format-version: 1.2
date:  06:11:2009 14:19
saved-by: IAO
auto-generated-by: http://purl.obolibrary.org/obo/obi/repository/trunk/src/tools/build/generate-obo.lisp
default-namespace: iao
idspace: RO http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry"
idspace: ROP http://purl.org/obo/owl/OBO_REL# "Relation ontology proposed terms"
idspace: PATO http://purl.org/obo/owl/PATO# "Phenotype Ontology"
idspace: snap http://www.ifomis.org/bfo/1.1/snap# "BFO SNAP ontology (continuants)"
idspace: span http://www.ifomis.org/bfo/1.1/span# "BFO SPAN ontology (occurrents)"
idspace: OBI http://purl.obolibrary.org/obo/OBI_ "Ontology for Biomedical Investigations"
idspace: CHEBI http://purl.org/obo/owl/CHEBI# "Chemical Entities of Biological Interest"
idspace: CL http://purl.org/obo/owl/CL# "Cell Ontology"
idspace: NCBITaxon http://purl.org/obo/owl/NCBITaxon# "NCBI Taxonomy"
idspace: birn_anat http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl# "NIF Standard Anatomy"
idspace: IAO http://purl.obolibrary.org/obo/IAO "Information Artifact Ontology"
idspace: BFO http://www.ifomis.org/bfo/1.1/ "Basic Formal Ontology"
idspace: GO http://purl.org/obo/owl/GO# "Gene Ontology"
idspace: FMA http://purl.org/obo/owl/FMA# "Foundational Model of Anatomy"
idspace: PRO http://purl.org/obo/owl/PRO# "Protein Ontology"
idspace: UO http://purl.org/obo/owl/UO# "Unit Ontology"
idspace: ENVO http://purl.org/obo/owl/ENVO# "Environment Ontology"
idspace: VO http://purl.obolibrary.org/obo/VO "Vaccine Ontology"
idspace: SO http://purl.org/obo/owl/SO# "Sequence Ontology"
idspace: HPO http://purl.org/obo/owl/HP# "Human Phenotype Ontology"
remark: This file is a subset of IAO adequate for indexing using the OLS service. It does not include all logical assertions present in the OWL file, which can be obtained at http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000013
name: journal article
def:"a report that is published in a journal" [OBO:sourced "OBI:0000159", GROUP:OBI ]
is_a: IAO:0000088 ! report

[Term]
id: snap:ObjectBoundary
name: object_boundary
def:"Comment: Boundaries are theoretically difficult entities to account for\, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.; Synonyms: substance boundary; Examples: the surface of the skin\, the surface of the earth\, the surface of the interior of the stomach\, the outer surface of a cell or cell wall; Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity\, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:IndependentContinuant ! independent_continuant

[Term]
id: IAO:0000415
name: hypothesis textual entity
def:"A textual entity that expresses an assertion that is intended to be tested." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: IAO:0000304
name: caption
def:"A textual entity that describes a figure" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: IAO:0000005
name: objective specification
def:"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." [OBO:sourced "OBI Plan and Planned Process/Roles Branch", OBO:sourced "OBI:0000217"]
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000017
name: model number
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000028 ! symbol

[Term]
id: IAO:0000029
name: numeral
def:"A symbol that denotes a number." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000028 ! symbol

[Term]
id: IAO:0000010
name: software
def:"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." [GROUP:OBI ]
is_a: IAO:0000104 ! plan specification

[Term]
id: IAO:0000300
name: textual entity
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000006
name: narrative object
def:"A narrative object is an information content entity that is a set of propositions." [OBO:sourced "OBI:0000013", GROUP:OBI ]
is_a: IAO:0000030 ! information content entity

[Term]
id: oboInOwl:Synonym
name: Synonym
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000327
name: table of contents
def:"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)." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000306 ! table

[Term]
id: IAO:0000310
name: document
def:"A collection of information content entities intended to be understood together as a whole" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000186
name: photographic print
def:"A photographic print is a material entity upon which a photograph generically depends." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000178 ! material information bearer

[Term]
id: bfo:Entity
name: entity

[Term]
id: IAO:0000027
name: data item
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: span:ScatteredTemporalRegion
name: scattered_temporal_region
def:"Examples: the time occupied by the individual games of the World Cup\, the time occupied by the individual liaisons in a romantic affair; Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:TemporalRegion ! temporal_region

[Term]
id: IAO:0000317
name: methods section
def:"A part of a publication about an investigation that is about the study design of the investigation" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: span:SpatiotemporalInstant
name: spatiotemporal_instant
def:"Definition: A connected space time region [span:ConnectedSpaceTimeRegion] at a specific moment.; Examples: the space time region occupied by a single instantaneous temporal slice (part) of a process" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region

[Term]
id: IAO:0000034
name: time trigger
def:"revisit?" [OBO:sourced "OBI:0000331", OBO:sourced "OBI branch derived"]
is_a: IAO:0000001 ! conditional specification

[Term]
id: IAO:0000308
name: figure
def:"An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000323
name: author contributions section
def:"A part of a publication that is about the specific contributions of each author" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: oboInOwl:DbXref
name: DbXref
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: OBI:0000066
name: OBI_0000066

[Term]
id: IAO:0000104
name: plan specification
def:"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.; 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them" [OBO:sourced "OBI:0000344", OBO:sourced "OBI Plan and Planned Process branch"]
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000315
name: abstract
def:"A summary of the entire document that is substantially smaller than the document it summarizes.  It is about the document it summarizes." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: snap:IndependentContinuant
name: independent_continuant
def:"Synonyms: substantial entity; Examples: an organism\, a heart\, a leg\, a person\, a symphony orchestra\, a chair\, the bottom right portion of a human torso\, the lawn and atmosphere in front of our building; Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities\, in which other entities inhere and which itself cannot inhere in anything." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:Continuant ! continuant

[Term]
id: IAO:0000179
name: histogram
def:"A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." [GROUP:OBI ]
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000132
name: lot number
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000028 ! symbol

[Term]
id: IAO:0000322
name: institution list
def:"part of a document that has parts that are institution identifications associated with the authors of the document" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: span:FiatProcessPart
name: fiat_process_part
def:"Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.; Examples: chewing during a meal\, the middle part of a rainstorm\, the worst part of a heart-attack\, the most interesting part of Van Gogh's life" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ProcessualEntity ! processual_entity

[Term]
id: IAO:0000321
name: author list
def:"part of a document that enumerates the authors of the document" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: oboInOwl:Subset
name: Subset
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000033
name: directive information entity
def:"An information content entity whose concretizations indicate to their bearer how to realize them in a process." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000183
name: dendrogram
def:"A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." [WEB:http://en.wikipedia.org/wiki/Dendrogram ]
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000301
name: citation
def:"a textual entity intended to identify a particular publication" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: IAO:0000184
name: scatter plot
def:"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." [WEB:http://en.wikipedia.org/wiki/Scatterplot ]
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000101
name: image
def:"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." [OBO:sourced "OBI:0000030", GROUP:OBI ]
is_a: IAO:0000308 ! figure

[Term]
id: span:Occurrent
name: occurrent
def:"Definition: An entity [bfo:Entity] that has temporal parts and that happens\, unfolds or develops through time. Sometimes also called perdurants.; Examples: the life of an organism\, a surgical operation as processual context for a nosocomical infection\, the spatiotemporal context occupied by a process of cellular meiosis\, the most interesting part of Van Gogh's life\, the spatiotemporal region occupied by the development of a cancer tumor; Synonyms: perdurant" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: bfo:Entity ! entity

[Term]
id: IAO:0000007
name: action specification
def:"a directive information entity that describes an action the bearer will take" [OBO:sourced "OBI Plan and Planned Process branch"]
is_a: IAO:0000033 ! directive information entity

[Term]
id: snap:Disposition
name: disposition
def:"Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres\, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform\, initiate a process) R under conditions C.; Examples: the disposition of vegetables to decay when not refrigerated\, the disposition of a vase to brake if dropped\, the disposition of blood to coagulate\, the disposition of a patient with a weakened immune system to contract disease\, the disposition of metal to conduct electricity." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:RealizableEntity ! realizable_entity

[Term]
id: IAO:0000403
name: three dimensional cartesian spatial coordinate datum
def:"A cartesion spatial coordinate datum that  uses three values to specify a position within a three dimensional spatial region" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000400 ! cartesian spatial coordinate datum

[Term]
id: IAO:0000314
name: document part
def:"an information content entity that is part of a document" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000078
name: curation status specification
def:"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." [OBO:sourced "OBI:0000266", GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: OBI:0000471
name: OBI_0000471

[Term]
id: IAO:0000098
name: data format specification
def:"A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" [OBO:sourced "OBI:0000187", OBO:sourced "OBI branch derived"]
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000079
name: density plot
def:"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." [OBO:sourced "OBI:0000179", OBO:sourced "group:Flow Cytometry community"]
is_a: IAO:0000038 ! graph

[Term]
id: snap:ZeroDimensionalRegion
name: zero_dimensional_region
def:"Examples: a point; Definition: A spatial region [snap:SpatialRegion] with no dimensions." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:SpatialRegion ! spatial_region

[Term]
id: IAO:0000037
name: dot plot
def:"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." [GROUP:OBI , OBO:sourced "OBI:0000123"]
is_a: IAO:0000038 ! graph

[Term]
id: span:ConnectedTemporalRegion
name: connected_temporal_region
def:"Examples: the 1970s years\, the time from the beginning to the end of a heart attack\, the time taken up by cellular meiosis; Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:TemporalRegion ! temporal_region

[Term]
id: IAO:0000320
name: references section
def:"A part of a document that has citations as parts" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: IAO:0000414
name: mass measurement datum
def:"A scalar measurement datum that is the result of measurement of mass quality" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000032 ! scalar measurement datum

[Term]
id: IAO:0000144
name: conclusion textual entity
def:"A textual entity that expresses the results of reasoning about a problem\, for instance as typically found towards the end of scientific papers." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: span:TemporalInstant
name: temporal_instant
def:"Examples: right now\, the moment at which a finger is detached in an industrial accident\, the moment at which a child is born\, the moment of death; Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ConnectedTemporalRegion ! connected_temporal_region

[Term]
id: IAO:0000325
name: footnote
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: IAO:0000303
name: institutional identification
def:"A textual entity intended to identify a particular institution" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: snap:ThreeDimensionalRegion
name: three_dimensional_region
def:"Examples: a cube-shaped part of space\, a sphere-shaped part of space; Definition: A spatial region [snap:SpatialRegion] with three dimensions." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:SpatialRegion ! spatial_region

[Term]
id: span:ProcessAggregate
name: process_aggregate
def:"Examples: the beating of the hearts of each of seven individuals in the room\, the playing of each of the members of an orchestra\, a process of digestion and a process of thinking taken together; Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ProcessualEntity ! processual_entity

[Term]
id: oboInOwl:SynonymType
name: SynonymType
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000180
name: heatmap
def:"A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." [GROUP:OBI ]
is_a: IAO:0000038 ! graph

[Term]
id: snap:Object
name: object
def:"Synonyms: substance; Definition: A material entity [snap:MaterialEntity] that is spatially extended\, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.; Examples: an organism\, a heart\, a chair\, a lung\, an apple" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:MaterialEntity ! material_entity

[Term]
id: span:ScatteredSpatiotemporalRegion
name: scattered_spatiotemporal_region
def:"Examples: the space and time occupied by the individual games of the World Cup\, the space and time occupied by the individual liaisons in a romantic affair; Definition: A space time region [span:SpaceTimeRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:SpatiotemporalRegion ! spatiotemporal_region

[Term]
id: IAO:0000402
name: two dimensional cartesian spatial coordinate datum
def:"A cartesion spatial coordinate datum that  uses two values to specify a position within a two dimensional spatial region" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000400 ! cartesian spatial coordinate datum

[Term]
id: IAO:0000181
name: Venn diagram
def:"A Venn diagram is a report graph showing all hypothetically possible\nlogical relations between a finite collection of sets." [WEB:http://en.wikipedia.org/wiki/Venn_diagram ]
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000408
name: length measurement datum
def:"A scalar measurement datum that is the result of measurement of length quality" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000032 ! scalar measurement datum

[Term]
id: IAO:0000416
name: time measurement datum
def:"A scalar measurement datum that is the result of measuring a temporal interval" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000032 ! scalar measurement datum

[Term]
id: snap:FiatObjectPart
name: fiat_object_part
def:"Examples: upper and lower lobes of the left lung\, the dorsal and ventral surfaces of the body\, the east side of Saarbruecken\, the lower right portion of a human torso; Synonyms: fiat substance part; Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:MaterialEntity ! material_entity

[Term]
id: IAO:0000100
name: data set
def:"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." [OBO:sourced "OBI:0000042", GROUP:OBI ]
is_a: IAO:0000027 ! data item

[Term]
id: span:TemporalRegion
name: temporal_region
def:"Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].; Examples: the time it takes to run a marathon\, the duration of a surgical procedure\, the moment of death; Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe\, a designated individual\, which is thus a temporal region itself.; Definition: An occurrent [span:Occurrent] that is part of time.; Comment: All instances of occurrent [span:Occurrent] are temporal entities\, that is\, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case\, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way\, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant]." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:Occurrent ! occurrent

[Term]
id: snap:Function
name: function
def:"Examples: the function of a birth canal to enable transport\, the function of the heart in the body: to pump blood\, to receive de-oxygenated and oxygenated blood\, etc.\, the function of reproduction in the transmission of genetic material\, the digestive function of the stomach to nutriate the body\, the function of a hammer to drive in nails\, the function of a computer program to compute mathematical equations\, the function of an automobile to provide transportation\, the function of a judge in a court of law; Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:RealizableEntity ! realizable_entity

[Term]
id: IAO:0000131
name: serial number
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000028 ! symbol

[Term]
id: IAO:0000129
name: version number
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000028 ! symbol

[Term]
id: IAO:0000055
name: rule
def:"a rule is an executable which guides\, defines\, restricts actions" [OBO:sourced "OBI:0500021", OBO:sourced "PRS"]
is_a: IAO:0000001 ! conditional specification

[Term]
id: span:TemporalInterval
name: temporal_interval
def:"Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.; Examples: any continuous temporal duration during which a process occurs" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ConnectedTemporalRegion ! connected_temporal_region

[Term]
id: IAO:0000032
name: scalar measurement datum
def:"a scalar measurement datum is a measurement datum that is composed of two parts\, numerals and a unit label." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000109 ! measurement datum

[Term]
id: OBI:0500000
name: OBI_0500000

[Term]
id: IAO:0000330
name: copyright section
def:"A document part that describes  legal restrictions on making or distributing copies of the document" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: IAO:0000001
name: conditional specification
def:"a directive information entity that specifies what should happen if the trigger condition is fulfilled" [OBO:sourced "OBI:0000349", OBO:sourced "OBI branch derived"]
is_a: IAO:0000033 ! directive information entity

[Term]
id: snap:MaterialEntity
name: material_entity
def:"Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object]\, fiat object part [snap:FiatObjectPart]\, and object aggregate [snap:ObjectAggregate]\, which assume a three level theory of granularity\, which is inadequate for some domains\, such as biology.; Examples: collection of random bacteria\, a chair\, dorsal surface of the body" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:IndependentContinuant ! independent_continuant

[Term]
id: snap:SpecificallyDependentContinuant
name: specifically_dependent_continuant
def:"Synonyms: property\, trope\, mode; Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.; Examples: the mass of a cloud\, the smell of mozzarella\, the liquidity of blood\, the color of a tomato\, the disposition of fish to decay\, the role of being a doctor\, the function of the heart in the body: to pump blood\, to receive de-oxygenated and oxygenated blood\, etc." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:DependentContinuant ! dependent_continuant

[Term]
id: IAO:0000109
name: measurement datum
def:"A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [OBO:sourced "OBI:0000305", GROUP:OBI ]
is_a: IAO:0000027 ! data item

[Term]
id: snap:Role
name: role
def:"Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural\, social or institutional contexts.; Examples: the role of a person as a surgeon\, the role of a chemical compound in an experiment\, the role of a patient relative as defined by a hospital administrative form\, the role of a woman as a legal mother in the context of system of laws\, the role of a biological grandfather as legal guardian in the context of a system of laws\, the role of ingested matter in digestion\, the role of a student in a university" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:RealizableEntity ! realizable_entity

[Term]
id: IAO:0000306
name: table
def:"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" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: IAO:0000064
name: algorithm
def:"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." [OBO:sourced "OBI:0000270", OBO:sourced "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"]
is_a: IAO:0000104 ! plan specification

[Term]
id: IAO:0000312
name: publication about an investigation
def:"A publication that is about an investigation" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000311 ! publication

[Term]
id: IAO:0000401
name: one dimensional cartesian spatial coordinate datum
def:"A cartesion spatial coordinate datum that  uses one value to specify a position along a one dimensional spatial region" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000400 ! cartesian spatial coordinate datum

[Term]
id: IAO:0000309
name: diagram
def:"A figure that expresses one or more propositions" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000308 ! figure

[Term]
id: IAO:0000003
name: measurement unit label
def:"A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000009 ! label

[Term]
id: IAO:0000305
name: document title
def:"A textual entity that names a document" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: IAO:0000324
name: acknowledgements section
def:"Part of a publication that is about the contributions of people or institutions other than the authors." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: IAO:0000102
name: data about an ontology part
def:"data about an ontology part is a data item about a part of an ontology\, for example a term" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000027 ! data item

[Term]
id: IAO:0000182
name: survival curve
def:"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." [WEB:http://www.graphpad.com/www/book/survive.htm ]
is_a: IAO:0000038 ! graph

[Term]
id: span:Process
name: process
def:"Examples: the life of an organism\, the process of sleeping\, the process of cell-division; Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ProcessualEntity ! processual_entity

[Term]
id: snap:Continuant
name: continuant
def:"Examples: a heart\, a person\, the color of a tomato\, the mass of a cloud\, a symphony orchestra\, the disposition of blood to coagulate\, the lawn and atmosphere in front of our building; Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all\, persists through time while maintaining its identity and has no temporal parts.; Synonyms: endurant" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: bfo:Entity ! entity

[Term]
id: IAO:0000015
name: information carrier
def:"A quality of an information bearer that imparts the information content" [OBO:sourced "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"]
is_a: snap:Quality ! quality

[Term]
id: IAO:0000326
name: supplementary material to a document
def:"part of a document that is segregated from the rest of the document due to its size" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: IAO:0000328
name: table of figures
def:"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)." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000306 ! table

[Term]
id: oboInOwl:ObsoleteClass
name: ObsoleteClass

[Term]
id: snap:Quality
name: quality
def:"Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).; Examples: the color of a tomato\, the ambient temperature of air\, the circumference of a waist\, the shape of a nose\, the mass of a piece of gold\, the weight of a chimpanzee" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant

[Term]
id: IAO:0000316
name: introduction to a publication about an investigation
def:"A part of a publication about an investigation that is about the objective specification (why the investigation is being done)" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: IAO:0000009
name: label
def:"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" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: oboInOwl:Definition
name: Definition
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000307
name: table of abbreviations
def:"A table where the constituent texts are abbreviations and their expansions" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000306 ! table

[Term]
id: span:SpatiotemporalInterval
name: spatiotemporal_interval
def:"Definition: A connected space time region [span:ConnectedSpaceTimeRegion] that endures for more than a single moment of time.; Examples: the space time region occupied by a process or by a fiat processual part" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region

[Term]
id: IAO:0000302
name: author identification
def:"A textual entity intended to identify a particular author" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000300 ! textual entity

[Term]
id: IAO:0000442
name: author role
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: snap:Role ! role

[Term]
id: IAO:0000185
name: photograph
def:"A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film\, CCD receptor\, etc." [WEB:http://en.wiktionary.org/wiki/photograph ]
is_a: IAO:0000101 ! image

[Term]
id: IAO:0000409
name: denotator type
def:"A denotator type indicates how a term should be interpreted from an ontological perspective." [OBO:sourced "Barry Smith, Werner Ceusters"]
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: snap:Site
name: site
def:"Examples: a particular room in a particular hospital\, Maria's nostril or her intestines for a variety of bacteria.; Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.; Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities\, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which\, then\, are sites) through a relation of "occupation". That relation is connected to\, but distinct from\, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO\, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class)." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:IndependentContinuant ! independent_continuant

[Term]
id: IAO:0000318
name: results section
def:"A part of a publication about an investigation that is about a study design execution" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: snap:GenericallyDependentContinuant
name: generically_dependent_continuant
def:"Examples: a certain PDF file that exists in different and in several hard drives; Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:DependentContinuant ! dependent_continuant

[Term]
id: snap:RealizableEntity
name: realizable_entity
def:"Examples: the role of being a doctor\, the function of the reproductive organs\, the disposition of blood to coagulate\, the disposition of metal to conduct electricity; Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant]\, this does not imply that it is actually realized.; Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation\, functioning or process that occurs under certain circumstances." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant

[Term]
id: snap:ObjectAggregate
name: object_aggregate
def:"Synonyms: substance aggregate; Examples: a heap of stones\, a group of commuters on the subway\, a collection of random bacteria\, a flock of geese\, the patients in a hospital; Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:MaterialEntity ! material_entity

[Term]
id: IAO:0000311
name: publication
def:"A document that has been accepted by a publisher" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000310 ! document

[Term]
id: snap:DependentContinuant
name: dependent_continuant
def:"Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:Continuant ! continuant

[Term]
id: IAO:0000178
name: material information bearer
def:"An information bearer is a material_entity\, such as a hard drive\, upon which an information content entity generically depends." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: snap:MaterialEntity ! material_entity

[Term]
id: span:SpatiotemporalRegion
name: spatiotemporal_region
def:"Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO\, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime\, that is to say\, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO\, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.; Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular\, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe\, a designated individual\, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.; Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.; Examples: the spatiotemporal region occupied by a human life\, the spatiotemporal region occupied by the development of a cancer tumor\, the spatiotemporal context occupied by a process of cellular meiosis; Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities\, that is\, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case\, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:Occurrent ! occurrent

[Term]
id: IAO:0000057
name: contour plot
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000088
name: report
def:"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)" [OBO:sourced "OBI:0000099", GROUP:OBI ]
is_a: IAO:0000310 ! document

[Term]
id: span:ConnectedSpatiotemporalRegion
name: connected_spatiotemporal_region
def:"Definition: A space time region [span:SpaceTimeRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same space time region [span:SpaceTimeRegion].; Examples: the spatial and temporal location of an individual organism's life\, the spatial and temporal location of the development of a fetus" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:SpatiotemporalRegion ! spatiotemporal_region

[Term]
id: IAO:0000096
name: source code module
def:"A source code module is a directive information entity that specifies\, using a programming language\, some algorithm." [OBO:sourced "OBI:0000039", GROUP:OBI ]
is_a: IAO:0000033 ! directive information entity

[Term]
id: snap:SpatialRegion
name: spatial_region
def:"Examples: the sum total of all space in the universe\, parts of the sum total of all space in the universe; Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO\, the class site [snap:Site] allows for a so-called relational view of space\, that is to say\, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities\, they are nevertheless spatial entities.; Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.; Comment: All instances of continuant [snap:Continuant] are spatial entities\, that is\, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case\, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.; Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe\, a designated individual\, which is thus itself a spatial region [snap:SpatialRegion]." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:Continuant ! continuant

[Term]
id: IAO:0000030
name: information content entity
def:"an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [OBO:sourced "OBI:0000142"]
is_a: snap:GenericallyDependentContinuant ! generically_dependent_continuant

[Term]
id: IAO:0000025
name: programming language
def:"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." [GROUP:OBI , OBO:sourced "OBI:0000058"]
is_a: IAO:0000104 ! plan specification

[Term]
id: IAO:0000028
name: symbol
def:"a smallish\, word-like datum..." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000313
name: patent
def:"A document that has been accepted by a patent authority" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000310 ! document

[Term]
id: span:ProcessBoundary
name: process_boundary
def:"Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.; Examples: birth\, death\, the forming of a synapse\, the onset of REM sleep\, the detaching of a finger in an industrial accident\, the final separation of two cells at the end of cell-division\, the incision at the beginning of a surgery" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ProcessualEntity ! processual_entity

[Term]
id: snap:TwoDimensionalRegion
name: two_dimensional_region
def:"Examples: the surface of a cube-shaped part of space\, the surface of a sphere-shaped part of space\, the surface of a rectilinear planar figure-shaped part of space; Definition: A spatial region [snap:SpatialRegion] with two dimensions." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:SpatialRegion ! spatial_region

[Term]
id: snap:OneDimensionalRegion
name: one_dimensional_region
def:"Definition: A spatial region [snap:SpatialRegion] with one dimension.; Examples: the part of space that is a line stretching from one end of absolute space to the other\, an edge of a cube-shaped part of space" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: snap:SpatialRegion ! spatial_region

[Term]
id: IAO:0000400
name: cartesian spatial coordinate datum
def:"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" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000027 ! data item

[Term]
id: span:ProcessualEntity
name: processual_entity
def:"Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening\, has temporal parts and always involves and depends on some entity.; Examples: the life of an organism\, the process of meiosis\, the course of a disease\, the flight of a bird" [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:Occurrent ! occurrent

[Term]
id: IAO:0000140
name: setting datum
def:"A settings datum is a datum that denotes some configuration of an instrument." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000027 ! data item

[Term]
id: IAO:0000038
name: graph
def:"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." [GROUP:OBI , OBO:sourced "OBI:0000240"]
is_a: IAO:0000309 ! diagram

[Term]
id: IAO:0000065
name: software interpreter
def:"An algorithmy that takes\, as input\, some digital entity\, and takes action driven by the information content of that algorithm" [GROUP:OBI , OBO:sourced "OBI:0000199"]
is_a: IAO:0000064 ! algorithm

[Term]
id: IAO:0000319
name: discussion section of a publication about an investigation
def:"A part of a publication about an investigation that is about the study interpretation of the investigation" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000314 ! document part

[Term]
id: span:ProcessualContext
name: processual_context
def:"Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.; Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.; Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel\, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment." [OBO:imported "http://www.ifomis.org/bfo/1.1/"]
is_a: span:ProcessualEntity ! processual_entity

[Term]
id: UO:0000001
name: UO_0000001

[Term]
id: IAO:0000031
name: integer numeral
def:"a numeral that denotes an integer" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000029 ! numeral

[Term]
id: IAO:0000329
name: running title
def:"A shorter version of a document title" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000305 ! document title

[Typedef]
id: IAO:0000116
name: editor note
def:"An administrative note intended for its editor. It may not be included in the publication version of the ontology\, so it should contain nothing necessary for end users to understand the ontology." [GROUP:OBI:<HTTP://purl.obfoundry.org/obo/obi> ]

[Typedef]
id: IAO:0000231
name: has obsolescence reason

[Typedef]
id: IAO:0000117
name: definition editor
def:"Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be\, but is not always\, the author of the definition\, which may have been worked upon by several people" [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0000115
name: definition
def:"The official definition\, explaining the meaning of a class or property. Shall be Aristotelian\, formalized and normalized. Can be augmented with colloquial definitions." [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0000412
name: imported from
def:"For external terms/classes\, the ontology from which the term was imported" [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0000114
name: has curation status

[Typedef]
id: IAO:0000112
name: example of usage
def:"A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics\, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms\, examples for low level terms (e.g.\, Affymetrix HU133 array) are not" [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0000119
name: definition source
def:"formal citation\, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name\, URI\, MeSH Term C04\, PUBMED ID\, Wiki uri on 31.01.2007" [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0000113
name: in branch

[Typedef]
id: IAO:0000118
name: alternative term
def:"An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)" [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0000111
name: editor preferred term
def:"The concise\, meaningful\, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" [GROUP:OBI:<HTTP://purl.obolibrary.org/obo/obi> ]

[Typedef]
id: IAO:0100001
name: term replaced by
def:"Use on obsolete terms\, relating the term to another term that can be used as a substitute" [OBO:sourced "Person:Alan Ruttenberg"]

[Typedef]
id: IAO:0000232
name: curator note
def:"An administrative note of use for a curator but of no use for a user" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]

[Typedef]
id: IAO:0000411
name: is denotator type
def:"relates an class defined in an ontology\, to the type of it's denotator" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]

[Typedef]
id: IAO:0000004
name: has measurement value

[Typedef]
id: IAO:0000404
name: has x coordinate value

[Typedef]
id: IAO:0000405
name: has z coordinate value

[Typedef]
id: IAO:0000406
name: has y coordinate value

[Typedef]
id: RO:has_participant
name: has_participant
def:"Has_participant is a primitive instance-level relation between a process\, a continuant\, and a time at which the continuant participates in some way in the process. The relation obtains\, for example\, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: RO:has_part
name: has_part

[Typedef]
id: RO:agent_in
name: agent_in
is_a: RO:participates_in ! participates_in

[Typedef]
id: RO:proper_part_of
name: proper_part_of
is_a: RO:part_of ! part_of

[Typedef]
id: RO:transformation_of
name: transformation_of
def:"When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte\, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed\, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells\, for example\, from reticulocyte to erythrocyte\, and by processes of development\, for example\, from larva to pupa\, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations\, for example\, of normal colon into carcinomatous colon. In each such case\, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: RO:part_of
name: part_of
def:"Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception.    This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p\, p part_of p); anti-symmetry (for all p\, p1\, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p\, p1\, p2\, if p part_of p1 and p1 part_of p2\, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions.    For parthood as a relation between continuants\, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t\, then also c part_of c2 at t.    Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes\, even though the explicit reference to instants of time now falls away. For continuants\, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time\, as for example in: cell nucleus part_ of cell." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: RO:participates_in
name: participates_in

[Typedef]
id: IAO:0000221
name: is quality measurement of
def:"m is a quality measurement of q at t when\nq is a quality \nthere is a measurement process p that has specified output m\, a measurement datum\, that is about q" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
inverse_of: IAO:0000417 ! is quality measured as
is_a: IAO:0000136 ! is about

[Typedef]
id: RO:adjacent_to
name: adjacent_to
def:"Note that adjacent_to as thus defined is not a symmetric relation\, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: RO:derived_into
name: derived_into

[Typedef]
id: RO:integral_part_of
name: integral_part_of
is_a: RO:part_of ! part_of

[Typedef]
id: RO:has_agent
name: has_agent
is_a: RO:has_participant ! has_participant

[Typedef]
id: RO:derives_from
name: derives_from
def:"Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation\, on the instance level\, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely\, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: IAO:0000039
name: has measurement unit label
is_a: RO:has_part ! has_part

[Typedef]
id: RO:has_proper_part
name: has_proper_part
is_a: RO:has_part ! has_part

[Typedef]
id: IAO:0000417
name: is quality measured as
def:"inverse of the relation of is quality measurement of" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
inverse_of: IAO:0000221 ! is quality measurement of

[Typedef]
id: OBI:0000294
name: is_concretization_of
inverse_of: OBI:0000297 ! is_concretized_as

[Typedef]
id: RO:location_of
name: location_of

[Typedef]
id: RO:contains
name: contains

[Typedef]
id: IAO:0000418
name: is quality specification of
def:"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." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
inverse_of: IAO:0000419 ! quality is specified as
is_a: IAO:0000136 ! is about

[Typedef]
id: OBI:0000297
name: is_concretized_as
inverse_of: OBI:0000294 ! is_concretization_of

[Typedef]
id: IAO:0000413
name: is duration of
def:"relates a process to a time-measurement-datum that represents the duration of the process" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000136 ! is about

[Typedef]
id: RO:located_in
name: located_in
def:"Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region\, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies\, but rather between one continuant and another. c is located in c1\, in this sense\, whenever the spatial region occupied by c is part_of the spatial region occupied by c1.    Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example\, when a portion of fluid exactly fills a cavity)\, as well as those sorts of inexact location relations which obtain\, for example\, between brain and head or between ovum and uterus" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: RO:contained_in
name: contained_in
def:"Containment obtains in each case between material and immaterial continuants\, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation.    If c part_of c1 at t then we have also\, by our definition and by the axioms of mereology applied to spatial regions\, c located_in c1 at t. Thus\, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood\, and arises only where some immaterial continuant is involved. To understand this relation\, we first define overlap for continuants as follows:    c1 overlap c2 at t =def for some c\, c part_of c1 at t and c part_of c2 at t.    The containment relation on the instance level can then be defined (see definition):" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: RO:precedes
name: precedes

[Typedef]
id: RO:has_integral_part
name: has_integral_part
is_a: RO:has_part ! has_part

[Typedef]
id: IAO:0000419
name: quality is specified as
def:"inverse of the relation of is quality specification of" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
inverse_of: IAO:0000418 ! is quality specification of

[Typedef]
id: IAO:0000219
name: denotes
def:"denotes is a primitive\, instance-level\, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [OBO:sourced "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan"]
is_a: IAO:0000136 ! is about

[Typedef]
id: RO:preceded_by
name: preceded_by
def:"An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants\, preceded_by links classes of processes. Clearly\, however\, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C\, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is\, it tells us something about what happened earlier\, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction\, concerning instances of P1 in general; that is\, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations\, for example in the relation immediately_preceded_by\, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants\, or that their participants are connected by relations of derivation\, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example\, initiates or regulates) the other." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"]

[Typedef]
id: IAO:0000142
name: mentions
def:"An information artifact IA mentions an entity E exactly when it has a component/part that denotes E" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: IAO:0000136 ! is about

[Typedef]
id: IAO:0000407
name: has coordinate unit label
def:"relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"]
is_a: RO:has_part ! has_part

[Typedef]
id: IAO:0000136
name: is about
def:"is_about is a (currently) primitive relation that relates an information artifact to an entity." [OBO:sourced "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"]

[Typedef]
id: ROP:bearer_of
name: bearer_of