Preferences for Environments Ontology (PrefEnvO)
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Preferences for Environments Ontology (PrefEnvO)

Release: 2024-06-12

Modified on: 2024-05-30
This version:
http://purl.org/spatialai/prefenvo/v1/core/
Latest version:
http://purl.org/spatialai/prefenvo/v1/core/
Revision:
1.0
Issued on:
2024-06-12
Creators:
Kingsley Wiafe-Kwakye, Kate Beard, Torsten Hahmann
Publisher:
Spatial Knowledge and Artificial Intelligence (SKAI) Lab, University of Maine,
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
http://insertlicenseURIhere.example.org
Repository:
https://github.com/theSKAILab/PrefEnvO
Visualization:
Visualize with WebVowl
Cite as:
. . .
Ontology Specification Draft
The Preferences for Environments Ontology (PrefEnvO) provides a detailed framework for capturing and analyzing species-environment relationships, addressing the granularity needed to represent diverse organisms' preferences across varied environmental conditions. It offers a structured vocabulary for specifying species' environmental preferences, considering spatial and temporal dimensions.

Introduction back to ToC

Understanding the dynamics influencing species distribution and predicting their consequences has become a critical focus within ecology, especially amid growing concerns about rapid environmental change and its impact on endangered species and ecosystem functions. Environmental conditions like climate significantly influence organism diversity across large spatial scales, and species exhibit varying responses to these variables across space and time. Better comprehension of the spatio-temporal responses of organisms to environmental variables is crucial for elucidating their distributions. Ontologies facilitate data integration and enrichment essential for understanding these interactions, but questions remain about specific environmental conditions influencing organisms' well-being. To address this, we introduce the Preferences for Environments Ontology (PrefEnvO) pattern, designed to model interactions between organisms and environmental variables, enabling detailed querying and analysis for various practical applications.

Namespace declarations

Table 1: Namespaces used in the document
[Ontology NS Prefix]<http://purl.org/spatialai/prefenvo/v1/core/>
dcterms<http://purl.org/dc/terms/>
owl<http://www.w3.org/2002/07/owl#>
prov<http://www.w3.org/ns/prov#>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
skos<http://www.w3.org/2004/02/skos/core#>
stad<http://purl.org/spatialai/stad/v2/core/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

Ontology Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Description back to ToC

PrefEnvO allows the capturing of organisms’ habitat requirements and interactions with various environmental factors. This ontology pattern facilitates a detailed and structured representation of the specific environmental conditions in which organisms thrive, allowing for precise querying and analysis of these preferences. Key components of the PrefEnvO pattern include representations of organisms and specific environmental variables, such as “Summer Mean Temperature” or “Soil pH.” It also includes detailed descriptions of the conditions under which organisms can thrive, which can be expressed as ranges, single thresholds, or qualitative summaries. Additionally, the pattern accounts for the relative significance of each environmental variable’s influence on an organism’s distribution, as well as the geographical region and time period relevant to the environmental preferences. By integrating these elements, PrefEnvO provides a comprehensive and flexible approach to understanding and modeling the environmental preferences of organisms, essential for various applications in ecology and environmental management. Description diagrams of PrefEnvO

Cross-reference for classes, object properties and data properties back to ToC

This section provides details for each class and property defined by Preferences for Environments Ontology (PrefEnvO).

Classes

Agentc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Agent

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.
Is defined by
http://www.w3.org/ns/prov-o#
is in range of
wasAttributedTo op

Algorithmc back to ToC or Class ToC

IRI: http://purl.org/spatialai/stad/v2/core/Algorithm

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has sub-classes
Data Transformation c
is in range of
implements op, realizes op

Algorithm Executionc back to ToC or Class ToC

IRI: http://purl.org/spatialai/stad/v2/core/AlgorithmExecution

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has super-classes
is in domain of
executes op, realizes op
is in range of
generated By op

Authoritative Environmental Preference Setc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/AuthoritativeEnvironmentalPreferenceSet

Environmental preferences derived from literature sources
has super-classes
Environmental Preference Set c
is in domain of
has Authoritative Source Description op

Authoritative Source Descriptionc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/AuthoritativeSourceDescription

Provides provenance information for an AuthoritativeEnvironmentalPreferenceSet regarding the source of the information
has super-classes
is in range of
has Authoritative Source Description op

Computational Environmental Preference Setc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/ComputationalEnvironmentalPreferenceSet

Environmental preferences derived directedly from observation data
has super-classes
Environmental Preference Set c

Correlation Clusterc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/CorrelationCluster

correlation cluster groups environmental variables based on their similar influence or importance for an organism
has super-classes
is in domain of
correlating Quality op
is in range of
associated Cluster op

Data Transformationc back to ToC or Class ToC

IRI: http://purl.org/spatialai/stad/v2/core/DataTransformation

has super-classes
Algorithm c

Entityc back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Entity

An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.
Is defined by
http://www.w3.org/ns/prov-o#
is in domain of
hadPrimarySource op, wasAttributedTo op
is in range of
hadPrimarySource op

Environmental Preferencec back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/EnvironmentalPreference

Specific preference of an organism regarding a specific environmental variable
has super-classes
is in domain of
associated Cluster op, has Predictor Importance op, has Preference Description op, has Spatial Coverage op, has Temporal Coverage op, preference For op
is in range of
contains Preference op, has Environmental Preference op

Environmental Preference Setc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/EnvironmentalPreferenceSet

A set of Environmental preferences of an organism for specific location and time
has super-classes
has sub-classes
Authoritative Environmental Preference Set c, Computational Environmental Preference Set c
is in domain of
contains Preference op, has Spatial Coverage op, has Temporal Coverage op
is in range of
has Environmental Preference op, importance Within op

Implementationc back to ToC or Class ToC

IRI: http://purl.org/spatialai/stad/v2/core/Implementation

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has super-classes
is in domain of
has Parameter op, implements op
is in range of
executes op

Parameterc back to ToC or Class ToC

IRI: http://purl.org/spatialai/stad/v2/core/Parameter

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
is in range of
has Parameter op, specified By op

Parameter Settingc back to ToC or Class ToC

IRI: http://purl.org/spatialai/stad/v2/core/ParameterSetting

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has super-classes
is in domain of
specified By op

Predictor Importancec back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/PredictorImportance

Provides an indication of the influence of an environmental variable on an organism or group of organisms
has super-classes
is in domain of
has Importance Rank op, importance Within op
is in range of
has Predictor Importance op

Predictor Importance Rankc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/PredictorImportanceRank

Provides importance of each preference by assigning a rank to indicate the extent of a preference relative to other preferences of the organism

Preference Descriptionc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/PreferenceDescription

Provides an indication of the influence of an environmental variable on an organism or group of organisms
has sub-classes
Qualitative Preference Description c, Quantitative Preference Description c
is in range of
has Preference Description op

Qualitative Preference Descriptionc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/QualitativePreferenceDescription

Preferences of environmental variables that are measured qualitatively, typically non-numeric, attributes that denote categorical distinctions such as different soil types
has super-classes
Preference Description c
is in domain of
preference Value op

Quantitative Preference Descriptionc back to ToC or Class ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/QuantitativePreferenceDescription

Preferences that can be expressed and measured in numerical terms, encompassing specific quantitative values for environmental variables
has super-classes
Preference Description c
is in domain of
maximum Preference op, minimum Preference op

Object Properties

associated Clusterop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/associatedCluster

links an prefernce environment to its associated correlation cluster.
has domain
Environmental Preference c
has range
Correlation Cluster c

contains Preferenceop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/containsPreference

Links EnvironmentalPreferenceSet with every EnvironmentalPreference that is part of the set.
has domain
Environmental Preference Set c
has range
Environmental Preference c

correlating Qualityop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/correlatingQuality

connects to every environmental variable that is part of a correlation cluster.
has domain
Correlation Cluster c
has range
Quality Kind c
has sub-property chains
o preference For op

environmental Preference Ofop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/environmentalPreferenceOf

links an organism to its prefernce environment.
is inverse of
has Environmental Preference op
has sub-property chains
o environmental Preference Of op

executesop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/executes

Links an AlgorithmExecution to the specific Implementaion of the Algorithm executed.
Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has domain
Algorithm Execution c
has range
Implementation c

generated Byop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/generatedBy

Links anything that is generated by an Algorithm to the specific AlgorithmExecution that was used
has domain
Thing c
has range
Algorithm Execution c

hadPrimarySourceop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#hadPrimarySource

Is defined by
http://www.w3.org/ns/prov-o#
has domain
Entity c
has range
Entity c

has Authoritative Source Descriptionop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasAuthoritativeSourceDescription

links an authoritative preference preference set to the authoritative entity that published the information.
has domain
Authoritative Environmental Preference Set c
has range
Authoritative Source Description c

has Environmental Preferenceop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasEnvironmentalPreference

This is the inverse of environmentalPreferenceOf; it links an organism to its preferences.
has domain
Thing c
has range
Environmental Preference c or Environmental Preference Set c
is inverse of
environmental Preference Of op

has Importance Rankop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasImportanceRank

Assigns a rank to a PredictorImportance instance.
has domain
Predictor Importance c
has range
Importance Rank c

has Inputop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/hasInput

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf

has Parameterop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/hasParameter

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has domain
Implementation c
has range
Parameter c

has Predictor Importanceop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasPredictorImportance

Links EnvironmentalPreference to PredictorImportance.
has domain
Environmental Preference c
has range
Predictor Importance c

has Preference Descriptionop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasPreferenceDescription

Links EnvironmentalPreference to PreferenceDescription.
has domain
Environmental Preference c
has range
Preference Description c

has Spatial Coverageop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasSpatialCoverage

Links EnvironmentalPreference or EnvironmentalPreferenceSet to spatial region the preference refers.
has domain
Environmental Preference c or Environmental Preference Set c
has range
Spatial Coverage c
has sub-property chains
o has Spatial Coverage op

has Temporal Coverageop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/hasTemporalCoverage

Links EnvironmentalPreference or EnvironmentalPreferenceSet to time interval the preference refers.
has domain
Environmental Preference c or Environmental Preference Set c
has range
Temporal Coverage c
has sub-property chains
o has Temporal Coverage op

implementsop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/implements

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has domain
Implementation c
has range
Algorithm c

importance Withinop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/importanceWithin

Connects PredictorImportance to the EnvironmentalPreferenceSet within which relative ranking is valid.
has domain
Predictor Importance c
has range
Environmental Preference Set c
has sub-property chains
o

maximum Preferenceop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/maximumPreference

Expresses the maximum value of a quantitative preference.
has domain
Quantitative Preference Description c
has range
Quantitative Value c

minimum Preferenceop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/minimumPreference

Expresses the minimum value of a quantitative preference.
has domain
Quantitative Preference Description c
has range
Quantitative Value c

preference Forop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/preferenceFor

Links EnvironmentalPreference to the quality kind for which the preference refers.
has domain
Environmental Preference c
has range
Quality Kind c

preference Valueop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/prefenvo/v1/core/preferenceValue

used in preference description to link preference to categorical values.
has domain
Qualitative Preference Description c
has range
Qualitative Value c

realizesop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/realizes

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has domain
Algorithm Execution c
has range
Algorithm c

specified Byop back to ToC or Object Property ToC

IRI: http://purl.org/spatialai/stad/v2/core/specifiedBy

Is defined by
http://ontologydesignpatterns.org/wiki/images/4/41/WOP2016_paper_07.pdf
has domain
Parameter Setting c
has range
Parameter c

wasAttributedToop back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasAttributedTo

Attribution is the ascribing of an entity to an agent.
Attribution is the ascribing of an entity to an agent.
Is defined by
http://www.w3.org/ns/prov-o#
has domain
Entity c
has range
Agent c

Legend back to ToC

c: Classes
op: Object Properties

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.