PHASES provides an ontology for integrating research in solitude and gerotranscendence. By integrating these areas of study, we aim to deepen our understanding of each and how they promote healthy aging.
Promoting Health Aging through Semantic Enrichment of Solitude Research (PHASES) Ontology
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
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.
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
definition source
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
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
Chris Mungall
expand assertion to
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)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
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 .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
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"
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)
Person:Alan Ruttenberg
has ID range allocated
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
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
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.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
logical characteristic of object property
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
A provenance property that denotes a synonym to be the preferred one for a specific community.
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
A synonym type for describing ambiguous synonyms
A synonym type for describing dubious synonyms
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
A synonym type for describing Latin term synonyms.
NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
GERO
SOLO
tooth SubClassOf 'never in taxon' value 'Aves'
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Class: ?X DisjointWith: RO_0002162 some ?Y
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
A relation that links an individual human behaviour to a behavioural attribute.
Realises the human life function of an individual human behaviour.
Causally relation between two entities in which a behaviour brings into existence, causes to occur, destroys, prevents from occurring, or changes an entity.
Has participant that relates a behaviour to the person enacting the behaviour.
Has participant that relates a behaviour to a material entity that the person enacting the behaviour intends to enable or facilitate the behaviour.
Has participant that relates a behaviour to another sentient being that accompanies the person enacting the behaviour.
Has participant that relates the behaviour to an object that the person enacting the behaviour intends to influence.
Inverse of has behavioural outcome relation.
A relation between an occurrent x and a one-dimensional temporal entity such that the one-dimensional temporal entity designates the latest boundary of x's existence or manifestation.
A relation between an occurrent x and a one-dimensional temporal entity such that the one-dimensional temporal entity designates the earliest boundary of x's existence or manifestation.
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
To say that b realizes c at t is to assert that there is some material entity d and b is a process which has participant d at t and c is a disposition or role of which d is bearer_of at tand the type instantiated by b is correlated with the type instantiated by c.
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
b occurs_in c =def b is a process and c is a material entity or immaterial entityand there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.and forall(t) if b exists_at t then c exists_at t and there exist spatial regions s and s’ where and b spatially_projects_onto s at tand c is occupies_spatial_region s’ at tand s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
Inverse of occurrent_part_of which is defined as: b occurrent_part_of c =Def. b is a part of c and b and c are occurrents.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects.
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
A relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Involves use of products, services, activities, rules or environmental objects.
An intervention that has the aim of influencing human behaviour.
A <mental disposition> to perceive or experience oneself as isolated from and not meaningfully involved in social groups.
"Coping" in the Health Behaviour Internalisation Model
"Hierarchy of Walking Needs" in the Social Ecological Model of Walking
"Needs" in the Needs-Opportunity-Abilities Model
"Needs" in the Self-Determination Theory
"Ownership" in the Health Behaviour Internalisation Model
"Support" in the Health Behaviour Internalisation Model
"Preference" in the Health Behaviour Internalisation Model
A <mental disposition> of a person to act to obtain or maintain a particular state due to this state’s importance to the person’s wellbeing.
Psychological needs can be satisfied or thwarted.
A spatial <quality> that inheres in a bearer by virtue of its position relative to other entities.
An intervention could be used to rearrange objects in an environment, changing the location of a person relative to these objects and thereby increasing the likelihood of a behaviour.
A plan that is realized in a BCI scenario process.
behaviour change intervention scenario plan
An aggregate of individual human behaviours of members of a population.
The class human behaviour [BCIO:042000] has been made obsolete. If you want to refer to the behaviour of an individual, refer to individual human behaviour . If you want to refer to the behaviour of a group, refer to population behaviour.
Also referred to in definitions as human behaviour or just behaviour.
walks for 15 mins/day, never eats meat, attends school daily
A <bodily process> of a human that involves co-ordinated contraction of striated muscles controlled by the brain.
A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain.
it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle)
The class human behaviour [BCIO:042000] has been made obsolete. If you want to refer to the behaviour of an individual, refer to individual human behaviour . If you want to refer to the behaviour of a group, refer to population behaviour. Striated muscles referred to in the definition do not ordinarily involve cardiac muscles. Behaviours are usually in response to an internal or external stimuli. Every behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour. 'behaviours' can involve a series of activities (e.g., more granular behaviours). 'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations
Learning function (e.g., knowledge development function and skill development function), knowledge or skill maintenance, protection of self, others and the environment, aesthetics function, bodily health function, spiritual function, social organisation function,, excretion function, nutrition function, reproductive function, respiration function,, rest function, travel function, thermoregulation function
A function that inheres in a human being and is realised in processes that enable the human to survive and thrive.
There are complex sets of processes involved in the realisation of human life functions, only some which would behaviours. An example for a human life function that is not a behaviour function: human thermoregulation via sweating function. However, some behaviours can fulfil 'human life functions'. The term 'survive' refers to continuing one's existence (e.g., staying alive), while 'thrive' includes a wide range of processes that improve an animal's life, including physical and mental wellbeing and experiencing positive social interactions, as well as being able to reproduce. Many processes can contribute to a human surviving and thriving.
An occurrent consisting exactly of a plurality of processes that are process_aggregate_member_parts_of that occurrent for all times at which it exists.
Process aggregate extends BFO in the same way that object aggregate extends its coverage of material entities. It is required to be able to classify occurrents such as behaviour patterns that are repeated occurrences of classes of process that have properties such as average frequency of occurrence (not to be confused with frequency as a process profile) and temporal patterning of occurrences.
Examples of interventions are putting health warnings on cigarette packets, providing free stop smoking services and banning smoking in public places.
A planned process that has the aim of influencing an outcome.
A process that is an individual human behaviour or a population behaviour.
This is intended to provide a user-friendly way of representing the way in which processes are manifest. This is somewhat similar to, but not the same as, the class 'specifically dependent continuant' in Basic Formal Ontology which provides a way of representing features of material entities such as age and size. It is formally equivalent to process profile in Basic Formal Ontology.
A process profile that is an attribute of a process.
physical performance behaviour has_behavioural_attribute behavioural attribute
A process attribute of an individual human behaviour.
entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
An entity is anything that exists or has existed or will exist.
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entities
entitātem
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
A specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized.
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
b is a specifically dependent continuant = Def. b is a continuant and there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
characteristic
generically dependent continuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
A disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An <independent continuant> that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
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.
PERSON: Chris Stoeckert
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
data about an ontology part is a data item about a part of an ontology, for example a term
obsolescence reason specification
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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Melanie Courtot
denotator type
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.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
"Regulatory fit" in the Regulatory Fit Theory
An <affective process> that involves the experience of internal or external sensory stimuli.
An affective process that involves the experience of internal or external sensory stimuli.
The subjective emotional feeling is that (fiat) part of the emotion process by which the organism experiences its own emotion.
'Subjective affective feeling can have greater or weaker physiological or mental components. The bodily process that are experienced will usually involve some mental process. Bodily sensation and the experiences of emotions (e.g., feeling calm) would both qualify as examples of 'subjective affective feeling'. As a subclass of 'affective process', subjective affective feelings have valence. Valence refers to the 'the subjective value of an event, object, person, or other entity in the life space of the individual' (https://dictionary.apa.org/valence). Valence ranges from negative to positive.
As a subclass of 'affective process', subjective affective feelings have valence. Valence refers to the 'the subjective value of an event, object, person, or other entity in the life space of the individual' (https://dictionary.apa.org/valence). Valence ranges from negative to positive.
Bodily sensations and the experiences of emotions (e.g., feeling calm) would both qualify as examples of 'subjective affective feeling'.
Excluded the following subjective feelings which appear on the GRID questionnaire since they seem debatable to what extent they are really *feelings* and to what extent they are actually *evaluations* or other things: -- felt submissive/dominant -- felt powerless/powerful
Subjective affective feeling can have greater or weaker physiological or mental components. The bodily processes that are experienced will usually involve some mental process.
"Mood / arousal" in the Social Action Theory (Ewart)
A <mental process> that has positive or negative valence.
A mental process that has positive or negative valence.
An affective process is any process that has positive or negative valence.
Valence refers to the 'the subjective value of an event, object, person, or other entity in the life space of the individual' (https://dictionary.apa.org/valence). Valence ranges from negative to positive.
affective process
An extended organism that is a member of the species Homo sapiens.
A <bodily process> that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour.
A bodily process that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour.
Valence is a process profile of an emotion, mood, or affective bodily feeling (such as pleasure and pain). Valence can be positive or negative, with different strengths in both directions. For example, pleasure is positively valenced while pain is negatively valenced.
A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain.
A bodily process which brings into being, sustains or modifies a cognitive representation or a behavior inducing state.
Examples include thinking, feeling pain, remembering and emotion as occurrent experiences.
Mental processes can vary in the degree to which they involve consciousness. A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain.
Mental processes can varying in the degree to which they involve consciousness.
GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.'
"Internal environment" in the PRIME theory
A <disposition> that inheres in some extended organism.
A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language.
A disposition that inheres in some extended organism.
Bodily disposition includes features that can be used in a specific context, such as a person's strength, but not a person's weight. A person has a specific weight independent of the circumstances they are in.
Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system) Bodily disposition would include features, such as a person's strength (which can be used in a specific context), but not weight. A person would have a certain weight independent of most circumstances they are in.
Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system).
bodily disposition
"Psychological" in the Health Promotion Model
"Psychological factors" in the I-Change Model
A <bodily disposition> that is realized in a mental process.
A bodily disposition that is realized in a mental process.
A mental disposition is a bodily disposition that is realized in a mental process.
'Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body.
Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body.
mental disposition
A bodily quality is a quality that inheres in some extended organism.
bodily quality
A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning.
mental quality
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
AR, BP, JM, MC, PRS
branch derived
The phrase 'bodily component of an organism in the definition refers to a part of the body.
A <process> in which at least one bodily component of an organism participates.
A process in which at least one bodily component of an organism participates.
A process in which at least one bodily component of an organsim participates.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060
The phrase 'bodily component of an organism’ in the definition refers to ‘a part of the body’.
An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087
A behavior change intervention that uses life histories—written, oral, or both—to improve psychological well-being. The therapy is often used with older people.
reminiscence therapy process
cognitive appraisal representational pattern quality
A cognitive representational pattern quality which consists of an evaluation of the relevance of some entity to another entity.
self-appraisal representational pattern quality
A cognitive appraisal representational pattern quality consisting of an evaluation of the appraiser themselves.
self-efficacy representational pattern quality
A self-appraisal representational pattern quality consisting of an evaluation of the agent's capability to achieve objectives or satisfy desires.
psychological construct information content entity
psychological construct
psychoanalytic psychological identity construct information content entity
A psychological construct in which it is hypothesized that human consciousness consists of the id, ego, and superego.
psychoanalytic psychological identity construct
performative identity quality
A personal identity quality formed as a result of the agent's performative behaviors as influencing and influenced by the formation of one's psychological identity.
social withdrawal disposition
A mental disposition that, if realized, is realized in the consistent avoidance of social interactions with both familiar and unfamiliar peers due to psychological traits such as social fear or anxiety.
self-transcendence disposition
A transcendence disposition that, if realized, is realized in shifting one’s focus beyond the self toward broader existential, moral, or spiritual concerns, including care for others, connection with nature, or alignment with perceived universal values.
elective solitude disposition
A mental disposition that, if realized, is realized in intentionally withdrawing from social interaction in order to pursue self-reflection, restoration, or personal goals.
imposed solitude characteristic
A characteristic of a person that is physically or socially alone due to external constraints or circumstances, and not by personal choice.
ambient sociability disposition
A mental disposition that is realized in retaining the sense of social presence without direct social engagement with others in a public or semi-public space.
healthy aging process
A biological process that is realized in maintaining functional ability, emotional well-being, and social engagement in later life, relative to cultural and personal expectations.
successful aging construct information content entity
A psychological construct information content entity that describes achieving physical health, cognitive vitality, and continued involvement with life, as measured against individual and cultural standards of aging well.
aloneliness disposition
A mental disposition that, if realized, is realized in experiencing discomfort or distress due to a perceived lack of desired time alone.
social detachment disposition
A mental disposition that, if realized, is realized in reduced motivation to engage in or maintain social relationships, often without distress or social fear.
shyness behavior disposition
A mental disposition to social anxiety that, if realized, is realized in the inhibition of behavior during potential social interaction due to fear of negative evaluation.
solitude affinity disposition
A mental disposition that, if realized, is realized in seeking out and enjoying time spent alone for reflection, creativity, or restoration.
A quality that concretizes some information content entity.
representational pattern quality
A mental representational pattern quality that has mind-to-world direction of fit.
cognitive representational pattern quality
A representational pattern quality that specifically depends on the cognitive system of its bearer.
mental representational pattern quality
A mental quality that is defined by (a) a set of physical, psychological, and interpersonal characteristics that is not wholly shared with any other person and (b) a range of affiliations (e.g., ethnicity) and social roles.
personal identity quality
self-concept
A personal identity quality consisting of the internalized, evolving, story of oneself that individuals construct to make sense and meaning out of life.
narrative identity quality
A personal identity quality consisting of the recognition of oneself as a persisting entity, resulting from the integration of one's ego-ideal, life roles, and adjustments to reality.
ego identity quality
A psychological construct that is putatively about biologically-based dispositions to avoid others due to social fears and anxieties
How are behavioral inhibition and anxious-solitude related to and distinct from solitude? (anxious-solitude, and behavioral inhibition are all constructs reflecting biologically-based dispositions to avoid others due to social fears and anxieties)
anxious solitude construct information content entity
A directive information content entity that prescribes any of various established rules, methods, procedures, and practices which have been accepted as guides for social conduct over a relatively long period.
social convention directive information entity
Everyone conforms to R Everyone believes others conform to R This belief gives everyone a good reason to conform to R himself Everyone believes others are doing the best they can to conform to R R is not the only possible regularity meeting (3) and (4) Each of the preceding factors are in principle common knowledge
A mental disposition that, if realized, is realized in being physical alone or in lacking social interactions, whether desired or not.
Solitude is most often linked to low levels of loneliness and positive emotions when it is chosen solitude (due to enjoying solitude) and spent in active ways; people with a propensity to ruminate and those who choose solitude because they do not like being with others tend to suffer the most in solitude - Julie
What are the different motivations that explain why some seek solitude? Here there are so many overlapping terms (ie., unsociability, preference for solitude, avoidance, social anhedonia, affinity for solitude, affinity for aloneness, aversion to aloneness, autonomous solitude, not self-motivated solitude), but I have a recent study suggesting that the constructs tend to load into three larger factors: shyness, affinity for solitude, and social detachment.
solitude
Oliveira, J., Guerra, S., Sousa, L., & Ribeiro, O. (2024). Solitude in old age: a scoping review of conceptualisations, associated factors and impacts. Aging & Mental Health, 29(2), 220–227. https://doi.org/10.1080/13607863.2024.2379408
A mental disposition borne by older adults such that, if realized, is realized in shifting in goals, values, and perspectives towards connections to past and future generations and in seeking coherence in one's life narrative.
gerotranscendence disposition
Social alienation that, if realized, is realized in being physically alone and desiring not to be.
social isolation behavior disposition
A subjective affective feeling of dissatisfaction with a lack of social interactions and relationships.
feeling of loneliness
Asher, S. R., Hymel, S., & Renshaw, P. D. (1984). Loneliness in children. Child development, 1456-1464.
An information content entity that is a principle or body of interrelated principles that purports to explain or predict a number of interrelated phenomena.
theory information content entity
theory
A theory that summarizes and explains mental and behavioral patterns within the context of society and culture.
psychological theory
A mental disposition borne by agents such that, if realized, is realized in shifting in goals, values, and attachments towards connections to past and future generations and in seeking coherence in one’s life narrative.
transcendence disposition
A process in which an individual objectively lacks social connection such that there is little or no opportunity for social interaction.
social isolation process
A psychological need to feel connected to and accepted by a group.
need for a sense of belonging to a community
example to be eventually removed
failed exploratory term
The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification.
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
The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
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 is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
core
obsolete_core
placeholder removed
The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.
This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.
terms merged
The term has been combined with one or more other terms to create a more encompassing (merged) term.
An editor note should explain what were the merged terms and the reason for the merge.
The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.
term imported
The term has been replaced by a term imported from another ontology.
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.
This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.
term split
The term has been split into two or more new terms.
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.
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. The deprecated term should reference the replacement terms with obo:IAO_0100001.
universal
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.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"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.
named class expression
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.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.
The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
Self-Transcendence Scale
Gerotranscendence Scale
Adult Self-Transcendence Inventory
Quiet Ego Scale
Narrative Identity Indicators of Self-Transcendence
Cloninger Temperament and Character Inventory
The Nondual Awareness Dimensional Assessment
NADA
The Non-attachment to Self Scale
Loneliness Scale
Social Preference Scale-Revised
The Likert scale designed to assess an individual's subjective feelings of loneliness and social isolation, as well as perceived disconnects between desired and actual social relationships.
UCLA Loneliness Scale
The Likert scale designed to assess the degree to which individuals experience solitude as a beneficial, reflecting dimensions such as emotional restoration, creativity, inner peace, and personal growth in the absence of social interaction.
Positive Solitude Scale
The behaviour change intervention that uses life histories to improve well-being
reminiscence therapy
Damayanthi Jesudas
Oliver He
Bill Duncan
John Beverley
Jie Zheng
Leo Yeh
Sam Smith
A psychological theory positing that social connections differ in levels of closeness and stability, where peripheral relationships are most vulnerable to change and termination, especially with increased age.
social convoy model
Antonucci, T. C., Ajrouch, K. J., & Birditt, K. S. (2014). The convoy model: Explaining social relations from a multidisciplinary perspective. The Gerontologist, 54(1), 82-92.
A psychological theory that posits the acceptance of life as it has been lived, including acceptance of death, as the major driving psychological goal of older adults.
ego integrity theory (Erikson)
Erikson E.H. The Life Cycle Completed. Norton; New York, NY, USA: 1982.
A psychological theory that posits self-transcendence as a mediating role between vulnerability and well-being, influenced by personal and contextual factors.
self-transcendence theory
Reed, P.G. (1991). Toward a nursing theory of self-transcendence: Deductive reformulation using developmental theories. Advances in Nursing Science, 13 (4), 64-77.