Information Artifact Ontology (IAO)
type: Ontology
version IRI: iao-edit.owl
imports: bfo.owl
imports: omo.owl
imports: externalByHand.owl
imports: import OBI.owl
imports: import PATO.owl
imports: import RO.owl
imports: import UO.owl
imports: obsolete.owl
imports: core.owl
default language: en
contributor: Adam Goldstein
contributor: Alan Ruttenberg
contributor: Albert Goldfain
contributor: Barry Smith
contributor: Bjoern Peters
contributor: Carlo Torniai
contributor: Chris Mungall
contributor: Chris Stoeckert
contributor: Christian A. Boelling
contributor: Clint Dowland
contributor: Darren Natale
contributor: David Osumi-Sutherland
contributor: Gwen Frishkoff
contributor: Holger Stenzhorn
contributor: James A. Overton
contributor: James Malone
contributor: Jennifer Fostel
contributor: Jie Zheng
contributor: Jonathan Rees
contributor: Larisa Soldatova
contributor: Lawrence Hunter
contributor: Mathias Brochhausen
contributor: Matt Brush
contributor: Melanie Courtot
contributor: Michel Dumontier
contributor: Paolo Ciccarese
contributor: Pat Hayes
contributor: Philippe Rocca-Serra
contributor: Randy Dipert
contributor: Ron Rudnicki
contributor: Satya Sahoo
contributor: Sivaram Arabandi
contributor: Werner Ceusters
contributor: William Duncan
contributor: William Hogan
contributor: Yongqun (Oliver) He
description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.
license: http://creativecommons.org/licenses/by/4.0/
comment: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
comment: IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
comment: IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999

retired from use as of
type: AnnotationProperty
IAO_0000111: retired from use as of
IAO_0000115: relates a class of CRID to the date after which further instances should not be made, according to the central authority
IAO_0000116: In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
IAO_0000117: Alan Ruttenberg

has measurement unit label
type: ObjectProperty
sub property of: BFO_0000051
type: FunctionalProperty
range: measurement unit label

is about
type: ObjectProperty
domain: information content entity
IAO_0000112: This document is about information artifacts and their representations
IAO_0000114: IAO_0000125
IAO_0000115: A (currently) primitive relation that relates an information artifact to an entity.
IAO_0000116: 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.
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

mentions
type: ObjectProperty
sub property of: is about
inverse of: mentioned by
IAO_0000114: IAO_0000125
IAO_0000115: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
IAO_0000116: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
IAO_0000116: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
IAO_0000117: PERSON: Jonathan Rees
IAO_0000117: Person: Alan Ruttenberg

mentioned by
type: ObjectProperty
IAO_0000115: Inverse of the relation 'mentions'
IAO_0000117: http://orcid.org/0000-0002-8844-9165
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/250
date: 2022-01-28T07:20:08Z

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: BFO_0000001
IAO_0000112: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
IAO_0000115: 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
IAO_0000116: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

is quality measurement of
type: ObjectProperty
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: BFO_0000019
IAO_0000115: m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
IAO_0000116: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
IAO_0000116: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
IAO_0000116: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
IAO_0000116: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
IAO_0000116: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
IAO_0000117: Alan Ruttenberg

denoted by
type: ObjectProperty
domain: BFO_0000001
range: information content entity
IAO_0000115: inverse of the relation 'denotes'
IAO_0000117: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/206

has coordinate unit label
type: ObjectProperty
sub property of: BFO_0000051
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: UO_0000001
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: BFO_0000015
IAO_0000114: IAO_0000120
IAO_0000115: relates a process to a time-measurement-datum that represents the duration of the process
IAO_0000117: Person:Alan Ruttenberg

is quality measured as
type: ObjectProperty
IAO_0000114: IAO_0000120
IAO_0000115: inverse of the relation of is quality measurement of
IAO_0000116: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
IAO_0000117: Person:Alan Ruttenberg

is quality specification of
type: ObjectProperty
sub property of: is about
inverse of: quality is specified as
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Bjoern Peters

quality is specified as
type: ObjectProperty
IAO_0000114: IAO_0000120
IAO_0000115: inverse of the relation of is quality specification of
IAO_0000116: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Bjoern Peters

has time stamp
type: ObjectProperty
sub property of: BFO_0000051
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
IAO_0000114: IAO_0000123
IAO_0000115: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
IAO_0000117: Alan Ruttenberg

has measurement datum
type: ObjectProperty
sub property of: BFO_0000051
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
IAO_0000114: IAO_0000123
IAO_0000115: relates a time stamped measurement datum to the measurement datum that was measured
IAO_0000117: Alan Ruttenberg

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

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

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

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

software development
type: Class
equivalent class: Class
  intersection of: OBI_0000011
  intersection of: Restriction
    on property: OBI_0000299
    some values from: Class
      union of: software
      union of: source code module
subclass of: OBI_0000011
IAO_0000115: A planned process that has specified output a software product and that involves the creation of source code.
IAO_0000117: Mathias Brochhausen
IAO_0000117: William R. Hogan
IAO_0000119: http://en.wikipedia.org/wiki/Software_development
IAO_0000600: A planned process resulting in a software product involving the creation of source code.

count
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: OBI_0000312
    some values from: counting
subclass of: measurement datum
IAO_0000115: A measurement datum that is the output of counting.
IAO_0000117: Mathias Brochhausen
IAO_0000600: A measurement datum that is the output of counting.

counting
type: Class
equivalent class: Class
  intersection of: OBI_0000011
  intersection of: Restriction
    on property: OBI_0000299
    some values from: count
subclass of: OBI_0000011
IAO_0000115: The planned process of finding the number of elements in a finite set of objects.
IAO_0000117: Mathias Brochhausen
IAO_0000119: http://en.wikipedia.org/wiki/Counting
IAO_0000600: The planned process of finding the number of elements in a finite set of objects.

source code repository
type: Class
subclass of: document
subclass of: Restriction
  on property: BFO_0000051
  some values from: source code module
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: source code module
IAO_0000111: software source code version control repository
IAO_0000115: A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
IAO_0000117: William R. Hogan
comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based

compiling software
type: Class
subclass of: OBI_0000011
subclass of: Class
  intersection of: Restriction
    on property: OBI_0000293
    some values from: Class
      union of: software
      union of: source code module
  intersection of: Restriction
    on property: OBI_0000299
    some values from: software
IAO_0000111: process of compiling software
IAO_0000115: A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
IAO_0000117: William R. Hogan
comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.

dataset creating
type: Class
equivalent class: Class
  intersection of: OBI_0000011
  intersection of: Restriction
    on property: OBI_0000299
    some values from: data set
subclass of: OBI_0000011
IAO_0000111: creating a data set
IAO_0000115: A planned process that has a data set as its specified output.
IAO_0000117: William R. Hogan
IAO_0000118: data set creation
IAO_0000118: dataset creation

conditional specification
type: Class
subclass of: directive information entity
IAO_0000111: conditional specification
IAO_0000114: IAO_0000120
IAO_0000115: A directive information entity that specifies what should happen if the trigger condition is fulfilled.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived
IAO_0000119: OBI_0000349

measurement unit label
type: Class
subclass of: datum label
IAO_0000111: measurement unit label
IAO_0000112: Examples of measurement unit labels are liters, inches, weight per volume.
IAO_0000114: IAO_0000125
IAO_0000115: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
IAO_0000116: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
IAO_0000116: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot

objective specification
type: Class
subclass of: directive information entity
IAO_0000111: objective specification
IAO_0000112: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000116: 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."
IAO_0000116: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
IAO_0000116: Answers the question, why did you do this experiment?
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Barry Smith
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000118: goal specification
IAO_0000119: OBI Plan and Planned Process/Roles Branch
IAO_0000119: OBI_0000217

narrative object
type: Class
subclass of: information content entity
IAO_0000111: narrative object
IAO_0000112: Examples of narrative objects are reports, journal articles, and patents submission.
IAO_0000114: IAO_0000123
IAO_0000115: A narrative object is an information content entity that is a set of propositions.
IAO_0000116: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
IAO_0000116: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000013
IAO_0000119: group:OBI

action specification
type: Class
subclass of: directive information entity
IAO_0000112: Pour the contents of flask 1 into flask 2
IAO_0000114: IAO_0000122
IAO_0000115: A directive information entity that describes an action the bearer will take.
IAO_0000117: Alan Ruttenberg
IAO_0000119: OBI Plan and Planned Process branch

datum label
type: Class
subclass of: information content entity
IAO_0000111: datum label
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: http://www.golovchenko.org/cgi-bin/wnsearch#4n
IAO_0000117: GROUP: IAO
IAO_0000232: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.

software
type: Class
subclass of: plan specification
IAO_0000111: software
IAO_0000114: IAO_0000120
IAO_0000115: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
IAO_0000116: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: GROUP: OBI

journal article
type: Class
subclass of: report
subclass of: Restriction
  on property: OBI_0000312
  some values from: publishing process
subclass of: Restriction
  on property: OBI_0000312
  all values from: publishing process
IAO_0000111: journal article
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A report that is published in a journal.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: OBI_0000159
IAO_0000119: group:OBI

information carrier
type: Class
equivalent class: Class
  intersection of: BFO_0000019
  intersection of: Restriction
    on property: RO_0000059
    some values from: information content entity
IAO_0000111: information carrier
IAO_0000112: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
IAO_0000114: IAO_0000125
IAO_0000115: A quality of an information bearer that imparts the information content
IAO_0000116: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
IAO_0000116: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000119: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

model number
type: Class
subclass of: symbol
IAO_0000111: model number
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
IAO_0000117: Person: Alan Ruttenberg

programming language
type: Class
subclass of: plan specification
IAO_0000111: programming language
IAO_0000112: R, Perl, Java
IAO_0000114: IAO_0000120
IAO_0000115: A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
IAO_0000117: person:Alan Ruttenberg
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000058
IAO_0000119: group:OBI

data item
type: Class
subclass of: information content entity
IAO_0000111: data item
IAO_0000112: Data items include counts of things, analyte concentrations, and statistical summaries.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
IAO_0000116: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jonathan Rees
IAO_0000118: data

symbol
type: Class
subclass of: information content entity
IAO_0000111: symbol
IAO_0000112: a serial number such as "12324X"
IAO_0000112: a stop sign
IAO_0000112: a written proper name such as "OBI"
IAO_0000114: IAO_0000125
IAO_0000115: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
IAO_0000116: 20091104, MC: this needs work and will most probably change
IAO_0000116: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
IAO_0000117: PERSON: James A. Overton
IAO_0000117: PERSON: Jonathan Rees
IAO_0000119: based on Oxford English Dictionary

numeral
type: Class
subclass of: symbol
IAO_0000111: numeral
IAO_0000114: IAO_0000123
IAO_0000115: A symbol that denotes a number.
IAO_0000117: PERSON: Jonathan Rees

information content entity
type: Class
subclass of: BFO_0000031
subclass of: Restriction
  on property: is about
  some values from: BFO_0000001
IAO_0000111: information content entity
IAO_0000112: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000114: IAO_0000122
IAO_0000115: A generically dependent continuant that is about some thing.
IAO_0000116: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
IAO_0000116: 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.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: OBI_0000142

integer numeral
type: Class
subclass of: numeral
IAO_0000111: integer numeral
IAO_0000114: IAO_0000123
IAO_0000115: A numeral that denotes an integer
IAO_0000117: PERSON: Jonathan Rees

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
IAO_0000112: 10 feet. 3 ml.
IAO_0000114: IAO_0000120
IAO_0000115: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
IAO_0000116: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
IAO_0000116: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: BFO_0000017
IAO_0000114: IAO_0000122
IAO_0000115: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
IAO_0000116: 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.
IAO_0000116: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
IAO_0000116: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters

time trigger
type: Class
subclass of: conditional specification
IAO_0000111: time trigger
IAO_0000114: IAO_0000124
IAO_0000117: PlanAndPlannedProcess Branch

dot plot
type: Class
subclass of: graph
IAO_0000111: dot plot
IAO_0000112: Dot plot of SSC-H and FSC-H.
IAO_0000114: IAO_0000002
IAO_0000115: 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.
IAO_0000117: person:Allyson Lister
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000123
IAO_0000119: group:OBI

graph
type: Class
subclass of: diagram
IAO_0000111: graph
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000117: person:Alan Ruttenberg
IAO_0000117: person:Allyson Lister
IAO_0000119: OBI_0000240
IAO_0000119: group:OBI

rule
type: Class
subclass of: conditional specification
IAO_0000111: rule
IAO_0000112: example to be added
IAO_0000114: IAO_0000123
IAO_0000115: A rule is an executable which guides, defines, restricts actions.
IAO_0000116: MSI
IAO_0000117: PRS
IAO_0000119: OBI_0500021
IAO_0000119: PRS

contour plot
type: Class
subclass of: graph
IAO_0000111: contour plot
IAO_0000112: Contour plot of SSC-H, FSC-H, and FL1-H.
IAO_0000114: IAO_0000002
IAO_0000116: generically_dependent_continuants
IAO_0000117: person:Allyson Lister
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000246
IAO_0000119: group:Flow Cytometry community

algorithm
type: Class
subclass of: plan specification
IAO_0000111: algorithm
IAO_0000112: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
IAO_0000114: IAO_0000120
IAO_0000115: A plan specification which describes the inputs and 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.
IAO_0000117: Philippe Rocca-Serra
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI_0000270
IAO_0000119: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

software interpreter
type: Class
subclass of: algorithm
IAO_0000111: software interpreter
IAO_0000112: R program, Perl interpreter, Java virtual machine
IAO_0000114: IAO_0000120
IAO_0000115: A software interpreter is a software application that executes some specified input software.
IAO_0000116: 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
IAO_0000117: person:Alan Ruttenberg
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000199
IAO_0000119: group:OBI

density plot
type: Class
subclass of: graph
IAO_0000111: density plot
IAO_0000112: Density plot of SSC-H and FSC-H.
IAO_0000114: IAO_0000002
IAO_0000115: 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.
IAO_0000117: person:Allyson Lister
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000179
IAO_0000119: group:Flow Cytometry community

report
type: Class
subclass of: document
IAO_0000111: report
IAO_0000112: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
IAO_0000114: IAO_0000125
IAO_0000115: 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).
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 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
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: GROUP: OBI
IAO_0000119: OBI_0000099

source code module
type: Class
subclass of: directive information entity
IAO_0000111: source code module
IAO_0000112: 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.
IAO_0000114: IAO_0000123
IAO_0000115: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
IAO_0000117: person:Alan Ruttenberg
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000039
IAO_0000119: group:OBI

data format specification
type: Class
subclass of: directive information entity
IAO_0000111: data format specification
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: 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"
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived
IAO_0000119: OBI_0000187
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/172

data set
type: Class
subclass of: data item
IAO_0000111: data set
IAO_0000112: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000116: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
IAO_0000117: person:Allyson Lister
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000042
IAO_0000119: group:OBI

image
type: Class
subclass of: figure
IAO_0000111: image
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: person:Alan Ruttenberg
IAO_0000117: person:Allyson
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000030
IAO_0000119: group:OBI

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: BFO_0000051
  some values from: objective specification
subclass of: Restriction
  on property: BFO_0000051
  some values from: action specification
IAO_0000111: plan specification
IAO_0000112: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
IAO_0000114: IAO_0000122
IAO_0000115: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
IAO_0000116: 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.
IAO_0000116: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
IAO_0000116: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
IAO_0000116: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
IAO_0000117: Alan Ruttenberg
IAO_0000117: Clint Dowland
IAO_0000119: OBI Plan and Planned Process branch
IAO_0000119: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
IAO_0000111: measurement datum
IAO_0000112: 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,}.
IAO_0000114: IAO_0000125
IAO_0000115: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
IAO_0000116: 2/2/2009 is_specified_output of some assay?
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000305
IAO_0000119: group:OBI

version number
type: Class
subclass of: symbol
IAO_0000111: version number
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000117: GROUP: IAO

serial number
type: Class
subclass of: symbol
IAO_0000111: serial number
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: 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 :-)
IAO_0000117: GROUP: IAO

lot number
type: Class
subclass of: symbol
IAO_0000111: lot number
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: GROUP: IAO
IAO_0000118: batch number

setting datum
type: Class
subclass of: data item
IAO_0000114: IAO_0000123
IAO_0000115: A settings datum is a datum that denotes some configuration of an instrument.
IAO_0000116: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
IAO_0000116: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.

conclusion textual entity
type: Class
subclass of: textual entity
IAO_0000111: conclusion textual entity
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
IAO_0000116: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
IAO_0000116: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
IAO_0000117: Person:Alan Ruttenberg

material information bearer
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: RO_0000053
    some values from: Restriction
      on property: RO_0000059
      some values from: information content entity
IAO_0000111: material information bearer
IAO_0000112: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
IAO_0000112: a brain
IAO_0000112: a hard drive
IAO_0000114: IAO_0000122
IAO_0000115: A material entity in which a concretization of an information content entity inheres.
IAO_0000117: GROUP: IAO

histogram
type: Class
subclass of: graph
IAO_0000111: histogram
IAO_0000114: IAO_0000122
IAO_0000115: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:James Malone
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: GROUP:OBI

heatmap
type: Class
subclass of: graph
IAO_0000111: heatmap
IAO_0000114: IAO_0000122
IAO_0000115: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:James Malone
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: GROUP:OBI

Venn diagram
type: Class
subclass of: graph
IAO_0000111: Venn diagram
IAO_0000114: IAO_0000122
IAO_0000115: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:James Malone
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Venn_diagram

dendrogram
type: Class
subclass of: graph
IAO_0000111: dendrogram
IAO_0000112: Dendrograms are often used in computational biology to illustrate the clustering of genes.
IAO_0000114: IAO_0000122
IAO_0000115: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:James Malone
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
IAO_0000111: scatter plot
IAO_0000112: Comparison of gene expression values in two samples can be displayed in a scatter plot
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:James Malone
IAO_0000117: PERSON:Melanie Courtot
IAO_0000118: scattergraph
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Scatterplot

photograph
type: Class
subclass of: image
IAO_0000114: IAO_0000122
IAO_0000115: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000117: PERSON:Joanne Luciano
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: WEB: http://en.wiktionary.org/wiki/photograph

photographic print
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: RO_0000053
    some values from: Restriction
      on property: RO_0000059
      some values from: photograph
IAO_0000111: photographic print
IAO_0000114: IAO_0000125
IAO_0000115: A photographic print is a material entity upon which a photograph generically depends.
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000117: PERSON:Melanie Courtot

textual entity
type: Class
subclass of: information content entity
IAO_0000111: textual entity
IAO_0000112: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: text

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
IAO_0000111: citation
IAO_0000112: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
IAO_0000114: IAO_0000125
IAO_0000115: A textual entity intended to identify a particular publication.
IAO_0000117: PERSON: Lawrence Hunter

author identification
type: Class
subclass of: written name
IAO_0000111: author identification
IAO_0000112: L. Hunter
IAO_0000114: IAO_0000125
IAO_0000115: A textual entity intended to identify a particular author
IAO_0000117: PERSON: Lawrence Hunter

institutional identification
type: Class
subclass of: textual entity
IAO_0000111: institutional identification
IAO_0000112: University of Colorado Denver School of Medicine
IAO_0000114: IAO_0000125
IAO_0000115: A textual entity intended to identify a particular institution
IAO_0000117: PERSON: Lawrence Hunter

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
IAO_0000111: caption
IAO_0000112: 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.
IAO_0000114: IAO_0000125
IAO_0000115: A textual entity that describes a figure
IAO_0000117: PERSON: Lawrence Hunter

document title
type: Class
subclass of: textual entity
IAO_0000111: document title
IAO_0000112: Textual characteristics of traditional and Open Access scientific journals are similar
IAO_0000114: IAO_0000125
IAO_0000115: A textual entity that names a document
IAO_0000117: PERSON: Lawrence Hunter

table
type: Class
subclass of: textual entity
IAO_0000111: table
IAO_0000112: | T F --+----- T | T F F | F F
IAO_0000114: IAO_0000125
IAO_0000115: 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
IAO_0000117: PERSON: Lawrence Hunter

table of abbreviations
type: Class
subclass of: table
IAO_0000111: table of abbreviations
IAO_0000112: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
IAO_0000114: IAO_0000125
IAO_0000115: A table where the constituent texts are abbreviations and their expansions
IAO_0000117: PERSON: Lawrence Hunter

figure
type: Class
subclass of: information content entity
IAO_0000111: figure
IAO_0000112: Any picture, diagram or table
IAO_0000114: IAO_0000120
IAO_0000115: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
IAO_0000117: PERSON: Lawrence Hunter

diagram
type: Class
subclass of: figure
IAO_0000111: diagram
IAO_0000112: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
IAO_0000114: IAO_0000120
IAO_0000115: A figure that expresses one or more propositions
IAO_0000117: PERSON: Lawrence Hunter

document
type: Class
subclass of: information content entity
IAO_0000111: document
IAO_0000112: A journal article, patent application, laboratory notebook, or a book
IAO_0000114: IAO_0000120
IAO_0000115: A collection of information content entities intended to be understood together as a whole
IAO_0000117: PERSON: Lawrence Hunter

publication
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: OBI_0000312
    all values from: publishing process
subclass of: document
IAO_0000111: publication
IAO_0000112: journal article, newspaper story, book, etc.
IAO_0000114: IAO_0000120
IAO_0000115: A document that is the output of a publishing process.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: published document
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/232
comment: Revisit the term in Octorber 2020. Improve the defintion.

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: OBI_0000066
IAO_0000111: publication about an investigation
IAO_0000112: Most scientific journal articles
IAO_0000114: IAO_0000120
IAO_0000115: A publication that is about an investigation
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: scientific publication

patent
type: Class
subclass of: document
IAO_0000111: patent
IAO_0000112: US Patent 6,449,603
IAO_0000114: IAO_0000120
IAO_0000115: A document that has been accepted by a patent authority
IAO_0000117: PERSON: Lawrence Hunter

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: BFO_0000050
  some values from: document
IAO_0000111: document part
IAO_0000112: An abstract, introduction, method or results section.
IAO_0000114: IAO_0000120
IAO_0000115: An information content entity that is part of a document.
IAO_0000117: PERSON: Lawrence Hunter

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
IAO_0000111: abstract
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: precis
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
IAO_0000111: introduction to a publication about an investigation
IAO_0000112: Section labelled 'introduction' of a typical scientific journal article
IAO_0000114: IAO_0000120
IAO_0000115: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: background
IAO_0000118: introduction
IAO_0000118: overview
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
IAO_0000111: methods section
IAO_0000112: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
IAO_0000114: IAO_0000120
IAO_0000115: A part of a publication about an investigation that is about the study design of the investigation
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: experimental
IAO_0000118: experimental methods
IAO_0000118: experimental procedures
IAO_0000118: experimental section
IAO_0000118: method
IAO_0000118: methodology
IAO_0000118: methods
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: OBI_0000471
IAO_0000111: results section
IAO_0000112: The section labelled 'results' in a typical scientific journal article
IAO_0000114: IAO_0000120
IAO_0000115: A part of a publication about an investigation that is about a study design execution
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: results

discussion section of a publication about an investigation
type: Class
subclass of: document part
IAO_0000111: discussion section of a publication about an investigation
IAO_0000114: IAO_0000120
IAO_0000115: A part of a publication about an investigation that is about the study interpretation of the investigation
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: discussion
IAO_0000118: discussion section
IAO_0000118: discussions
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: citation
IAO_0000111: references section
IAO_0000112: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
IAO_0000114: IAO_0000120
IAO_0000115: A part of a document that has citations as parts
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: literature cited
IAO_0000118: reference
IAO_0000118: reference list
IAO_0000118: references
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: author identification
IAO_0000111: author list
IAO_0000112: Lawrence Hunter and Kevin Brettonel Cohen
IAO_0000114: IAO_0000120
IAO_0000115: A part of a document that enumerates the authors of the document
IAO_0000117: PERSON: Lawrence Hunter

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: institutional identification
IAO_0000111: institution list
IAO_0000112: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
IAO_0000114: IAO_0000120
IAO_0000115: A part of a document that has parts that are institution identifications associated with the authors of the document
IAO_0000117: PERSON: Lawrence Hunter

author contributions section
type: Class
subclass of: document part
IAO_0000111: author contributions section
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A part of a publication that is about the specific contributions of each author
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: author contributions
IAO_0000118: authors' contribution
IAO_0000118: authors' contributions
IAO_0000118: authors' roles
IAO_0000118: contributions by the authors
IAO_0000118: contributorship
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

acknowledgements section
type: Class
subclass of: document part
IAO_0000111: acknowledgements section
IAO_0000112: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
IAO_0000114: IAO_0000120
IAO_0000115: Part of a publication that is about the contributions of people or institutions other than the authors.
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: acknowledgement
IAO_0000118: acknowledgements
IAO_0000118: acknowledgment
IAO_0000118: acknowledgments
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
IAO_0000111: footnote
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: endnote
IAO_0000118: footnotes
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

supplementary material to a document
type: Class
subclass of: document part
IAO_0000111: supplementary material to a document
IAO_0000114: IAO_0000120
IAO_0000115: A part of a document that is segregated from the rest of the document due to its size
IAO_0000117: PERSON: Lawrence Hunter
IAO_0000118: additional file
IAO_0000118: additional files
IAO_0000118: additional information
IAO_0000118: appendix
IAO_0000118: electronic supplementary material
IAO_0000118: electronic supplementary materials
IAO_0000118: supplemental data
IAO_0000118: supplemental information
IAO_0000118: supplemental material
IAO_0000118: supplementary data
IAO_0000118: supplementary files
IAO_0000118: supplementary information
IAO_0000118: supplementary material
IAO_0000118: supplementary materials
IAO_0000118: supporting information
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

table of contents
type: Class
subclass of: table
IAO_0000111: table of contents
IAO_0000114: IAO_0000125
IAO_0000115: 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).
IAO_0000117: PERSON: Lawrence Hunter

table of figures
type: Class
subclass of: table
IAO_0000111: table of figures
IAO_0000114: IAO_0000125
IAO_0000115: 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).
IAO_0000117: PERSON: Lawrence Hunter

running title
type: Class
subclass of: document title
IAO_0000111: running title
IAO_0000114: IAO_0000125
IAO_0000115: A shorter version of a document title
IAO_0000117: PERSON: Lawrence Hunter

copyright section
type: Class
subclass of: document part
IAO_0000111: copyright section
IAO_0000112: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
IAO_0000114: IAO_0000120
IAO_0000115: A document part that describes legal restrictions on making or distributing copies of the document
IAO_0000117: PERSON: Lawrence Hunter

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: BFO_0000018
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000116: 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
IAO_0000117: Alan Ruttenberg
IAO_0000232: AR notes: We need to discuss whether it should include site.

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: BFO_0000018
    intersection of: Restriction
      on property: BFO_0000050
      some values from: BFO_0000026
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
IAO_0000114: IAO_0000123
IAO_0000115: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
IAO_0000117: Alan Ruttenberg

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: BFO_0000018
    intersection of: Restriction
      on property: BFO_0000050
      some values from: BFO_0000009
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
IAO_0000114: IAO_0000123
IAO_0000115: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
IAO_0000117: Alan Ruttenberg

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: BFO_0000018
    intersection of: Restriction
      on property: BFO_0000050
      some values from: BFO_0000028
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
IAO_0000114: IAO_0000123
IAO_0000115: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
IAO_0000117: Alan Ruttenberg

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000001
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0000122
IAO_0000114: IAO_0000123
IAO_0000115: A scalar measurement datum that is the result of measurement of length quality
IAO_0000117: Alan Ruttenberg

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000002
  intersection of: Restriction
    on property: is quality measurement of
    all values from: PATO_0000125
IAO_0000114: IAO_0000123
IAO_0000115: A scalar measurement datum that is the result of measurement of mass quality
IAO_0000116: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
IAO_0000117: Person:Alan Ruttenberg

hypothesis textual entity
type: Class
subclass of: textual entity
IAO_0000111: hypothesis textual entity
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: A textual entity that expresses an assertion that is intended to be tested.
IAO_0000116: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
IAO_0000117: Person:Alan Ruttenberg

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000003
  intersection of: Restriction
    on property: is duration of
    all values from: BFO_0000015
IAO_0000114: IAO_0000123
IAO_0000115: A scalar measurement datum that is the result of measuring a temporal interval
IAO_0000116: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
IAO_0000117: Person:Alan Ruttenberg

postal address
type: Class
subclass of: textual entity
IAO_0000114: IAO_0000123
IAO_0000115: A textual entity that is used as directive to deliver something to a person, or organization
IAO_0000116: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59

email address
type: Class
subclass of: information content entity
IAO_0000111: email address
IAO_0000114: IAO_0000123
IAO_0000116: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Chris Stoeckart

author role
type: Class
subclass of: BFO_0000023
IAO_0000111: author role
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot

data item extraction from journal article
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000293
  some values from: journal article
subclass of: Restriction
  on property: OBI_0000299
  some values from: data item
IAO_0000114: IAO_0000120
IAO_0000115: A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
IAO_0000117: Person:Alan Ruttenberg

publishing process
type: Class
subclass of: OBI_0000011
IAO_0000114: IAO_0000120
IAO_0000115: A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
IAO_0000117: Person: Jie Zheng
IAO_0000119: https://en.wikipedia.org/wiki/Publishing
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/232
IAO_0000234: VEuPathDB

document in preparation for publication
type: Class
subclass of: document
IAO_0000114: IAO_0000120
IAO_0000115: A document that is in preparation for submission to be published.
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: EFO_0001795 in preparation
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/232
IAO_0000234: VEuPathDB

documenting
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000293
  some values from: information content entity
subclass of: Restriction
  on property: OBI_0000299
  some values from: document
IAO_0000112: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
IAO_0000114: IAO_0000125
IAO_0000115: A planned process in which a document is created or added to by including the specified input in it.
IAO_0000116: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
IAO_0000117: Bjoern Peters
IAO_0000119: wikipedia http://en.wikipedia.org/wiki/Documenting

line graph
type: Class
subclass of: graph
IAO_0000111: line graph
IAO_0000114: IAO_0000122
IAO_0000115: A line graph is a type of graph created by connecting a series of data points together with a line.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:Melanie Courtot
IAO_0000118: line chart
IAO_0000119: GROUP:OBI
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Line_chart

assigning a centrally registered identifier
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000299
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: RO_0000057
  some values from: centrally registered identifier registry
IAO_0000112: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
IAO_0000116: 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Bjoern Peters
IAO_0000117: Person:Melanie Courtot
IAO_0000118: assigning a CRID

associating information with a centrally registered identifier in its registry
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000293
  some values from: information content entity
subclass of: Restriction
  on property: OBI_0000293
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: RO_0000057
  some values from: centrally registered identifier registry
IAO_0000112: Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process in which a CRID registry associates an information content entity with a CRID symbol
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000118: associating information with a CRID in the CRID registry

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: BFO_0000050
  some values from: centrally registered identifier
IAO_0000112: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
IAO_0000114: IAO_0000120
IAO_0000115: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000118: CRID symbol
IAO_0000119: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: BFO_0000051
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: BFO_0000051
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
IAO_0000112: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
IAO_0000114: IAO_0000120
IAO_0000115: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
IAO_0000116: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
IAO_0000116: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
IAO_0000116: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000118: CRID
IAO_0000119: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: code set
IAO_0000112: PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
IAO_0000114: IAO_0000120
IAO_0000115: A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: Justin Whorton
IAO_0000118: CRID registry
IAO_0000119: Original proposal from Bjoern, discussions at IAO calls
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237

looking up a centrally registered identifier
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000293
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: OBI_0000299
  some values from: information content entity
subclass of: Restriction
  on property: RO_0000057
  some values from: centrally registered identifier registry
IAO_0000112: Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bill Hogan
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Melanie Courtot
IAO_0000118: looking up a CRID

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
IAO_0000114: IAO_0000123

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: BFO_0000051
  some values from: time stamped measurement datum
IAO_0000112: pmid:20604925 - time-lapse live cell microscopy
IAO_0000114: IAO_0000120
IAO_0000115: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
IAO_0000117: Alan Ruttenberg
IAO_0000118: experimental time series

written name
type: Class
subclass of: textual entity
IAO_0000111: written name
IAO_0000112: "Bill Clinton"
IAO_0000112: "The Eiffel Tower"
IAO_0000112: "United States of America"
IAO_0000114: IAO_0000125
IAO_0000115: A textual entity that denotes a particular in reality.
IAO_0000117: PERSON: Bill Hogan
IAO_0000119: https://github.com/information-artifact-ontology/IAO/issues/114
IAO_0000232: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.

software method
type: Class
subclass of: software
IAO_0000114: IAO_0000123
IAO_0000115: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Michel Dumontier
IAO_0000119: https://github.com/information-artifact-ontology/IAO/issues/80

software module
type: Class
subclass of: software
IAO_0000114: IAO_0000123
IAO_0000115: A software module is software composed of a collection of software methods.
IAO_0000117: PERSON: Melanei Courtot
IAO_0000117: PERSON: Michel Dumontier
IAO_0000119: https://github.com/information-artifact-ontology/IAO/issues/80

software library
type: Class
subclass of: software
IAO_0000114: IAO_0000123
IAO_0000115: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Michel Dumontier
IAO_0000119: https://github.com/information-artifact-ontology/IAO/issues/80

software application
type: Class
subclass of: software
IAO_0000114: IAO_0000123
IAO_0000115: A software application is software that can be directly executed by some processing unit.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Michel Dumontier
IAO_0000119: https://github.com/information-artifact-ontology/IAO/issues/80

software script
type: Class
subclass of: software
IAO_0000114: IAO_0000123
IAO_0000115: A software script is software whose instructions can be executed using a software interpreter.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Michel Dumontier
IAO_0000119: https://github.com/information-artifact-ontology/IAO/issues/80

abbreviation textual entity
type: Class
subclass of: textual entity
IAO_0000111: abbreviation textual entity
IAO_0000112: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
IAO_0000115: A textual entity listing abbreviations and their expansions that are used in a document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

abbreviations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: abbreviation textual entity
IAO_0000111: abbreviations section
IAO_0000112: The section labelled 'abbreviations' in a typical scientific journal article.
IAO_0000115: A part of a document where abbreviations and their long-forms used within the document are listed.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: abbreviation and acronyms
IAO_0000118: abbreviation list
IAO_0000118: abbreviations
IAO_0000118: abbreviations and acronyms
IAO_0000118: abbreviations list
IAO_0000118: abbreviations used
IAO_0000118: definitions for abbreviations
IAO_0000118: list of abbreviations
IAO_0000118: list of abbreviations used
IAO_0000118: non-standard abbreviations
IAO_0000118: nonstandard abbreviations
IAO_0000118: nonstandard abbreviations and acronyms
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

author information section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: author information textual entity
IAO_0000111: author information section
IAO_0000112: The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
IAO_0000115: A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: author information
IAO_0000118: authors’ information
IAO_0000118: biographies
IAO_0000118: contributor information
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

author information textual entity
type: Class
subclass of: textual entity
IAO_0000111: author information textual entity
IAO_0000112: From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
IAO_0000115: A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

author summary section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: author summary textual entity
IAO_0000111: author summary section
IAO_0000112: The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
IAO_0000115: A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: author summary
IAO_0000118: summary
IAO_0000118: synopsis
IAO_0000119: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

author summary textual entity
type: Class
subclass of: textual entity
IAO_0000111: author summary textual entity
IAO_0000112: From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
IAO_0000115: A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000119: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

availability section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: availability textual entity
IAO_0000111: availability section
IAO_0000112: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
IAO_0000115: A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: availability
IAO_0000118: availability of data
IAO_0000118: data archiving
IAO_0000118: data availability
IAO_0000118: data availability statement
IAO_0000118: data sharing statement
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

availability textual entity
type: Class
subclass of: textual entity
IAO_0000111: availability textual entity
IAO_0000112: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
IAO_0000115: A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

case report section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: case report textual entity
IAO_0000111: case report section
IAO_0000112: The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
IAO_0000115: A part of a document about the medical history of a specific patient as it relates to the topic of the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: case presentation
IAO_0000118: case report
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

case report textual entity
type: Class
subclass of: textual entity
IAO_0000111: case report textual entity
IAO_0000112: Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
IAO_0000115: A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

conclusion section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: conclusion textual entity
IAO_0000111: conclusion section
IAO_0000112: The section labelled 'conclusion' in a typical scientific journal article.
IAO_0000115: A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: concluding remarks
IAO_0000118: conclusion
IAO_0000118: conclusions
IAO_0000118: findings
IAO_0000118: summary
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

conflict of interest section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: conflict of interest textual entity
IAO_0000111: conflict of interest section
IAO_0000112: The section labelled 'conflict of interest statement' in a typical scientific journal article.
IAO_0000115: A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: authors' disclosures of potential conflicts of interest
IAO_0000118: competing financial interests
IAO_0000118: competing interests
IAO_0000118: conflict of interest
IAO_0000118: conflict of interest statement
IAO_0000118: conflict of interests
IAO_0000118: conflicts of interest
IAO_0000118: declaration of competing interest
IAO_0000118: declaration of competing interests
IAO_0000118: declaration of interest
IAO_0000118: declaration of interests
IAO_0000118: disclosure of conflict of interest
IAO_0000118: disclosure of potential conflicts of interest
IAO_0000118: duality of interest
IAO_0000118: statement of interest
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

conflict of interest textual entity
type: Class
subclass of: textual entity
IAO_0000111: conflict of interest statement
IAO_0000112: SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
IAO_0000115: A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

consent section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: consent textual entity
IAO_0000111: consent section
IAO_0000112: The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
IAO_0000115: A part of a document about the consent process that was used to enroll patients in a study.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: consent
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

consent textual entity
type: Class
subclass of: textual entity
IAO_0000111: consent textual entity
IAO_0000112: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
IAO_0000115: A textual entity that documents the consenting process used to enroll patients in a study.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

ethical approval section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: ethical approval textual entity
IAO_0000111: ethical approval section
IAO_0000112: The section labelled 'ethical approval' in a typical scientific journal article.
IAO_0000115: A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: ethical approval
IAO_0000118: ethical requirements
IAO_0000118: ethics
IAO_0000118: ethics statement
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

ethical approval textual entity
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
IAO_0000111: ethical approval textual entity
IAO_0000112: From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
IAO_0000115: A textual entity that documents the ethical approval of some study design.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

figures section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: figure
IAO_0000111: figures section
IAO_0000112: The section labelled 'figures' in a typical scientific journal article.
IAO_0000115: A part of a document that contains one or more figures.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: figures
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

funding source declaration section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: funding source declaration textual entity
IAO_0000111: funding source declaration section
IAO_0000112: The section labelled 'funding' in a typical scientific journal article.
IAO_0000115: A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: financial support
IAO_0000118: funding
IAO_0000118: funding information
IAO_0000118: funding sources
IAO_0000118: funding statement
IAO_0000118: funding/support
IAO_0000118: grants
IAO_0000118: role of the funding source
IAO_0000118: source of funding
IAO_0000118: sources of funding
IAO_0000118: study funding
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

funding source declaration textual entity
type: Class
subclass of: textual entity
IAO_0000111: funding souce declaration textual entity
IAO_0000112: From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
IAO_0000115: A textual entity documenting the source of funding that supported some study.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

future directions section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: future directions textual entity
IAO_0000111: future directions section
IAO_0000112: The section labelled 'future directions' in a typical scientific journal article.
IAO_0000115: A part of a document detailing extensions of the described work that may be implemented at some future point in time.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: future challenges
IAO_0000118: future considerations
IAO_0000118: future developments
IAO_0000118: future directions
IAO_0000118: future outlook
IAO_0000118: future perspectives
IAO_0000118: future plans
IAO_0000118: future prospects
IAO_0000118: future research
IAO_0000118: future research directions
IAO_0000118: future studies
IAO_0000118: future work
IAO_0000118: outlook
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234

future directions textual entity
type: Class
subclass of: textual entity
IAO_0000111: future directions textual entity
IAO_0000112: Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
IAO_0000115: A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: genome announcement textual entity
IAO_0000111: genome announcement section
IAO_0000112: The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
IAO_0000115: A document part announcing the publication of a novel draft genome sequence.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: genome announcement
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement textual entity
type: Class
subclass of: textual entity
IAO_0000111: genome announcement textual entity
IAO_0000112: Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
IAO_0000115: A textual entity that describes the generation and public release of a novel, draft genome sequence.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

keyword textual entity
type: Class
subclass of: textual entity
IAO_0000111: keyword textual entity
IAO_0000112: From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
IAO_0000115: A textual entity listing keywords indicating the major theme(s) of a document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

keywords section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: keyword textual entity
IAO_0000111: keywords section
IAO_0000112: The section labelled 'keywords' in a typical scientific journal article.
IAO_0000115: A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: keywords
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: study limitations textual entity
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
IAO_0000111: study limitations section
IAO_0000112: The section labelled 'limitations' in a typical scientific journal article.
IAO_0000115: A part of a document about biases or short comings related to the study design and execution.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: limitations
IAO_0000118: study limitations
IAO_0000119: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations textual entity
type: Class
subclass of: textual entity
IAO_0000111: study limitations textual entity
IAO_0000112: Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
IAO_0000115: A textual entity addressing a shortcoming or bias of a study design or execution.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000119: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

materials section
type: Class
subclass of: document part
IAO_0000111: materials section
IAO_0000112: The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
IAO_0000115: A part of a document about the materials required to reproduce the content of the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: materials
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

notes section
type: Class
subclass of: document part
IAO_0000111: notes section
IAO_0000112: The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
IAO_0000115: A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: notes
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

patients section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: patients textual entity
IAO_0000111: patients section
IAO_0000112: The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
IAO_0000115: A part of a document about the patients that participated in a study.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

patients textual entity
type: Class
subclass of: textual entity
IAO_0000111: patients textual entity
IAO_0000112: Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
IAO_0000115: A textual entity expressing information regarding the patients used in a study.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: pre-publication history textual entity
IAO_0000111: pre-publication history section
IAO_0000112: The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
IAO_0000115: A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: notice of republication
IAO_0000118: pre-publication history
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history textual entity
type: Class
subclass of: textual entity
IAO_0000111: pre-publication history textual entity
IAO_0000112: From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
IAO_0000115: A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

related work section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: related work textual entity
IAO_0000111: related work section
IAO_0000112: The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
IAO_0000115: A part of a document about work in other publications that is relevant to the content of the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: related literature
IAO_0000118: related work
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

related work textual entity
type: Class
subclass of: textual entity
IAO_0000111: related work textual entity
IAO_0000112: Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
IAO_0000115: A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

requirements section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: requirements textual entity
IAO_0000111: requirements section
IAO_0000112: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
IAO_0000115: A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: requirements
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

requirements textual entity
type: Class
subclass of: textual entity
IAO_0000111: requirements textual entity
IAO_0000112: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
IAO_0000115: A textual entity that expresses the requirements necessary to use a resource, e.g. software.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis textual entity
type: Class
subclass of: textual entity
IAO_0000111: statistical analysis textual entity
IAO_0000112: From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
IAO_0000115: A textual entity documenting statistical analysis tools and techniques employed.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: statistical analysis textual entity
IAO_0000111: statistical analysis section
IAO_0000112: The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
IAO_0000115: A part of the document used to describe the statistical methodologies employed in the work presented in the document.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: statistical analysis
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

tables section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: table
IAO_0000111: tables section
IAO_0000112: The section labelled 'tables' in a typical scientific journal article.
IAO_0000115: A part of a document that contains one or more tables.
IAO_0000117: PERSON: Bill Baumgartner
IAO_0000118: tables
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

postal code
type: Class
subclass of: identifier
IAO_0000115: An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
IAO_0000117: Mathias Brochhausen

Postal delivery route
type: Class
subclass of: plan specification
IAO_0000115: A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
IAO_0000117: Mathias Brochhausen

zone improvement plan code
type: Class
subclass of: postal code
IAO_0000115: A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
IAO_0000117: Mathias Brochhausen
IAO_0000118: ZIP code

database extract, transform, and load process
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000293
  some values from: information content entity
subclass of: Restriction
  on property: OBI_0000299
  some values from: information content entity
IAO_0000111: database extract, transform, and load process
IAO_0000115: A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
IAO_0000116: Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
IAO_0000116: Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000118: ETL
IAO_0000119: WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/187

descriptive data section
type: Class
subclass of: document part
IAO_0000111: descriptive data section
IAO_0000114: IAO_0000120
IAO_0000115: A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
IAO_0000117: PERSON: Chen Yang
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: https://www.equator-network.org/reporting-guidelines/prisma/
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/235
IAO_0000234: ONE ontology

additional results section
type: Class
subclass of: results section
IAO_0000111: additional results section
IAO_0000114: IAO_0000120
IAO_0000115: A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
IAO_0000117: PERSON: Chen Yang
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: https://www.equator-network.org/reporting-guidelines/consort/
IAO_0000119: https://www.equator-network.org/reporting-guidelines/prisma/
IAO_0000119: https://www.equator-network.org/reporting-guidelines/strobe/
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/235
IAO_0000234: ONE ontology

research participants section
type: Class
subclass of: document part
IAO_0000111: research participants section
IAO_0000114: IAO_0000120
IAO_0000115: A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
IAO_0000117: PERSON: Chen Yang
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: https://www.equator-network.org/reporting-guidelines/consort/
IAO_0000119: https://www.equator-network.org/reporting-guidelines/prisma/
IAO_0000119: https://www.equator-network.org/reporting-guidelines/strobe-nut/
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/235
IAO_0000234: ONE ontology

measurement methods section
type: Class
subclass of: methods section
IAO_0000111: measurement methods section
IAO_0000114: IAO_0000120
IAO_0000115: A methods section that describes details of data assessment methods (data measurement).
IAO_0000117: PERSON: Chen Yang
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: https://www.equator-network.org/reporting-guidelines/strobe/
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/235
IAO_0000234: ONE ontology

research settings section
type: Class
subclass of: document part
IAO_0000111: research settings section
IAO_0000114: IAO_0000120
IAO_0000115: A document part that describes the physical/social/cultural conditions around a research trial.
IAO_0000117: PERSON: Chen Yang
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK262175/
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/235
IAO_0000234: ONE ontology

study bias section
type: Class
subclass of: study limitations section
IAO_0000111: study bias section
IAO_0000114: IAO_0000120
IAO_0000115: A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
IAO_0000117: PERSON: Chen Yang
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: DOI: 10.1097/PRS.0b013e3181de24bc
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/235
IAO_0000234: ONE ontology

graphical abstract
type: Class
subclass of: abstract
IAO_0000111: graphical abstract
IAO_0000114: IAO_0000120
IAO_0000115: An abstract that is pictorial summary of the main findings described in the document.
IAO_0000117: PERSON: Jie Zheng
IAO_0000117: PERSON: Tim Beck
IAO_0000118: visual abstract
IAO_0000119: https://www.elsevier.com/authors/journal-authors/graphical-abstract
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/234
IAO_0000234: Biomedical literature NLP project

ORCID identifier
type: Class
subclass of: centrally registered identifier
IAO_0000114: IAO_0000125
IAO_0000115: A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
IAO_0000116: "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]
IAO_0000116: This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)
IAO_0000117: http://orcid.org/0000-0002-1595-3213
IAO_0000118: ORCID ID
IAO_0000118: ORCiD
IAO_0000118: Open Researcher and Contributor ID
IAO_0000118: Open Researcher and Contributor Identifier
IAO_0000119: https://orcid.org/
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/259

identifier
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: denotes
    some values from: BFO_0000001
  intersection of: Restriction
    on property: OBI_0000312
    some values from: identifier creating process
subclass of: information content entity
IAO_0000111: identifier
IAO_0000115: An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
IAO_0000117: Mathias Brochhausen
IAO_0000117: Justin Whorton
IAO_0000118: proper name
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen
comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)

grapheme
type: Class
subclass of: information content entity
IAO_0000112: alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems
IAO_0000115: An information content entity that is a fundamental unit in a written language.
IAO_0000117: Justin Whorton
IAO_0000119: http://en.wikipedia.org/wiki/Grapheme
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen
comment: Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there.

identifier creating process
type: Class
equivalent class: Class
  intersection of: OBI_0000011
  intersection of: Restriction
    on property: OBI_0000299
    some values from: identifier
subclass of: OBI_0000011
IAO_0000115: A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
IAO_0000117: Mathias Brochhausen
IAO_0000117: Justin Whorton
IAO_0000118: dubbing process
IAO_0000118: naming
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen

personal name
type: Class
subclass of: identifier
IAO_0000115: An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.
IAO_0000117: Mathias Brochhausen
IAO_0000117: Justin Whorton
IAO_0000119: http://en.wikipedia.org/wiki/Personal_name
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
comment: Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
comment: Personal names to not include names of fictional characters, e.g. Sherlock Holmes.

given name
type: Class
subclass of: personal name
IAO_0000115: A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
IAO_0000117: Mathias Brochhausen
IAO_0000117: Justin Whorton
IAO_0000118: first name
IAO_0000119: http://en.wikipedia.org/wiki/Given_name
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237

family name
type: Class
subclass of: identifier
IAO_0000115: An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
IAO_0000117: Mathias Brochhausen
IAO_0000117: Justin Whorton
IAO_0000118: last name
IAO_0000118: surname
IAO_0000119: http://en.wikipedia.org/wiki/Family_name
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237

code set
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: BFO_0000051
  some values from: identifier
IAO_0000115: An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
IAO_0000117: Mathias Brochhausen
IAO_0000117: Justin Whorton
IAO_0000117: Alan Ruttenberg
IAO_0000118: code map
IAO_0000118: code system
IAO_0000118: codeset
IAO_0000118: coding system
IAO_0000118: controlled vocabulary
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/237
contributor: Clint Dowland
contributor: Matt Diller
contributor: Sarah Bost
contributor: William R. Hogan
contributor: Alan Ruttenberg
comment: Does not imply absence vs. presence of any taxonomy.
comment: Code sets might include non-entities/things (e.g. missing thumbs).
comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
comment: The information content entities do not denote each other.