Class
BFOEntity
BFO entity (root).
Schema Graph
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Namespaces 14
Namespace prefixes used in this ontology.
| Prefix | Namespace IRI |
|---|---|
|
http://scimantic.io/schema
|
cco |
https://www.commoncoreontologies.org/
|
dcat |
http://www.w3.org/ns/dcat#
|
dcterms |
http://purl.org/dc/terms/
|
linkml |
https://w3id.org/linkml/
|
np |
http://www.nanopub.org/nschema#
|
oa |
http://www.w3.org/ns/oa#
|
obo |
http://purl.obolibrary.org/obo/
|
rdfs |
http://www.w3.org/2000/01/rdf-schema#
|
scimantic |
http://scimantic.io/
|
urref |
https://raw.githubusercontent.com/adelphi23/urref/469137/URREF.ttl#
|
xsd |
http://www.w3.org/2001/XMLSchema#
|
owl |
http://www.w3.org/2002/07/owl#
|
rdf |
http://www.w3.org/1999/02/22-rdf-syntax-ns#
|
Classes 49
Classes defined in this ontology.
Act
ActOfEstimation
ActOfInformationProcessing
ActOfObservation
ActOfPlanning
Agent
Aleatory
Ambiguity
Analysis
Annotation
BFOContinuant
BFOEntity
BFOGenericallyDependentContinuant
BFOOccurrent
BFOProcess
BFOQuality
BFOSpecificallyDependentContinuant
Conclusion
DCATDataset
Dataset
DescriptiveICE
DesignOfExperiment
DesignativeICE
DirectiveICE
Evidence
EvidenceAssessment
EvidenceExtraction
ExperimentalMethod
Experimentation
Hypothesis
HypothesisFormation
Identifiable
Incompleteness
InformationContentEntity
LiteratureSearch
Nanopublication
Parameter
PlannedAct
Premise
Question
QuestionFormation
Result
ResultAssessment
TextSelector
URREFEvidence
UncertaintyDerivation
UncertaintyModel
UncertaintySubject
Vagueness
-
- Superclass of
- BFOContinuant, BFOOccurrent
-
Class
BFOContinuant
BFO continuant. Persists through time while maintaining identity.
- Subclass of
- BFOEntity
- Superclass of
- Agent, BFOGenericallyDependentContinuant, BFOSpecificallyDependentContinuant
-
Class
Agent
CCO Agent. A material entity capable of intentional action.
- Subclass of
- BFOContinuant
-
Class
BFOGenericallyDependentContinuant
BFO generically dependent continuant (e.g., information content).
- Subclass of
- BFOContinuant
- Superclass of
- InformationContentEntity
-
Class
InformationContentEntity
CCO Information Content Entity (ICE).
- Subclass of
- BFOGenericallyDependentContinuant
- Superclass of
- Dataset, DescriptiveICE, DesignativeICE, DirectiveICE
-
Class
Dataset
Raw data, observations, or measurements produced by an Experimentation.
- Subclass of
- InformationContentEntity
- Mixes in
- DCATDataset, UncertaintySubject
- Slots
-
hasUncertainty
:
UncertaintyModel
Links an UncertaintySubject (continuant) to the UncertaintyModel (BFO quality) it bears. Effectively a restriction of BFO 'bearer of' (obo:BFO_0000196) to UncertaintyModel range.
-
isOutputOf
:
Experimentation required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
Class
DescriptiveICE
CCO Descriptive Information Content Entity. Describes some aspect of reality.
- Subclass of
- InformationContentEntity
- Superclass of
- Conclusion, Evidence, Hypothesis, Premise, Result
-
Class
Conclusion
The final claim derived from a ResultAssessment.
- Subclass of
- DescriptiveICE
- Mixes in
- Nanopublication
- Slots
-
content
:
string
The text content of an ICE (used by Evidence and Conclusion).
-
isOutputOf
:
ResultAssessment required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
Class
Evidence
A descriptive ICE articulating a factual claim extracted from one or more Annotations.
- Subclass of
- DescriptiveICE
- Mixes in
- URREFEvidence, Nanopublication, UncertaintySubject
- Slots
-
accessLevel
:
string
Publishing scope (e.g., local, institutional, public).
-
citation
:
string
Bibliographic reference.
-
content
:
string
The text content of an ICE (used by Evidence and Conclusion).
-
contradicts
:
Hypothesis refined here
An entity (Evidence/Result) that provides negative evidence against a Hypothesis.
-
hasUncertainty
:
UncertaintyModel
Links an UncertaintySubject (continuant) to the UncertaintyModel (BFO quality) it bears. Effectively a restriction of BFO 'bearer of' (obo:BFO_0000196) to UncertaintyModel range.
-
isOutputOf
:
EvidenceExtraction required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
publishable
:
boolean
Flag indicating if this is ready for public promotion.
-
source
:
string
Source URL or identifier.
-
supports
:
Hypothesis refined here
An entity (Evidence/Result) that provides positive evidence for a Hypothesis.
-
Class
Hypothesis
A testable claim about the world, synthesized from one or more Premises.
- Subclass of
- DescriptiveICE
- Mixes in
- Nanopublication
- Slots
-
isOutputOf
:
HypothesisFormation required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
Class
Premise
An evaluated proposition derived from Evidence via an EvidenceAssessment.
- Subclass of
- DescriptiveICE
- Slots
-
isOutputOf
:
EvidenceAssessment required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
Class
Result
A descriptive ICE summarizing the outcome of an Analysis.
- Subclass of
- DescriptiveICE
- Mixes in
- URREFEvidence, Nanopublication, UncertaintySubject
- Slots
-
contradicts
:
Hypothesis refined here
An entity (Evidence/Result) that provides negative evidence against a Hypothesis.
-
hasUncertainty
:
UncertaintyModel
Links an UncertaintySubject (continuant) to the UncertaintyModel (BFO quality) it bears. Effectively a restriction of BFO 'bearer of' (obo:BFO_0000196) to UncertaintyModel range.
-
isOutputOf
:
Analysis required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
refines
:
Hypothesis refined here
A Result that suggests a specific modification to a Hypothesis.
-
supports
:
Hypothesis refined here
An entity (Evidence/Result) that provides positive evidence for a Hypothesis.
-
unit
:
string
Unit of measurement.
-
value
:
string
The numeric or categorical result.
-
Class
DesignativeICE
CCO Designative Information Content Entity. Designates (names/identifies) some entity.
- Subclass of
- InformationContentEntity
- Superclass of
- Annotation, Parameter, TextSelector
-
Class
Annotation
A text annotation or highlight that designates a specific span of source text. Follows W3C Web Annotation Data Model.
- Subclass of
- DesignativeICE
- Slots
-
createdAt
:
datetime
When this entity was created (ISO 8601 datetime).
-
hasBody
:
string
The content or comment of the annotation (optional for highlights).
-
hasSelector
:
TextSelector refined here
The selector specifying which part of the target is annotated.
-
hasTarget
:
string required refined here
The source document being annotated (DOI, URL, or local file reference).
-
isOutputOf
:
LiteratureSearch required refined here
The LiteratureSearch that produced this annotation.
-
label required
The human-readable label or text.
-
Class
Parameter
A configured parameter value within an ExperimentalMethod.
- Subclass of
- DesignativeICE
- Slots
-
label required
The human-readable label or text.
-
Class
TextSelector
A selector identifying text by exact quote with surrounding context. Follows W3C Web Annotation TextQuoteSelector.
- Subclass of
- DesignativeICE
- Slots
-
endOffset
:
integer
Character offset where the selection ends.
-
exact
:
string required
The exact text that was selected/highlighted.
-
pageNumber
:
integer
Page number in PDF documents where the selection appears.
-
prefix
:
string
Text immediately before the selection (for disambiguation).
-
startOffset
:
integer
Character offset where the selection starts (within the target or page).
-
suffix
:
string
Text immediately after the selection (for disambiguation).
-
Class
DirectiveICE
CCO Prescriptive (a.k.a. Directive) Information Content Entity. Prescribes some behavior, state, or plan.
- Subclass of
- InformationContentEntity
- Superclass of
- ExperimentalMethod, Question
-
Class
ExperimentalMethod
A directive ICE specifying an experimental or computational method.
- Subclass of
- DirectiveICE
- Slots
-
isOutputOf
:
DesignOfExperiment required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
method
:
string
Name or description of the method.
-
parameter
:
Parameter multivalued
Structured configuration parameter.
-
Class
Question
An interrogative ICE representing a research query. As a directive, a Question prescribes inquiry behaviors (e.g., a LiteratureSearch).
- Subclass of
- DirectiveICE
- Slots
-
isOutputOf
:
QuestionFormation required refined here
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
-
label required
The human-readable label or text.
-
prescribes
:
LiteratureSearch multivalued refined here
CCO 'prescribes'. A directive ICE prescribes a behavior, plan, or process.
-
Class
BFOSpecificallyDependentContinuant
BFO specifically dependent continuant. Inheres in a specific independent continuant.
- Subclass of
- BFOContinuant
- Superclass of
- BFOQuality
-
Class
BFOQuality
BFO quality.
- Subclass of
- BFOSpecificallyDependentContinuant
- Superclass of
- UncertaintyModel
-
Class
UncertaintyModel
A reified uncertainty model. As a BFO quality (SDC), it inheres in some independent continuant (the UncertaintySubject).
- Subclass of
- BFOQuality
- Superclass of
- Aleatory, Ambiguity, Incompleteness, Vagueness
- Slots
-
derivationOfUncertainty
:
UncertaintyDerivation
How the uncertainty was derived.
-
natureOfUncertainty
:
UncertaintyNature required refined here
The nature of the uncertainty (Aleatory or Epistemic).
-
Class
Aleatory
Aleatory uncertainty entities must have nature Aleatory.
- Subclass of
- UncertaintyModel
- Slots
- derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
- natureOfUncertainty : UncertaintyNature required from UncertaintyModel
-
Class
Ambiguity
Ambiguity is inherently Epistemic uncertainty.
- Subclass of
- UncertaintyModel
- Slots
- derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
- natureOfUncertainty : UncertaintyNature required from UncertaintyModel
-
Class
Incompleteness
Incompleteness is inherently Epistemic uncertainty.
- Subclass of
- UncertaintyModel
- Slots
- derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
- natureOfUncertainty : UncertaintyNature required from UncertaintyModel
-
Class
Vagueness
Vagueness is inherently Epistemic uncertainty.
- Subclass of
- UncertaintyModel
- Slots
- derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
- natureOfUncertainty : UncertaintyNature required from UncertaintyModel
-
Class
BFOOccurrent
BFO occurrent. Unfolds in time.
- Subclass of
- BFOEntity
- Superclass of
- BFOProcess
-
Class
BFOProcess
BFO process.
- Subclass of
- BFOOccurrent
- Superclass of
- Act
-
Class
Act
CCO Act. A process with an agent participant.
- Subclass of
- BFOProcess
- Superclass of
- PlannedAct
- Slots
-
status
:
ActStatus
Optional lifecycle status of a PlannedAct. Captures planning/execution phase as data; does NOT change the act's BFO/CCO type. A single Act individual spans its planning, execution, and completion as one occurrent; this enum records which phase its temporal region is in.
-
Class
PlannedAct
CCO Planned Act. An Act prescribed by a plan specification (intentional, agent-driven), in contrast to natural processes. NOTE: "Planned" denotes intentionality, NOT lifecycle phase. A PlannedAct individual spans its design, execution, and completion as a single occurrent; lifecycle state is captured by the ActStatus enum on the
statusslot, not by class.- Subclass of
- Act
- Superclass of
- ActOfEstimation, ActOfInformationProcessing, ActOfObservation, ActOfPlanning
- Slots
- status : ActStatus from Act
-
Class
ActOfEstimation
CCO Act of Estimation.
- Subclass of
- PlannedAct
- Superclass of
- EvidenceAssessment, ResultAssessment
- Slots
- status : ActStatus from Act
-
Class
EvidenceAssessment
The act of evaluating credibility or relevance of Evidence, producing a Premise.
- Subclass of
- ActOfEstimation
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
:
Evidence refined here
CCO 'has input'. Links a process to an entity it takes as input.
-
precededBy
:
EvidenceExtraction refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
ResultAssessment
The act of comparing a Result to the originating Hypothesis to produce a Conclusion.
- Subclass of
- ActOfEstimation
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
:
Result refined here
CCO 'has input'. Links a process to an entity it takes as input.
-
precededBy
:
Analysis refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
ActOfInformationProcessing
CCO Act of Information Processing.
- Subclass of
- PlannedAct
- Superclass of
- Analysis, EvidenceExtraction, HypothesisFormation
- Slots
- status : ActStatus from Act
-
Class
Analysis
The act of processing a Dataset to produce a Result.
- Subclass of
- ActOfInformationProcessing
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
:
Dataset refined here
CCO 'has input'. Links a process to an entity it takes as input.
-
precededBy
:
Experimentation refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
EvidenceExtraction
The act of articulating Evidence claims from one or more Annotations. Separates reading/highlighting from formulating evidence statements.
- Subclass of
- ActOfInformationProcessing
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
:
Annotation multivalued refined here
The annotations from which evidence is extracted.
-
precededBy
:
LiteratureSearch refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
HypothesisFormation
The act of synthesizing one or more Premises into a Hypothesis.
- Subclass of
- ActOfInformationProcessing
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
:
Premise multivalued refined here
CCO 'has input'. Links a process to an entity it takes as input.
-
precededBy
:
EvidenceAssessment refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
ActOfObservation
CCO Act of Observation.
- Subclass of
- PlannedAct
- Superclass of
- Experimentation, LiteratureSearch
- Slots
- status : ActStatus from Act
-
Class
Experimentation
The act of executing an ExperimentalMethod to produce a Dataset.
- Subclass of
- ActOfObservation
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
:
ExperimentalMethod refined here
CCO 'has input'. Links a process to an entity it takes as input.
-
precededBy
:
DesignOfExperiment refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
LiteratureSearch
The act of searching literature and producing Annotations (highlights, notes) on source text. Treated as an Act of Observation since it consists of structured observation of source material.
- Subclass of
- ActOfObservation
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
precededBy
:
QuestionFormation refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
ActOfPlanning
CCO Act of Planning.
- Subclass of
- PlannedAct
- Superclass of
- DesignOfExperiment, QuestionFormation
- Slots
- status : ActStatus from Act
-
Class
DesignOfExperiment
The act of creating an ExperimentalMethod from a Hypothesis (and possibly supporting Evidence).
- Subclass of
- ActOfPlanning
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
: any of [Hypothesis, Evidence
] refined here
CCO 'has input'. Links a process to an entity it takes as input.
-
precededBy
: any of [HypothesisFormation, LiteratureSearch
] refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
QuestionFormation
The act of forming or refining a research Question. Can be informed by prior assessments (iterating on findings) or by literature search.
- Subclass of
- ActOfPlanning
- Slots
-
hasAgent
:
Agent
CCO 'has agent'. Links a process to its agent participant.
-
hasInput
: any of [Question, Annotation, Evidence
] multivalued refined here
Prior inputs that informed this question (a refined-from question, supporting annotations, or evidence).
-
precededBy
: any of [ResultAssessment, LiteratureSearch
] refined here
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
- status : ActStatus from Act
-
Class
DCATDataset
A collection of data, published or curated by a single agent (DCAT mixin).
-
Class
Identifiable
A mixin for objects that have a unique identifier slot.
- Slots
-
id
:
string
Unique identifier (URI) for this node.
-
Class
Nanopublication
A nanopublication object (mixin).
-
Class
URREFEvidence
URREF Evidence (mixin reference).
-
Class
UncertaintyDerivation
Describes how the uncertainty was assessed.
-
Class
UncertaintySubject
A mixin for continuants that can bear a reified uncertainty model (a BFO quality).
Slots 33
Slots defined in this ontology.
accessLevel
citation
content
contradicts
createdAt
derivationOfUncertainty
endOffset
exact
hasAgent
hasBody
hasInput
hasSelector
hasTarget
hasUncertainty
id
isOutputOf
label
method
natureOfUncertainty
pageNumber
parameter
precededBy
prefix
prescribes
publishable
refines
source
startOffset
status
suffix
supports
unit
value
Slot
accessLevel
Publishing scope (e.g., local, institutional, public).
Slot
citation
Bibliographic reference.
Slot
content
The text content of an ICE (used by Evidence and Conclusion).
Slot
contradicts
An entity (Evidence/Result) that provides negative evidence against a Hypothesis.
Slot
createdAt
When this entity was created (ISO 8601 datetime).
Slot
derivationOfUncertainty
How the uncertainty was derived.
Slot
endOffset
Character offset where the selection ends.
Slot
exact
The exact text that was selected/highlighted.
Slot
hasAgent
CCO 'has agent'. Links a process to its agent participant.
Slot
hasBody
The content or comment of the annotation (optional for highlights).
Slot
hasInput
CCO 'has input'. Links a process to an entity it takes as input.
Slot
hasSelector
The selector identifying the specific part of the target.
Slot
hasTarget
The source being annotated (DOI, URL, or file reference).
Slot
hasUncertainty
Links an UncertaintySubject (continuant) to the UncertaintyModel (BFO quality) it bears. Effectively a restriction of BFO 'bearer of' (obo:BFO_0000196) to UncertaintyModel range.
Slot
id
Unique identifier (URI) for this node.
Slot
isOutputOf
CCO 'is output of'. Inverse of 'has output'. Links a continuant to the process that produced it.
Slot
label
The human-readable label or text.
Slot
method
Name or description of the method.
Slot
natureOfUncertainty
The nature of the uncertainty (Aleatory or Epistemic).
Slot
pageNumber
Page number in PDF documents where the selection appears.
Slot
parameter
Structured configuration parameter.
Slot
precededBy
BFO 'preceded by'. An occurrent temporally preceded by another occurrent.
Slot
prefix
Text immediately before the selection (for disambiguation).
Slot
prescribes
CCO 'prescribes'. A directive ICE prescribes a behavior, plan, or process.
Slot
publishable
Flag indicating if this is ready for public promotion.
Slot
refines
A Result that suggests a specific modification to a Hypothesis.
Slot
source
Source URL or identifier.
Slot
startOffset
Character offset where the selection starts (within the target or page).
Slot
status
Optional lifecycle status of a PlannedAct. Captures planning/execution phase as data; does NOT change the act's BFO/CCO type. A single Act individual spans its planning, execution, and completion as one occurrent; this enum records which phase its temporal region is in.
Slot
suffix
Text immediately after the selection (for disambiguation).
Slot
supports
An entity (Evidence/Result) that provides positive evidence for a Hypothesis.
Slot
unit
Unit of measurement.
Slot
value
The numeric or categorical result.
Enumerations 2
Enumerations defined in this ontology.
Enum
ActStatus
Lifecycle status of a PlannedAct. Optional metadata; does NOT change the act's BFO/CCO classification. A single Act individual is the same instance regardless of which phase its temporal region is in.
-
abandoned
The act was started but did not reach completion.
-
completed
The act has ended successfully.
-
in_progress
The act has begun but has not ended.
-
planned
The act has been designed but execution has not begun.
Enum
UncertaintyNature
-
Aleatory
Uncertainty due to inherent randomness.
-
Epistemic
Uncertainty due to lack of knowledge.
Individuals 0
Named individuals defined in this ontology.
No individuals defined in this ontology.