Description
An account of the content of the resource.
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
term replaced by
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
Contributor
An entity responsible for making contributions to the content of the resource.
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
OBO foundry unique label
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
An alternative name for a class or property which is unique across the OBO Foundry.
GROUP:OBO Foundry <http://obofoundry.org/>
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
Creator
An entity primarily responsible for making the content of the resource.
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
BrightonFormula
AngEdGenLoc - angioedema, localized or generalized
An annotation property reflecting the string used by Brighton in their ABC tool to encode the term
Subject and Keywords
The topic of the content of the resource.
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
Resource Identifier
An unambiguous reference to the resource within a given context.
Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
Date
A date associated with an event in the life cycle of the resource.
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
Title
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Relation
Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a related resource.
definition
PERSON:Daniel Schober
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
expand expression to
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
has curation status
PERSON:Bill Bug
Language
A language of the intellectual content of the resource.
Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
antisymmetric property
Alan Ruttenberg
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
Resource Type
The nature or genre of the content of the resource.
Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
first order logic expression
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
expand assertion to
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
Source
A reference to a resource from which the present resource is derived.
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
example
Publisher
An entity responsible for making the resource available
Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.
Coverage
Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
The extent or scope of the content of the resource.
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
relates an class defined in an ontology, to the type of it's denotator
is denotator type
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID range allocated to
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
imported from
For external terms/classes, the ontology from which the term was imported
has ID digit count
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Format
The physical or digital manifestation of the resource.
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
Rights Management
Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
Information about rights held in and over the resource.
has component
is part of
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
part of
part_of
domain of part of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates_in
has participant
has_participant
is concretization of
concretization of
concretization_of
concretizes
is immediately preceded by
immediately preceded by
immediately_preceded_by
immediately precedes
immediately_precedes
is preceded by
preceded by
preceded_by
precedes
is course of
course of
course_of
has course
has_course
occurs in
occurs_in
has site of
has_site_of
begins to exist during
begins_to_exist_during
ceases to exist during
ceases_to_exist_during
s depends on
s_depends_on
has granular part
has_granular_part
has granular process part
has_granular_process_part
is granular part of
granular part of
granular_part_of
is granular part of process
granular part of process
granular_part_of_process
is aggregate of
aggregate of
aggregate_of
is fiat part of
fiat part of
fiat_part_of
has participant beginning to exist
has_participant_beginning_to_exist
has participant ceasing to exist
has_participant_ceasing_to_exist
is function of
function of
function_of
is quality of
quality of
quality_of
is role of
role of
role_of
is located in
located in
located_in
is located at
located at
located_at
g depends on
g_depends_on
has function
has_function
has quality
has_quality
has role
has_role
has measurement unit label
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
is about
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.
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
mentions
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)
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
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
PERSON: Jonathan Rees
Person: Alan Ruttenberg
denotes
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
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.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
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
is quality measurement of
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
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.
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.
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.
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.
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
has coordinate unit label
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
is quality measured as
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
inverse of the relation of is quality measurement of
is quality specification of
Person:Bjoern Peters
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.
quality is specified as
inverse of the relation of is quality specification of
has time stamp
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has measurement datum
relates a time stamped measurement datum to the measurement datum that was measured
is_specified_output_of
regulates
A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process
stimulates
unfolds_in
P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
diagnosis guideline
A directive information entity that specifies how to establish a diagnosis based on clinical findings
disorder resulting from an AEFI process
MC, 20110120: AR mentioned that the use of is_specified_output is not appropriate, as this would indicate that the adverse event process is a planned process - specified output are things that are specified in the plan to realize a process. Adverse events are not planned process but processual entities, and therefore this should be updated. AR mentioned that BFO will include an appropriate relation.
MC, 20110120: This class should have a different label for OBO Foundry unique label. "adverse event following immunization" is a term in use by the clinician community, however in the context if the Foundry it may be confusing to associate the word "event" which seem to refer to a process with the hierarchical position under continuant. Proposed OBO Foundry label: disorder resulting from an AEFI
MC, 20110126: class renamed from "adverse event following immunization continuant" following AR suggestion
Brighton case definition
A diagnosis guideline specifying how to establish a diagnosis of adverse event with an associated degree of certainty, as developed by the Brighton Collaboration, http://www.brightoncollaboration.org/
MC, 20110126: this should be linked to the different adverse events reported. AR suggests using a new relation to appear in BFO2, maybe "ascription"
Brighton assessment of generalized convulsive seizure as an adverse event following immunization
a categorical measurement datum whose instances are used to classify adverse events according to whether or not they have some likelihood of being a seizure and if so, to what degree
PMID:14741144#Generalized convulsive seizure as an adverse event following immunization: case definition and guidelines for data collection, analysis, and presentation.
disorder resulting from an adverse event process
MC, 20110120: This class was initially labeled "adverse event continuant". After discussion with AR, and due to the fact that the word "event" implicitely refers to a process, we renamed this class.
adverse event rash
MC, 20110120: This class should have a different label for OBO Foundry unique label. "adverse event rash" is a term in use by the clinician community, however in the context if the Foundry it may be confusing to associate the word "event" which seem to refer to a process with the hierarchical position under continuant. Proposed OBO Foundry label: rash resulting from an adverse event
AEFI rash
MC, 20110120: This class should have a different label for OBO Foundry unique label. "AEFI_rash" is a term in use by the clinician community, however in the context if the Foundry it may be confusing to associate the word "event" which seem to refer to a process with the hierarchical position under continuant. Proposed OBO Foundry label: rash resulting from an AEFI process
rash
A rash is a change of the skin which affects its color, appearance or texture.
WEB: http://en.wikipedia.org/wiki/Rash
adverse event
An adverse event is an undesirable, unfavorable and unintended medical occurrence presenting in a predetermined time frame following administration of a compound or usage of a device
I initialy made adverse event a defined class: is_a sign and preceded by administration. However, by doing so, and as the range of preceded by is processual entities, I was implicitely making adverse event a subclass of processual entity, therfore making adverse event rash (a continuant) inconsistent.
ICH Topic E 2 A Clinical Safety Data Management: Definitions and Standards for Expedited Reporting
adverse event following immunization
An adverse event is an undesirable, unfavorable and unintended medical occurrence presenting in a predetermined time frame following administration of a vaccine
Adapted from ICH Topic E 2 A Clinical Safety Data Management: Definitions and Standards for Expedited Reporting
_manifestations
temporary placeholder - to be removed This class just helps me group some terms during development of the structure
Idiopathic thrombocytopenic purpura
Idiopathic thrombocytopenic purpura (ITP) is the condition of having a low platelet count (thrombocytopenia) of no known cause (idiopathic).v
encephalitis
Encephalitis is an inflammation of the brain. It may be caused by a number of different factors. One of the most common causes is direct infection of the brain by a virus or bacterium. Inflammation can also occur as a complication of some other disorder, such as mumps (see mumps entry) or herpes simplex (see herpes infections entry).
motor manifestation
A _manifestation involving the motor system
adverse event process
An adverse event process is a processual entity occurring in a pre determined time frame following administration of a compound or usage of a device
I included the usage of a device into the definition of adverse event as I am aiming at being inclusive, and cover cases such as those described by MAUDE - Manufacturer and User Facility Device Experience. See for example http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfMAUDE/detail.cfm?mdrfoi__id=1942591 - a patient get fitted with bioprosthetic heart valves and dies within the following 4 months.
Note that this definition of adverse event doesn't imply any type of causality between the sign observed and the coumpond administration/device utilization. For our purposes, we consider any type of sign presenting within a specific time frame after the coumpound administration/device utilization to be an adverse event.
adverse event following immunization process
generalized convulsive seizure according to Brighton criteria
AEFI generalized convulsive seizure according to Brighton guideline
seizure level 1 of certainty according to the Brighton criteria
MC, 20110126: this needs to be linked to the Brighton guideline defined under directive information entity
witnessed sudden loss of consciousness AND generalized, tonic, clonic, tonic–clonic, or atonic motor manifestations. (atonic In the absence of: hypotonic hyporesponsive episode (as deﬁned by the Brighton Collaboration), syncope, and myoclonic jerks.
seizure level 2 of certainty according to the Brighton criteria
history of unconsciousness AND generalized, tonic, clonic, tonic–clonic, or atonic motor manifestations. (atonic In the absence of: hypotonic hyporesponsive episode (as deﬁned by the Brighton Collaboration), syncope, and myoclonic jerks.
seizure level 3 of certainty according to the Brighton criteria
history of unconsciousness AND other generalized motor manifestations.
atonic motor manifestation
A sudden loss of tone in postural muscle, often preceded by a myoclonic jerk and precipitated by hyperventilation
Brighton Collaboration, http://www.brightoncollaboration.org/
generalized atonic motor manifestation
clonic motor manifestation
Sudden, brief (100ms) involuntary contractions of the same muscle groups, regularly repetitive at a frequency of about two to three contractions per second.
generalized motor manifestation
bilateral motor manifestation, more than minimal muscle involvement
generalized clonic motor manifestation
generalized tonic motor manifestation
generalized tonic-clonic motor manifestation
hypotonic-hyporesponsive episode
HHE
HHE is characterized by sudde onset of reduced muscle tone, hyporesponsiveness (i.e., less responsive than usual to verbal or other sensorial stimuli) and change of skin color (pallor or cyanosis)
Affecting or undertaken by two sides equally; binding on both parties
diagnosing generalized convulsive seizure according to Brighton guidelines
performing a diagnosis specified by the Brighton case definition for convulsive seizure as an adverse event following immunization
Brighton case definition of generalized convulsive seizure as an adverse event following immunization
A Brighton case definition of generalized convulsive seizure as an adverse event following immunization
shaking
quivering
repetitive, cyclical movements of the body or a body part; usually involuntary, but can also manifest in response to an attempt at movement
shivering
trembling
tremor
bilateral shaking
A shaking process which unfolds in both sides of an organism
syncope
MC, 20110126: The Brighton guideline on which this is based needs to be checked. Email correspondance with Brighton: [MC] One thing is unclear to me: Level 1 of diagnostic certainty is defined as "witnessed sudden loss of consciousness AND generalized, tonic, clonic, tonicâclonic, or atonic motor manifestations." A footnote adds: atonic in the absence of: hypotonic hyporesponsive episode (as deï¬ned by the Brighton Collaboration), syncope, and myoclonic jerks. If we define syncope as being a loss of consciousness, how can I have a witnessed sudden loss of consciousness and a generalized atonic motor manifestation in the absence of syncope? [Brighton] Thank you for your question. You are right, that there is an overlap between the clinical presentation of an atonic seizure and a Syncope. This is also true for HHE. This is the very reasonf or the footnote to alert the user of the definition to this differential diagnosis. If you are working on a database and only have the clinical criteria vailable, you may have some false positives for the atonic seizure cases, unless you obtain additional information, e.g. that the Syncope was vasovagal or orthostatic, or arrhythmic, etc.
loss of consciousness, fainting
myoclonic jerk
A myoclonic jerk is the brief, involuntary twitching of a muscle or group of muscles. It may be caused either by a sudden muscle contraction, or a sudden lapse of contraction. This happens when a person is on the verge of falling asleep, and suddenly have a sensation or feeling that they are free falling through the air. Contractions are called positive myoclonus; relaxations are called negative myoclonus. When falling asleep, it is common for people to experience a type of myoclonic jerk known as a hypnic jerk. Hiccups are also a kind of myoclonic jerk specifically affecting the diaphragm.
tonic motor manifestation
tonic-clonic motor manifestation
A sequence consisting of a tonic followed by a clonic phase
A sustained increase in muscle contraction lasting a few seconds to minutes
loss of consciousness
i.e., unreactive to verbal and painful stimuli
history of unconsciousness
MC, 20110126: AR suggest that "history of consciousness is not a process. definition reads "the sudden loss of consciousness was not observed, but the patient was found unconscious", so maybe updating the label would be better : "unwitnessed loss of consciousness with history of unconsciousness" would help
the sudden loss of consciousness was not observed, but the patient was found unconscious
witnessed sudden loss of consciousness
bilateral site
witness role
A role inhering in a person that is realized when the bearer sees an event and reports what happened
adapted from http://golovchenko.org/cgi-bin/wnsearch?q=witness
AEFI encephalitis
AEFI Idiopathic thrombocytopenic purpura
AEFI: hypotonic-hyporesponsive episode
adverse side effect
side effect is an adverse event of a type that has been determined by a review board to be causally related to the intervention.
while in some cases the particular may not be actually caused by the intervention, it is an adverse side effect nonetheless.
device malfunction
A process in which the device doesn't perform as expected
adverse event report
A report as submitted in an adverse event reporting system
MC, 20110719: not all adverse event report are about adverse event. See for example cases in MAUDE database that are about potential adverse events such as device malfunctions.
reporting process
The process of creating documentation about something and adding it to a system allowing further analysis of the reported entity
sudden onset
The term sudden onsets refers to an event that occurred unexpectedly and without warning leading to a marked change in a subjects previously stable condition
Anaphylaxis: Case definition and guidelines for data collection, analysis, and presentation of immunization safety data. Vaccine 25 (2007) 5675–5684
rapid progression
The term rapid progression is a conventional clinical term. An exact timeframe sould not be offered since it would have to refer to a wide range of signs and symptoms without a scientific evidence base. Using an arbitrarily restrictive setpoint might bias future data collection unnecessarily.
anaphylaxis
generalized urticaria
generalized erythema
angioedema
generalized pruritus
skin rash
measured hypotension
tachycardia
capillary refill time > 3s
reduced central pulse volume
decreased level of consciousness or loss of consciousness
bilateral wheeze
stridor
a harsh or vibrating noise when breathing caused by obstruction of the windpipe or larynx.
upper airway swelling
tachypnoea
increased use of accessory respiratory muscles
recession
cyanosis
grunting
respiratory distress
respiratory distress—2 or more of the following: • tachypnoea • increased use of accessory respiratory muscles (sternocleidomastoid, intercostals, etc.) • recession • cyanosis • grunting
respiratory distress sign
a helper class which allows us to define a qualified cardinality restriction for respiratory distress such as used in the case definition of anaphylaxis.Respiratory distress is defined as having at least 2 respiratory distress signs
infected abscess
A localized collection of pus in a cavity formed by the disintegration of tissue, usually caused by microorganisms that invade the tissues.
PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf
sterile abscess
An abscess whose contents are not caused by pyogenic bacteria.
cellulitis
A diffuse inflammatory process within solid tissues, characterized by edema, redness, pain, and interference with function, usually caused by infection with streptococci, staphylococci, or similar organisms.
nodule
A firm, small mass of tissue at the injection site with discrete or well demarcated borders in the absence of abscess formation, erythema and warmth.
lymphadenitis
Inflammation of one or more lymph nodes, usually caused by a primary focus of infection elsewhere in the body.
erythema
Abnormal redness of the skin.
induration
Palpable thickening, firmness or hardening of soft tissue that is assessed by a health care provider
performing a diagnosis according to a Brighton case definition
Brighton assessment
The assessment performed upon review of an adverse event report according to the Brighton case definitions
adverse event reporting process
The process of creating documentation about an adverse event and adding it to a system allowing further analysis of the event
clinical diagnosis of uncompensated shock
combination of at least 3 of the following: - tachycardia - capillary refill time > 3s - reduced central pulse volume - decreased level of consciousness or loss of consciousness
uncompensated shock sign
a helper class which allows us to define a qualified cardinality restriction for uncompensated shock such as used in the case definition of anaphylaxis. Clinical diagnosis of uncompensated shock is defined as having at least 3 uncompensated shock signs
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
a heart
a person
a symphony orchestra
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
a surgical operation as processual context for a nosocomical infection
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a leg
an organism
substantial entity
the bottom right portion of a human torso
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
spatial region
A continuant that is neither bearer of quality entities nor inheres in any other entities.
All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
parts of the sum total of all space in the universe
the sum total of all space in the universe
process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
the process of cell-division
the process of sleeping
temporal region
All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
An occurrent that is part of time.
Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
the duration of a surgical procedure
the moment of death
the time it takes to run a marathon
two dimensional region
A spatial region with two dimensions.
the surface of a cube-shaped part of space
the surface of a rectilinear planar figure-shaped part of space
the surface of a sphere-shaped part of space
disposition
A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
the disposition of a patient with a weakened immune system to contract disease
the disposition of a vase to brake if dropped
the disposition of metal to conduct electricity
the disposition of vegetables to decay when not refrigerated
realizable entity
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
the function of the reproductive organs
the role of being a doctor
zero dimensional region
A spatial region with no dimensions.
a point
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
the ambient temperature of air
the circumference of a waist
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the smell of mozzarella
trope
temporal instant
A connected temporal region comprising a single moment of time.
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
connected temporal region
A temporal region every point of which is mediately or immediately connected with every other point of which.
the 1970s years
the time from the beginning to the end of a heart attack
the time taken up by cellular meiosis
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
object boundary
An independent continuant that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object entities that exist at exactly the point where the object is separated off from the rest of the existing entities in the world.
Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
substance boundary
the outer surface of a cell or cell wall
the surface of the earth
the surface of the interior of the stomach
the surface of the skin
one dimensional region
A spatial region with one dimension.
an edge of a cube-shaped part of space
the part of space that is a line stretching from one end of absolute space to the other
three dimensional region
A spatial region with three dimensions.
a cube-shaped part of space
a sphere-shaped part of space
site
An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.
An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are sites) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
Maria's nostril or her intestines for a variety of bacteria
a particular room in a particular hospital
generically dependent continuant
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
a certain PDF file that exists in different and in several hard drives
scattered temporal region
A temporal region every point of which is not mediately or immediately connected with every other point of which.
the time occupied by the individual games of the World Cup
the time occupied by the individual liaisons in a romantic affair
function
A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
the digestive function of the stomach to nutriate the body
the function of a birth canal to enable transport
the function of a computer program to compute mathematical equations
the function of a hammer to drive in nails
the function of a judge in a court of law
the function of an automobile to provide transportation
the function of reproduction in the transmission of genetic material
process boundary
A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
birth
death
the detaching of a finger in an industrial accident
the final separation of two cells at the end of cell-division
the forming of a synapse
the incision at the beginning of a surgery
the onset of REM sleep
temporal interval
A connected temporal region lasting for more than a single moment of time.
any continuous temporal duration during which a process occurs
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
geographical location
A reference to a place on the Earth, by its name or by its geographical location.
conditional specification
OBI branch derived
PlanAndPlannedProcess Branch
a directive information entity that specifies what should happen if the trigger condition is fulfilled
measurement unit label
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.
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.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
PERSON: Melanie Courtot
objective specification
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."
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
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.
purpose of a study; support of hypothesis, discovery of new information
narrative object
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
A narrative object is an information content entity that is a set of propositions.
Examples of narrative objects are reports, journal articles, and patents submission.
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
person:Chris Stoeckert
action specification
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
datum label
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.
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
GROUP: IAO
software
GROUP: OBI
PERSON: Chris Stoeckert
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
obsolete2_digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
obsolete_digital entity
journal article
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.
a report that is published in a journal
information carrier
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'.
A quality of an information bearer that imparts the information content
The pattern in ink on a page of a paperback novel.
model number
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.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
obsolete2_binary digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
MS Word document, ZIP file, DICOM file, JPEG file
binary digital entity
digital_entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
programming language
A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
R, Perl, Java
data item
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
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
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.
data
symbol
20091104, MC: this needs work and will most probably change
a smallish, word-like datum...
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
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.
integer numeral
a numeral that denotes an integer
scalar measurement datum
10 feet. 3 ml.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
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.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
directive information entity
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
time trigger
revisit?
obsolete_study interpretation
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
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.
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
Lawrence Hunter
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
dot plot
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.
Dot plot of SSC-H and FSC-H.
person:Allyson Lister
graph
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.
PERSON: Lawrence Hunter
obsolete2_text based digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
XML file, C++ source code file
text based digital entity
rule
MSI
PRS
a rule is an executable which guides, defines, restricts actions
example to be added
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
obsolete2_report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
report figure
algorithm
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
A software interpreter is a software application that executes some specified input software.
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
R program, Perl interpreter, Java virtual machine
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
density plot
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.
Density plot of SSC-H and FSC-H.
report
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.
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.
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
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
PERSON:Chris Stoeckert
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)
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
obsolete_report element
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
PERSON: Allyson Lister
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
report element
obsolete2_binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
binary executable
person:Jennifer Fostel
source code module
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
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.
obsolete_report table
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
report table
data format specification
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"
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
data set
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
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.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
image
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.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
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
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
obsolete2_digital document
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
digital document
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
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,}.
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
version number
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.
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
serial number
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.
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 :-)
lot number
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.
batch number
setting datum
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.
A settings datum is a datum that denotes some configuration of an instrument.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
Need to rework digital entity. Digital quality was suggested by Barry.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
conclusion textual entity
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
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
material information bearer
An information bearer is a material_entity in which a concretization of an information content entity inheres.
a hard drive, a piece of paper with writing on it, a brain
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:James Malone
heatmap
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.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
dendrogram
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.
Dendrograms are often used in computational biology to illustrate the clustering of genes.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
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.
Comparison of gene expression values in two samples can be displayed in a scatter plot
WEB: http://en.wikipedia.org/wiki/Scatterplot
scattergraph
photograph
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
obsolescence reason specification
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
textual entity
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.
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.
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.
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
a textual entity intended to identify a particular publication
author identification
A textual entity intended to identify a particular author
L. Hunter
institutional identification
A textual entity intended to identify a particular institution
University of Colorado Denver School of Medicine
caption
A textual entity that describes a figure
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.
document title
A textual entity that names a document
Textual characteristics of traditional and Open Access scientific journals are similar
table
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
| T F --+----- T | T F F | F F
table of abbreviations
A table where the constituent texts are abbreviations and their expansions
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Any picture, diagram or table
diagram
A figure that expresses one or more propositions
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
publication
A document that has been accepted by a publisher
A journal article or book
publication about an investigation
A publication that is about an investigation
Most scientific journal articles
scientific publication
patent
A document that has been accepted by a patent authority
US Patent 6,449,603
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
abstract
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
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.
introduction to a publication about an investigation
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
Section labelled 'introduction' of a typical scientific journal article
introduction
methods section
A part of a publication about an investigation that is about the study design of the investigation
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
results section
A part of a publication about an investigation that is about a study design execution
The section labelled 'results' in a typical scientific journal article
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion section
references section
A part of a document that has citations as parts
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
author list
Lawrence Hunter and Kevin Brettonel Cohen
part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
A part of a publication that is about the specific contributions of each author
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.
acknowledgements section
Part of a publication that is about the contributions of people or institutions other than the authors.
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
footnote
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.
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.
endnote
supplementary material to a document
appendix
part of a document that is segregated from the rest of the document due to its size
supplementary material
table of contents
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).
table of figures
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).
running title
A shorter version of a document title
copyright section
A document part that describes legal restrictions on making or distributing copies of the document
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
cartesian spatial coordinate datum
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
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
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
three dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
A denotator type indicates how a term should be interpreted from an ontological perspective.
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
mass measurement datum
A scalar measurement datum that is the result of measurement of mass quality
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
postal address
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
Person:Chris Stoeckart
author role
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.
data item extraction from journal article
a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
documenting
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
Bjoern Peters
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
wikipedia http://en.wikipedia.org/wiki/Documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
WEB: http://en.wikipedia.org/wiki/Line_chart
line chart
assigning a centrally registered identifier
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.
Person:Melanie Courtot
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
associating information with a CRID in the CRID registry
A planned process in which a CRID registry associates an information content entity with a CRID symbol
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
CRID symbol
A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Bill Hogan
PMID:12345, 12345 in a database column which has header "pubmedID"
CRID
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
Entries in a Column of which the header is "Pubmed ID"
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.
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
CRID registry
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.
IAO call, 20101124: PubMed registry is an instance of CRID registry
looking up a CRID
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
time stamped measurement datum
time sampled measurement data set
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.
experimental time series
pmid:20604925 - time-lapse live cell microscopy
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
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
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software module
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software library
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.
software application
A software application is software that can be directly executed by some processing unit.
software script
A software script is software whose instructions can be executed using a software interpreter.
planned process
A processual entity that realizes a plan which is the concretization of a plan specification.
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
material processing
A planned process which results in physical changes in a specified input material
adding a material entity into a target
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
a planned process that realizes the concretization of a study design
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
categorical measurement datum
device
performing a diagnosis
anatomical entity
An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
data transformation
study design
A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
administering substance in vivo
A process by which a substance is intentionally given to an organism
clinical finding
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
A process in an organism that leads to a subsequent disorder.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
Vaccination is: an 'administering substance in vivo' that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intend to invoke a protective immune response.
_BrightonMidLevelTerms
fever
A rise in body temperature above the normal, often as a response to infection.
inflammatory response
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
behavior
The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
peripheral nervous system
Nervous structures including ganglia outside of the central nervous system. Divided into somatic nervous system and autonomic nervous system [FB:gg, OMD:peripheral+nervous+system, Wikipedia:Peripheral_nervous_system, ZFIN:curator] comment: This class was created automatically from a combination of ontologies
brain
def: "The supra-esophageal ganglion of the central nervous system, composed of three primitive ganglia known as protocerebrum, deutocerebrum and tritocerebrum. In the context of Drosophila refers to the preoral ganglionic mass of the central nervous system containing the ventral ganglia. // Organ component of neuraxis that has as its parts gray matter and white matter that surround the cerebral ventricular system; Examples: There is only one brain. // Organ that is a component of the central nervous system and is responsible for the coordination and control of bodily activities and the interpretation of information from the senses. It appears when the neural tube segregates in forebrain, midbrain, and hindbrain at NF stage 22. The general pattern of the brain has been mainly established at NF stage 28. Yolky material is consumed and the fibre tracts and later the commissures develop. In general all of its parts are well developed at NF stage 53 and later development consists mainly of growth and some further cytological differentiation. In the period of metamorphosis only topographical changes take place." [FB:gg, ISBN:0815318960, ISBN:3110148986, OMD:brain, Wikipedia:Brain] comment: This class was created automatically from a combination of ontologies
nervous system
MC, 20100112: I am using the UBERON term as this one is non human specific, compared to FMA.
a network of specialized cells that communicate information about an organism's surroundings and itself[Wikipedia].
Level 1 of certainty of generalized convulsive seizure as an adverse event following immunization
Level 2 of certainty of generalized convulsive seizure as an adverse event following immunization
Level 3 of certainty of generalized convulsive seizure as an adverse event following immunization
Reported generalized convulsive seizure with insufficient evidence to meet the case definition
not a case of generalized convulsive seizure
example to be eventually removed
failed exploratory term
The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
other
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations"
Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO"
Institute for Formal Ontology and Medical Information Science (IFOMIS)
Barry Smith: "Basic Tools of Formal Ontology"
Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE"
Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization"