tmo-external.owl
type: Ontology
has default namespace: relationship
contributor: Alan Ruttenberg
default language: en
contributor: Pierre Grenon
contributor: Holger Stenzhorn
contributor: Andrew Spear
language: en

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

data format specification
type: Class
editor preferred term: data format specification
definition source: OBI_0000187
definition source: OBI branch derived
has curation status: http://purl.obolibrary.org/obo/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"

directive information entity
type: Class
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: http://purl.obolibrary.org/obo/IAO_0000123
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#13
definition editor: PERSON: Alan Ruttenberg

software interpreter
type: Class
definition source: group:OBI
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
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.

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#1
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#2
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: http://purl.obolibrary.org/obo/IAO_0000124

cartesian spatial coordinate datum
type: Class
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
definition editor: Alan Ruttenberg

http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#1
type: Restriction
on property: has x coordinate value
cardinality: 1

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

http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#2
type: Restriction
on property: has y coordinate value
cardinality: 1

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

zero_dimensional_region
type: Class
subclass of: spatial_region
comment: Definition: A spatial region [snap:SpatialRegion] with no dimensions.
comment: Examples: a point

spatial_region
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#54
subclass of: continuant
comment: 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: 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].
comment: 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.
comment: Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
comment: Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe

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

information content entity
type: Class
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#28
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
editor preferred term: information content entity
subclass of: generically_dependent_continuant
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: http://purl.obolibrary.org/obo/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

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

document part
type: Class
subclass of: information content entity
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#44
editor preferred term: document part
example of usage: An abstract, introduction, method or results section.
definition editor: PERSON: Lawrence Hunter
definition: an information content entity that is part of a document

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

caption
type: Class
subclass of: textual entity
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#3
editor preferred term: caption
has curation status: http://purl.obolibrary.org/obo/IAO_0000125
definition: A textual entity that describes a figure
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
definition editor: PERSON: Lawrence Hunter

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

is about
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
has curation status: http://purl.obolibrary.org/obo/IAO_0000125
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
definition editor: person:Alan Ruttenberg
domain: information content entity

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

processual_entity
type: Class
comment: Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird
subclass of: occurrent
disjoint with: spatiotemporal_region
disjoint with: temporal_region
comment: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.

occurrent
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#24
subclass of: entity
comment: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
comment: 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
comment: Synonyms: perdurant

spatiotemporal_region
type: Class
comment: 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
subclass of: occurrent
comment: 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.
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#21
comment: Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
comment: 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.
disjoint with: temporal_region
comment: 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.

temporal_region
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#7
subclass of: occurrent
comment: 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].
comment: 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.
comment: 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].
comment: Definition: An occurrent [span:Occurrent] that is part of time.
comment: Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#4
has curation status: http://purl.obolibrary.org/obo/IAO_0000124
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#5
subclass of: cartesian spatial coordinate datum
definition editor: Alan Ruttenberg
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#6
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region

http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#4
type: Restriction
on property: has y coordinate value
cardinality: 1

http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#5
type: Restriction
on property: has z coordinate value
cardinality: 1

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

http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#6
type: Restriction
on property: has x coordinate value
cardinality: 1

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
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
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#14
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: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#15
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

realizable_entity
type: Class
subclass of: specifically_dependent_continuant
comment: Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
comment: 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.
comment: 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

specifically_dependent_continuant
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#10
subclass of: dependent_continuant
comment: 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.
comment: 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.
comment: Synonyms: property, trope, mode

label
type: Class
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
definition editor: GROUP: IAO
has curation status: http://purl.obolibrary.org/obo/IAO_0000123
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
editor preferred term: label

journal article
type: Class
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 source: OBI_0000099
definition editor: PERSON: Melanie Courtot
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: 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: http://purl.obolibrary.org/obo/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 role
type: Class
subclass of: role
editor preferred term: author role
has curation status: http://purl.obolibrary.org/obo/IAO_0000125
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: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

role
type: Class
subclass of: realizable_entity
comment: 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.
comment: 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

one_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: three_dimensional_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with one dimension.
comment: 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

three_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with three dimensions.
comment: Examples: a cube-shaped part of space, a sphere-shaped part of space

two_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with two dimensions.
comment: 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

connected_temporal_region
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#45
subclass of: temporal_region
disjoint with: scattered_temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
comment: Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis

scattered_temporal_region
type: Class
subclass of: temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
comment: Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair

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

quality
type: Class
subclass of: specifically_dependent_continuant
disjoint with: realizable_entity
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
comment: 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

dependent_continuant
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#41
subclass of: continuant
disjoint with: independent_continuant
disjoint with: spatial_region
comment: 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.

disposition
type: Class
subclass of: realizable_entity
disjoint with: function
disjoint with: role
comment: 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.
comment: 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.

function
type: Class
subclass of: realizable_entity
disjoint with: role
comment: 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.
comment: 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

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

generically_dependent_continuant
type: Class
subclass of: dependent_continuant
disjoint with: specifically_dependent_continuant
comment: 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.
comment: Examples: a certain PDF file that exists in different and in several hard drives

has part
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000003
type: TransitiveProperty

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: http://purl.obolibrary.org/obo/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."

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

temporal_interval
type: Class
subclass of: connected_temporal_region
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
comment: Examples: any continuous temporal duration during which a process occurs

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

independent_continuant
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#16
subclass of: continuant
disjoint with: spatial_region
comment: 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.
comment: 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
comment: Synonyms: substantial entity

material_entity
type: Class
comment: Examples: collection of random bacteria, a chair, dorsal surface of the body
subclass of: independent_continuant
disjoint with: object_boundary
disjoint with: site
comment: 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.

object_boundary
type: Class
subclass of: independent_continuant
disjoint with: site
comment: 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.
comment: 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.
comment: 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
comment: Synonyms: substance boundary

site
type: Class
subclass of: independent_continuant
comment: 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 site [snap:Site] entities) 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).
comment: 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: Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.

continuant
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#37
subclass of: entity
disjoint with: occurrent
comment: 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.
comment: 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
comment: Synonyms: endurant

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: http://purl.obolibrary.org/obo/IAO_0000125
definition source: OBI_0000240

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

citation
type: Class
subclass of: textual entity
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#20
editor preferred term: citation
has curation status: http://purl.obolibrary.org/obo/IAO_0000125
definition editor: PERSON: Lawrence Hunter
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication

connected_spatiotemporal_region
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#30
subclass of: spatiotemporal_region
disjoint with: scattered_spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] 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 spatiotemporal region [span:SpatiotemporalRegion].
comment: Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus

scattered_spatiotemporal_region
type: Class
subclass of: spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] 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.
comment: 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

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
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.

entity
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#34

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

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

institution list
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#29
editor preferred term: institution list
definition editor: PERSON: Lawrence Hunter
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
definition: part of a document that has parts that are institution identifications associated with the authors of the document

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

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

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

spatiotemporal_instant
type: Class
subclass of: connected_spatiotemporal_region
disjoint with: spatiotemporal_interval
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
comment: Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process

spatiotemporal_interval
type: Class
subclass of: connected_spatiotemporal_region
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
comment: Examples: the spatiotemporal region occupied by a process or by a fiat processual part

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

author list
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#33
editor preferred term: author list
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
definition editor: PERSON: Lawrence Hunter
definition: part of a document that enumerates the authors of the document

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

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

temporal_instant
type: Class
subclass of: connected_temporal_region
disjoint with: temporal_interval
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
comment: 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

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

image
type: Class
has curation status: http://purl.obolibrary.org/obo/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

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: http://purl.obolibrary.org/obo/IAO_0000124
editor note: MSI
definition editor: PRS

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

lot number
type: Class
subclass of: symbol
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
alternative term: batch number
has curation status: http://purl.obolibrary.org/obo/IAO_0000124
editor preferred term: lot number

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

part of
type: ObjectProperty
comment: 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.
editor note: There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
has OBO namespace: relationship
has alternative id: OBO_REL:0000002
inverse of: has part
type: TransitiveProperty

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

serial number
type: Class
subclass of: symbol
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
has curation status: http://purl.obolibrary.org/obo/IAO_0000124
editor preferred term: serial number

model number
type: Class
subclass of: symbol
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: Person: Alan Ruttenberg
has curation status: http://purl.obolibrary.org/obo/IAO_0000125
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
editor preferred term: model number

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: http://purl.obolibrary.org/obo/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

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

table
type: Class
has curation status: http://purl.obolibrary.org/obo/IAO_0000125
editor preferred term: table
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
definition editor: PERSON: Lawrence Hunter
example of usage: | T F --+----- T | T F F | F F

methods section
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#48
editor preferred term: methods section
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.

version number
type: Class
subclass of: symbol
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
definition editor: GROUP: IAO
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
has curation status: http://purl.obolibrary.org/obo/IAO_0000124
editor preferred term: version number

data set
type: Class
definition source: OBI_0000042
editor preferred term: data set
definition editor: person:Chris Stoeckert
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).

time trigger
type: Class
subclass of: conditional specification
definition source: OBI_0000331
has curation status: http://purl.obolibrary.org/obo/IAO_0000124
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
definition: revisit?
editor preferred term: time trigger

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

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#49
editor preferred term: introduction to a publication about an investigation
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
definition editor: PERSON: Lawrence Hunter
example of usage: Section labelled 'introduction' of a typical scientific journal article
alternative term: introduction

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

references section
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#50
editor preferred term: references section
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"

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

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#51
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: http://purl.obolibrary.org/obo/IAO_0000124

http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#51
type: Restriction
on property: has x coordinate value
cardinality: 1

footnote
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#52
editor preferred term: footnote
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
definition editor: PERSON: Lawrence Hunter
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
alternative term: endnote

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: plan specification
definition source: group:OBI
subclass of: directive information entity

abstract
type: Class
subclass of: document part
subclass of: http://lodlaundromat.org/.well-known/genid/c0dff512475ff0037b37130d7bf2ae65#53
editor preferred term: abstract
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
definition editor: PERSON: Lawrence Hunter
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.

contained in
type: ObjectProperty
comment: 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):
has OBO namespace: relationship
has alternative id: OBO_REL:0000010
inverse of: contains

contains
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000011

proper part of
type: ObjectProperty
has alternative id: OBO_REL:0000006
has OBO namespace: relationship
inverse of: has proper part
sub property of: part of
type: TransitiveProperty

has proper part
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000007
sub property of: has part
type: TransitiveProperty

location of
type: ObjectProperty
has alternative id: OBO_REL:0000009
has OBO namespace: relationship
type: TransitiveProperty

is concretized as
type: ObjectProperty
inverse of: is concretization of
domain: generically_dependent_continuant
range: specifically_dependent_continuant

is concretization of
type: ObjectProperty
range: generically_dependent_continuant
domain: specifically_dependent_continuant

precedes
type: ObjectProperty
has alternative id: OBO_REL:0000018
has OBO namespace: relationship
type: TransitiveProperty

integral part of
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000004
inverse of: has integral part

has integral part
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000005

bearer of {en}
type: ObjectProperty
range: dependent_continuant
domain: independent_continuant

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

derives from
type: ObjectProperty
comment: 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.
has OBO namespace: relationship
has alternative id: OBO_REL:0000015
inverse of: derived into
type: TransitiveProperty

derived into
type: ObjectProperty
has alternative id: OBO_REL:0000016
has OBO namespace: relationship
type: TransitiveProperty

agent in
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000022
sub property of: participates in

participates in
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000020

transformation of
type: ObjectProperty
comment: 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.
has alternative id: OBO_REL:0000013
has OBO namespace: relationship
type: TransitiveProperty

adjacent to
type: ObjectProperty
comment: 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
has alternative id: OBO_REL:0000012
has OBO namespace: relationship

preceded by
type: ObjectProperty
comment: 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.
has alternative id: OBO_REL:0000017
has OBO namespace: relationship
inverse of: precedes
type: TransitiveProperty

located in
type: ObjectProperty
comment: 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
has OBO namespace: relationship
has alternative id: OBO_REL:0000008
inverse of: location of
type: TransitiveProperty

has agent
type: ObjectProperty
has alternative id: OBO_REL:0000021
has OBO namespace: relationship
inverse of: agent in
sub property of: has participant

has participant
type: ObjectProperty
comment: 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.
has alternative id: OBO_REL:0000019
has OBO namespace: relationship
inverse of: participates in

is duration of
type: ObjectProperty
definition editor: Person:Alan Ruttenberg
definition: relates a process to a time-measurement-datum that represents the duration of the process
sub property of: is about

has measurement value
type: DatatypeProperty
range: float
type: FunctionalProperty

title
type: AnnotationProperty

example of usage
type: AnnotationProperty

rights
type: AnnotationProperty

editor preferred term
type: AnnotationProperty

format
type: AnnotationProperty

creator
type: AnnotationProperty

has curation status
type: AnnotationProperty

source
type: AnnotationProperty

identifier
type: AnnotationProperty

definition editor
type: AnnotationProperty

publisher
type: AnnotationProperty

imported from
type: AnnotationProperty

alternative term
type: AnnotationProperty

definition source
type: AnnotationProperty

language
type: AnnotationProperty

definition
type: AnnotationProperty

contributor
type: AnnotationProperty

editor note
type: AnnotationProperty