PREBIOTIC ORIGINS OF LIFE ONTOLOGY (POLO): A FORMAL, DOMAIN-SPECIFIC ONTOLOGY FOR EXPERIMENTAL PREBIOTIC CHEMISTRY

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Ontology Specification Draft

Abstract

The study of life's origins is underpinned by the vast literature in prebiotic chemistry, which is the study of the chemistry that proceeded on the early Earth prior to life's emergence. Such research focuses on experiments and models, and this vast and complex field poses challenges due to the significant diversity of experimental input and outcome parameters. To overcome this challenge, we introduce an ontology for the field of prebiotic chemistry. The primary objective of this approach is to organize data in a systematic way, thereby providing a framework to study the experimental landscape of prebiotic chemistry more effectively. An ontology-based on experimental workflows relevant to prebiotic chemistry has been developed. The ontology framework is adaptable and can be readily expanded to accommodate additional workflows and their parameters. The ontology is an effective solution that can be used as a foundation for developing new tools and technologies. By implementing semantic technologies into a scientific discipline, this work aims to serve as an example of the implementation of semantic eScience pipelines. It is expected that the use of this ontology will be positively adopted by the prebiotic chemistry community and will help streamline the data generated from the experiments of prebiotic chemistry. This approach will play an essential role in consolidating the heterogeneous data that comes with the multidisciplinary nature of the field, thereby facilitating a more efficient and effective research approach.

Introduction back to ToC

Prebiotic chemistry investigates the chemical processes that may have given rise to life on early Earth. The field is inherently multidisciplinary, drawing on geology, chemistry, biology, and planetary science, and generates heterogeneous experimental data that is difficult to compare and query across studies. POLO addresses this challenge by providing a formal, machine-readable vocabulary for representing prebiotic chemistry experiments as linked data. POLO was developed at Rensselaer Polytechnic Institute as part of the NASA Earth First Origins project, under the supervision of Dr. James A. Hendler and Dr. Karyn L. Rogers. It is the first ontology specifically designed for experimental prebiotic chemistry and is intended to serve as the semantic layer for the EORE (Executable Online Resource of Experimental Data) framework.

Description back to ToC

POLO provides a structured vocabulary for annotating and querying experimental prebiotic chemistry data, covering batch and continuous flowthrough experiment types.

Cross-Reference back to ToC

This section provides details for each class and property defined by Prebiotic Origins of Life Ontology (POLO).

Classes

Analysisc back to ToC or Class ToC

IRI: https://purl.org/polo#Analysis

The analysis component of a flowthrough experiment.
has super-classes
Flowthrough c

Batchc back to ToC or Class ToC

IRI: https://purl.org/polo#Batch

A batch experiment where a measured amount of chemical compositions interact over a fixed duration with no additions during the process.
has super-classes
ExperimentType c
is in domain of
hasState op

Conditionsc back to ToC or Class ToC

IRI: https://purl.org/polo#Conditions

System conditions for an experiment at a given state.
has sub-classes
FinalSystemConditions c, InitialSystemConditions c, LoadingConditions c

Continuousc back to ToC or Class ToC

IRI: https://purl.org/polo#Continuous

The continuous component of a flowthrough experiment where fluid passes through the stationary stage.
has super-classes
Flowthrough c

Experimentc back to ToC or Class ToC

IRI: https://purl.org/polo#Experiment

The top-level class representing a prebiotic chemistry experiment reported in a scientific paper.
has super-classes
is in domain of
hasMetadata op, hasSetup op

ExperimentSetupc back to ToC or Class ToC

IRI: https://purl.org/polo#ExperimentSetup

Describes the experimental setup parameters for a given experiment.
has sub-classes
ExperimentType c
is in domain of
durationHrs dp, hasExperimentType op, replicatesCount dp, systemType dp, unknownReplicatesCount dp
is in range of
hasSetup op

ExperimentStatec back to ToC or Class ToC

IRI: https://purl.org/polo#ExperimentState

A state of a batch experiment, either initial or final.
has sub-classes
FinalState c, InitialState c
is in range of
hasState op

ExperimentTypec back to ToC or Class ToC

IRI: https://purl.org/polo#ExperimentType

The type of prebiotic chemistry experiment.
has super-classes
ExperimentSetup c
has sub-classes
Batch c, Flowthrough c
is in range of
hasExperimentType op

FinalStatec back to ToC or Class ToC

IRI: https://purl.org/polo#FinalState

The final state of a batch experiment after conditions have been applied.
has super-classes
ExperimentState c

FinalSystemConditionsc back to ToC or Class ToC

IRI: https://purl.org/polo#FinalSystemConditions

System conditions recorded at the final state of a batch experiment.
has super-classes
Conditions c

Flowthroughc back to ToC or Class ToC

IRI: https://purl.org/polo#Flowthrough

A continuous flowthrough experiment.
has super-classes
ExperimentType c
has sub-classes
Analysis c, Continuous c, Stationary c

GasPhasec back to ToC or Class ToC

IRI: https://purl.org/polo#GasPhase

The gas phase component of an experiment.
has super-classes
Phases c
is in domain of
ambientAtmosphere dp, gasConcentration dp, gasIsMeasured dp, gasName dp

InitialStatec back to ToC or Class ToC

IRI: https://purl.org/polo#InitialState

The initial state of a batch experiment before conditions are applied.
has super-classes
ExperimentState c

InitialSystemConditionsc back to ToC or Class ToC

IRI: https://purl.org/polo#InitialSystemConditions

System conditions recorded at the initial state of a batch experiment.
has super-classes
Conditions c

LiquidPhasec back to ToC or Class ToC

IRI: https://purl.org/polo#LiquidPhase

The liquid phase component of an experiment.
has super-classes
Phases c
is in domain of
freqOfMonomer dp, isPolymer dp, liquidIsMeasured dp, monomerName dp, noOfUniqueMonomers dp, polymerLength dp, polymerLengthUnknown dp, soluteConcentration dp, soluteConcentrationUnknown dp, soluteName dp, solventName dp, solventType dp

LoadingConditionsc back to ToC or Class ToC

IRI: https://purl.org/polo#LoadingConditions

Conditions at the loading stage of a batch experiment.
has super-classes
Conditions c
is in domain of
containerMaterial dp

PaperMetadatac back to ToC or Class ToC

IRI: https://purl.org/polo#PaperMetadata

Provenance information about the scientific paper in which the experiment was reported.
is in domain of
paperAuthor dp, paperDoi dp, paperJournal dp, paperTitle dp, paperYear dp
is in range of
hasMetadata op

Phasesc back to ToC or Class ToC

IRI: https://purl.org/polo#Phases

The phases of matter present in an experiment.
has sub-classes
GasPhase c, LiquidPhase c, SolidPhase c

SolidPhasec back to ToC or Class ToC

IRI: https://purl.org/polo#SolidPhase

The solid phase component of an experiment.
has super-classes
Phases c
is in domain of
formOfAmorphSolid dp, maxGrainSize dp, minGrainSize dp, particleSizeUnknown dp, solidIsMeasured dp, solidMass dp, solidName dp, solidType dp

Stationaryc back to ToC or Class ToC

IRI: https://purl.org/polo#Stationary

The stationary component of a flowthrough experiment.
has super-classes
Flowthrough c

Object Properties

hasConditionsop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasConditions

Links an experiment state to its system conditions.

hasExperimentTypeop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasExperimentType

has domain
ExperimentSetup c
has range
ExperimentType c

hasMeasurementop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasMeasurement

Links a phase or condition to its method of measurement.

hasMetadataop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasMetadata

Links an experiment to its paper metadata provenance.
has domain
Experiment c
has range
PaperMetadata c

hasPhaseop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasPhase

Links an experiment state to one of its phases (gas, liquid, solid).

hasSetupop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasSetup

Links an experiment to its experimental setup.
has domain
Experiment c
has range
ExperimentSetup c

hasStateop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasState

Links a batch experiment to its initial or final state.
has domain
Batch c
has range
ExperimentState c

hasUnitop back to ToC or Object Property ToC

IRI: https://purl.org/polo#hasUnit

Links a measurement to its unit of measurement from the Units Ontology.

Data Properties

ambientAtmospheredp back to ToC or Data Property ToC

IRI: https://purl.org/polo#ambientAtmosphere

has domain
GasPhase c
has range
boolean

containerMaterialdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#containerMaterial

has domain
LoadingConditions c
has range
string

durationHrsdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#durationHrs

Duration of the experiment in hours.
has domain
ExperimentSetup c
has range
decimal

formOfAmorphSoliddp back to ToC or Data Property ToC

IRI: https://purl.org/polo#formOfAmorphSolid

Form of amorphous solid e.g. chunk or powder.
has domain
SolidPhase c
has range
string

freqOfMonomerdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#freqOfMonomer

has domain
LiquidPhase c
has range
integer

gasConcentrationdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#gasConcentration

has domain
GasPhase c
has range
decimal

gasIsMeasureddp back to ToC or Data Property ToC

IRI: https://purl.org/polo#gasIsMeasured

has domain
GasPhase c
has range
boolean

gasNamedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#gasName

has domain
GasPhase c
has range
string

isIsobaricdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#isIsobaric

has range
boolean

isIsochoricdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#isIsochoric

has range
boolean

isIsothermaldp back to ToC or Data Property ToC

IRI: https://purl.org/polo#isIsothermal

has range
boolean

isPolymerdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#isPolymer

has domain
LiquidPhase c
has range
boolean

isRoomTemperaturedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#isRoomTemperature

has range
boolean

liquidIsMeasureddp back to ToC or Data Property ToC

IRI: https://purl.org/polo#liquidIsMeasured

has domain
LiquidPhase c
has range
boolean

maxGrainSizedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#maxGrainSize

Maximum grain size in micrometres.
has domain
SolidPhase c
has range
decimal

minGrainSizedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#minGrainSize

Minimum grain size in micrometres.
has domain
SolidPhase c
has range
decimal

monomerNamedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#monomerName

has domain
LiquidPhase c
has range
string

noOfUniqueMonomersdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#noOfUniqueMonomers

has domain
LiquidPhase c
has range
integer

paperAuthordp back to ToC or Data Property ToC

IRI: https://purl.org/polo#paperAuthor

has domain
PaperMetadata c
has range
string

paperDoidp back to ToC or Data Property ToC

IRI: https://purl.org/polo#paperDoi

has domain
PaperMetadata c
has range
string

paperJournaldp back to ToC or Data Property ToC

IRI: https://purl.org/polo#paperJournal

has domain
PaperMetadata c
has range
string

paperTitledp back to ToC or Data Property ToC

IRI: https://purl.org/polo#paperTitle

has domain
PaperMetadata c
has range
string

paperYeardp back to ToC or Data Property ToC

IRI: https://purl.org/polo#paperYear

has domain
PaperMetadata c
has range
integer

particleSizeUnknowndp back to ToC or Data Property ToC

IRI: https://purl.org/polo#particleSizeUnknown

has domain
SolidPhase c
has range
boolean

polymerLengthdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#polymerLength

Maximum or average polymer length observed.
has domain
LiquidPhase c
has range
decimal

polymerLengthUnknowndp back to ToC or Data Property ToC

IRI: https://purl.org/polo#polymerLengthUnknown

has domain
LiquidPhase c
has range
boolean

pressuredp back to ToC or Data Property ToC

IRI: https://purl.org/polo#pressure

System pressure in bars.
has range
decimal

replicatesCountdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#replicatesCount

has domain
ExperimentSetup c
has range
integer

solidIsMeasureddp back to ToC or Data Property ToC

IRI: https://purl.org/polo#solidIsMeasured

has domain
SolidPhase c
has range
boolean

solidMassdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#solidMass

Solid mass in milligrams.
has domain
SolidPhase c
has range
decimal

solidNamedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#solidName

has domain
SolidPhase c
has range
string

solidTypedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#solidType

Type of solid e.g. mineral, amorphous, rock, other.
has domain
SolidPhase c
has range
string

soluteConcentrationdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#soluteConcentration

Solute concentration in mM/L.
has domain
LiquidPhase c
has range
decimal

soluteConcentrationUnknowndp back to ToC or Data Property ToC

IRI: https://purl.org/polo#soluteConcentrationUnknown

has domain
LiquidPhase c
has range
boolean

soluteNamedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#soluteName

has domain
LiquidPhase c
has range
string

solventNamedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#solventName

has domain
LiquidPhase c
has range
string

solventTypedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#solventType

Type of solvent e.g. organic or inorganic.
has domain
LiquidPhase c
has range
string

systemTypedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#systemType

has domain
ExperimentSetup c
has range
string

temperaturedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#temperature

System temperature in Celsius.
has range
decimal

unknownReplicatesCountdp back to ToC or Data Property ToC

IRI: https://purl.org/polo#unknownReplicatesCount

has domain
ExperimentSetup c
has range
boolean

volumedp back to ToC or Data Property ToC

IRI: https://purl.org/polo#volume

System volume in millilitres.
has range
decimal

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

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.