iao-main.owl
type: Ontology
version IRI: iao-main.owl
imports: import-OBO.owl
imports: bfo.owl
imports: externalByHand.owl
imports: core.owl
imports: ontology-metadata.owl
contributor: Mathias Brochhausen
contributor: Pat Hayes
license: http://creativecommons.org/licenses/by/4.0/
contributor: Jie Zheng
contributor: Albert Goldfain
contributor: William Duncan
contributor: Philippe Rocca-Serra
contributor: Gwen Frishkoff
comment: The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html
contributor: Matt Brush
contributor: James A. Overton
contributor: Jonathan Rees
contributor: Satya Sahoo
contributor: David Osumi-Sutherland
contributor: Sivaram Arabandi
contributor: Ron Rudnicki
contributor: Paolo Ciccarese
contributor: Darren Natale
contributor: Bjoern Peters
contributor: Melanie Courtot
contributor: Chris Stoeckert
contributor: Jennifer Fostel
contributor: Adam Goldstein
contributor: Michel Dumontier
contributor: James Malone
contributor: Chris Mungall
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
contributor: Carlo Torniai
contributor: Christian A. Boelling
contributor: William Hogan
contributor: Barry Smith
contributor: Holger Stenzhorn
contributor: Yongqun (Oliver) He
contributor: Werner Ceusters
contributor: Randy Dipert
contributor: Larisa Soldatova
default language: en
contributor: Alan Ruttenberg
contributor: Lawrence Hunter

editor preferred term
type: AnnotationProperty

in branch
type: AnnotationProperty

has curation status
type: AnnotationProperty

definition
type: AnnotationProperty

editor note
type: AnnotationProperty

term editor
type: AnnotationProperty

alternative term
type: AnnotationProperty

definition source
type: AnnotationProperty

has obsolescence reason
type: AnnotationProperty

imported from
type: AnnotationProperty

retired from use as of
type: AnnotationProperty
editor preferred term: retired from use as of
definition: relates a class of CRID to the date after which further instances should not be made, according to the central authority
editor note: In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
term editor: 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
has curation status: IAO_0000125
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

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

denotes
type: ObjectProperty
sub property of: is about
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.
definition: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
editor note: 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
term editor: person:Alan Ruttenberg
definition source: 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
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
term editor: Alan Ruttenberg

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
has curation status: IAO_0000120
definition: relates a process to a time-measurement-datum that represents the duration of the process
term editor: Person:Alan Ruttenberg

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

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

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

has time stamp
type: ObjectProperty
sub property of: BFO_0000051
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
has curation status: IAO_0000123
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
term editor: 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
has curation status: IAO_0000123
definition: relates a time stamped measurement datum to the measurement datum that was measured
term editor: 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

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

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

objective specification
type: Class
subclass of: directive information entity
editor preferred term: objective specification
IAO_0000112: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: IAO_0000122
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 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.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

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

action specification
type: Class
subclass of: directive information entity
IAO_0000112: Pour the contents of flask 1 into flask 2
has curation status: IAO_0000122
definition: a directive information entity that describes an action the bearer will take
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

datum label
type: Class
subclass of: information content entity
editor preferred term: datum label
has curation status: IAO_0000123
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: 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
editor preferred term: software
has curation status: IAO_0000120
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

journal article
type: Class
subclass of: report
editor preferred term: 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.
has curation status: IAO_0000120
definition: a report that is published in a journal
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000159
definition source: 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
editor preferred term: 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.
has curation status: IAO_0000125
definition: A quality of an information bearer that imparts the information content
editor note: 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'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

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

programming language
type: Class
subclass of: plan specification
editor preferred term: programming language
IAO_0000112: R, Perl, Java
has curation status: IAO_0000120
definition: 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.
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000058
definition source: group:OBI

data item
type: Class
subclass of: information content entity
editor preferred term: data item
IAO_0000112: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data

symbol
type: Class
subclass of: information content entity
editor preferred term: symbol
IAO_0000112: a serial number such as "12324X"
IAO_0000112: a stop sign
IAO_0000112: a written proper name such as "OBI"
has curation status: IAO_0000125
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 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).
term editor: PERSON: James A. Overton
term editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary

numeral
type: Class
subclass of: symbol
editor preferred term: numeral
has curation status: IAO_0000123
definition: A symbol that denotes a number.
term editor: PERSON: Jonathan Rees

information content entity
type: Class
subclass of: BFO_0000031
subclass of: Restriction
  on property: is about
  some values from: BFO_0000001
editor preferred term: information content entity
IAO_0000112: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
definition: A generically dependent continuant that is about some thing.
editor note: 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).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142

integer numeral
type: Class
subclass of: numeral
editor preferred term: integer numeral
has curation status: IAO_0000123
definition: a numeral that denotes an integer
term editor: 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.
has curation status: IAO_0000120
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
term editor: PERSON: Alan Ruttenberg
term editor: 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
has curation status: IAO_0000122
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters

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

dot plot
type: Class
subclass of: graph
editor preferred term: dot plot
IAO_0000112: Dot plot of SSC-H and FSC-H.
has curation status: IAO_0000002
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI

graph
type: Class
subclass of: diagram
editor preferred term: graph
has curation status: IAO_0000125
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
term editor: PERSON: Lawrence Hunter
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

rule
type: Class
subclass of: conditional specification
editor preferred term: rule
IAO_0000112: example to be added
has curation status: IAO_0000123
definition: a rule is an executable which guides, defines, restricts actions
editor note: MSI
term editor: PRS
definition source: OBI_0500021
definition source: PRS

contour plot
type: Class
subclass of: graph
editor preferred term: contour plot
IAO_0000112: Contour plot of SSC-H, FSC-H, and FL1-H.
has curation status: IAO_0000002
editor note: generically_dependent_continuants
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000246
definition source: group:Flow Cytometry community

algorithm
type: Class
subclass of: plan specification
editor preferred term: algorithm
IAO_0000112: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: IAO_0000120
definition: 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.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

software interpreter
type: Class
subclass of: algorithm
editor preferred term: software interpreter
IAO_0000112: R program, Perl interpreter, Java virtual machine
has curation status: IAO_0000120
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000199
definition source: group:OBI

density plot
type: Class
subclass of: graph
editor preferred term: density plot
IAO_0000112: Density plot of SSC-H and FSC-H.
has curation status: IAO_0000002
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000179
definition source: group:Flow Cytometry community

report
type: Class
subclass of: document
editor preferred term: 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.
has curation status: IAO_0000125
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term editor: PERSON:Chris Stoeckert
definition source: GROUP: OBI
definition source: OBI_0000099

source code module
type: Class
subclass of: directive information entity
editor preferred term: 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.
has curation status: IAO_0000123
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000039
definition source: group:OBI

data format specification
type: Class
subclass of: directive information entity
editor preferred term: data format specification
has curation status: IAO_0000123
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187

data set
type: Class
subclass of: data item
editor preferred term: 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).
has curation status: IAO_0000125
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 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.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

image
type: Class
subclass of: figure
editor preferred term: image
has curation status: IAO_0000122
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: 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
editor preferred term: plan specification
IAO_0000112: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000122
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
editor preferred term: 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,}.
has curation status: IAO_0000125
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI

version number
type: Class
subclass of: symbol
editor preferred term: version number
has curation status: IAO_0000123
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
term editor: GROUP: IAO

serial number
type: Class
subclass of: symbol
editor preferred term: serial number
has curation status: IAO_0000123
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
term editor: GROUP: IAO

lot number
type: Class
subclass of: symbol
editor preferred term: lot number
has curation status: IAO_0000123
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: GROUP: IAO
alternative term: batch number

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

conclusion textual entity
type: Class
subclass of: textual entity
editor preferred term: 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
has curation status: IAO_0000120
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
term editor: 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
editor preferred term: 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
has curation status: IAO_0000122
definition: A material entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO

histogram
type: Class
subclass of: graph
editor preferred term: histogram
has curation status: IAO_0000122
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

heatmap
type: Class
subclass of: graph
editor preferred term: heatmap
has curation status: IAO_0000122
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

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

dendrogram
type: Class
subclass of: graph
editor preferred term: dendrogram
IAO_0000112: Dendrograms are often used in computational biology to illustrate the clustering of genes.
has curation status: IAO_0000122
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
editor preferred term: scatter plot
IAO_0000112: Comparison of gene expression values in two samples can be displayed in a scatter plot
has curation status: IAO_0000122
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
alternative term: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

photograph
type: Class
subclass of: image
has curation status: IAO_0000122
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Joanne Luciano
term editor: PERSON:Melanie Courtot
definition source: 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
editor preferred term: photographic print
has curation status: IAO_0000125
definition: A photographic print is a material entity upon which a photograph generically depends.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

textual entity
type: Class
subclass of: information content entity
editor preferred term: textual entity
IAO_0000112: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: IAO_0000123
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
term editor: PERSON: Lawrence Hunter
alternative term: text

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

author identification
type: Class
subclass of: written name
editor preferred term: author identification
IAO_0000112: L. Hunter
has curation status: IAO_0000125
definition: A textual entity intended to identify a particular author
term editor: PERSON: Lawrence Hunter

institutional identification
type: Class
subclass of: textual entity
editor preferred term: institutional identification
IAO_0000112: University of Colorado Denver School of Medicine
has curation status: IAO_0000125
definition: A textual entity intended to identify a particular institution
term editor: PERSON: Lawrence Hunter

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

document title
type: Class
subclass of: textual entity
editor preferred term: document title
IAO_0000112: Textual characteristics of traditional and Open Access scientific journals are similar
has curation status: IAO_0000125
definition: A textual entity that names a document
term editor: PERSON: Lawrence Hunter

table
type: Class
subclass of: textual entity
editor preferred term: table
IAO_0000112: | T F --+----- T | T F F | F F
has curation status: IAO_0000125
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
term editor: PERSON: Lawrence Hunter

table of abbreviations
type: Class
subclass of: table
editor preferred term: table of abbreviations
IAO_0000112: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
has curation status: IAO_0000125
definition: A table where the constituent texts are abbreviations and their expansions
term editor: PERSON: Lawrence Hunter

figure
type: Class
subclass of: information content entity
editor preferred term: figure
IAO_0000112: Any picture, diagram or table
has curation status: IAO_0000120
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter

diagram
type: Class
subclass of: figure
editor preferred term: diagram
IAO_0000112: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has curation status: IAO_0000120
definition: A figure that expresses one or more propositions
term editor: PERSON: Lawrence Hunter

document
type: Class
subclass of: information content entity
editor preferred term: document
IAO_0000112: A journal article, patent application, laboratory notebook, or a book
has curation status: IAO_0000120
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter

publication
type: Class
subclass of: document
editor preferred term: publication
IAO_0000112: A journal article or book
has curation status: IAO_0000120
definition: A document that has been accepted by a publisher
term editor: PERSON: Lawrence Hunter

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: OBI_0000066
editor preferred term: publication about an investigation
IAO_0000112: Most scientific journal articles
has curation status: IAO_0000120
definition: A publication that is about an investigation
term editor: PERSON: Lawrence Hunter
alternative term: scientific publication

patent
type: Class
subclass of: document
editor preferred term: patent
IAO_0000112: US Patent 6,449,603
has curation status: IAO_0000120
definition: A document that has been accepted by a patent authority
term editor: PERSON: Lawrence Hunter

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: BFO_0000050
  some values from: document
editor preferred term: document part
IAO_0000112: An abstract, introduction, method or results section.
has curation status: IAO_0000120
definition: an information content entity that is part of a document
term editor: PERSON: Lawrence Hunter

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

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
editor preferred term: introduction to a publication about an investigation
IAO_0000112: Section labelled 'introduction' of a typical scientific journal article
has curation status: IAO_0000120
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
term editor: PERSON: Lawrence Hunter
alternative term: background
alternative term: introduction

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
editor preferred term: methods section
IAO_0000112: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
has curation status: IAO_0000120
definition: A part of a publication about an investigation that is about the study design of the investigation
term editor: PERSON: Lawrence Hunter
alternative term: experimental
alternative term: experimental procedures
alternative term: experimental section
alternative term: methods

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: OBI_0000471
editor preferred term: results section
IAO_0000112: The section labelled 'results' in a typical scientific journal article
has curation status: IAO_0000120
definition: A part of a publication about an investigation that is about a study design execution
term editor: PERSON: Lawrence Hunter
alternative term: results

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

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: citation
editor preferred term: 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"
has curation status: IAO_0000120
definition: A part of a document that has citations as parts
term editor: PERSON: Lawrence Hunter

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: author identification
editor preferred term: author list
IAO_0000112: Lawrence Hunter and Kevin Brettonel Cohen
has curation status: IAO_0000120
definition: part of a document that enumerates the authors of the document
term editor: PERSON: Lawrence Hunter

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: institutional identification
editor preferred term: institution list
IAO_0000112: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
has curation status: IAO_0000120
definition: part of a document that has parts that are institution identifications associated with the authors of the document
term editor: PERSON: Lawrence Hunter

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

acknowledgements section
type: Class
subclass of: document part
editor preferred term: acknowledgements section
IAO_0000112: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
has curation status: IAO_0000120
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
term editor: PERSON: Lawrence Hunter
alternative term: acknowledgements
alternative term: acknowledgments

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
editor preferred term: 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.
has curation status: IAO_0000120
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
term editor: PERSON: Lawrence Hunter
alternative term: endnote

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

table of contents
type: Class
subclass of: table
editor preferred term: table of contents
has curation status: IAO_0000125
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
term editor: PERSON: Lawrence Hunter

table of figures
type: Class
subclass of: table
editor preferred term: table of figures
has curation status: IAO_0000125
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
term editor: PERSON: Lawrence Hunter

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

copyright section
type: Class
subclass of: document part
editor preferred term: copyright section
IAO_0000112: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
has curation status: IAO_0000120
definition: A document part that describes legal restrictions on making or distributing copies of the document
term editor: 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
has curation status: IAO_0000120
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
term editor: 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
has curation status: IAO_0000123
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
term editor: 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
has curation status: IAO_0000123
definition: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
term editor: 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
has curation status: IAO_0000123
definition: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
term editor: 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
has curation status: IAO_0000123
definition: A scalar measurement datum that is the result of measurement of length quality
term editor: 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
has curation status: IAO_0000123
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg

hypothesis textual entity
type: Class
subclass of: textual entity
editor preferred term: 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
has curation status: IAO_0000120
definition: A textual entity that expresses an assertion that is intended to be tested.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: 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
has curation status: IAO_0000123
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: GAZ_00000448
has curation status: IAO_0000123
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 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
editor preferred term: email address
has curation status: IAO_0000123
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart

author role
type: Class
subclass of: BFO_0000023
editor preferred term: author role
has curation status: IAO_0000125
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
term editor: PERSON: Alan Ruttenberg
term editor: 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
has curation status: IAO_0000120
definition: a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
term editor: Person:Alan Ruttenberg

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.
has curation status: IAO_0000125
definition: a planned process in which a document is created or added to by including the specified input in it.
editor note: 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
term editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting

line graph
type: Class
subclass of: graph
editor preferred term: line graph
has curation status: IAO_0000122
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:Melanie Courtot
alternative term: line chart
definition source: GROUP:OBI
definition source: 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.
has curation status: IAO_0000120
definition: 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
editor note: 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
term editor: Person:Melanie Courtot
alternative term: 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.
has curation status: IAO_0000120
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
term editor: PERSON:Alan Ruttenberg
alternative term: 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.
has curation status: IAO_0000120
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier
type: Class
subclass of: information content entity
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.
has curation status: IAO_0000120
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 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').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: data set
IAO_0000112: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has curation status: IAO_0000120
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls

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.
has curation status: IAO_0000120
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: 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
has curation status: 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
has curation status: IAO_0000120
definition: 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.
term editor: Alan Ruttenberg
alternative term: experimental time series

written name
type: Class
subclass of: textual entity
editor preferred term: written name
IAO_0000112: "Bill Clinton"
IAO_0000112: "The Eiffel Tower"
IAO_0000112: "United States of America"
has curation status: IAO_0000125
definition: A textual entity that denotes a particular in reality.
term editor: PERSON: Bill Hogan
definition source: 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
has curation status: IAO_0000123
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software module
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software module is software composed of a collection of software methods.
term editor: PERSON: Melanei Courtot
term editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software library
type: Class
subclass of: software
has curation status: IAO_0000123
definition: 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.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software application
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software application is software that can be directly executed by some processing unit.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software script
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software script is software whose instructions can be executed using a software interpreter.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

abbreviation textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity listing abbreviations and their expansions that are used in a document.
term editor: 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
editor preferred term: abbreviations section
IAO_0000112: The section labelled 'abbreviations' in a typical scientific journal article.
definition: A part of a document where abbreviations and their long-forms used within the document are listed.
term editor: PERSON: Bill Baumgartner
alternative term: abbreviations
alternative term: abbreviations list
alternative term: abbreviations used
alternative term: list of abbreviations
alternative term: list of abbreviations used
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

author information section
type: Class
subclass of: document part
subclass of: Restriction
  on property: BFO_0000051
  some values from: author information textual entity
editor preferred term: 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/)
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: author information
alternative term: authors’ information
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

author information textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: 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.
term editor: 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
editor preferred term: 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/)
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: author summary
alternative term: summary
alternative term: synopsis
definition source: 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
editor preferred term: 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.
definition: 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).
term editor: PERSON: Bill Baumgartner
definition source: 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
editor preferred term: 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/).
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: availability
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

availability textual entity
type: Class
subclass of: textual entity
editor preferred term: 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
definition: A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
term editor: 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
editor preferred term: 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/)
definition: A part of a document about the medical history of a specific patient as it relates to the topic of the document.
term editor: PERSON: Bill Baumgartner
alternative term: case presentation
alternative term: case report
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

case report textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
term editor: 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
editor preferred term: conclusion section
IAO_0000112: The section labelled 'conclusion' in a typical scientific journal article.
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: concluding remarks
alternative term: conclusion
alternative term: conclusions
alternative term: findings
alternative term: 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
editor preferred term: conflict of interest section
IAO_0000112: The section labelled 'conflict of interest statement' in a typical scientific journal article.
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: competing interests
alternative term: conflict of interest
alternative term: conflict of interest statement
alternative term: declaration of competing interests
alternative term: disclosure of potential conflicts of interest
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

conflict of interest textual entity
type: Class
subclass of: textual entity
editor preferred term: 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/)]
definition: 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.
term editor: 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
editor preferred term: 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/)
definition: A part of a document about the consent process that was used to enroll patients in a study.
term editor: PERSON: Bill Baumgartner
alternative term: consent
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

consent textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity that documents the consenting process used to enroll patients in a study.
term editor: 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
editor preferred term: ethical approval section
IAO_0000112: The section labelled 'ethical approval' in a typical scientific journal article.
definition: A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
term editor: PERSON: Bill Baumgartner
alternative term: ethical approval
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

ethical approval textual entity
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
editor preferred term: 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.
definition: A textual entity that documents the ethical approval of some study design.
term editor: 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
editor preferred term: figures section
IAO_0000112: The section labelled 'figures' in a typical scientific journal article.
definition: A part of a document that contains one or more figures.
term editor: PERSON: Bill Baumgartner
alternative term: 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
editor preferred term: funding source declaration section
IAO_0000112: The section labelled 'funding' in a typical scientific journal article.
definition: A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
term editor: PERSON: Bill Baumgartner
alternative term: funding
alternative term: funding information
alternative term: funding sources
alternative term: funding statement
alternative term: funding/support
alternative term: source of funding
alternative term: sources of funding
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

funding source declaration textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity documenting the source of funding that supported some study.
term editor: 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
editor preferred term: future directions section
IAO_0000112: The section labelled 'future directions' in a typical scientific journal article.
definition: A part of a document detailing extensions of the described work that may be implemented at some future point in time.
term editor: PERSON: Bill Baumgartner
alternative term: future challenges
alternative term: future considerations
alternative term: future developments
alternative term: future directions
alternative term: future outlook
alternative term: future perspectives
alternative term: future plans
alternative term: future prospects
alternative term: future research
alternative term: future research directions
alternative term: future studies
alternative term: future work
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

future directions textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
term editor: 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
editor preferred term: 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/)
definition: A document part announcing the publication of a novel draft genome sequence.
term editor: PERSON: Bill Baumgartner
alternative term: genome announcement
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement textual entity
type: Class
subclass of: textual entity
editor preferred term: 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).
definition: A textual entity that describes the generation and public release of a novel, draft genome sequence.
term editor: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

keyword textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity listing keywords indicating the major theme(s) of a document.
term editor: 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
editor preferred term: keywords section
IAO_0000112: The section labelled 'keywords' in a typical scientific journal article.
definition: A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
term editor: PERSON: Bill Baumgartner
alternative term: 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
editor preferred term: study limitations section
IAO_0000112: The section labelled 'limitations' in a typical scientific journal article.
definition: A part of a document about biases or short comings related to the study design and execution.
term editor: PERSON: Bill Baumgartner
alternative term: limitations
alternative term: study limitations
definition source: 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
editor preferred term: 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.
definition: A textual entity addressing a shortcoming or bias of a study design or execution.
term editor: PERSON: Bill Baumgartner
definition source: 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
editor preferred term: 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/)
definition: A part of a document about the materials required to reproduce the content of the document.
term editor: PERSON: Bill Baumgartner
alternative term: materials
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

notes section
type: Class
subclass of: document part
editor preferred term: 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/):
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: footnotes
alternative term: 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
editor preferred term: 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/)
definition: A part of a document about the patients that participated in a study.
term editor: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

patients textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity expressing information regarding the patients used in a study.
term editor: 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
editor preferred term: 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/)
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: notice of republication
alternative term: 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
editor preferred term: 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
definition: 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.
term editor: 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
editor preferred term: 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/)
definition: A part of a document about work in other publications that is relevant to the content of the document.
term editor: PERSON: Bill Baumgartner
alternative term: related literature
alternative term: related work
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

related work textual entity
type: Class
subclass of: textual entity
editor preferred term: 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).
definition: A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
term editor: 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
editor preferred term: 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/).
definition: 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.
term editor: PERSON: Bill Baumgartner
alternative term: requirements
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

requirements textual entity
type: Class
subclass of: textual entity
editor preferred term: 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
definition: A textual entity that expresses the requirements necessary to use a resource, e.g. software.
term editor: PERSON: Bill Baumgartner
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis textual entity
type: Class
subclass of: textual entity
editor preferred term: 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.
definition: A textual entity documenting statistical analysis tools and techniques employed.
term editor: 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
editor preferred term: 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/)
definition: A part of the document used to describe the statistical methodologies employed in the work presented in the document.
term editor: PERSON: Bill Baumgartner
alternative term: 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
editor preferred term: tables section
IAO_0000112: The section labelled 'tables' in a typical scientific journal article.
definition: A part of a document that contains one or more tables.
term editor: PERSON: Bill Baumgartner
alternative term: tables
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/183

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
editor preferred term: database extract, transform, and load process
definition: 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.
editor note: 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
editor note: 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.
term editor: PERSON:Alan Ruttenberg
alternative term: ETL
definition source: WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
IAO_0000233: https://github.com/information-artifact-ontology/IAO/issues/187