Ontology for Scientific Evidence and Provenance Information
type: Ontology
version IRI: sepio.owl
contributor: https://orcid.org/0000-0002-1048-5019
description: The SEPIO ontology is in its early stages of development, undergoing iterative refinement as new requirements emerge and alignment with existing standards is explored.
license: https://creativecommons.org/licenses/by/3.0/
version info: 2023-06-13

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred term: example of usage
has curation status: ready for release
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: ready for release
definition: 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: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: ready for release
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred term: alternative label
has curation status: pending final vetting
definition: 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.
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: 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).
label: alternative term

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: ready for release
definition: 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred term: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
has curation status: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

consider
type: AnnotationProperty

SEPIO_editor_note
type: AnnotationProperty
comment: Used to capture development notes and design decisions or questions. All annotations using this property should be removed before publishing / releasing the ontology to the public (but ideally retained in some place as valuable documentation).

usage note
type: AnnotationProperty

in_value_set
type: AnnotationProperty

sepio_preferred_label
type: AnnotationProperty
sub property of: alternative label

is_shortcut
type: AnnotationProperty
definition: Annotation indicating whether a property represents a "shortcut" relation that can be used to directly link two objects that are indirectly linked through a longer path of two or more edges. Shortcut relations can be logically expanded to be expressed in terms of this longer path, e.g. has_evidence_from_source = has_evidence_line o has_evidence_item o source.
range: boolean

eco subset
type: AnnotationProperty
sub property of: SubsetProperty

description
type: AnnotationProperty
range: string
type: DatatypeProperty
definition: An account of a resource.

description
type: AnnotationProperty
definition: An account of the resource.
comment: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."

source
type: AnnotationProperty
range: information
type: ObjectProperty
definition: A related resource from which the described resource is derived.
comment: The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.

title
type: AnnotationProperty
type: DatatypeProperty

database_cross_reference
type: AnnotationProperty

in_subset
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative label: part_of
imported from: ro.owl
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable
RO_0040042: quality
RO_0040042: characteristic
RO_0040042: generically dependent continuant
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative label: has_part
imported from: ro.owl
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
IAO_0000600: [copied from inverse property 'realizes'] 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])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, 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

realizes
type: ObjectProperty
sub property of: topObjectProperty
domain: process
range: realizable
range: characteristic
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
IAO_0000600: 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])
comment: 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

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred term: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative label: is preceded by
alternative label: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: eco subset

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred term: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: eco subset

executed by
type: ObjectProperty
inverse of: executes

concretizes
type: ObjectProperty
inverse of: is concretized as

intended to realize
type: ObjectProperty

realizes
type: ObjectProperty
domain: process
range: realizable

is about
type: ObjectProperty
domain: information
definition: Is_about is a (currently) primitive relation that relates an information artifact to an entity.
label: is_about

has specified input
type: ObjectProperty
sub property of: has participant
inverse of: is specified input of
domain: completely executed planned process

is specified input of
type: ObjectProperty
sub property of: participates in

has specified output
type: ObjectProperty
sub property of: has participant
inverse of: is specified output of
domain: completely executed planned process

is specified output of
type: ObjectProperty
sub property of: participates in

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: this red color is a characteristic of this apple
definition: 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.
alternative label: inheres_in
RO_0001900: RO_0001901
comment: 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.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: characteristic
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in
imported from: ro.owl

has participant
type: ObjectProperty
domain: occurrent
domain: process
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative label: has_participant
imported from: ro.owl
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative label: function_of
alternative label: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative label: is role of
alternative label: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative label: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative label: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in_subset: RO_0002259
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: dos
creation date: 2017-05-24T09:49:21Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
database_cross_reference: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
database_cross_reference: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: GOC:dos

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
in_subset: eco subset
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
term editor: David Osumi-Sutherland
alternative label: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: https://orcid.org/0000-0002-7073-9172
term editor: David Osumi-Sutherland
alternative label: ends_at_start_of
alternative label: meets
RO_0002575: precedes
in_subset: eco subset
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: eco subset

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

has component
type: ObjectProperty
sub property of: has part
has curation status: pending final vetting
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
in_subset: eco subset

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
term editor: https://orcid.org/0000-0001-9114-8737
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
term editor: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
has curation status: pending final vetting
definition: inverse of develops from
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
term editor: https://orcid.org/0000-0003-1980-3228
in_subset: RO_0002259

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
term editor: https://orcid.org/0000-0001-7476-6306
term editor: https://orcid.org/0000-0002-3837-8864
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in_subset: eco subset

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allen's interval algebra
curator note: 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.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: eco subset
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
has curation status: pending final vetting
definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
alternative label: consumes
imported from: ro.owl
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: eco subset

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
has curation status: pending final vetting
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
alternative label: produces
imported from: ro.owl
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: eco subset

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops from
example of usage: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
has curation status: pending final vetting
definition: x has developmental contribution from y iff x has some part z such that z develops from y
term editor: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
has curation status: pending final vetting
definition: inverse of has developmental contribution from
term editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
has curation status: pending final vetting
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
editor note: false
term editor: https://orcid.org/0000-0002-6601-2165
curator note: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in_subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has related synonym: affects
in_subset: valid for go gp2term

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: pending final vetting
definition: Inverse of developmentally preceded by
term editor: https://orcid.org/0000-0002-6601-2165

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
RO_0004049: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO_0004050: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing
curator note: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in_subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: https://orcid.org/0000-0002-6601-2165
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: actively involved in
alternative label: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
term editor: https://orcid.org/0000-0002-6601-2165
in_subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
term editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
term editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: Is member of is a mereological relation between a item and a collection.
definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: Has member is a mereological relation between a collection and an item.
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
imported from: ro.owl
in_subset: RO_0002259
in_subset: eco subset

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
imported from: ro.owl
in_subset: RO_0002259
in_subset: eco subset

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
has curation status: requires discussion
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
term editor: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: requires discussion
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
term editor: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: requires discussion
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
term editor: https://orcid.org/0000-0002-6601-2165

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
has curation status: requires discussion
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
term editor: https://orcid.org/0000-0002-6601-2165

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
has curation status: requires discussion
definition: inverse of upstream of
term editor: https://orcid.org/0000-0002-6601-2165

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
term editor: https://orcid.org/0000-0002-6601-2165

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly activates
RO_0002579: positively regulates

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly inhibits
RO_0002579: negatively regulates

causally related to
type: ObjectProperty
definition: 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.
editor note: 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 yie…
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: 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.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
term editor: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
term editor: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
in_subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: involved in or reguates

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
editor note: Considering relabeling as 'pairwise interacts with'
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has exact synonym: in pairwise interaction with
in_subset: eco subset

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: binds
alternative label: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
has exact synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly inhibits
has exact synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly activates
has exact synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165
curator note: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
term editor: https://orcid.org/0000-0002-6601-2165

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
editor note: 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
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
term editor: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
term editor: https://orcid.org/0000-0002-6601-2165

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
definition source: causal-relations
IAO_0000589: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
domain: evidence line
example of usage: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
definition: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
alternative label: is_evidence_supported_by
comment: In the Gene Ontology association model, this corresponds to the With/From field
label: is_evidence_with_support_from

related via evidence or inference to
type: ObjectProperty
curator note: Do not use this relation directly. It is a grouping relation.

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
definition source: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
definition source: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable
range: material entity
property chain axiom: realized in response to
property chain axiom: has input
definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:45:49Z

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable
range: process
property chain axiom: realized in
property chain axiom: causally downstream of
example of usage: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
example of usage: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
example of usage: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: https://orcid.org/0000-0001-6996-0040
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-7073-9172
contributor: https://orcid.org/0000-0002-8461-9745
has exact synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: hasExactSynonym
annotated target: triggered by process
database_cross_reference: RO:cjm

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
term editor: https://orcid.org/0000-0003-4639-4431

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
definition: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
created by: pg
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: pg
creation date: 2022-09-26T06:08:01Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
example of usage: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
term editor: https://orcid.org/0000-0001-9625-1899
term editor: https://orcid.org/0000-0003-2620-0345
curator note: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
curator note: See github ticket https://github.com/oborel/obo-relations/issues/497
creation date: 2021-11-08T12:00:00Z
has broad synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

has_evidence_line
type: ObjectProperty
inverse of: is_evidence_line_for
domain: Class
  union of: proposition
  union of: assertion
range: evidence line
definition: A relationship between an assertion or proposition and an evidence line used in evaluating its validity.
editor note: Consider re-use of http://purl.obolibrary.org/obo/RO_0002558 ! 'has evidence'. Definition = "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." See also http://semanticscience.org/resource/SIO_000772 ! 'has evidence'.
alternative label: has_evidence

has_supporting_evidence_line
type: ObjectProperty
sub property of: has_evidence_line
property chain axiom: is_equilavent_to
definition: A relation between a proposition and information that supports its validity, based on the evaluation of some agent.
editor note: Mapping to related terms: Consider: http://semanticscience.org/resource/SIO_000206 ! 'is supported by'

has_disputing_evidence_line
type: ObjectProperty
sub property of: has_evidence_line
property chain axiom: strongly_contradicts
property chain axiom: has_supporting_evidence_line
definition: A relation between a proposition and information that contradicts its validity, based on the evaluation and conclusion of some agent.
editor note: Mapping to related terms: Consider: http://semanticscience.org/resource/SIO_000774 ! 'is refuted by'
alternative label: has_conflicting_evidence
alternative label: has_refuting_evidence_line

has_inconclusive_evidence_line
type: ObjectProperty
sub property of: has_evidence_line
property chain axiom: is_equilavent_to
definition: A relation between a proposition and information that was used to evaluate a particular proposition, but failed to provide conclusive support for or against its validity.
editor note: Mapping to related terms: Consider: http://semanticscience.org/resource/SIO_000207 ! 'is disputed by'
alternative label: has_insignificant_evidence_line
comment: A relation between a proposition and information that does not conclusively support or contradict its validity, based on evaluation of some agent.

proposition_asserted_in
type: ObjectProperty
inverse of: asserts_proposition
domain: proposition
range: assertion
definition: A relation holding between a proposition and an assertion in which it is expressed.
alternative label: is_asserted_in
comment: A particular proposition can be asserted in more than one assertion - in cases where assertions made by different agents, or on different occasions, put forth the same proposition as true.

has_agent
type: ObjectProperty
sub property of: has participant
range: Agent
editor note: Consider use of http://purl.obolibrary.org/obo/RO_0002217 ! actively participates in. Definition = "actively participates in y if and only if x participates in y and x realizes some active role"

assertion_has_subject
type: ObjectProperty
sub property of: ObsoleteProperty
domain: assertion
property chain axiom: asserts_proposition
property chain axiom: association has subject
has obsolescence reason: Decided that a more generic has_subject property should suffice to cover links from either an assertion or a proposition to an entity representing the subject of the statement made. But wanted to maintain the text in the comment here for future reference/use.
comment: Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_subject :thing1). The assertion_has_subject property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the subject of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_subject). This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.

assertion_has_object
type: ObjectProperty
sub property of: ObsoleteProperty
domain: assertion
property chain axiom: asserts_proposition
comment: Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_object :thing1). The assertion_has_object property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the object of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_object). This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.

assertion_has_predicate
type: ObjectProperty
sub property of: ObsoleteProperty
domain: assertion
property chain axiom: asserts_proposition
property chain axiom: association has predicate
comment: Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_predicate :thing1). The assertion_has_predicate property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the predicate of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_predicate). This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.

asserts_proposition
type: ObjectProperty
domain: assertion
range: proposition
definition: A relation holding between an assertion and the proposition that it puts forth as true.
consider: Mapping to related terms: Consider: http://purl.org/see/rdo#is_assertion_asserting
sepio_preferred_label: assertsProposition
comment: In practice, SEPIO recommends that data is captured at the assertion level, and post-processed as needed to aggregate assertions making the same claim under a single proposition using this property.

was_specified_by
type: ObjectProperty
inverse of: specified_creation_of
range: plan specification
definition: A relation holding between a planned process, or the artifact it generates, and a plan specification that specifies all or part of the process (e.g. a protocol, guideline, rule set)
editor note: Consider SIO:00339 (a relation between a product and the information content entity that specifies it.)
comment: In SEPIO, this property is most often used to link an assertion (the generated artifact) to an 'assertion method' that may specified how it was created. This assertion method may describe what types of data may be used as evidence, what weight to give a particular type of evidence, and how to combine different lines of evidence in generating the final assertion.

has_role
type: ObjectProperty
editor note: Consider RO:0000087 ! has_role (def = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence). However, this property is defined as a relation between an independent continuant and a role. In BFO, dependent continuants (such as information) cannot bear roles.

has_evidence_item
type: ObjectProperty
sub property of: is evidence with support from
inverse of: evidence_item_for
domain: evidence line
range: evidence item
property chain axiom: describes_study_data
definition: A relation holding between an evidence line and an individual information entity that contributes to the argument it represents.
alternative label: has_supporting_information

Axiom
annotated source: has_evidence_item
annotated property: propertyChainAxiom
annotated target: has_evidence_item
annotated target: describes_study_data
SEPIO_editor_note: If we start using the 'study data set' class in a similar way to organize data items from a partiular study, we should create a similar property chain that traverses the property we use to link study data sets to their data item parts. Can this just be "has part" . . .or is a specific/unique relation needed here to avoid unwanted entailments?
comment: This property chain ensures that any evidence items that are organized into groups using a 'study finding' object will still be classified as evidence items for the relevant evidence line, and returned by queries for evidence items for a particular evidence line.

evidence_has_supporting_activity
type: ObjectProperty
sub property of: is evidence with support from
domain: evidence line
range: Activity
property chain axiom: has_evidence_item
property chain axiom: output of
definition: A relation that links an evidence line to any activities (studies, assays, computational tasks, curation) that generated evidence items contributing to it.
alternative label: has_evidence_item_output_from
alternative label: has_supporting_activity
is_shortcut: true

is_equilavent_to
type: ObjectProperty
sub property of: aligns_with
type: SymmetricProperty
alternative label: has_equivalent_proposition

is_consistent_with
type: ObjectProperty
sub property of: aligns_with
type: SymmetricProperty
alternative label: has_consistent_proposition

strongly_contradicts
type: ObjectProperty
sub property of: conflicts_with
type: SymmetricProperty
domain: proposition
range: proposition
editor note: Previosly implemented property chains: is_asserted_in o strongly_contradicts o asserts -> strongly_contradicts asserts o strongly_contradicts o is_asserted_in -> strongly_contradicts But these broke reasoner - "the given hierarchy is not regular" error message". Apparently breaks rule that "in property chains of 3 or larger, the inner property must not also appear as the composite property". (https://arxiv.org/pdf/1212.2902.pdf)
alternative label: has_contradicting_proposition
comment: Relation between two propositions that make opposing claims (e.g. proposition1 holds that variant1 is pathogenic for disease1, and proposition2 holds that variant1 is benign for disease1).

contradicts
type: ObjectProperty
sub property of: conflicts_with
alternative label: has_inconsistent_proposition

is_expressed_in
type: ObjectProperty
inverse of: expresses
domain: Class
  union of: proposition
  union of: statement
range: document
definition: Relationship between a statement or proposition and a document in which it is expressed (e.g. a publication, report, or database record).
alternative label: is_reported_in

expresses
type: ObjectProperty
domain: document
range: Class
  union of: proposition
  union of: assertion
definition: Relationship between a document (e.g. a publication, report, database record) and an assertion or proposition that is stated in its content.

has_compatability
type: ObjectProperty
sub property of: ExploratoryObjectProperty
editor note: Grouping class to hold exploratory relationships linking assertions or propositions based on the compatability or degree of agreement in their meaning. Has utility toward inferring links between evidence lines and propositions.
alternative label: has_concordance
alternative label: propositional relationships

measures_parameter
type: ObjectProperty
sub property of: ExploratoryObjectProperty
definition: A relation between a planned process and a parameter that it measures as part of an assay or observation.

conflicts_with
type: ObjectProperty
sub property of: has_compatability

aligns_with
type: ObjectProperty
sub property of: has_compatability

evidence_has_supporting_reference
type: ObjectProperty
sub property of: is evidence with support from
domain: evidence line
range: document
definition: A relation that holds between an evidence line and a citable document from which information supporting the evidence line was obtained (i.e. a "supporting reference").
editor note: Note that this relation only links an evidence line to publications actually consulted by the asserting agent to find and interpret evidence items. There may be other publications that describe the same evidence item that the asserting agent did not consult, which would not qualify as supporting references. For example, consider a GO curator's use of sequence data for the rat Vegfa gene in a line of evidence supporting their assertion that the human VEGFA ortholog exhibited the same angiogeneic activity. There may be multiple publications that report this same rat gene sequence, but only the publication that the curator consulted in making this assertion would qualify as a supporting reference for this evidence line. For this resaon, we are not able to create a property chain declaring "has_evidence_item o is_described_by -> has_evidence_item_described_by". . . because this would entail that any publication describing this rat Vegfa gene sequence was a supporting reference for the assertion.
alternative label: has_support_from_source
alternative label: has_supporting_reference
SEPIO_editor_note: Keeping the label has_supporting_reference instead of has_evidence_item_described_by because the later follows the pattern we use for true shortcut relations (i.e. that can be defined using property chains). For reasons outlined in the editor note, this is not such a shortcut relation.

is_inconsistent_with
type: ObjectProperty
sub property of: has_compatability

authored_by
type: ObjectProperty
sub property of: has_contributor
example of usage: As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge. The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above. The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above.
definition: A relation between an information content entity (or concrete manifestation of it as a particular resource/digital artifact), and the agent that originally generated the information content.
SEPIO_editor_note: Older note - remove before releasing: We intentionally avoid use of a more generic "creator" property here, as this term is used in established standards such as PAV and DC to specifically describe agents who generated a specific representation of an information content entity. For example, the pav:createdBy property is used specifically to describe agents contributing to a specific representation. SEPIO, by contrast, aims to describe the agent(s) responsible for generating the abstract information content these concretized artifacts express. For this reason, SEPIO creates the more specific "stated_by" relation to explicitly distinguish the act of making a statement (generating its information content) from the act of creating a specific digital representation of the statement (generating a particular concretized artifact). A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice.
comment: In the case that the information artifact is an assertion, the responsible agent is the one who originally generated an assertion based on their evaluation of relevant evidence. If more than one agent is involved in this process, we may consider them collectively as a group or organization representing a single agent.

evidence_line_strength
type: ObjectProperty
domain: evidence line
range: evidence strength
definition: A relation describing the degree of support provided by an evidence line for a target assertion or proposition.
editor note: The value of this property is typically a term from some defined set of values that enumerates categorical degrees of evidence strength (e.g. the CIViC five-teired 'evidence level' scale). Different systems or applications can create terms representing the levels of strength they wish to define for their use case.

evaluated_by
type: ObjectProperty
sub property of: has_contributor
definition: A relation holding between a generated artifact and an agent who evaluated its quality, completeness, or utility.
editor note: In SEPIO, the agent responsible for a particular evidence line is linked via the "evaluated_by" property. This reflects that perspective that evaluation of the relevance, strength, and direction of an evidence line w.r.t. a particular assertion are the key acts inherent in the evidence line's "creation". We avoid using a "creator" relation here because this label is used in established standards such as PAV and DC to specifically describe agents contributing to a specific digital representation, as opposed to agents responsible for generating the underlying information content these concrete representations express. A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice.
alternative label: assessed_by

has_qualifier
type: ObjectProperty
sub property of: is about
domain: Class
  union of: proposition
  union of: statement
definition: A relation used to indicate context in which a particular assertion or proposition applies.

has_evidence_from_source
type: ObjectProperty
domain: Class
  union of: proposition
  union of: assertion
range: information
property chain axiom: has_evidence_line
property chain axiom: has_evidence_item
property chain axiom: is_described_by
property chain axiom: source
definition: A relation used to link an assertion or proposition to a source where evidence for it was found (i.e. a document, document part, database, etc)
consider: cito:cites_as_evidence
SEPIO_editor_note: Note that this may not qualify as a proper shortcut (i.e. it may not be valid to define using a property chain) for the same reason has_supporting reference is not defined as a property chain called has_evidence_item_described_by.
is_shortcut: true
comment: This is a shortcut relation to be used when publications are referenced as providing support for an assertion, but it is not clear how many evidence lines are described across these publications. In such cases, discrete evidence lines cannot be created, and the has_evidence_from_source relation is used to directly link the assertion to publications providing some form of evidence information.

has_evidence_level
type: ObjectProperty
domain: Class
  union of: proposition
  union of: assertion
range: evidence strength
definition: A relation used to link an assertion or proposition directly to some indicator of the strength of the total evidence that asserting agent beleives to support it.
alternative label: has_total_evidence_strength
comment: This relation links an assertion or proposition directly to some indicator of the strength of the total evidence supporting it. It is used when there is not enough information to create evidence line(s) for the assertion, but the source provides some indication of the strength of the evidence supporting it. Note that this is different than the notion of statement confidence, which describes how confident an agent is that a statement is true. Confidence may depend on factors in addition to the strength of the evidence (e.g. who made the prior probability that the asserted proposition could be true, who made the assertion and when, etc.)

has_contributor
type: ObjectProperty
inverse of: contributes_to
range: Agent
definition: A relation between an information content entity and an agent who made a contribution to its information content, or to its subsequent modification or assessment.
editor note: SEPIO intentionally creates its own hierarchy of contributor properties, instead of re-using terms from existing standards like PAV or Dublin Core - whose domain is structured digital resources. This is because properties such as pav:createdBy specifically describe agents who generated a specific digital representation of information, while SEPIO aims to describe agents responsible for generating the abstract information content that such a concrete representation may express. The subject of 'contributor' relations in the SEPIO are explicitly abstract in nature - considered at the level of their information content as opposed to concretizations in particular digital resources or representations. For example, the SEPIO "stated_by" relation explicitly refers toan agent originally putting forth a statement as true (generating its information content), as opposed to an agent creating a specific digital representation of the statement (generating a particular concretized artifact such as a json object returned by an API). Should further clarification become available with respect to whether PAV or DC contributor properties accommodate the nuanced definitions we require, we will re-consider their inclusion in SEPIO. For example, the pav:authoredBy property seems to refer specifically to the agent who generated information content expressed in a resource - and thus may be appropriate in the context of SEPIO. But even here, the range of the property is a particular authored digital resource, and not the information content it expresses. DC properties such as dc:contributor and dc:creator are ambiguous as to which level of contribution they describe.

validated_by
type: ObjectProperty
sub property of: has_contributor
definition: A relation holding between a statement and an agent that validates its truth or accuracy - typically by reviewing the provenance and data on which it is based.
alternative label: validity_assessed_by

obsolete_evidence_assessed_by
type: ObjectProperty
sub property of: ObsoleteProperty
alternative label: evidence_strength_assessed_by
has obsolescence reason: ClinGen not using this, as they create contrigution objects and assign roles to capture such information. Can bring it back if there is need in some other use case/application.
deprecated: true

qualified_contribution
type: ObjectProperty
range: contribution
definition: A relation holding between an artifact and a contribution made by a particular agent to its creation, modification, assessment, or destruction.
editor note: Consider sup-properties specific to the type of contribuion make, to support property chains for inferring a direct realtiomnship between the artifact/entitiy contributed to, and a related agent or date. At present, we could only support: - qualified_contribution o date_of_contribution -> dc:date Want to be able to support inferences such as: - qualified_creation o date_of_contribution -> date_created - qualified_evaluation o date_of_contribution -> date_evaluated - qualified_modification o date_of_contribution -> date_modified
alternative label: has_contribution
comment: Analogous to PROV qualified Attribution - use to capture additional information about the contribution made by an agent, such as a role they played, or organization on behalf of which the contribution was made.

has_confidence_level
type: ObjectProperty
domain: information
range: confidence level
definition: A relation between an information entity and an indicator of degree of confidence that the information it represents is true.
alternative label: trust_rating
comment: Confidence in an information entity can mean different things for different types of information. For example, for assertions this reflects the confidence an agent has that the proposition it puts forth is true. For things like data items, it reflects the confidence an agent has that the data accurately reflects the aspect of reality its was intended to measure.

performed_for
type: ObjectProperty
domain: contribution
range: Agent
definition: A relation between an agent and an other agent, typically an organization, on whose behalf a Contribution is made.
alternative label: performed_on_behalf_of

is_described_by
type: ObjectProperty
definition: A relation between one entity and an informtion content entity that provides a description of it.
editor note: Consider: http://semanticscience.org/resource/SIO_000557 ! 'is described by'

evidence_direction
type: ObjectProperty
domain: evidence line
range: evidence direction
definition: A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).
sepio_preferred_label: evidenceDirection

contributes_to
type: ObjectProperty
sepio_preferred_label: contributesTo
comment: A relation between an agent and an entity toward which the agent made a contribution.

has_evidence
type: ObjectProperty
domain: Class
  union of: proposition
  union of: assertion
range: evidence item
property chain axiom: has_evidence_line
property chain axiom: has_evidence_item
definition: A relation that directly connects an assertion and an evidence item that contributes to one or more of its evidence lines. This evidence provided by this item may support or dispute the target assertion.
alternative label: assertion_has_evidence_item
alternative label: has_evidence_information
alternative label: has_evidence_line_with_item
comment: This relation can be used to link an assertion directly to evidence items that support it. Evidence items are typically organized into 'evidence lines' that group them according to the argument(s) to which they contribute. This shortcut relation supports use cases where it is desirable to elide over this level of organization and create direct links from an assertion to the fundamental pieces of information that represent evidence supporting it. A property chain (has_evidence_line o has_evidence_item -> has_evidence_with_item) is defined that can be used to infer this direct edge, facilitating interoperability between data sets that do and don't implement evidence lines to organize evidence items.

asserted_conclusion
type: ObjectProperty
domain: assertion
definition: A relationship that holds between an assertion and a term that summarizes its asserted conclusion.
alternative label: asserted_outcome
sepio_preferred_label: assertedConclusion

obsolete_has_quantifier
type: ObjectProperty
sub property of: ObsoleteProperty
has obsolescence reason: Deprecate until there is a specific use case requiring this relation.
deprecated: true

describes_study_data
type: ObjectProperty
sub property of: is about
domain: study finding
range: information
definition: A relation that holds between a study finding and a data item it describes (i.e. a data item generated by the study whose results are described by the finding).
alternative label: describes_supporting_data

evidence_item_for
type: ObjectProperty
domain: evidence item
range: evidence line
sepio_preferred_label: evidenceItemFor

created_by
type: ObjectProperty
sub property of: has_contributor
example of usage: As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge. The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above. The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above.
definition: A relation between a particular information resource / digital artifact and an agent who made a primary contribution to its original creation.
comment: With respect to information resources, this property is used to capture a creator of a particular representation/manifestation of the information content - e.g. as a web resource or digital artifact. To describe the creator of the information content carried by such a digital artifact or resource, us the 'authored_by' property.

has_subject
type: ObjectProperty
sub property of: is about
definition: A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the entity that representing the subject of this relationship.

has_predicate
type: ObjectProperty
sub property of: is about
definition: A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the property serving as the predicate in this relationship.

has_object
type: ObjectProperty
sub property of: is about
definition: A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the entity that representing the object or value of this relationship.

has_evidence_of_type
type: ObjectProperty
definition: A shortcut relation that links an assertion directly to a term representing the type of evidence that supports it.
is_shortcut: true
comment: Relation expands to has_evidence_line o rdf:type -> has_evidence_type

ExploratoryObjectProperty
type: ObjectProperty

specified_creation_of
type: ObjectProperty
domain: plan specification
definition: A relation holding between a plan specification and a planned process it specifies, or the artifact the process generates.

information_quality
type: ObjectProperty
domain: information
definition: A relation describing the quality of a piece of information, wich may or may not be used as evidence by an agent making an assertion.
editor note: This property is used to indicate the inherent quality of a piece of data, based on the rigor of the experiment that produced it. It is not a direct indicator of the strength of evidence the data may provide for an assertion. The value of this property is typically a term from some defined set of values that enumerates categorical degrees of quality (e.g. the CIViC five star 'trust rating' scale) Different systems or applications can create terms representing the levels of quality they wish to define for their use case.

is_evidence_line_for
type: ObjectProperty
alternative label: evidence_for

provided_by
type: ObjectProperty
definition: A relationship between an information resource found in some information system, and the agent (person, organization, computational agent) who is responsible for sharing/providing it to that information system.
editor note: Consider: pav:providedBy
comment: Note that this property connects a resource to an agent, not to some other information resource from which it came (e.g. another database or an API from which the resource in question was obtained). Use the 'source' property to capture this type of relationship.

has_supporting_evidence_from_source
type: ObjectProperty
sub property of: has_evidence_from_source
definition: A relation used to link an assertion or proposition to a source where supporting evidence for it was found (i.e. a document, document part, database, etc)

has_disputing_evidence_from_source
type: ObjectProperty
sub property of: has_evidence_from_source
definition: A relation used to link an assertion or proposition to a source where disputing evidence for it was found (i.e. a document, document part, database, etc)

has_supporting_evidence
type: ObjectProperty
sub property of: has_evidence
definition: A relation that directly connects an assertion and a piece of information that contributes to an evidence line interpreted to support the truth of the assertion.

has_disputing_evidence
type: ObjectProperty
sub property of: has_evidence
definition: A relation that directly connects an assertion and a piece of information that contributes to an evidence line interpreted to dispute the truth of the assertion.

reference
type: ObjectProperty
definition: Links an entity to a document that describes it.

executes
type: ObjectProperty
property chain axiom: realizes
property chain axiom: concretizes

association has object
type: ObjectProperty
sub property of: has_object
domain: association
editor note: Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to their object (sensu RDF). It is therefore a more specific relation than its has_object parent, which can be used to link a statement or proposition to its object.

association has predicate
type: ObjectProperty
sub property of: has_predicate
domain: association
editor note: Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to the property representing the predicate of the reified triple. It is therefore a more specific relation than its has_predicate parent, which can be used to link a statement or proposition to its predicate.

association has subject
type: ObjectProperty
sub property of: has_subject
domain: association
editor note: Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents. This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to their subject (sensu RDF). It is therefore a more specific relation than its has_subject parent, which can be used to link a statement or proposition to its subject.

Authored by
type: ObjectProperty
sub property of: ObsoleteProperty
comment: An agent that originated or gave existence to the work that is expressed by the digital resource. The author of the content of a resource may be different from the creator of the resource representation (although they are often the same). See pav:createdBy for a discussion. pav:authoredBy is more specific than its superproperty dct:creator - which might or might not be interpreted to also cover the creation of the representation of the artifact. The author is usually not a software agent (which would be indicated with pav:createdWith, pav:createdBy or pav:importedBy), unless the software actually authored the content itself; for instance an artificial intelligence algorithm which authored a piece of music or a machine learning algorithm that authored a classification of a tumor sample. The date of authoring can be expressed using pav:authoredOn - note however in the case of multiple authors that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy.

Created by
type: ObjectProperty
sub property of: ObsoleteProperty
property chain axiom: output of
property chain axiom: has_agent
editor note: SEPIO creates this relation distinct from existing PAV and PROV relations (e.g. pcav:createdBy), which are too specific about whether a relation refers to the agent who created the abstract information content, vs who serialized and documented in concrete form.
database_cross_reference: http://purl.org/dc/terms/creator
comment: An agent primary responsible for making the digital artifact or resource representation. This property is distinct from forming the content, which is indicated with pav:contributedBy or its subproperties; pav:authoredBy, which identifies who authored the knowledge expressed by this resource; and pav:curatedBy, which identifies who curated the knowledge into its current form. pav:createdBy is more specific than its superproperty dct:creator - which might or might not be interpreted to cover this creator. For instance, the author wrote 'this species has bigger wings than normal' in his log book. The curator, going through the log book and identifying important knowledge, formalizes this as 'locus perculus has wingspan > 0.5m'. The creator enters this knowledge as a digital resource in the knowledge system, thus creating the digital artifact (say as JSON, RDF, XML or HTML). A different example is a news article. pav:authoredBy indicates the journalist who wrote the article. pav:contributedBy can indicate the artist who added an illustration. pav:curatedBy can indicate the editor who made the article conform to the news paper's style. pav:createdBy can indicate who put the article on the web site. The software tool used by the creator to make the digital resource (say Protege, Wordpress or OpenOffice) can be indicated with pav:createdWith. The date the digital resource was created can be indicated with pav:createdOn. The location the agent was at when creating the digital resource can be made using pav:createdAt.

Curated by
type: ObjectProperty
sub property of: ObsoleteProperty
definition: Specifies an agent specialist responsible for shaping the expression in an appropriate format. Often the primary agent responsible for ensuring the quality of the representation. The curator may be different from the author (pav:authoredBy) and creator of the digital resource (pav:createdBy). The curator may in some cases be a software agent, for instance text mining software which adds hyperlinks for recognized genome names. The date of curating can be expressed using pav:curatedOn - note however in the case of multiple curators that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy

Derived from
type: ObjectProperty
sub property of: source
comment: Derived from a different resource. Derivation conserns itself with derived knowledge. If this resource has the same content as the other resource, but has simply been transcribed to fit a different model (like XML -> RDF or SQL -> CVS), use pav:importedFrom. If a resource was simply retrieved, use pav:retrievedFrom. If the content has however been further refined or modified, pav:derivedFrom should be used. Details about who performed the derivation (e.g. who did the refining or modifications) may be indicated with pav:contributedBy and its subproperties.

Imported from
type: ObjectProperty
sub property of: source
definition: The original source of imported information. Import means that the content has been preserved, but transcribed somehow, for instance to fit a different representation model by converting formats. Examples of import are when the original was JSON and the current resource is RDF, or where the original was an document scan, and this resource is the plain text found through OCR. The imported resource does not have to be complete, but should be consistent with the knowledge conveyed by the original resource. If additional knowledge has been contributed, pav:derivedFrom would be more appropriate. If the resource has been copied verbatim from the original representation (e.g. downloaded), use pav:retrievedFrom. To indicate which agent(s) performed the import, use pav:importedBy. Use pav:importedOn to indicate when it happened.

Retrieved from
type: ObjectProperty
sub property of: source
comment: The URI where a resource has been retrieved from. The retrieving agent is usually a software entity, which has done the retrieval from the original source without performing any transcription. Retrieval indicates that this resource has the same representation as the original resource. If the resource has been somewhat transformed, use pav:importedFrom instead. The time of the retrieval should be indicated using pav:retrievedOn. The agent may be indicated with pav:retrievedBy.

Source accessed at
type: ObjectProperty
sub property of: ObsoleteProperty
comment: The resource is related to a given source which was accessed or consulted (but not retrieved, imported or derived from). This access can be detailed with pav:sourceAccessedBy and pav:sourceAccessedOn. For instance, a curator (pav:curatedBy) might have consulted figures in a published paper to confirm that a dataset was correctly pav:importedFrom the paper's supplementary CSV file. Another example: I can access the page for tomorrow weather in Boston (http://www.weather.com/weather/tomorrow/Boston+MA+02143) and I can blog ‘tomorrow is going to be nice’. The source does not make any claims about the nice weather, that is my interpretation; therefore the blog post has pav:sourceAccessedAt the weather page.

has_url
type: DatatypeProperty
definition: Web address of the resource

obsolete_date_created
type: DatatypeProperty
editor note: SEPIO creates a relation separate from existing PAV and PROV relations (e.g. pav:createdOn) which are too specific about whether a relation refers to the date on which the abstract information content was created, or when it was serialized and documented as a concrete digital artifact or resource with a particular format.
alternative label: created_on
consider: Consider: 1. http://purl.org/dc/terms/created 2. http://purl.org/pav/createdOn ! Created on Def: The date of creation of the resource representation. The agents responsible can be indicated with pav:createdBy. This property is normally used in a functional way, indicating the time of creation, although PAV does not formally restrict this. pav:lastUpdateOn can be used to indicate minor updates that did not affect the creating date. 3. prov:generatedAtTime: The time at which an entity was completely created and is available for use.
deprecated: true

date_modified
type: DatatypeProperty
sub property of: date
domain: continuant
definition: The date that a particular resource or artifact was last modified or updated.
alternative label: date_last_updated
consider: http://purl.org/dc/terms/modified ! Date Modified Definition: Date on which the resource was changed.
comment: Examples of modification include adding or removing content to/from a document, updating information in a data record, fixing errors in a manuscript, etc. The important thing is that the modification retains the identity of the artifact.

date_evaluated
type: DatatypeProperty
sub property of: date
domain: continuant
definition: The date that a particular resource or artifact was last evaluated - typically to assess its quality, completeness, accuracy, conformance, etc.
comment: Evaluating an artifact does not involve its modification - however the suggestion of alterations can be a separate outcome of an evaluation. If the artifact is modified by the agent during or subsequent to the evaluation, this date can be captured using the date_modified property.

date_submitted
type: DatatypeProperty
sub property of: date
domain: continuant
definition: The date that a particular resource or artifact was formally submitted to be reviewed and/or included in some larger resource (e.g. database, registry, collection, etc.).
consider: http://purl.org/dc/terms/dateSubmitted

start_date
type: DatatypeProperty
sub property of: activity_date
domain: process
editor note: Consider: http://www.w3.org/ns/prov#startedAtTime

date_created_before
type: DatatypeProperty
sub property of: ExploratoryDataProperty

has_textual_part
type: DatatypeProperty
comment: Relation between a report and a string of text that it contains

date_authored
type: DatatypeProperty
sub property of: date
definition: A relation holding between an information content entity and the date on which the information it expresses was initially generated.
editor note: Consider http://purl.org/pav/authoredOn

activity_date
type: DatatypeProperty
domain: process
range: dateTime
alternative label: occurredAtTime
alternative label: process_date
alternative label: time_of_activity

end_date
type: DatatypeProperty
sub property of: activity_date
editor note: Consider: http://www.w3.org/ns/prov#endedAtTime

obsolete_date_curated
type: DatatypeProperty
editor note: Consider: http://purl.org/pav/curatedOn Definition: The date this resource was curated. pav:curatedBy gives the agent(s) that performed the curation. This property is normally used in a functional way, indicating the last curation date, although PAV does not formally restrict this. The value is of type xsd:dateTime, for instance "2013-03-26T14:49:00+01:00"^^xsd:dateTime. The timezone information (Z for UTC, +01:00 for UTC+1, etc) SHOULD be included unless unknown. If the time (or parts of time) is unknown, use 00:00:00Z. If the day/month is unknown, use 01-01, for instance, if we only know September 1983, then use "1983-09-01T00:00:00Z"^^xsd:dateTime.
deprecated: true

date_updated
type: DatatypeProperty
sub property of: date
editor note: Consider: http://purl.org/pav/lastUpdateOn

date_validated
type: DatatypeProperty
sub property of: date
domain: assertion
definition: The date that a particular resource or digital artifact was formally validated as meeting some standard for quality, completeness, relevance, etc..

has_confidence_score
type: DatatypeProperty
domain: information
definition: A quantitative value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about.
editor note: This property has a similar intent as assertion_confidence_level, but used for quantitative numerical values.
comment: The 'confidence score' property does not only include statistical measures such as p-values that explicitly indicate a level of confidence. It also includes any quantitative score against which a threshold for making an assertion is defined - where the distance of this score from this threshold can be interpreted as an indicator of how much confidence we might have that the asserted conclusion is true. For example, many silico prediction tools such as SIFT interrogate biological sequence data to calculate a score that reflects the likelihood that a particular sequence variant negatively impacts gene product function. A variant is interpreted to be 'Tolerated', 'Damaging', or 'Deleterious' based on how its score compares against pre-defined thresholds. Here, we may have less confidence that a variant with a score just above the 'Damaging' threshold is truly damaging, versus a variant whose score is well above the threshold.

statement quantifier
type: DatatypeProperty
definition: A relation used to link a statement to some quantitative measure about the statement itself (e.g. a confidence score)

statement qualifier
type: DatatypeProperty
definition: A relation used to qualify the meaning of a statement.
comment: Most commonly used with a "NOT" value to negate a statement - i.e. indicate that the claim implied by its strucuted representation is not true. For example, the negation qualifier on the following OBAN-style association would make the claim that BRCA2 is NOT linked to the phenotype 'abnormal lymphocyte count': <:assertion1> a OBAN:association; OBAN:association_has_object HP_0040088 (abnormal lymphocyte count); OBAN:association_has_predicate RO:0002200 (has_phenotype); OBAN:association_has_subject HGNC:1101 (BRCA2); SEPIO:0000346(quallifier) "NOT".

date_created_after
type: DatatypeProperty
sub property of: ExploratoryDataProperty

probabilistic quantifier
type: DatatypeProperty
sub property of: has_confidence_score

evidence_line_strength_score
type: DatatypeProperty
domain: evidence line
definition: A numerical value that quantifies the strength of evidence provided by a line of evidence. This is a counterpart to the evidence_line_strength object property - for use when the strength of evidence is captured using a quantitiative score/measure.

activity_location
type: DatatypeProperty
alternative label: occurred_in
alternative label: process_location

ExploratoryDataProperty
type: DatatypeProperty

ObsoleteDataProperty
type: DatatypeProperty
deprecated: true

date_created
type: DatatypeProperty
sub property of: date
definition: Date that a particular representation/manifestation of an information content entity was created - e.g. as a web resource or digital artifact. To describe the date that the information content carried by a digital artifact or resource as generated, use the 'date_authored' property.

has_value
type: DatatypeProperty
consider: http://www.w3.org/ns/prov#value 'This property serves the same purpose as rdf:value, but has been reintroduced to avoid some of the definitional ambiguity in the RDF specification (specifically, 'may be used in describing structured values'). The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue'

date
type: DatatypeProperty
domain: continuant
range: dateTime
definition: A point or period of time associated with an event in the lifecycle of an information entity or resource.
editor note: Consider: http://purl.org/pav/contributedOn

identifier
type: DatatypeProperty

digital object identifier (doi)
type: DatatypeProperty
sub property of: identifier
alternative label: doi

version
type: DatatypeProperty
comment: The version number of a resource. This is a freetext string, typical values are "1.5" or "21". The URI identifying the previous version can be provided using prov:previousVersion. This property is normally used in a functional way, although PAV does not formally restrict this.

name
type: DatatypeProperty
definition: A name for some thing.

entity
type: Class
BFO_0000179: entity
BFO_0000180: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
IAO_0000600: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: IAO_0000600
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
definition: 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.
editor note: 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
editor note: 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
IAO_0000600: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0000602: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0000602: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO_0000179: occurrent
BFO_0000180: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
IAO_0000600: 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])
IAO_0000601: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0000601: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0000602: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0000602: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: characteristic
disjoint with: generically dependent continuant
BFO_0000179: ic
BFO_0000180: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0000602: (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]
IAO_0000602: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  all values from: process
BFO_0000179: process
BFO_0000180: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
IAO_0000602: (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]

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable
disjoint with: role

realizable
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: realizable
disjoint with: quality
BFO_0000179: realizable
BFO_0000180: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
IAO_0000600: 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])
IAO_0000601: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0000602: (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]
IAO_0000602: (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]
label: realizable entity

Axiom
annotated source: realizable
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable
annotated property: IAO_0000601
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

quality
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: quality
BFO_0000179: quality
BFO_0000180: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
IAO_0000600: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0000602: (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]

Axiom
annotated source: quality
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000601
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

characteristic
type: Class
subclass of: continuant
subclass of: Restriction
subclass of: Restriction
  on property: part of
  all values from: characteristic
subclass of: Restriction
  on property: has part
  all values from: characteristic
disjoint with: generically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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.
definition: 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])
editor note: 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.
IAO_0000602: (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]
label: specifically dependent continuant

Axiom
annotated source: characteristic
annotated property: subClassOf
annotated target: Restriction
comment: We should name the inverse in COB and avoid the confusing inverse(..) construct

Axiom
annotated source: characteristic
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: characteristic
annotated property: editor note
annotated target: 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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: characteristic
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable
BFO_0000179: role
BFO_0000180: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
IAO_0000600: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
IAO_0000602: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: IAO_0000600
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: IAO_0000602
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: generically dependent continuant
BFO_0000179: gdc
BFO_0000180: GenericallyDependentContinuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: 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])
IAO_0000602: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: IAO_0000602
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
BFO_0000179: material
BFO_0000180: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
IAO_0000600: 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])
IAO_0000601: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0000601: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0000602: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0000602: (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]
IAO_0000602: (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]

Axiom
annotated source: material entity
annotated property: IAO_0000600
annotated target: 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

history
type: Class
subclass of: process
BFO_0000179: history
BFO_0000180: History
IAO_0000600: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
comment: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: IAO_0000600
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/138-001

anatomical entity
type: Class
subclass of: independent continuant
definition: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
id: CARO:0000000
comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
database_cross_reference: CAROC:Brownsville2014

action specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: action specification

planned process
type: Class
subclass of: process
subclass of: Restriction
  on property: intended to realize
  some values from: plan
subclass of: Restriction
  on property: realizes
  some values from: agent role
definition: A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.

evaluant role
type: Class
subclass of: role
COB based on: OBI:0000067

information representation
type: Class
equivalent class: Restriction
  on property: concretizes
  some values from: information
subclass of: characteristic
subclass of: Restriction
  on property: concretizes
  some values from: information
COB based on: http://purl.obolibrary.org/obo/IAO_0000015
comment: Pier 'representational entity'
comment: This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc

measurement datum
type: Class
subclass of: data item
COB based on: measurement datum

physical information carrier
type: Class
equivalent class: Restriction
  on property: has characteristic
  some values from: Restriction
    on property: concretizes
    some values from: information
subclass of: material entity
subclass of: Restriction
  on property: has characteristic
  some values from: Restriction
    on property: concretizes
    some values from: information

database
type: Class
subclass of: information
definition: A database is an organized collection of data, today typically in digital form.
database_cross_reference: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Database

molecular_function
type: Class
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
has exact synonym: molecular function
id: GO:0003674
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
database_cross_reference: GOC:pdt

biological_process
type: Class
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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.
created by: jl
creation date: 2012-09-19T15:05:24Z
database_cross_reference: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has related synonym: single organism process
has related synonym: single-organism process
id: GO:0008150
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use 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.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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.
database_cross_reference: GOC:pdt

kinase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: Reactome:R-HSA-6788855
database_cross_reference: Reactome:R-HSA-6788867
has exact synonym: phosphokinase activity
id: GO:0016301
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788867

objective specification
type: Class
subclass of: directive information entity

journal article
type: Class
subclass of: publication
editor preferred term: journal article
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
has curation status: metadata complete
definition: a report that is published in a journal
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000159
definition source: group:OBI
imported from: obi.owl

data item
type: Class
subclass of: information
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative label: data
imported from: obi.owl

information
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
subclass of: Restriction
  on property: created_by
  some values from: Agent
subclass of: Restriction
  on property:
    inverse of: concretizes
  some values from: information representation
subclass of: Restriction
  on property: date
  qualified cardinality: 1
  on data range: dateTime
editor preferred term: information content entity
example of usage: - Data Items: A '548.5 mg/dl' measurement of blood glucose in mutant mice. - Protocols: A blood glucose assay protocol that describes how the measurement was taken. - Calculations: A 1.3951e-24 p-value statistic indicating a significant increase relative to wild-type mice. - Assertions: An assertion stating that "Lpr1 leptin receptor mutations can lead to diabetes". - Publications: A journal article that publishes this assertion. - Figure/Tables: A figure or table from this article that present data supporting it. - Software/Algorithms: A text-mining algorithm that mines the literature to identify and extract the assertion. - Databases: The MGI (Mouse Genome Informatics) database that stores the assertion as a structured gene-disease annotation.
definition: A generically dependent continuant that is about some thing.
comment: ICEs are abstract entities that convey information about things in the world. ICEs represent the information encoded in physical artifacts such as photographs, books, or digital storage medium (as opposed to the physical medium itself). A particular ICE can be encoded simultaneously in many physical or digital mediums and formats. For example, only one instance of the first edition of "War and Peace" exists as an ICE, representing information conveyed in this work. But many instances of "War and Peace" exist at the level of their physical concretizations in printed books or digital devices.
comment: Pier: 'data, information or knowledge'. OR 'representation
label: information content entity

directive information entity
type: Class
subclass of: information

algorithm
type: Class
subclass of: plan specification
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred term: curation status specification
has curation status: pending final vetting
definition: 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.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

report
type: Class
subclass of: document
editor preferred term: report
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
has curation status: pending final vetting
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term editor: PERSON:Chris Stoeckert
definition source: GROUP: OBI
definition source: OBI_0000099
imported from: obi.owl

data set
type: Class
subclass of: information
editor preferred term: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
imported from: obi.owl

data about an ontology part
type: Class
subclass of: data item
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: action specification
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
sepio_preferred_label: method

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

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
  one of: out of scope
subclass of: data about an ontology part
editor preferred term: obsolescence reason specification
has curation status: pending final vetting
definition: 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.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

table
type: Class
subclass of: information
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
comment: MHB: A figure depicting a tabular representation of data, typically created to highlight a particular aspect or view of a larger data set. They may include derived statistical measures summarizing the primary data. The concept described here represents a tables generated for purposes of documentation or publication of results, as opposed to database tables defined as structures for primary storage of source data in some information system.

figure
type: Class
subclass of: information
editor preferred term: figure
example of usage: Any picture, diagram or table
has curation status: metadata complete
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter
imported from: obi.owl
comment: MHB: A figure is a graphical presentation of information created as a vehicle to share with an audience, e.g. in a publication or report. Figures may include raw and/or summarized/derived data, or diagrammatic abstractions of results, conclusions, or hypotheses. Figures often present data in a form that is summarized or abstracted for human consumption, using graphical conventions that may sacrifice detail of underlying data for ease or understanding.

document
type: Class
subclass of: information
editor preferred term: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: metadata complete
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

publication
type: Class
subclass of: document
editor preferred term: publication
example of usage: A journal article or book
has curation status: metadata complete
definition: A document that has been accepted by a publisher
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

patent
type: Class
subclass of: document
editor preferred term: patent
example of usage: US Patent 6,449,603
has curation status: metadata complete
definition: A document that has been accepted by a patent authority
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
editor preferred term: denotator type
example of usage: 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.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

completely executed planned process
type: Class
subclass of: planned process
subclass of: Activity
subclass of: Restriction
  on property: realizes
  some values from: plan
subclass of: Restriction
  on property: has_agent
  some values from: Agent
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: '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.)
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: 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)
imported from: obi.owl
label: planned process

investigation
type: Class
subclass of: research activity
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).

assay
type: Class
subclass of: research activity
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has characteristic
      some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction

p-value
type: Class
subclass of: statistic
editor preferred term: p-value
has curation status: organizational term
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
editor note: May be outside the scope of OBI long term, is needed so is retained
term editor: PERSON:Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/P-value
imported from: obi.owl

standard error
type: Class
subclass of: statistic
editor preferred term: standard error
has curation status: pending final vetting
definition: A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
term editor: person:Chris Stoeckert
definition source: group:OBI
curator note: see P-Value
imported from: obi.owl

plan
type: Class
subclass of: realizable
subclass of: information representation
subclass of: Restriction
  on property: concretizes
  some values from: plan specification
subclass of: Restriction
  on property:
    inverse of: realizes
  all values from: planned process

protocol
type: Class
subclass of: plan specification
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
sepio_preferred_label: experimental protocol

drawing a conclusion based on data
type: Class
subclass of: assertion process
editor preferred term: drawing a conclusion based on data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: ready for release
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters
imported from: obi.owl

binding assay
type: Class
subclass of: assay
editor preferred term: binding assay
example of usage: Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
has curation status: metadata complete
definition: An assay with the objective to characterize the disposition of two or more material entities to form a complex.
term editor: PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
definition source: PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
imported from: obi.owl

protein localization assay
type: Class
subclass of: assay
editor preferred term: protein localization assay
has curation status: metadata complete
definition: An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied.
term editor: Rebecca Tauber
definition source: OBI development call
imported from: obi.owl

quality
type: Class
subclass of: characteristic
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
database_cross_reference: PATOC:GVG

proposition
type: Class
subclass of: entity
example of usage: The proposition that BRCA1:2685T>A causes familial breast cancer.
definition: An abstract entity representing the sharable meaning of what is expressed in a particular assertion.
editor note: In the SEPIO model, an assertion is akin to an act in speech or text that expresses beleif in the truth of a proposition. It is the proposition that represents the semantic content of a claim, and bears truth value. Mappings to terms from related models: 1. http://purl.org/see/rdo#proposition A SEPIO proposition is equivalent to a 'proposition' from the Semantic EvidencE framework. "The class rdo:proposition represents propositions i.e. the sharable objects of propositional attitudes like belief or desire and the bearers of truth values. As truth bearers they are either true or false. They are taken to represent the semantic content of sentences or larger lexical entities formulated in some natural or artificial language.") 2. http://purl.org/mp/Holotype The notion of a holotype from the Micropublications model is related to a SPEIO proposition - in that it represents a statement that is selcted to all other statements expressing the same meaning. 3. http://purl.org/oban/association An OBAN proposition is a more type of proposition, that is structured/expressed according to the specifications laid out in the OBAN ontology.
definition source: http://plato.stanford.edu/entries/propositions
comment: The notion of a proposition, and its relationship to an assertion, derives from the domain of logic and philosophy [12]. Propositions are abstract entities that, like numbers, are independent of space and time. They represent only the meaning that is expressed in a particular agent’s assertion, and are ‘sharable’ in that the same proposition can be expressed in many different assertions. Propositions are primary bearers of truth value, in that they are true or false. From http://plato.stanford.edu/entries/propositions/: "Propositions are the sharable objects of the attitudes and the primary bearers of truth and falsity. This stipulation rules out certain candidates for propositions, including thought- and utterance-tokens, which presumably are not sharable, and concrete events or facts, which presumably cannot be false."

assertion
type: Class
subclass of: statement
subclass of: Restriction
  on property: output of
  some values from: assertion process
subclass of: Restriction
  on property: has_evidence_line
  some values from: evidence line
subclass of: Restriction
  on property: asserts_proposition
  some values from: proposition
example of usage: The following are three seperate assertion instances, that assert the same proposition (that BRCA1:2685T>A causes familial breast cancer) 1. Counsyl's assertion on October 5, 2009 that BRCA1:2685T>A causes familial breast cancer. 2. The ENIGMA consortium’s assertion on September 18, 2010 that BRCA1:2685T>A causes familial breast cancer. 3. A later assertion by the ENIGMA consortium on May 9, 2013, based on new evidence, that BRCA1:2685T>A causes familial breast cancer.
definition: A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence.
editor note: SEPIO distinguishes two high-level subtypes of statements: 1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from the act of reporting or summarizing these direct observations, calculations, or measurements. 2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and the act of interpretating as evidence.
alternative label: claim
alternative label: evidence-based assertion
alternative label: propostional assertion
definition source: Derived from http://purl.org/see/rdo#assertion
usage note: The identity of a particular assertion is dependent upon (1) what it claims to be true (its semantic content, aka its ‘proposition’), (2) the agent asserting it, and (3) the occasion on which the assertion is made. Many agents can make assertions expressing belief in the same proposition (e.g. ENIGMA’s assertion that that BRCA1:2685T>A causes familial breast cancer is a separate instance than Counsyl’s assertion of the same underlying proposition). Likewise, a single agent can make more than one assertion of belief in the same proposition on different occasions (e.g. ENIGMA may make a separate assertion of the same proposition that BRCA1:2685T>A causes familial breast cancer at a later date, based on additional evidence).
comment: Assertions as defined in SEPIO are the result of some logical inference made based on the interpretation of evidence. They put forth a proposition that may or may not be true - the validity of which ultimately rests on the quantity, quality, diversity, and concordance of evidence supporting it. Statements directly reporting study results or observations are not considered assertions in this sense, as they merely report what was observed or recorded, but do not rely on a leap of logical inference (see 'study finding').

evidence line
type: Class
subclass of: information
subclass of: Restriction
  on property: has_evidence_item
  some values from: evidence item
subclass of: Restriction
  on property: evidence_line_strength
  some values from: evidence strength
subclass of: Restriction
  on property: evidence_direction
  some values from: evidence direction
example of usage: An example of an evidence line would be the argument that a finding such as "Lepr1 KO mice exhibit lower blood glucose levels than matched WT controls" makes in support of the proposition that "Lepr1 gene is involved in diabetes". The Evidence Items supporting this line of evidence could include experimental data from a study exploring blood glucose levels in Lepr1 KO mice, such as a 548.5 mg/dl measurement of blood glucose in a Lepr<tm1b/tm1b> mutant mouse, or a 1.3951e-24 p-value indicating this measure to be significantly different from wild-type mice. Here, the finding and its supporting data exist independently of their use as evidence. An evidence line based on this finding comes into existence only when an agent interprets this finding as providing a meaningful argument for a particular proposition, in the act of making an assertion. (This example is based on data from the IMPC record here: http://bit.ly/2t4J1TI)
definition: An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence.
alternative label: evidence-based argument
comment: An evidence line is created through the interpretation of one or more pieces of information that collectively support a meaningful argument for or against a proposition. To qualify as an Evidence Line, this argument must be independently significant as evidence - i.e. it must be capable of affecting the probability of accepting the target proposition as true. This does not mean, however, that it is independently sufficient to establish belief in the proposition, as additional evidence lines may be required to ultimately accept the proposition as true. For example, in the ACMG framework for variant interpretations establishes "absence in population databases" as a type of evidence line that can argue for the pathogenicty of a particular variant. But this argument alone is not considered sufficient to establish a variant's pathogencity, as the other types of evidence are additionally required to establish the truth of this Proposition (e.g. a line of evidence demonstrating the variant to have a deleterious effect on protein function, or showing it to segregate with disease features in a family tree).

assertion process
type: Class
subclass of: completely executed planned process
subclass of: Restriction
  on property: has input
  some values from: evidence line
subclass of: Restriction
  on property: has output
  some values from: assertion
definition: An act of interpreting evidence to make an assertion of belief that a particular proposition is true
editor note: Mappings to terms from related models: Likely equivalent to http://purl.org/see/rdo#act_of_inference. May be equivalent to http://purl.obolibrary.org/obo/ECO_0000217 ! assertion method.
alternative label: act of assertion
comment: An assertion process includes the processes of interpreting data and evaluating it as evidence for the validity of a proposition. They are affected by a particular agents on a particular occasions, and can be specified by assertion methods or guidelines.

research activity
type: Class
subclass of: completely executed planned process
subclass of: Restriction
  on property: has output
  some values from: information
definition: A planned process executed in the performance of scientific research wherein systematic investigations are performed to establish facts and reach new conclusions about phenomena in the world.
comment: Data generation process are typically experimental studies or observations, but can include any process generating information used to evaluate a claim. This is an organizational class that groups more specific types of such processes that are most commonly used in generating data used as evidence to support claims. These processes produce informational artifacts such as measured data values, derived statistical calculations and confidence measures, or statements representing summaries or conclusions drawn from such data.

assertion method
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: specified_creation_of
  some values from: assertion
definition: A directive information entity that specifies an algorithm or heuristics for evaluating evidence in the process of making an assertion.
editor note: SEPIO implements several OWL individuals representing instances of commonly applied assertion methods, primarily those used in pathogenic variant classification such as the ACMG variant classification criteria.
comment: Assertion methods can be informal guidlines or heuristics that support manual evaluation of evidence, e.g. the ACMG Variant Classification Guidelines. Assertion methods can also be formally encoded as algorithms that allow computational or statistical analysis of data as evidence in support of making an assertion - e.g. multifactorial analysis algorithms that operate on specified data to generate a quantitative score indicating the validity of a particular proposition.

agent role
type: Class
subclass of: role
definition: A role borne by a person, group, organization, or information processing entity (e.g. software, algorithms) in virtue of its active participation in a process leading to some outcome (e.g the generation, modification, or provision of some entity).
editor note: A role realized by a participant in a process such that the participant causes the process.
alternative label: agent role
consider: http://purl.org/see/rdo#agent_role
comment: In the context of evidence and proveannce, agents are persons, groups, organizations, or software that are responsible for making assertions or generating the evidence and data that support them.
label: contributor role

resource role
type: Class
subclass of: role
definition: A role inhering in any material or information artifact that is used by an agent as specified input into a planned process.
comment: In the context of evidence and provenance for scientific claims, resources are entities that are used by agents to facilitate processes aimed at the generation of assertions or the evidence and data that support them. Examples include instruments, reagents, model systems, software, and protocols.

obsolete_manual assertion process
type: Class
subclass of: ObsoleteClass
editor note: Mappings to related terms: 1. http://purl.obolibrary.org/obo/ECO_0000218 ! manual assertion ECO Definition/Comment: A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
deprecated: true

obsolete_automated assertion process
type: Class
subclass of: ObsoleteClass
definition: An assertion process performed through algorithmic analysis by a computational agent, independent of human review.
editor note: Mappings to related terms: 1. http://purl.obolibrary.org/obo/ECO_0000203 ! automatic assertion ECO Definition/Comment: An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
comment: Ultimately even automated assertions require a human agent to set a confidence threshhold that determines when a computational output (e.g. a sequence similarity p-value) justifies an assesrtion being made.
deprecated: true

provenance
type: Class
subclass of: history
definition: The process history leading to the creation and current condition of an artifact.
editor note: Consider whether it is appropriate to place this under the BFO:history class, which may apply only to histories of "material entities or sites". And consider if we want/need to define this class at all - as it is not used to model data - only as a means to record what SEPIO considers provenance to be, and how it is different from evidence.
comment: For scientific assertions/claims, this is the process history leading to the asseertion being made, including processes through which evidence is evaluated, and processes through which information used as evidence is created. The transitive nature of provenance means that the provenance history of informtion used as supporting data becomes provenance for an assertion that uses this information as evidence. Provenance metadata describes these processes, including accounts of who conducted these processes, what entities participated in them, and when/where they occurred.

primary research study
type: Class
subclass of: research study
definition: A study that involves primary research of subjects or specimens in a natural, cliniclal, or laboratory setting.

clinical study
type: Class
subclass of: primary research study
definition: Formal clinical study performed using cohorts of multiple patients

interventional clinical study
type: Class
subclass of: clinical study
consider: http://purl.org/net/OCRe/research.owl#Interventional_study

observational clinical study
type: Class
subclass of: clinical study
consider: http://purl.org/net/OCRe/research.owl#Observational_study

case-control clinical study
type: Class
subclass of: observational clinical study
consider: http://purl.org/net/OCRe/research.owl#Case_control_study

experimental model study
type: Class
subclass of: primary research study
definition: A research dtudy perfomred using an experimental model system such as a cell line, or model organism.

in vitro study
type: Class
subclass of: experimental model study

in vivo study
type: Class
subclass of: experimental model study

cell-based in vivo study
type: Class
subclass of: in vivo study

tissue-based in vivo study
type: Class
subclass of: in vivo study

organism-based in vivo study
type: Class
subclass of: in vivo study
alternative label: whole organism in vivo study

secondary research study
type: Class
subclass of: research study
definition: A study based only on analysis of existing data, as found in artifacts such as community/curated databases, raw datasets, or publications.
alternative label: data-driven study

literature-based study
type: Class
subclass of: secondary research study
definition: A curation-based study that uses only one or more literature publication as input data source.
editor note: Based on ClinVar 'literature only' collection method: "for submissions that provide the interpretation of a variant from one or more publications. No additional curation has been performed by the submitter; the interpretation is from the publication(s) only."

curation-based study
type: Class
subclass of: secondary research study
editor note: Based on Clinvar 'curation' collection method: "for variants that were not directly observed by the submitter, but were interpreted by curation of multiple sources, including clinical testing laboratory reports, publications, private case data, and public databases."

reference population data study
type: Class
subclass of: secondary research study
definition: A study based on analysis of data gathered from baseline studies of a population group of apparently unaffected individuals to assess allele frequencies
definition source: ClinVar

research study
type: Class
subclass of: research activity
definition: A planned process that executes some study design or protocol to generate scientific data that is interpreted to test or generate a hypothesis.
SEPIO_editor_note: Explore the classification of study types here as a possibility to implement in SEPIO. https://mcw.libguides.com/evidencebased/studies Useful because these map to the strength of the evidence each might provide.
comment: A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study.
comment: A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of related experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study. 'Study' here is broadly considered to include any defined activity performed to address a scientific question or generate a scientific hypothesis. It covers scientific inquiry at different scales of complexity, from a single assay, experiment or observation, to a complex research investigation addressing a broader scientific question. Studies can be based on a broad range of methods, including in silico algorithms, in vitro or in vivo experimentation on model systems, clinical studies on human subjects, or curation and analysis of existing knowledge, e.g. from publications, datasets, or knowledegbases, to derive novel insight.

obsolete_study group
type: Class
subclass of: ObsoleteClass
definition: A group of individuals (organisms, specimens, samples) that are subjects in an observational or intervention study, and whose members represent experimental replicates as defined in a study design by the same independent variable specifications (i.e. subjected to the same selction criteria or set of experimental interventions).
editor note: Consider: STATO_0000193, OBI_0000174
deprecated: true

curation
type: Class
subclass of: research activity
definition: A planned process in which existing data is collected, organized, and improved in preparation for subsequent use.

evidence strength
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: evidence line
definition: A data item that quantifies the degree of support an agent believes an evidence line to provide for a particular proposition.
SEPIO_editor_note: Consider also framing as categorical measurement values?: A categorical measurement reflecting an agent's cognitive quantification of the degree of support (s)he believes an evidence line to provide for a particular proposition.
comment: The strength of a line of evidence typically depends on the *type* and *quality* of the study(ies) that generate its supporting evidence items. 1. Type of Study: In a particular domain of research, certain types of studies are commonly held to produce data that is more meaningful and reliable than others, as evidence for a particular type of assertion. These more reliable studies tend to draw on experimental systems that more accurately replicate the natural phenomenon being studied, and experimental designs that reduce confounding variables and biases. For example, in vivo studies of gene function provide stronger evidence than in vitro systems that may not replicate all aspects of the biology of a living system, and randomized controlled clinical trials are held to be more reliable than retrospective or case control studies that are more susceptible to confounding factors. 2. Quality of Study: A given study can be performed to varying degrees of rigor and comprehensiveness, irrespective of the type of study it represents. This is another important factor in assessing the overall strength of evidence it may produce. Higher quality studies will have carefully defined controls, and be replicated numerous times to ensure reproducibility. Other factors that are often used as secondary indicators of the quality of research data include the quality of the journal in which it is published, and the reputation of the lab or institution performing the study. In SEPIO, the notion of evidence quality is captured in an attribute separate from the notion of evidence strength. And the notion of study type can be represented in the type assigned to a study instance, or the evidence code used to type an evidence line (which are often based on the type of study that produced the evidence data). Evidence strength typically relies on assessment of one or both of these more fundamental attributes of evidence.

patient case study
type: Class
subclass of: primary research study
definition: A study that documents observations or findings from a single patent.
alternative label: case reporting

evidence role
type: Class
subclass of: role

evidence item
type: Class
equivalent class: Class
  intersection of: information
  intersection of: Restriction
    on property: evidence_item_for
    some values from: evidence line
subclass of: information
subclass of: Restriction
  on property: has_role
  some values from: evidence role
subclass of: Restriction
  on property: evidence_item_for
  some values from: evidence line
example of usage: - the raw count data from a case-control study comparing the frequency of an allele in two cohorts or populations - the calculated p-value as a measure of statistical significance of the difference identified in the study - a published figure documenting these data - an author statement summarizing the outcomes of the study (i.e. a 'study finding') - a broader conclusion inferred from interpretation of the data reported in a study (i.e. an evidence-based 'assertion')
definition: An information content entity that is used as evidence to evaluate the validity of a target assertion or proposition.
alternative label: evidence
alternative label: evidence information
comment: 'Evidence Item' is a broad term covering any information interpreted as evidence in the act of making an assertion. Classes representing different types of evidence items are imported here from ontologies such as OBI, IAO, and STATO, and include: - measured data values - derived data values such as statistical calculations and confidence measures - figures presenting or describing such data - author statements representing summaries of or conclusions drawn from such data - established facts in a field of research Note that publications and reports are considered separately from 'evidence items', as a they *contain* information (data values, figures author statements) that can be used as evidence. But on its own a publication or report is merely a proxy for this information.

creator role
type: Class
subclass of: agent role

assessor role
type: Class
subclass of: agent role

approver role
type: Class
subclass of: assessor role
alternative label: validator role

curator role
type: Class
subclass of: agent role

obsolete software agent
type: Class
subclass of: ObsoleteClass
term replaced by: SoftwareAgent
deprecated: true

contribution
type: Class
subclass of: completely executed planned process
subclass of: Restriction
  on property: realizes
  some values from: agent role
subclass of: Restriction
  on property: has_agent
  qualified cardinality: 1
  on class: Agent
definition: The actions taken by a particular agent in the creation, modification, assessment, or deprecation of an artifact.
editor note: This concept is similar in meaning and usage to PROV:Attribution. Consider aligning or adopting.
comment: Contribution instances organize information about who, when, where, how (e.g. what roles were played), and on whose behalf these actions were performed. The scope of a Contribution instance includes only the actions of a single agent in contributing to a particular artifact - which may be performed in one continuous effort, or multiple discrete sessions of work. The contributing agent can be a single individual, or an organization of multiple individuals acting together.

study finding
type: Class
subclass of: statement
subclass of: Restriction
  on property: output of
  some values from: research study
example of usage: Findings statements tend to take the form of "We observed that . . . ", or "Assay X revelaned that . . . ", or "X was determined to be Y in a study of . . . ". For example: "Smith et. al observed that a positive response to imatinib treatment was two-fold higher in a cohort of leukemia patients bearing Bcr-Abl fusions compared to those lacking this driver mutaiton." A statement summarizing the outcome of a sequencing analysis: "DNA sequencing data from patient X revealed an A->T mutation at position 2143 in gene Y". A statement summarizing the outcome of a variant population frequency study: "The frequency of variant X was determined to be 0.00015 in a cohort of non-finnish european subjects described in the ExAC dataset."
definition: A statement describing the immediate results of a research study, describing what was directly observed, measured, or derived through mathematical calculation.
editor note: In SEPIO, a high-level distinction is made between statements that are 'findings' vs 'assertions'. Findings are statements that report/summarize what was directly observed or calculated in a study, and are about only the immediate participants in the experiment or study. As such, findings involve no interpretation or inference from the data to draw broader conclusions. Assertions, by contrast, are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence', and often make broader claims about the types or categories to which study participants belong. This distinction is important because the provenance and validity of a 'finding' statement does not depend on subjective interpretation of 'evidence' in the same way that of an assertion does. This has modeling implications for how findings and assertions are linked to information that supports them. In practices, instances of 'study findings' are used to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it.
alternative label: study outcome
SEPIO_editor_note: - While the act of generating a finding is simpler, it does involve some cognitive effort that could be guided by some method (i.e., one defining what experimental context should be included in the finding statement, and how this and the observed outcomes are reported). Which means that findings are not the direct output of an assay, which merely generates data. So perhaps in SEPIO we commit to only considering research processes at the level of studies - such that even assays would potentially involve some act of summarizing the results as a finding. - Note that at present 'study data sets' can serve the same 'organizational' purpose as 'study findings' - we should converge on one recommended way to perform this level of organization of evidence data.
comment: A study finding is a statement that summarizes the immediate results of a particular experiment or study. It describes only what was directly observed, measured, or calculated, and optionally the experimental context of these observations. It does not describe more general conclusions that may have been inferred from such results. As such, the scope of what a finding describes is limited to the direct participants in the study - i.e. it is about only the instances observed or measured in the study. It makes no broader inference or conclusion about types or classes to which these instances belong. This is not to say that the onserved findings are necessarily accurate or correct - only that they were indeed made in a particular study. For example, the finding that "Sequencing of DNA from patient X revealed an A->T mutation at position 2143 in gene Y" is a matter of fact - this was the outcome of the assay, even if the finding is an artifact of low sequencing coverage. Metadata about the finding (e.g. sequencing methods/reagents used, coverage or read depth) are recoded so users can judge for themselves whether the objectively reported finding accurtely reflects the biology it describes.
comment: SEPIO distinguishes two high-level subtypes of statements: 1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from an act of reporting or summarizing these direct observations, calculations, or measurements. 2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and its interpretation as evidence.

statement
type: Class
subclass of: information
subclass of: Restriction
  on property: authored_by
  some values from: Agent
example of usage: The following is derived from https://en.wikipedia.org/wiki/Statement_(logic): Examples of sentences that are (or make) statements: "Socrates is a man." "A triangle has three sides." "Madrid is the capital of Spain." "There are five ducks on the lake" "The BRAF V600E mutation causes breast cancer" Examples of sentences that are not (or do not make) statements: "Who are you?" "Run!" "Greenness perambulates." "I had one grunch but the eggplant over there." "The King of France is wise." "Broccoli tastes good." The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste.
definition: An information content entity expressing a declarative sentence that is either true or false.
comment: From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21): "A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities." ---- Note that the definition in (b) describes something closer to the notion of a 'Proposition' as defined in SEPIO?
comment: Statements are sentences (or, more precisely, the information content of sentences) that declare a definitive or proposed fact - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made. The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth.

obsolete_observation
type: Class
subclass of: ObsoleteClass
definition: A statement describing something that was observed or recorded.
editor note: In SEPIO, a high-level distinction is made between Statements that are 'Observations' vs 'Assertions'. Observations are statements that report what is observed, and are inherently true in the sense that they reflect an agents particular experience. Assertions are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence'. This distinction is important because the ultimate truth of observations or findings do not depend on evidence in the same way that the truth of assertions does. Accordingly, any data related to an observation is not treated as evidence, and captured as observations.
comment: An observation reflects only what an agent observed or device recorded. It is therefore considered a matter of fact, rather than a propositional assertion that may or may not be true. This does not mean that the observations or recordings were necessarily accurate or correct - only that they were indeed made by an agent. For example, the observation that "I counted six ducks in the pond" is a matter of fact, even if there are actually seven because I missed one that was hiding in the reeds.
deprecated: true

obsolete_evidence statement
type: Class
subclass of: ObsoleteClass
definition: A statement (ie an assertion or finding) that is used as evidence to evaluate the validity of a target assertion or proposition.
has obsolescence reason: Term is confusing and not required for current use cases. Main reason it was creaated is that his term is used in efforts like CIViC, and we wanted to be clear about how it fits into the SEPIO model. But this can be accomplished in documentation outside of the ontology. Axioms: Eq: statement and (contributes_to_evidence_line some 'evidence line') Sc: 'information content entity' has_role some 'evidence role'
comment: Evidence Statements can be 'findings' that summarize data and outcomes from a particular study, or evidence-based 'assertions' that make a broader claim, as inferred from the interpretation and evaluation of previously generated information.
deprecated: true

obsolete_evidence data
type: Class
subclass of: ObsoleteClass
definition: Research data, or a product derived from research data such as data sets or figures, that are used as evidence to evaluate the validity of a target assertion or proposition.
editor note: Evidence data is not classified as a 'data item' because it is intended to cover products derived from data such as figures, tables, and data sets.
alternative label: evidence datum
has obsolescence reason: Term is confusing and not required for current use cases. Axioms: Eq: ('data item' or table or figure) and (contributes_to_evidence_line some 'evidence line') Sc: 'information content entity' has_role some 'evidence role'
comment: Instances of this class can include elemental 'data items' such as experimental measurements or derived statistical calculations or scores (e.g. a 548.5 mg/dl blood glucose level, or a 1.3951e-24 p-value), data sets containing several such values and possibly metadata about them, or tables/figures that render such data for human consumption. The notion of 'evidence data' is meant to be contrasted with the notion of an 'evidence statement', which is a statement used as evidence. (Statements here are logical sentences with truth value that are typically supported by interpretation of more fundamental data).
deprecated: true

obsolete_data table
type: Class
subclass of: ObsoleteClass
alternative label: A set of data arranged in rows and columns.
definition source: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C48693 ! Data Table
has obsolescence reason: Not required for data models.
deprecated: true

patient phenotyping study
type: Class
subclass of: observational clinical study
definition: A study with the goal of assessing and documenting phenotypes exhibited by one or more patients.
comment: Source: ClinVar (" 'Phenotyping only' is intended for variants that are submitted to ClinVar to provide individual observations with detailed phenotype data, such as submissions from clinicians or patient registries, without an interpretation from the submitter. The interpretation from the testing laboratory may be provided in a separate field.") ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf

confidence level
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: information
definition: A measurement datum that quantifies the level of confidence an agent has that a particular piece of information is true.

provider interpretation
type: Class
subclass of: observational clinical study
comment: Source: ClinVar (" 'Provider interpretation' is intended for variants that were interpreted by a clinical provider. For example, the clinician may reclassify the variant using detailed patient phenotype information that was unavailable to the testing laborator") ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf

skos terms
type: Class
definition: Organizational class that groups classes imported from the skos model to support creation and definition of value sets for particular SEPIO data model implementations.

obsolete_method
type: Class
subclass of: ObsoleteClass
editor note: Consider IAO:0000104 (plan specification).
alternative label: plan specification
has obsolescence reason: Decided to use IAO:plan specification here. Will give this term 'method' as a SEPIO-preferred label.
comment: An information content entity that specifies instructions for how a particular objective can be achieved.
deprecated: true

study data set
type: Class
subclass of: data set
example of usage: The set of data output from a study of the frequency of a particular allele in a particular population, which includes the following data (and metadata) items: { "ascertainment": "ExAc ascertainment method" "population": "Non-Finnish European" "allele": "CAR:CA011797", "alleleCount": 66706, "alleleNumber": 1, "alleleFrequency": 0.00001499, "homozygousAlleleIndividualCount": 0 } This collection of data may be described by, but remains distinct from, a 'study finding' statement that summarizes the results in narrative form.
definition: A data set comprised of data items produced by a single research study.
editor note: Instances of this class are used in SEPIO to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it.
comment: The data items comprising a study data set may include primary measurements, derived calculations, metadata about study participants and methods, or parameters of execution. A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay.

obsolete_opinion
type: Class
subclass of: ObsoleteClass
definition: A declarative sentence that expresses a belief or judgement that is not necessarily based on fact or knowledge.
comment: Opinions are matters of subjective judgement or taste, and typically not able to be scientifically validated as objectively true based on empirical evidence. In this way, they are distinct from statements that have inherent truth value.
deprecated: true

evidence direction
type: Class
equivalent class: Class
  one of: supporting
  one of: disputing
  one of: inconclusive
subclass of: measurement datum
definition: A data item that indicates an agent's assessment of whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).
SEPIO_editor_note: Consider also treating this as an attribute/quality of an evidence line: An attribute of an evidence line describing whether it supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).

evidence quality
type: Class
subclass of: measurement datum
definition: A data item that indicates the quality of the data used as evidence by an agent making an assertion.
comment: The quality of an evidence item is a measure of the rigor applied in performing the study and anlysis tasks used to produce it. Higher quality studies will have carefully defined controls, and be replicated numerous times to ensure reproducibility. Other factors that are often used as secondary indicators of the quality of research data include the quality of the journal in which it is published, and the reputation of the lab or institution performing the study. Evidence qualitty is an important factor in assessing the overall strength of evidence it may produce.

recommendation
type: Class
subclass of: statement
comment: Recommendations are another type of statement besides assertions that can be supported by evidence. They don't put forth a proposed facts as true, but instead describe a recommended action on the foundation of evidence that it will be beneficial.

hypothesis
type: Class
subclass of: statement
comment: A hypothesis is another type of statement that, like an assertion, can be supported by evidence. It puts forward a possible fact as true, but does not express an agents belief in this fact. Rather, it is a possible fact whose truth will be explored via reasoning or experimentation.

record
type: Class
subclass of: document
definition: A document containing a collection of data or statements about some entity.
database_cross_reference: SIO:000088
comment: 'Record' here is broadly defined to include any document holding (typically) structured information about a particular entity. This can include individual records from a database or knowledgebase that hold information about the subject of the record. Specific examples include: - A single row of a table in a relational database. - A JSON or XML document holding information describing some entity. - A VCF File describing varaints in a patient, or a single row in this VCF file describinng a particular variant. - A Uniprot knowldgebase record describing the BRCA2 protein (http://www.uniprot.org/uniprot/P51587) - A ClinVar knwoledgebase record describing an assertion about the pathogenicity of the NM_000059.3(BRCA2):c.10G>T variant (https://www.ncbi.nlm.nih.gov/clinvar/variation/51063/) - An EHR record for a hospital patient.

statistic
type: Class
subclass of: data item
has curation status: ready for release
definition: a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
imported from: stato.owl

z-score
type: Class
subclass of: statistic
has curation status: ready for release
definition: A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores
imported from: stato.owl

obsolete_ratio
type: Class
subclass of: ObsoleteClass
definition: A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
deprecated: true

association
type: Class
subclass of: proposition
definition: Associations are a form of proposition, framed as a tuple linking two (or more) entities through defined relationships.

Concept
type: Class
subclass of: skos terms
definition: An idea or notion; a unit of thought.

Activity
type: Class
subclass of: process
subclass of: Restriction
  on property: has participant
  some values from: continuant
subclass of: Restriction
  on property: activity_date
  some values from: dateTime
definition: An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.

Agent
type: Class
equivalent class: Restriction
  on property: capable of
  some values from: contribution
subclass of: material entity
subclass of: Restriction
  on property: capable of
  some values from: contribution
definition: An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.
editor note: prov:Agent is considered equivalent to foaf:Agent (http://xmlns.com/foaf/0.1/Agent ) Def = "The Agent class is the class of agents; things that do stuff. A well known sub-class is Person, representing people. Other kinds of agents include Organization and Group."
comment: Agents typically persons, organizations, or software that perform tasks, including making assertions, or generating information used as evidence. In the execution of such tasks, an 'agent role' is realized that inheres in the agent.

Organization
type: Class
subclass of: Group
definition: An organization is a social or legal institution such as a company, society, etc.
editor note: Consider: http://xmlns.com/foaf/0.1/Organization

Person
type: Class
subclass of: Agent
definition: Person agents are people.
editor note: Consider: http://xmlns.com/foaf/0.1/Person

SoftwareAgent
type: Class
subclass of: Agent
subclass of: Restriction
  on property: has part
  some values from: algorithm
definition: A software agent is running software.
comment: Software agents are autonomous computer programs that carries out tasks. They designed to execute algorithm(s) that receive some input information and direct its processing to achieve a specified goal. Artificial intelligence is not required to be considered a software agent - only that it can autonomously execute programmed tasks.

Group
type: Class
subclass of: Agent
comment: The Group class represents a collection of individual agents (and may itself play the role of a Agent, ie. something that can perform actions). This concept is intentionally quite broad, covering informal and ad-hoc groups, long-lived communities, organizational groups within a workplace, etc. Some such groups may have associated characteristics which could be captured in RDF (perhaps a homepage, name, mailing list etc.).

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
type: curation status specification
editor preferred term: metadata complete
definition: 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
type: NamedIndividual
type: curation status specification
editor preferred term: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
editor preferred term: ready for release
definition: 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
type: NamedIndividual
type: curation status specification
editor preferred term: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
editor preferred term: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred term: pending final vetting
definition: 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.

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: term imported
editor note: 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
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: term split
editor note: 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.

universal
type: NamedIndividual
type: denotator type
editor preferred term: universal
editor note: 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.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
editor preferred term: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "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.
term editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
editor preferred term: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: 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
term editor: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
editor preferred term: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred term: requires discussion
definition: 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.
term editor: Alan Ruttenberg
definition source: group:OBI

out of scope
type: NamedIndividual
type: obsolescence reason specification
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: 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.
term editor: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/77
IAO_0000234: https://orcid.org/0000-0001-5208-3432

supporting
type: NamedIndividual
type: evidence direction
definition: An evidence direction indicating that an evidence line provides an argument that supports the validity of a target assertion.

disputing
type: NamedIndividual
type: evidence direction

inconclusive
type: NamedIndividual
type: evidence direction
definition: An evidence direction indicating that an evidence line lacks sufficient credibility, relevance, or completeness to argue for or against the validity of a target assertion.

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x