scimantic

Metadata

IRI: http://scimantic.io/schema
Version: 0.1.0
Description: A minimal domain ontology for representing the scientific method as provenance chains.

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Namespaces 13

Namespace prefixes used in this ontology.

Prefix	Namespace IRI
	`http://scimantic.io/schema`
`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#`
`prov`	`http://www.w3.org/ns/prov#`
`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 34

Classes defined in this ontology.

Class

Activity

prov:Activity

A provenance activity. Identified by its RDF URI.

Superclass of

Analysis, DesignOfExperiment, EvidenceAssessment, EvidenceExtraction, Experimentation, HypothesisFormation, LiteratureSearch, QuestionFormation, ResultAssessment
- Class
  
  Analysis
  
  scimantic:Analysis
  
  The activity of processing a Dataset to produce a Result.
  Subclass of
  
  Activity
  Slots
  
  used : Dataset refined here
  Entity used by an Activity.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : Experimentation refined here
  Activity that informed this Activity.
- Class
  
  DesignOfExperiment
  
  scimantic:DesignOfExperiment
  
  The activity of creating an ExperimentalMethod from a Hypothesis.
  Subclass of
  
  Activity
  Slots
  
  used : any of [Hypothesis, Evidence ] refined here
  Entity used by an Activity.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : any of [HypothesisFormation, LiteratureSearch ] refined here
  Activity that informed this Activity.
- Class
  
  EvidenceAssessment
  
  scimantic:EvidenceAssessment
  
  The activity of evaluating credibility or relevance of Evidence.
  Subclass of
  
  Activity
  Slots
  
  used : Evidence refined here
  Entity used by an Activity.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : EvidenceExtraction refined here
  Activity that informed this Activity.
- Class
  
  EvidenceExtraction
  
  scimantic:EvidenceExtraction
  
  The activity of articulating Evidence claims from one or more Annotations. Separates the act of reading/highlighting from the act of formulating evidence statements.
  Subclass of
  
  Activity
  Slots
  
  used : Annotation multivalued refined here
  The annotations from which evidence is extracted.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : LiteratureSearch refined here
  Activity that informed this Activity.
- Class
  
  Experimentation
  
  scimantic:Experimentation
  
  The activity of running an ExperimentalMethod to produce a Dataset.
  Subclass of
  
  Activity
  Slots
  
  used : ExperimentalMethod refined here
  Entity used by an Activity.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : DesignOfExperiment refined here
  Activity that informed this Activity.
- Class
  
  HypothesisFormation
  
  scimantic:HypothesisFormation
  
  The activity of synthesizing Evidence into a Hypothesis.
  Subclass of
  
  Activity
  Slots
  
  used : Premise refined here
  Entity used by an Activity.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : EvidenceAssessment refined here
  Activity that informed this Activity.
- Class
  
  LiteratureSearch
  
  scimantic:LiteratureSearch
  
  The activity of searching literature and creating Annotations (highlights, notes) on source text.
  Subclass of
  
  Activity
  Slots
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : QuestionFormation refined here
  Activity that informed this Activity.
- Class
  
  QuestionFormation
  
  scimantic:QuestionFormation
  
  The activity of creating or refining a Research Question. Can be informed by prior results (iterating on findings) or by literature search (refining questions based on discovered evidence).
  Subclass of
  
  Activity
  Slots
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : any of [ResultAssessment, LiteratureSearch ] refined here
  Activity that informed this Activity.
- Class
  
  ResultAssessment
  
  scimantic:ResultAssessment
  
  The activity of comparing a Result to the original Hypothesis.
  Subclass of
  
  Activity
  Slots
  
  used : Result refined here
  Entity used by an Activity.
  
  wasAssociatedWith : Agent
  The agent associated with an activity.
  
  wasInformedBy : Analysis refined here
  Activity that informed this Activity.
Class

Agent

prov:Agent

A provenance agent. Identified by its RDF URI.
Class

DCATDataset

dcat:Dataset

A collection of data, published or curated by a single agent.
Class

Entity

prov:Entity

A provenance entity. Identified by its RDF URI.

Superclass of

Annotation, Conclusion, Dataset, Evidence, ExperimentalMethod, Hypothesis, Parameter, Premise, Question, Result, TextSelector, UncertaintyModel
- Class
  
  Annotation
  
  oa:Annotation
  
  A text annotation or highlight that grounds Questions or Evidence in specific source text. Follows W3C Web Annotation Data Model.
  Subclass of
  
  Entity
  Slots
  
  generatedAtTime : datetime
  Time of generation.
  
  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).
  
  label required
  The human-readable label or text.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasGeneratedBy : LiteratureSearch refined here
  The literature search activity that produced this annotation.
- Class
  
  Conclusion
  
  scimantic:Conclusion
  
  The final claim or decision derived from the ResultAssessment.
  Subclass of
  
  Entity
  
  Mixes in
  
  Nanopublication
  Slots
  
  content : string
  The actual text content of the evidence.
  
  label required
  The human-readable label or text.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : Result refined here
  Entity derived from another Entity.
  
  wasGeneratedBy : ResultAssessment refined here
  The activity that generated this entity.
- Class
  
  Dataset
  
  scimantic:Dataset
  
  Raw data, observations, or measurements produced by experimentation.
  Subclass of
  
  Entity
  
  Mixes in
  
  DCATDataset, UncertaintySubject
  Slots
  
  hasUncertainty : UncertaintyModel
  Links an entity to its reified uncertainty model.
  
  label required
  The human-readable label or text.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : ExperimentalMethod refined here
  Entity derived from another Entity.
  
  wasGeneratedBy : Experimentation refined here
  The activity that generated this entity.
- Class
  
  Evidence
  
  scimantic:Evidence
  
  A factual claim extracted from a source.
  Subclass of
  
  Entity
  
  Mixes in
  
  URREFEvidence, Nanopublication, UncertaintySubject
  Slots
  
  accessLevel : string
  Publishing scope (e.g., local, institutional, public).
  
  citation : string
  Bibliographic reference.
  
  content : string
  The actual text content of the evidence.
  
  contradicts : Hypothesis refined here
  An Entity (Evidence/Result) that provides negative evidence against a Hypothesis.
  
  hasUncertainty : UncertaintyModel
  Links an entity to its reified uncertainty model.
  
  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.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : any of [Question, Annotation ] multivalued refined here
  Evidence can be derived from research questions or from annotations/highlights in literature.
  
  wasGeneratedBy : EvidenceExtraction refined here
  The activity that generated this entity.
- Class
  
  ExperimentalMethod
  
  scimantic:ExperimentalMethod
  
  A specification of the experimental or computational method.
  Subclass of
  
  Entity
  Slots
  
  label required
  The human-readable label or text.
  
  method : string
  Name or description of the method.
  
  parameter : Parameter multivalued
  Structured configuration parameter.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : any of [Hypothesis, Evidence ] refined here
  Entity derived from another Entity.
  
  wasGeneratedBy : DesignOfExperiment refined here
  The activity that generated this entity.
- Class
  
  Hypothesis
  
  scimantic:Hypothesis
  
  A testable claim derived from evidence.
  Subclass of
  
  Entity
  
  Mixes in
  
  Nanopublication
  Slots
  
  label required
  The human-readable label or text.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : Premise multivalued refined here
  Entity derived from another Entity.
  
  wasGeneratedBy : HypothesisFormation refined here
  The activity that generated this entity.
- Class
  
  Parameter
  
  scimantic:Parameter
  
  A configured parameter within an Experimental Method.
  
  Subclass of
  
  Entity
- Class
  
  Premise
  
  scimantic:Premise
  
  An evaluated proposition or insight derived from Evidence.
  Subclass of
  
  Entity
  Slots
  
  label required
  The human-readable label or text.
  
  wasDerivedFrom : Evidence refined here
  Entity derived from another Entity.
  
  wasGeneratedBy : EvidenceAssessment refined here
  The activity that generated this entity.
- Class
  
  Question
  
  scimantic:Question
  
  An interrogative sentence representing the research query.
  Subclass of
  
  Entity
  Slots
  
  label required
  The human-readable label or text.
  
  motivates : LiteratureSearch multivalued refined here
  A Question that triggers or motivates an Activity.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : any of [Question, Annotation, Evidence ] multivalued refined here
  Questions can be derived from prior questions (refinement), annotations/highlights in literature, or evidence claims.
  
  wasGeneratedBy : QuestionFormation refined here
  The activity that generated this entity.
- Class
  
  Result
  
  scimantic:Result
  
  The outcome of an analysis activity.
  Subclass of
  
  Entity
  
  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 entity to its reified uncertainty model.
  
  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.
  
  wasAttributedTo : Agent
  The agent who attributed this entity (Agent).
  
  wasDerivedFrom : Dataset refined here
  Entity derived from another Entity.
  
  wasGeneratedBy : Analysis refined here
  The activity that generated this entity.
- Class
  
  TextSelector
  
  oa:TextQuoteSelector
  
  A selector that identifies text by exact quote with surrounding context. Follows W3C Web Annotation TextQuoteSelector.
  Subclass of
  
  Entity
  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
  
  UncertaintyModel
  
  urref:UncertaintyModel
  
  A reified uncertainty model.
  Subclass of
  
  Entity
  
  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
    
    urref:Aleatory
    
    Aleatory uncertainty entities must have nature Aleatory.
    Subclass of
    
    UncertaintyModel
    
    Slots
    
    derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
    
    natureOfUncertainty : UncertaintyNature required from UncertaintyModel
  - Class
    
    Ambiguity
    
    urref:Ambiguity
    
    Ambiguity is inherently Epistemic uncertainty.
    Subclass of
    
    UncertaintyModel
    
    Slots
    
    derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
    
    natureOfUncertainty : UncertaintyNature required refined here from UncertaintyModel
  - Class
    
    Incompleteness
    
    urref:Incompleteness
    
    Incompleteness is inherently Epistemic uncertainty.
    Subclass of
    
    UncertaintyModel
    
    Slots
    
    derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
    
    natureOfUncertainty : UncertaintyNature required from UncertaintyModel
  - Class
    
    Vagueness
    
    urref:Vagueness
    
    Vagueness is inherently Epistemic uncertainty.
    Subclass of
    
    UncertaintyModel
    
    Slots
    
    derivationOfUncertainty : UncertaintyDerivation from UncertaintyModel
    
    natureOfUncertainty : UncertaintyNature required from UncertaintyModel
Class

Identifiable

scimantic:Identifiable

A mixin for objects that have a unique identifier.
Slots
id : string
Unique identifier (URI) for this node.
Class

Nanopublication

np:Nanopublication

A nanopublication object.
Class

URREFEvidence

urref:Evidence

Root evidence class from URREF ontology.
Class

UncertaintyDerivation

urref:UncertaintyDerivation

Describes how the uncertainty was assessed.
Class

UncertaintySubject

scimantic:UncertaintySubject

A mixin for objects that can have a reified uncertainty model.

Slots 34

Slots defined in this ontology.

Slot

accessLevel

scimantic:accessLevel

Publishing scope (e.g., local, institutional, public).

Domain

Nanopublication

Range

string

Slot

citation

dcterms:bibliographicCitation

Bibliographic reference.

Domain

Evidence

Range

string

Slot

content

scimantic:content

The actual text content of the evidence.

Domain

Evidence

Range

string

Slot

contradicts

scimantic:contradicts

An Entity (Evidence/Result) that provides negative evidence against a Hypothesis.

Domain

Evidence, Result

Slot

derivationOfUncertainty

urref:derivationOfUncertainty

How the uncertainty was derived.

Domain

UncertaintyModel

Range

UncertaintyDerivation

Slot

endOffset

oa:end

Character offset where the selection ends.

Domain

TextSelector

Range

integer

Slot

exact

oa:exact

The exact text that was selected/highlighted.

Domain

TextSelector

Range

string

Characteristics

Required

Slot

generatedAtTime

prov:generatedAtTime

Time of generation.

Domain

Entity

Range

datetime

Slot

hasBody

oa:hasBody

The content or comment of the annotation (optional for highlights).

Domain

Annotation

Range

string

Slot

hasSelector

oa:hasSelector

The selector identifying the specific part of the target.

Domain

Annotation

Slot

hasTarget

oa:hasTarget

The source being annotated (DOI, URL, or file reference).

Domain

Annotation

Range

string

Slot

hasUncertainty

scimantic:hasUncertainty

Links an entity to its reified uncertainty model.

Domain

UncertaintySubject

Range

UncertaintyModel

Slot

id

id

Unique identifier (URI) for this node.

Domain

Identifiable

Range

string

Characteristics

Identifier

Slot

label

rdfs:label

The human-readable label or text.

Domain

Annotation, Conclusion, Dataset, Evidence, ExperimentalMethod, Hypothesis, Premise, Question, Result

Characteristics

Required

Slot

method

scimantic:method

Name or description of the method.

Domain

ExperimentalMethod

Range

string

Slot

motivates

scimantic:motivates

A Question that triggers or motivates an Activity.

Domain

Question

Characteristics

Multivalued

Slot

natureOfUncertainty

urref:natureOfUncertainty

The nature of the uncertainty (Aleatory or Epistemic).

Domain

UncertaintyModel

Range

UncertaintyNature

Slot

pageNumber

scimantic:pageNumber

Page number in PDF documents where the selection appears.

Domain

TextSelector

Range

integer

Slot

parameter

scimantic:parameter

Structured configuration parameter.

Domain

ExperimentalMethod

Range

Parameter

Characteristics

Multivalued

Slot

prefix

oa:prefix

Text immediately before the selection (for disambiguation).

Domain

TextSelector

Range

string

Slot

publishable

scimantic:publishable

Flag indicating if this is ready for public promotion.

Domain

Nanopublication

Range

boolean

Slot

refines

scimantic:refines

A Result that suggests a specific modification to a Hypothesis.

Domain

Result

Slot

source

dcterms:source

Source URL or identifier.

Domain

Evidence

Range

string

Slot

startOffset

oa:start

Character offset where the selection starts (within the target or page).

Domain

TextSelector

Range

integer

Slot

suffix

oa:suffix

Text immediately after the selection (for disambiguation).

Domain

TextSelector

Range

string

Slot

supports

scimantic:supports

An Entity (Evidence/Result) that provides positive evidence for a Hypothesis.

Domain

Evidence, Result

Slot

unit

scimantic:unit

Unit of measurement.

Domain

Result

Range

string

Slot

used

prov:used

Entity used by an Activity.

Domain

Analysis, DesignOfExperiment, EvidenceAssessment, EvidenceExtraction, Experimentation, HypothesisFormation, ResultAssessment

Slot

value

scimantic:value

The numeric or categorical result.

Domain

Result

Range

string

Slot

wasAssociatedWith

prov:wasAssociatedWith

The agent associated with an activity.

Domain

Activity

Range

Agent

Slot

wasAttributedTo

prov:wasAttributedTo

The agent who attributed this entity (Agent).

Domain

Entity

Range

Agent

Slot

wasDerivedFrom

prov:wasDerivedFrom

Entity derived from another Entity.

Domain

Conclusion, Dataset, Evidence, ExperimentalMethod, Hypothesis, Premise, Question, Result

Slot

wasGeneratedBy

prov:wasGeneratedBy

The activity that generated this entity.

Domain

Annotation, Conclusion, Dataset, Evidence, ExperimentalMethod, Hypothesis, Premise, Question, Result

Slot

wasInformedBy

prov:wasInformedBy

Activity that informed this Activity.

Domain

Analysis, DesignOfExperiment, EvidenceAssessment, EvidenceExtraction, Experimentation, HypothesisFormation, LiteratureSearch, QuestionFormation, ResultAssessment

Enumerations 1

Enumerations defined in this ontology.

UncertaintyNature

Enum

UncertaintyNature

Permissible values

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.