definition source: OBI_0000246
definition source: group:Flow Cytometry community
editor note: generically_dependent_continuants
definition editor: person:Allyson Lister
editor preferred term: contour plot
has curation status: IAO_0000002
subclass of: graph
definition editor: person:Chris Stoeckert

software
type: Class
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
definition source: GROUP: OBI
has curation status: IAO_0000120
definition editor: PERSON: Bjoern Peters
editor preferred term: software
subclass of: plan specification
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
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.

plan specification
type: Class
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.
editor preferred term: plan specification
subclass of: Restriction
  on property: has part
  some values from: action specification
definition source: OBI_0000344
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.
definition editor: Alan Ruttenberg
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.
subclass of: Restriction
  some values from: objective specification
  on property: has part
subclass of: directive information entity
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
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
has curation status: IAO_0000120

acknowledgements section
type: Class
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
has curation status: IAO_0000120
definition editor: PERSON: Lawrence Hunter
subclass of: document part
editor preferred term: acknowledgements section
definition: Part of a publication that is about the contributions of people or institutions other than the authors.

document part
type: Class
has curation status: IAO_0000120
editor preferred term: document part
definition: an information content entity that is part of a document
example of usage: An abstract, introduction, method or results section.
subclass of: information content entity
subclass of: Restriction
  some values from: document
  on property: part of
definition editor: PERSON: Lawrence Hunter

copyright section
type: Class
editor preferred term: copyright section
definition editor: PERSON: Lawrence Hunter
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
definition: A document part that describes legal restrictions on making or distributing copies of the document
has curation status: IAO_0000120
subclass of: document part

information content entity
type: Class
subclass of: Restriction
  on property: is about
  some values from: Entity
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
subclass of: GenericallyDependentContinuant
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.
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000125
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity

table of figures
type: Class
has curation status: IAO_0000125
definition editor: PERSON: Lawrence Hunter
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).
editor preferred term: table of figures
subclass of: table

table
type: Class
has curation status: IAO_0000125
subclass of: textual entity
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
editor preferred term: table
definition editor: PERSON: Lawrence Hunter
example of usage: | T F --+----- T | T F F | F F

time measurement datum
type: Class
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    all values from: time unit
    on property: has measurement unit label
  intersection of: Restriction
    all values from: Process
    on property: is duration of
definition editor: Person:Alan Ruttenberg
definition: A scalar measurement datum that is the result of measuring a temporal interval
has curation status: IAO_0000123

scalar measurement datum
type: Class
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 editor: PERSON: Melanie Courtot
subclass of: measurement datum
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
subclass of: Restriction
  min cardinality: 1
  on property: has measurement value
has curation status: IAO_0000120
example of usage: 10 feet. 3 ml.
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
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

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

is duration of
type: ObjectProperty
definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg
has curation status: IAO_0000120
sub property of: is about
domain: time measurement datum
range: Process

citation
type: Class
has curation status: IAO_0000125
definition: a textual entity intended to identify a particular publication
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.
editor preferred term: citation
definition editor: PERSON: Lawrence Hunter
subclass of: textual entity
subclass of: Restriction
  some values from: document
  on property: is about

textual entity
type: Class
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
definition editor: PERSON: Lawrence Hunter
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.
alternative term: text
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.
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.
editor preferred term: textual entity
subclass of: information content entity

document
type: Class
has curation status: IAO_0000120
definition editor: PERSON: Lawrence Hunter
definition: A collection of information content entities intended to be understood together as a whole
subclass of: information content entity
editor preferred term: document
example of usage: A journal article, patent application, laboratory notebook, or a book

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
has curation status: IAO_0000125
definition editor: person:Alan Ruttenberg
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.

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

results section
type: Class
subclass of: document part
subclass of: Restriction
  some values from: study design execution
  on property: is about
has curation status: IAO_0000120
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
editor preferred term: results section

study design execution
type: Class
imported from: obi.owl
subclass of: planned process
definition: a planned process that realizes the concretization of a study design
editor preferred term: study design execution

image
type: Class
has curation status: IAO_0000122
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 editor: person:Alan Ruttenberg
subclass of: figure
definition editor: person:Chris Stoeckert
editor preferred term: image
definition source: group:OBI
definition editor: person:Allyson

figure
type: Class
has curation status: IAO_0000120
definition editor: PERSON: Lawrence Hunter
subclass of: information content entity
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
editor preferred term: figure

table of abbreviations
type: Class
has curation status: IAO_0000125
definition: A table where the constituent texts are abbreviations and their expansions
subclass of: table
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
editor preferred term: table of abbreviations
definition editor: PERSON: Lawrence Hunter

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: Restriction
  cardinality: 1
  on property: has y coordinate value
has curation status: IAO_0000124
subclass of: Restriction
  cardinality: 1
  on property: has z coordinate value
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: cartesian spatial coordinate datum
definition editor: Alan Ruttenberg
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1

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

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

denotes
type: ObjectProperty
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
definition editor: person:Alan Ruttenberg
example of usage: The word Boston on a traffic signn in Massachusetts generically denotes the city of Boston
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: 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
sub property of: is about

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

cartesian spatial coordinate datum
type: Class
subclass of: data item
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 editor: Alan Ruttenberg
subclass of: Restriction
  cardinality: 1
  on property: has coordinate unit label
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
has curation status: IAO_0000120

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

model number
type: Class
has curation status: IAO_0000125
editor preferred term: model number
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
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.
subclass of: symbol
definition editor: Person: Alan Ruttenberg

narrative object
type: Class
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: OBI_0000013
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
has curation status: IAO_0000124
definition source: group:OBI
editor preferred term: narrative object
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.
definition editor: person:Chris Stoeckert

serial number
type: Class
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 :-)
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
has curation status: IAO_0000124
subclass of: symbol
editor preferred term: serial number

supplementary material to a document
type: Class
alternative term: appendix
alternative term: supplementary material
definition: part of a document that is segregated from the rest of the document due to its size
has curation status: IAO_0000120
definition editor: PERSON: Lawrence Hunter
subclass of: document part
editor preferred term: supplementary material to a document

measurement datum
type: Class
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,}.
has curation status: IAO_0000120
definition editor: person:Chris Stoeckert
editor note: 2/2/2009 is_specified_output of some assay?
subclass of: data item
editor preferred term: measurement datum
definition source: OBI_0000305
definition source: group:OBI
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.

data item
type: Class
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor preferred term: data item
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: 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.
has curation status: IAO_0000125
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition editor: PERSON: Jonathan Rees
alternative term: data
subclass of: information content entity
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.
definition editor: PERSON: Chris Stoeckert
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 editor: PERSON: Alan Ruttenberg

hypothesis textual entity
type: Class
has curation status: IAO_0000120
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
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
subclass of: textual entity
editor preferred term: hypothesis textual entity
definition: A textual entity that expresses an assertion that is intended to be tested.

methods section
type: Class
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.
subclass of: document part
subclass of: Restriction
  some values from: study design
  on property: is about
has curation status: IAO_0000120
editor preferred term: methods section

study design
type: Class
subclass of: plan specification
imported from: obi.owl
editor preferred term: study design
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.

rule
type: Class
definition source: OBI_0500021
definition: a rule is an executable which guides, defines, restricts actions
definition source: PRS
example of usage: example to be added
editor preferred term: rule
subclass of: conditional specification
has curation status: IAO_0000124
editor note: MSI
definition editor: PRS

conditional specification
type: Class
editor preferred term: instruction trigger
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
definition source: OBI_0000349
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
subclass of: directive information entity
has curation status: IAO_0000120

institutional identification
type: Class
has curation status: IAO_0000125
definition: A textual entity intended to identify a particular institution
editor preferred term: institutional identification
definition editor: PERSON: Lawrence Hunter
example of usage: University of Colorado Denver School of Medicine
subclass of: textual entity

material information bearer
type: Class
has curation status: IAO_0000120
equivalent class: Class
  intersection of: MaterialEntity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: is_concretization_of
      some values from: information content entity
definition: An information bearer is a material_entity, such as a hard drive, upon which an information content entity generically depends.
definition editor: GROUP: IAO
editor preferred term: material information bearer

is_concretization_of
type: ObjectProperty
domain: SpecificallyDependentContinuant
range: GenericallyDependentContinuant

institution list
type: Class
definition: part of a document that has parts that are institution identifications associated with the authors of the document
has curation status: IAO_0000120
subclass of: document part
subclass of: Restriction
  some values from: institutional identification
  on property: has part
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.

directive information entity
type: Class
subclass of: information content entity
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.
definition editor: PERSON: Bjoern Peters
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: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
has curation status: IAO_0000123
subclass of: Restriction
  on property: is about
  some values from: RealizableEntity
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition editor: PERSON: Alan Ruttenberg

source code module
type: Class
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition source: OBI_0000039
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.
editor preferred term: source code module
definition editor: person:Chris Stoeckert
definition editor: person:Alan Ruttenberg
has curation status: IAO_0000124
definition source: group:OBI
subclass of: directive information entity

caption
type: Class
has curation status: IAO_0000125
definition: A textual entity that describes a figure
editor preferred term: caption
definition editor: PERSON: Lawrence Hunter
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.
subclass of: textual entity
subclass of: Restriction
  some values from: figure
  on property: is about

action specification
type: Class
definition editor: Alan Ruttenberg
has curation status: IAO_0000123
subclass of: directive information entity
definition source: OBI Plan and Planned Process branch
definition: a directive information entity that describes an action the bearer will take
example of usage: Pour the contents of flask 1 into flask 2

objective specification
type: Class
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Barry Smith
editor preferred term: objective specification
subclass of: directive information entity
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.
definition source: OBI Plan and Planned Process/Roles Branch
example of usage: purpose of a study; support of hypothesis, discovery of new information
definition editor: PERSON: Alan Ruttenberg
definition source: OBI_0000217
has curation status: IAO_0000125
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."

conclusion textual entity
type: Class
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 note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
subclass of: textual entity
editor preferred term: conclusion textual entity
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
has curation status: IAO_0000120
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

heatmap
type: Class
definition source: GROUP:OBI
subclass of: graph
definition editor: PERSON:Melanie Courtot
has curation status: IAO_0000122
editor preferred term: heatmap
definition editor: PERSON:Chris Stoeckert
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 editor: PERSON:James Malone

running title
type: Class
has curation status: IAO_0000125
editor preferred term: running title
definition: A shorter version of a document title
subclass of: document title
definition editor: PERSON: Lawrence Hunter

document title
type: Class
has curation status: IAO_0000125
definition editor: PERSON: Lawrence Hunter
subclass of: textual entity
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
definition: A textual entity that names a document
editor preferred term: document title

histogram
type: Class
editor preferred term: histogram
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 editor: PERSON:Chris Stoeckert
definition source: GROUP:OBI
subclass of: graph
has curation status: IAO_0000122
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot

information carrier
type: Class
example of usage: The pattern in ink on a page of a paperback novel.
definition editor: PERSON: Alan Ruttenberg
has curation status: IAO_0000125
definition: A quality of an information bearer that imparts the information content
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
editor preferred term: information carrier
subclass of: Quality

journal article
type: Class
has curation status: IAO_0000120
subclass of: report
editor preferred term: journal article
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 source: OBI_0000159
definition: a report that is published in a journal
definition editor: person:Chris Stoeckert
definition source: group:OBI
definition editor: person:Alan Ruttenberg

report
type: Class
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)
definition editor: PERSON: Melanie Courtot
definition source: OBI_0000099
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.
subclass of: document
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 editor: PERSON: Alan Ruttenberg
has curation status: IAO_0000125
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: 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.
definition editor: PERSON:Chris Stoeckert
definition source: GROUP: OBI
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
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.
editor preferred term: report

author identification
type: Class
has curation status: IAO_0000125
subclass of: textual entity
definition: A textual entity intended to identify a particular author
editor preferred term: author identification
example of usage: L. Hunter
definition editor: PERSON: Lawrence Hunter

author list
type: Class
definition: part of a document that enumerates the authors of the document
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author identification
editor preferred term: author list
definition editor: PERSON: Lawrence Hunter
has curation status: IAO_0000120
example of usage: Lawrence Hunter and Kevin Brettonel Cohen

two dimensional cartesian spatial coordinate datum
type: Class
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  cardinality: 1
  on property: has x coordinate value
subclass of: Restriction
  cardinality: 1
  on property: has y coordinate value
subclass of: Restriction
  some values from: Class
    intersection of: ZeroDimensionalRegion
    intersection of: Restriction
      some values from: TwoDimensionalRegion
      on property: part of
  on property: denotes
has curation status: IAO_0000124
definition editor: Alan Ruttenberg

dot plot
type: Class
editor preferred term: dot plot
definition source: group:OBI
definition editor: person:Chris Stoeckert
example of usage: Dot plot of SSC-H and FSC-H.
subclass of: graph
definition editor: person:Allyson Lister
has curation status: IAO_0000002
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.

data set
type: Class
definition source: OBI_0000042
editor preferred term: data set
definition editor: person:Chris Stoeckert
has curation status: IAO_0000120
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
subclass of: data item
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.
definition source: group:OBI
definition editor: person:Allyson Lister
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).

photographic print
type: Class
has curation status: IAO_0000125
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition: A photographic print is a material entity upon which a photograph generically depends.
editor preferred term: photographic print
equivalent class: Class
  intersection of: MaterialEntity
  intersection of: Restriction
    some values from: Restriction
      on property: is_concretization_of
      some values from: photograph
    on property: bearer of

photograph
type: Class
definition source: WEB: http://en.wiktionary.org/wiki/photograph
has curation status: IAO_0000122
subclass of: image
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.

data format specification
type: Class
editor preferred term: data format specification
definition source: OBI_0000187
definition source: OBI branch derived
has curation status: IAO_0000123
definition editor: PlanAndPlannedProcess Branch
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
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"

investigation
type: Class
subclass of: planned process
imported from: obi.owl
editor preferred term: investigation
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).

Venn diagram
type: Class
editor preferred term: Venn diagram
definition editor: PERSON:Chris Stoeckert
has curation status: IAO_0000122
subclass of: graph
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram
definition editor: PERSON:James Malone
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.

scatter plot
type: Class
definition editor: PERSON:James Malone
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
alternative term: scattergraph
has curation status: IAO_0000122
definition editor: PERSON:Melanie Courtot
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.
definition editor: PERSON:Chris Stoeckert
editor preferred term: scatter plot

survival curve
type: Class
definition editor: PERSON:James Malone
editor preferred term: survival curve
subclass of: graph
has curation status: IAO_0000122
definition editor: PERSON:Melanie Courtot
definition editor: PERSON:Chris Stoeckert
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 source: WEB: http://www.graphpad.com/www/book/survive.htm

programming language
type: Class
definition editor: person:Chris Stoeckert
example of usage: R, Perl, Java
definition editor: person:Alan Ruttenberg
editor preferred term: programming language
subclass of: plan specification
definition source: group:OBI
has curation status: IAO_0000120
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.
definition source: OBI_0000058

lot number
type: Class
subclass of: symbol
alternative term: batch number
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.
has curation status: IAO_0000124
definition editor: GROUP: IAO
editor preferred term: lot number

length measurement datum
type: Class
definition: A scalar measurement datum that is the result of measurement of length quality
has curation status: IAO_0000123
definition editor: Alan Ruttenberg
subclass of: scalar measurement datum
subclass of: Restriction
  some values from: length unit
  on property: has measurement unit label
subclass of: Restriction
  some values from: length
  on property: is quality measurement of

is quality measurement of
type: ObjectProperty
definition editor: Alan Ruttenberg
domain: measurement datum
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.
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.
range: 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: 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.
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
sub property of: is about
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

setting datum
type: Class
subclass of: data item
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.
definition: A settings datum is a datum that denotes some configuration of an instrument.
has curation status: IAO_0000124

introduction to a publication about an investigation
type: Class
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
subclass of: document part
alternative term: introduction
editor preferred term: introduction to a publication about an investigation
definition editor: PERSON: Lawrence Hunter
has curation status: IAO_0000120
example of usage: Section labelled 'introduction' of a typical scientific journal article
subclass of: Restriction
  on property: is about
  some values from: objective specification

time trigger
type: Class
definition editor: PlanAndPlannedProcess Branch
subclass of: conditional specification
editor preferred term: time trigger
definition source: OBI_0000331
definition source: OBI branch derived
has curation status: IAO_0000124
definition: revisit?

publication
type: Class
has curation status: IAO_0000120
subclass of: document
definition: A document that has been accepted by a publisher
editor preferred term: publication
definition editor: PERSON: Lawrence Hunter
example of usage: A journal article or book

footnote
type: Class
alternative term: endnote
has curation status: IAO_0000120
editor preferred term: footnote
subclass of: Restriction
  on property: is about
  some values from: document part
subclass of: document part
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.
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.

software interpreter
type: Class
definition source: group:OBI
has curation status: IAO_0000120
subclass of: algorithm
definition editor: person:Alan Ruttenberg
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
editor preferred term: software interpreter
definition source: OBI_0000199
example of usage: R program, Perl interpreter, Java virtual machine
definition editor: person:Chris Stoeckert
definition: An algorithmy that takes, as input, some digital entity, and takes action driven by the information content of that algorithm

algorithm
type: Class
definition editor: PlanAndPlannedProcess Branch
subclass of: plan specification
has curation status: IAO_0000120
definition editor: Philippe Rocca-Serra
definition source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
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.

measurement unit label
type: Class
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor preferred term: measurement unit label
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.
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.
definition editor: PERSON: Alan Ruttenberg
subclass of: label
definition editor: PERSON: Melanie Courtot
has curation status: IAO_0000125

label
type: Class
has curation status: IAO_0000123
definition editor: GROUP: IAO
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
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
subclass of: information content entity
editor preferred term: label

discussion section of a publication about an investigation
type: Class
definition editor: PERSON: Lawrence Hunter
subclass of: document part
alternative term: discussion section
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
has curation status: IAO_0000120
editor preferred term: discussion section of a publication about an investigation

version number
type: Class
subclass of: symbol
has curation status: IAO_0000124
definition editor: GROUP: IAO
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.
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

patent
type: Class
editor preferred term: patent
subclass of: document
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: IAO_0000120

author contributions section
type: Class
definition editor: PERSON: Lawrence Hunter
editor preferred term: author contributions section
has curation status: IAO_0000120
definition: A part of a publication that is about the specific contributions of each author
subclass of: document part
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.

mass measurement datum
type: Class
definition editor: Person:Alan Ruttenberg
subclass of: Class
  intersection of: Restriction
    all values from: mass unit
    on property: has measurement unit label
  intersection of: Restriction
    all values from: mass
    on property: is quality measurement of
subclass of: scalar measurement datum
has curation status: IAO_0000123
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality

abstract
type: Class
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
has curation status: IAO_0000120
subclass of: document part
subclass of: Restriction
  some values from: document
  on property: is about
definition editor: PERSON: Lawrence Hunter
editor preferred term: abstract
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.

publication about an investigation
type: Class
example of usage: Most scientific journal articles
definition: A publication that is about an investigation
subclass of: Restriction
  some values from: investigation
  on property: is about
subclass of: publication
has curation status: IAO_0000120
alternative term: scientific publication
editor preferred term: publication about an investigation
definition editor: PERSON: Lawrence Hunter

references section
type: Class
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"
definition editor: PERSON: Lawrence Hunter
definition: A part of a document that has citations as parts
subclass of: document part
subclass of: Restriction
  some values from: citation
  on property: has part
editor preferred term: references section
has curation status: IAO_0000120

table of contents
type: Class
has curation status: IAO_0000125
definition editor: PERSON: Lawrence Hunter
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).

density plot
type: Class
example of usage: Density plot of SSC-H and FSC-H.
subclass of: graph
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.
has curation status: IAO_0000002
definition source: OBI_0000179
editor preferred term: density plot
definition source: group:Flow Cytometry community
definition editor: person:Chris Stoeckert
definition editor: person:Allyson Lister

dendrogram
type: Class
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
editor preferred term: dendrogram
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.
definition editor: PERSON:James Malone
subclass of: graph
has curation status: IAO_0000122
definition editor: PERSON:Chris Stoeckert

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

one dimensional cartesian spatial coordinate datum
type: Class
definition editor: Alan Ruttenberg
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  cardinality: 1
  on property: has x coordinate value
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: ZeroDimensionalRegion
    intersection of: Restriction
      some values from: OneDimensionalRegion
      on property: part of
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
has curation status: IAO_0000124

author role
type: Class
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Alan Ruttenberg
editor preferred term: author role
subclass of: Role
has curation status: IAO_0000125

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

is quality measured as
type: ObjectProperty
definition editor: Person:Alan Ruttenberg
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
has curation status: IAO_0000120
definition: inverse of the relation of is quality measurement of
inverse of: is quality measurement of

mentions
type: ObjectProperty
definition: An information artifact IA mentions an entity E exactly when it has a component/part that geenerically denotes E
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition editor: PERSON: Jonathan Rees
definition editor: Person: Alan Ruttenberg
sub property of: is about
has curation status: IAO_0000125

is quality specification of
type: ObjectProperty
definition editor: Person:Bjoern Peters
definition editor: Person:Alan Ruttenberg
sub property of: is about
has curation status: IAO_0000120
definition: a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.

is_concretized_as
type: ObjectProperty
inverse of: is_concretization_of
range: SpecificallyDependentContinuant
domain: GenericallyDependentContinuant

materially denotes
type: ObjectProperty
sub property of: is about

specifically denotes
type: ObjectProperty
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
editor note: 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
sub property of: is about
has curation status: IAO_0000125
definition editor: Alan Ruttenberg
definition: c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.

quality is specified as
type: ObjectProperty
definition editor: Person:Bjoern Peters
definition editor: Person:Alan Ruttenberg
definition: inverse of the relation of is quality specification of
inverse of: is quality specification of
has curation status: IAO_0000120
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship

example of usage
type: AnnotationProperty

imported from
type: AnnotationProperty

alternative term
type: AnnotationProperty

has obsolescence reason
type: AnnotationProperty

definition editor
type: AnnotationProperty

in branch
type: AnnotationProperty

definition source
type: AnnotationProperty

editor note
type: AnnotationProperty

definition
type: AnnotationProperty

editor preferred term
type: AnnotationProperty

has curation status
type: AnnotationProperty

planned process
type: Class
imported from: obi.owl
subclass of: ProcessualEntity
editor preferred term: planned process
definition: A processual entity that realizes a plan which is the concretization of a plan specification.

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

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

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

length
type: Class
subclass of: Quality
imported from: PATO
definition: A 1-D extent quality which is equal to the distance between two points.
editor preferred term: length

mass
type: Class
subclass of: Quality
imported from: PATO
editor preferred term: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.