Linked Earth landing page

Here you can find a pointer to the main concepts and ontologies in the Linked Earth specification.

Overview

The Linked Earth specification is divided in several documents to facilitate its navigation.

• The LiPD Ontology provides the main concepts and relationships to describe a paleoclimate dataset and its values.
• The Proxy Archive Ontology describes a taxonomy of the most common types of archives.
• The Proxy Observation Ontology describes a taxonomy of the most common types of observed properties (e-g-, temperature, moisture, thickness, etc.
• The Proxy Sensor Ontology describes a taxonomy of the most common types of sensors.
• The Instrument Ontology describes a taxonomy of the most common instrument for taking measurements.
• The Inferred Variable Ontology describes a taxonomy of the most common types of inferred variables that can be found in a dataset.

Accessing the Linked Earth Ontology

The following table contains the pointers to the Linked Earth ontologies:

Ontology Serialization Version License Language Description
The LiPD Ontology TURTLE 1.2.0 BY/2.0 en The LiPD Ontology aims to provide a common vocabulary for annotating paleoclimatology data
The Proxy Archive Ontology TURTLE 1.0.0 BY/2.0 en The Proxy Archive Ontology defines different types of proxy archives that we can find in a paleo climate dataset.
The Proxy Observation Ontology TURTLE 1.0.0 BY/2.0 en The Proxy Observation Type Ontology defines different types of proxy observations that we can find in a paleo climate dataset.
The Proxy Sensor Ontology TURTLE 1.0.0 BY/2.0 en The Proxy Sensor Ontology defines different types of proxy sensors that we can find in a paleo climate dataset.
The Instrument Ontology TURTLE 1.0.0 BY/2.0 en The Instrument Ontology defines the different types of instruments that can be used to measure in a paleo climate dataset.
Inferred Variable Ontology TURTLE 1.0.0 BY/2.0 en Inferred Variable Ontology describes a taxonomy of the most common types of inferred variables that can be found in a dataset.

Alternatively, you can access programatically with the following commands:

• Turtle
• curl -sH "Accept: text/turtle" -L http://linked.earth/ontology#
• RDF/XML
• curl -sH "Accept: application/rdf+xml" -L http://linked.earth/ontology#

Contributing to the ontology

To suggest changes to a term in the core ontology, start a discussion on its wiki page (all terms and properties have associated wiki pages). Once a community consensus has been reached, use this form to contact the Editorial Board about the change.

The Linked Earth concepts and relationships

Here you can find a list of the main concepts and relationships in the Linked Earth Documents, sorted in alphabetical order.

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z |

A

AcceleratorMassSpectrometer

Defined in: The Instrument Ontology

AcceleratorMassSpectrometerInstrument

Defined in: The Instrument Ontology

age

The age of a sample

Defined in: The Inferred Variable Ontology

Al/Ca

Defined in: The Proxy Observation Type Ontology

Ar-Ar

Defined in: The Proxy Observation Type Ontology

Archea

Defined in: The Proxy Sensor Ontology

arcticOscillation

Defined in: The Inferred Variable Ontology

Assemblage

Defined in: The Proxy Observation Type Ontology

atlanticMultiDecadalOscillation

Defined in: The Inferred Variable Ontology

AtmosphericChemistry

Defined in: The Inferred Variable Ontology

author

Answers the question: Who wrote (i.e., created) the resource, such as a Publication?

Defined in: The LiPD Ontology

B

B/Ca

Defined in: The Proxy Observation Type Ontology

Ba/Ca

Defined in: The Proxy Observation Type Ontology

BinocularMicroscope

Defined in: The Instrument Ontology

Bivalves

Defined in: The Proxy Sensor Ontology

book

Answers the question: In which book was the resource published?

Defined in: The LiPD Ontology

bottomWaterTemperature

Defined in: The Inferred Variable Ontology

C

C

Defined in: The Proxy Observation Type Ontology

calibratedVia

Answers the question: What calibration process was used to relate the InferredVariable to the MeasuredVariable?

Defined in: The LiPD Ontology

CalibrationModel

Metadata about how the variable was calibrated to reflect an environmental variable

Defined in: The LiPD Ontology

calibrationReferences

Answers the question: In what Reference(s) is the Calibration described/justified?

Defined in: The LiPD Ontology

CarbonateIonConcentration

Defined in: The Inferred Variable Ontology

carbonateSaturation

Defined in: The Inferred Variable Ontology

carbonDioxideConcentration

Defined in: The Inferred Variable Ontology

CFAMS

Defined in: The Instrument Ontology

Chemical

Defined in: The Proxy Observation Type Ontology

Chironomids

Defined in: The Proxy Sensor Ontology

ChronData

The data, metadata, and Model that describe the set of Variables used to relate depth/position to time (chronological information)

Defined in: The LiPD Ontology

ChronDataTable

DataTable containing Variables pertaining to chronological information

Defined in: The LiPD Ontology

ChronModel

Model used to derive a time (or age) axis from the ChronDataModel

Defined in: The LiPD Ontology

chronModeledBy

Answers the question: What is the ChronModel for the ChronData or ProxySystem under consideration?

Defined in: The LiPD Ontology

ChronProxySystem

The combination of ProxyArchive, ProxySensor, and ProxyObservations pertaining to chronological information. For instance, measurements of radiocarbon on foraminiferal shells would have a ChronProxySystem consisting of ProxyArchive: marine sediment, ProxySensor: Foraminifera, ProxyObservations: Radiocarbon. (ref: Evans et al. [2013])

Defined in: The LiPD Ontology

ClayFraction

Defined in: The Proxy Observation Type Ontology

ClimateIndex

Defined in: The Inferred Variable Ontology

Coccolithophores

Defined in: The Proxy Sensor Ontology

collectedFrom

Answers the question: Where (in the world) was the data in the Dataset collected? Refers to the location of the ProxyArchive

Defined in: The LiPD Ontology

Color

Defined in: The Proxy Observation Type Ontology

Compilation

A curated aggregation of datasets

Defined in: The LiPD Ontology

compilationCitation

Answers the question: How should someone cite the compilation?

Defined in: The LiPD Ontology

compilationDate

Answers the question: At what date was the Compilation created?

Defined in: The LiPD Ontology

compilationVersion

Answers the question: What is the version of the Compilation?

Defined in: The LiPD Ontology

Composition

Defined in: The Proxy Observation Type Ontology

contributor

Answers the question: Who contributed the resource? A contributor may be the same as the authors of the resource or different. For instance, in the case of a legacy dataset, a Linked Earth member may contribute a previously-published dataset that he/she may not have authored

Defined in: The LiPD Ontology

coral

Defined in: The Proxy Archive Ontology

CRDS

Defined in: The Instrument Ontology

D

d13C

Defined in: The Proxy Observation Type Ontology

d15N

Defined in: The Proxy Observation Type Ontology

d170

Defined in: The Proxy Observation Type Ontology

d180

Oxygen has three naturally-occuring stable isotopes: 16O, 17O, 18O, with 16O being the most abundant (99.762%). Two international reference standards are used to report variations in oxygen isotope standards: PDB and SMOW. The use of the PDB standard in reporting oxygen isotope composition is restricted to carbonates of low-temperature origins (e.g., oceanic, lacustrine ). The conversion between SMOW and PDB scales is given by: \delta^{18}O_{SMOW} = 1.03091 (\delta^{18}O_{PDB}) +30.91 ?18O may be measured on the shells of foraminifera

Defined in: The Proxy Observation Type Ontology

d34S

Defined in: The Proxy Observation Type Ontology

Data

An aggregation of DataTables and Models with their supporting paleoenvironmental and/or chronological information

Defined in: The LiPD Ontology

Dataset

A structured collection of related information, including -but not limited to -measured and/or modelled geograhical, chronological, and environmental data

Defined in: The LiPD Ontology

datasetCitation

Sentence indicating how a dataset should be cited

Defined in: The LiPD Ontology

datasetDate

Answers the question: At what date was the Dataset created?

Defined in: The LiPD Ontology

datasetLicense

License associated to a dataset

Defined in: The LiPD Ontology

datasetVersion

Answers the question: What is the version of the Dataset? It should follow the x.y.z notation where x refers to changes in metadata and data following a publication (for instance, the creation of a new age model using a different code), y refers to changes to the data following a publication (for instance, adding data further back in time without changing the model underlying the interpretation), and z refers to changes not associated with a publication (for instance, typos).

Defined in: The LiPD Ontology

DataTable

A set of Variables organized in columns

Defined in: The LiPD Ontology

dD

Defined in: The Proxy Observation Type Ontology

Density

Defined in: The Proxy Observation Type Ontology

description

Answers the question: What additional details would you give about the resource?

Defined in: The LiPD Ontology

detail

Answers the "of what" question for an Interpretation. For intance, sea surface in sea surface temperature.

Defined in: The LiPD Ontology

deuteriumExcess

Defined in: The Inferred Variable Ontology

Diffraction

Defined in: The Proxy Observation Type Ontology

DiffuseSpectralReflectance

Defined in: The Proxy Observation Type Ontology

DistributionTable

DataTable containing the probability distribution of a single value of a Variable. Output of a Model

Defined in: The LiPD Ontology

distributionTableGeneratedByModel

Answers the question: In which DistributionTable is the Model output found?

Defined in: The LiPD Ontology

document

Defined in: The Proxy Archive Ontology

E

ElNinoIndex

Defined in: The Inferred Variable Ontology

email

Answers the question: What is the email address of the Person?

Defined in: The LiPD Ontology

EnergyDispersiveSpectrometer

Defined in: The Instrument Ontology

EnsembleTable

DataTable constaining many possible series of how the Variable is modeled. Output of a Model

Defined in: The LiPD Ontology

ensembleTableGeneratedByModel

Answers the question: In which EnsembleTable is the Model output found?

Defined in: The LiPD Ontology

equation

Answers the question: What is the mathematical formulation of the Model?

Defined in: The LiPD Ontology

F

Faunal

Defined in: The Proxy Observation Type Ontology

Fe/Ca

Defined in: The Proxy Observation Type Ontology

Floral

Defined in: The Proxy Observation Type Ontology

Fluorescence

Defined in: The Proxy Observation Type Ontology

Foraminifera

Because of their population size, foraminifera produce a significant amount of oceanic carbonate, making them a valuable source of paleoceanographic information. The following parameters are used in paleoceanographic applications: * Faunal Assemblage * Geochemical measurements: * Isotopes * Stable oxygen isotopes * Stable carbon isotopes * Radiocarbon * Trace Elements

Defined in: The Proxy Sensor Ontology

foundInMeasurementTable

Answers the question: In which MeasurementTable are the Variables found?

Defined in: The LiPD Ontology

foundInTable

Answers the question: In which DataTable can the information/data be found?

Defined in: The LiPD Ontology

freeOxygenLevels

Defined in: The Inferred Variable Ontology

fundedBy

Answers the question: What was the Funding source for the Dataset?

Defined in: The LiPD Ontology

Funding

Source of monetary support underlying the collection/creation/analysis/curation of the Dataset

Defined in: The LiPD Ontology

fundingAgency

Answers the question: Which entity was the Dataset fundedBy?

Defined in: The LiPD Ontology

fundingCountry

Answers the question: Which nation funded the Dataset?

Defined in: The LiPD Ontology

G

GasChromatograph

Defined in: The Instrument Ontology

GasChromatographyMassSpectrometer

Defined in: The Instrument Ontology

Gastropods

Defined in: The Proxy Sensor Ontology

GC-IR-MS

Defined in: The Instrument Ontology

GCMS

Defined in: The Instrument Ontology

generatedByModel

Answers the question: which model was used to generated this data table?

Defined in: The LiPD Ontology

GlacierIce

Defined in: The Proxy Archive Ontology

GrainSize

Defined in: The Proxy Observation Type Ontology

grantNumber

Answers the question: What is the unique identifier associated with the Funding for the Dataset?

Defined in: The LiPD Ontology

H

hasCode

Answers the question: What SoftwareCode was used to generate the Model output?

Defined in: The LiPD Ontology

hasColumnNumber

Answers the question: In which column of the csv file can the Variable be found?

Defined in: The LiPD Ontology

hasDatasetID

Property used to associate an identifier to a dataset

Defined in: The LiPD Ontology

hasDOI

Answers the question: What is the digital object identifier associated with the resource?

Defined in: The LiPD Ontology

hasExecutionCommand

Answers the question: What is the command to run the script or the code?

Defined in: The LiPD Ontology

hasExecutionEnvironment

Answers the question: In which environment is the script meant to be run in?

Defined in: The LiPD Ontology

hasFileName

Answers the question: What is the name of the csv file in which the Variable values are stored?

Defined in: The LiPD Ontology

hasIGSN

IGSN identifier associated to a physical sample

Defined in: The LiPD Ontology

hasIntegrationTime

Answers the question: What is the integration time needed for a ProxySensor to imprint environmental information on the ProxyArchive? Both are included as part of a ProxySystem

Defined in: The LiPD Ontology

hasISBN

Answers the question: What is the international book number of the Publication?

Defined in: The LiPD Ontology

hasISSN

Answers the question: What is the International Standard Serial Number of the Publication?

Defined in: The LiPD Ontology

Answers the question: What is the universal resource locator to a resource?

Defined in: The LiPD Ontology

hasMaxValue

Answers the question: What is the maximum value of the Variable?

Defined in: The LiPD Ontology

hasMeanValue

Answers the question: What is the mean value of the Variable?

Defined in: The LiPD Ontology

hasMedianValue

Answers the question: What is the median value of the Variable?

Defined in: The LiPD Ontology

hasMinValue

Answers the question: What is the minimum value of the Variable?

Defined in: The LiPD Ontology

hasMissingValue

Answers the question: How are the missing values of the Variable identified in the DataTable?

Defined in: The LiPD Ontology

hasProxySystem

Answers the question: What is the ProxySystem associated with this MeasuredVariable?

Defined in: The LiPD Ontology

hasRank

Answers the question: What is the importance of the Interpretation?

Defined in: The LiPD Ontology

hasResolution

Answers the question: What is the Resolution of the Variable?

Defined in: The LiPD Ontology

hasUncertainty

Answers the question: What is the Uncertainty associated with the Variable, Model, or Instrument?

Defined in: The LiPD Ontology

hasUnits

Answers the question: In what unit of measure is (are) the Variable(s) expressed?

Defined in: The LiPD Ontology

hasValue

Answers the question: What are the numerical values of the Variable, Uncertainty, and Model outputs?

Defined in: The LiPD Ontology

hasVariableID

Answers the question: What is the unique identifier for the Variable?

Defined in: The LiPD Ontology

Historic

Defined in: The Proxy Observation Type Ontology

housedAt

Answers the question: In which laboratory/repository is the Instrument/PhysicalSample located?

Defined in: The LiPD Ontology

hybrid

Defined in: The Proxy Archive Ontology

Hydrology

Defined in: The Inferred Variable Ontology

I

IceSheet

Defined in: The Proxy Sensor Ontology

ICP-AES

Inductively coupled plasma atomic emission spectroscopy (ICP-AES), also referred to as inductively coupled plasma optical emission spectrometry (ICP-OES), is an analytical technique used for the detection of trace metals.

Defined in: The Instrument Ontology

ICP-MS

Defined in: The Instrument Ontology

ICP-OES

Defined in: The Instrument Ontology

includesChronData

Answers the question: Which ChronData are included in the Dataset?

Defined in: The LiPD Ontology

includesData

Answers the question: Which Data are included in the Dataset?

Defined in: The LiPD Ontology

includesPaleoData

Answers the question: Which PaleoData are included in the Dataset?

Defined in: The LiPD Ontology

includesVariable

Answers the question: Which Variables are included in the DataTable?

Defined in: The LiPD Ontology

inferredFrom

Answers the question: From which MeasuredVariable(s) is (are) the InferredVariable inferred from?

Defined in: The LiPD Ontology

InferredVariable

A Variable that is inferred from one or more MeasuredVariable (s)

Defined in: The LiPD Ontology

inferredVariableType

Answers the question: What type of InferredVariable does the InferredVariable belongs to?

Defined in: The LiPD Ontology

InorganicProxySensor

An inorganic substrate sensing enviromental changes. Examples: karst, snow, watershed, ice sheet, rock, etc.

Defined in: The LiPD Ontology

Instrument

A tool used to produce MeasuredVariables

Defined in: The LiPD Ontology

IntegrationTime

The time it takes for the ProxySensor to imprint environmental information on the ProxyArchive. It may be further qualified with time periods and units

Defined in: The LiPD Ontology

Interpretation

A suite of metadata that describes which phenomena drove variability in this Variable (e.g. environmental drivers).

Defined in: The LiPD Ontology

interpretationDirection

Answers the question: Is the InferredVariable value increasing or decreasing as the value of the MeasuredVariable is increasing?

Defined in: The LiPD Ontology

interpretationReferences

Answers the question: In which Publication(s) is the Interpretation substantiated?

Defined in: The LiPD Ontology

interpretedAs

Answers the question: What is the Variable's Interpretation?

Defined in: The LiPD Ontology

IRMS

An isotope-ration mass spectrometer measures the relative abundance of isotopes in a given sample.

Defined in: The Instrument Ontology

isLocal

Answers the question: Does the Interpretation describe local variability, or far-field variability that may not reflect local conditions?

Defined in: The LiPD Ontology

Isotope

Atoms can be simply described as consisting of protons, electrons, and neutrons. Isotopes of the same element differ by the number of neutrons in the nucleus, resulting in different mass.

Defined in: The Proxy Observation Type Ontology

IsotopeRatioMassSpectrometer

Defined in: The Instrument Ontology

IsotopicComposition

Defined in: The Inferred Variable Ontology

issue

Answers the question: In what issue of the journal can the resource be found?

Defined in: The LiPD Ontology

J

journal

Answers the question: What is the name of the journal in which the resource can be found?

Defined in: The LiPD Ontology

julianDay

Defined in: The Inferred Variable Ontology

K

Karst

Defined in: The Proxy Sensor Ontology

L

LA-ICP-MS

Defined in: The Instrument Ontology

lakeSediment

Defined in: The Proxy Archive Ontology

LayerThickness

Defined in: The Proxy Observation Type Ontology

LeadIsotope

Defined in: The Proxy Observation Type Ontology

Li/Ca

Defined in: The Proxy Observation Type Ontology

Lithics

Defined in: The Proxy Observation Type Ontology

Location

The geographic data and metadata for the dataset

Defined in: The LiPD Ontology

Luminescence

Defined in: The Proxy Observation Type Ontology

M

MagneticSusceptibility

Defined in: The Proxy Observation Type Ontology

MajorElement

Defined in: The Proxy Observation Type Ontology

MarineSediment

Marine sediments are a type of proxy archives‏‎ that provide long, continuous records of past ocean variability. The timescales associated with this archive‏‎ are usually in the order of several tens to millions of years. The resolution of the sedimentary archive varies from annual to multi-century. Paleoceanographic data are derived from many sensors found in deep-sea sediments including trace metal and isotopic composition of foraminifera, alkenones, and TEX86.

Defined in: The Proxy Archive Ontology

MassSpectrometer

Defined in: The Instrument Ontology

MassSpectrometerInstrument

Defined in: The Instrument Ontology

MC-ICP-MS

Defined in: The Instrument Ontology

measuredBy

Answers the question: Which Instrument was used to produce the MeasuredVariable?

Defined in: The LiPD Ontology

measuredOn

Answers the question: On which PhysicalSample was the MeasuredVariable measured?

Defined in: The LiPD Ontology

MeasuredVariable

Variables that are measured by an Instrument. MeasuredVariables are ssn: Observations. They represent the values of a certain type of ProxyObservations

Defined in: The LiPD Ontology

MeasurementTable

DataTable that contains the Variables (both measured and inferred)

Defined in: The LiPD Ontology

methaneConcentration

Defined in: The Inferred Variable Ontology

method

Answers the question: How is the information obtained from the resource?

Defined in: The LiPD Ontology

Mg/Ca

Defined in: The Proxy Observation Type Ontology

Microscope

Defined in: The Instrument Ontology

MineralMatter

Defined in: The Proxy Observation Type Ontology

Mn/Ca

Defined in: The Proxy Observation Type Ontology

Model

A mathematical construct that is at least partially isomorphic to the target system, and is used to derive information about the structure and/or dynamics of the target system

Defined in: The LiPD Ontology

modeledBy

Answers the question: What is the Model for the Data, Compilation or ProxySystem under consideration?

Defined in: The LiPD Ontology

modelReferences

Answers the question: In which Publication is the model described/applied?

Defined in: The LiPD Ontology

MoistureContent

Defined in: The Proxy Observation Type Ontology

Mollusk

Defined in: The Proxy Sensor Ontology

MolluskShells

Defined in: The Proxy Archive Ontology

N

N

Defined in: The Proxy Observation Type Ontology

name

Answers the question: How is the resource called?

Defined in: The LiPD Ontology

Neodymium

Defined in: The Proxy Observation Type Ontology

nino1

Defined in: The Inferred Variable Ontology

Nino1Plus2

Defined in: The Inferred Variable Ontology

nino2

Defined in: The Inferred Variable Ontology

nino3

Defined in: The Inferred Variable Ontology

nino3_4

Defined in: The Inferred Variable Ontology

nino4

Defined in: The Inferred Variable Ontology

nitrousOxideConcentration

Defined in: The Inferred Variable Ontology

NonPeerReviewedPublication

A publication that has not undergone a formal review process; for instance, a Dataset attached to a dissertation.

Defined in: The LiPD Ontology

northAtlanticOscillation

Defined in: The Inferred Variable Ontology

NOSAMSTandetron

Defined in: The Instrument Ontology

notes

Answers the question: What additional information would you give about the Variable or DataTable ?

Defined in: The LiPD Ontology

O

OceanChemistry

Defined in: The Inferred Variable Ontology

oceanMixedLayerTemperature

Defined in: The Inferred Variable Ontology

orcidNumber

Answers the question: What is the persistent digital identifier of the Person?

Defined in: The LiPD Ontology

OrganicIndex

Paleoceanographers use the term biomarker to describe organic molecules found in marine sediments, initially produced by a variety of organisms either on land or in the marine environment [1]. A key characteristic of biomarkers is their ability to survive deposition in the archive in terms of their original structure and steroidal configuration (i.e., spatial distribution of the atoms) [1]. Their usefulness for paleoceanographic reconstructions largely depends on their degradation within the archive [1].

1. Rosell-Melé, A., & McClymont, E. L. (2007). Biomarkers as Paleoceanographic proxies. Developments in Marine Geology, 1, 441-490. doi:10.1016/S1572-5480(07)01016-0

Defined in: The Proxy Observation Type Ontology

OrganicMatter

Defined in: The Proxy Observation Type Ontology

OrganicProxySensor

Biologically-mediated ProxySensor. Examples include: foraminifera, trees, mollusks, polyps

Defined in: The LiPD Ontology

Ostracods

Defined in: The Proxy Sensor Ontology

P

P

Defined in: The Proxy Observation Type Ontology

pages

Answers the question: In what pages of the Publication can the reference to the resource be found?

Defined in: The LiPD Ontology

PaleoData

The Data pertaining to past environmental variability

Defined in: The LiPD Ontology

PaleoDataTable

DataTable containing PaleoData Variables

Defined in: The LiPD Ontology

PaleoModel

Model used to derive an environmental axis from the PaleoDataModel

Defined in: The LiPD Ontology

paleoModeledBy

Answers the question: What is the PaleoModel for the PaleoData or ProxySytem under consideration?

Defined in: The LiPD Ontology

PaleoProxySystem

Climate observations prior to the instrumental era are necessarily indirect. These observations are made on climate proxies in various geological (e.g. lake or marine sediments, living or fossil coral reefs, cave deposits), glaciological (ice cores or snow pits) or biological (trees) archives. Many types of measurements can be made on each archives, each sensing a different aspect of the environment (sometimes, several aspects at once). A paleoclimate dataset is a set of observations made on an archive.

Defined in: The LiPD Ontology

palmerDroughtIndex

Defined in: The Inferred Variable Ontology

palmerDroughtSeverityIndex

Defined in: The Inferred Variable Ontology

partOfCompilation

Answer the question: Which compilation does a dataset belong to?

Defined in: The LiPD Ontology

Peat

Defined in: The Proxy Archive Ontology

PeerReviewedPublication

A Publication that has undergone a formal peer-review process

Defined in: The LiPD Ontology

Permeability

Defined in: The Proxy Observation Type Ontology

Person

An individual who has participated directly or indirectly in the authoring of any resources on the LinkedEarth wiki

Defined in: The LiPD Ontology

pH

Defined in: The Inferred Variable Ontology

Physical

Defined in: The Proxy Observation Type Ontology

PhysicalSample

The actual sample on which the measurements are made. For instance, the lake core analyzed in the lab is the physical sample.

Defined in: The LiPD Ontology

Polyp

Defined in: The Proxy Sensor Ontology

Porosity

Defined in: The Proxy Observation Type Ontology

Precipitation

Defined in: The Inferred Variable Ontology

precipitationAmount

Defined in: The Inferred Variable Ontology

principalInvestigator

Answers the question: Who was the lead on the source of Funding for the Dataset?

Defined in: The LiPD Ontology

programmedIn

Answers the question: In which language was the software code written in?

Defined in: The LiPD Ontology

ProxyArchive

According to the Evans et al. (2013), the medium in which the response of a ProxySensor to environmental forcing is recorded. Example of archives include: marine sediments, corals, wood, lake sediments, speleothems, glacier ice

Defined in: The LiPD Ontology

ProxyArchiveModel

A Model of how the ProxySensor either creates or emplaces the signal into the ProxyArchive. Sensu Evans et al. (2013)

Defined in: The LiPD Ontology

proxyArchiveType

Answers the question: Which ProxyArchive underlies this ProxySystem?

Defined in: The LiPD Ontology

ProxyObservation

The type of MeasuredVariables measured on the ProxyArchive, whether chemical (e.g. Mg/Ca, D18O, Sr/Ca), physical (e.g. density, layer thickness), or biological (e.g. Species abundance)

Defined in: The LiPD Ontology

ProxyObservationModel

The Model of how ProxyObservations are made on the archive. Sensu Evans et al. (2013)

Defined in: The LiPD Ontology

proxyObservationType

Answers the question: What type of ProxyObservation does the MeasuredVariable or Proxy System belong to? For example, the measured value of 5.63 mmol/mol is of type Mg/Ca, or the proxy observation of the current prpoxy system is Mg/Ca

Defined in: The LiPD Ontology

ProxySensor

The sensor comprises physical, chemical, and/or biological components that react to environmental conditions. Sensors often respond to more than one environmental variable, and may have complex responses to the environment they sense, including thresholds (record only part of the range of environmental conditions), seasonal biases (record environmental conditions over a few months of the year), and/or nonlinear responses (Evans et al. (2013)). Signals recorded by the ProxySensor are imprinted onto the ProxyArchive.

Defined in: The LiPD Ontology

ProxySensorModel

A Model of the ProxySensor. Sensu Evans et al. (2013)

Defined in: The LiPD Ontology

proxySensorType

Answers the question: Which ProxySensor underlies this ProxySystem?

Defined in: The LiPD Ontology

ProxySystem

Climate observations prior to the instrumental era are necessarily indirect. These observations are made on climate proxies in various geological (e.g. lake or marine sediments, living or fossil coral reefs, cave deposits), glaciological (ice cores or snow pits) or biological (trees) archives. Many types of data can often be collected from each archives, each sensing a different aspect of the environment (sometimes, several aspects at once). A paleoclimate dataset is almost always a time series of observations made on an archive.

Evans et al. (2013) [1] define a proxy system as comprised of three components (Fig 1).:

• The sensor comprises physical, chemical, and/or biological components that react to environmental conditions. Sensors often respond to more than one environmental variable, and may have complex responses to the environment they sense, including thresholds (record only part of the range of environmental conditions), seasonal biases (record environmental conditions over a few months of the year), and/or nonlinear responses. For instance, foraminifera are an often used sensor for oceanic conditions. Multiple observations can be made on this sensor, recording different environmental variables. Similarly, picking foraminifera of a given species to conduct the measurements is part of the observation process, though it does affect the sensor definition : the habitat of these forams determines with environmental variable (e.g. surface, sub-surface, or thermocline temperature) they are most sensitive to.
• The archive is the medium in which the response of a sensor to environmental forcing is recorded. Marine sediments are a type of archive, on which many sensors and observations may be recorded (e.g. Foraminifera Mg/Ca, ?18O, TEX86)
• Observations are made on archives and are generally referred to as "proxies". The term "proxy" used ubiquitously, and often ambiguously, throughout the paleoclimate literature, is most commonly equivalent to "sensor + observation". "Observation" is the more explicit, and thus, preferred term, however "proxy" can be treated as a synonym of "observation". For instance, Foraminifera Mg/Ca is often used to investigate past changes in sea-surface temperature but depends also on sea-surface salinity and deep-ocean carbonate saturation [2]. Furthermore, its temperature and salinity dependence is exponential [3] [4] [5] while its response to carbonate saturation is thresholded [6].

These three major components may be individually modeled, and linked together within a Proxy System Model [1] [7]. Some sensors are common to multiple archives (e.g. ?18O), and all archives support more than one possible sensor.

References

1. Evans, M. N., Tolwinski-Ward, S. E., Thompson, D. M., & Anchukaitis, K. J. (2013). Applications of proxy system modeling in high resolution paleoclimatology. Quaternary Science Reviews, 76, 16-28. doi:10.1016/j.quascirev.2013.05.024
2. Jump up ? Khider, D., Huerta, G., Jackson, C., Stott, L. D., & Emile-Geay, J. (2015). A Bayesian, multivariate calibration for Globigerinoides ruber Mg/Ca. Geochemistry Geophysics Geosystems, 16(9), 2916-2932. doi:10.1002/2015GC005844
3. Jump up ? Anand, P., Elderfield, H., & Conte, M. H. (2003). Calibration of Mg/Ca thermometry in planktonic foraminifera from a sediment trap time series. Paleoceanography, 18(2), 1050. doi:10.1029/2002PA000846
4. Jump up ? Lea, D. W., Mashiotta, T. A., & Spero, H. J. (1999). Controls on magnesium and strontium uptake in planktonic foraminifera determined by live culturing. Geochimica et cosmochimica acta, 63(16), 2369-2379.
5. Jump up ? Kisakürek, B., Eisenhauer, A., Böhm, F., Garbe-Schönberg, D., & Erez, J. (2008). Controls on shell Mg/Ca and Sr/Ca in cultured planktonic foraminiferan, Globigeriniodes ruber (white). Earth and Planetary Science Letters, 273, 260-269. doi:10.1016/j.epsl.2008.06.026
6. Jump up ? Regenberg, M., Regenberg, A., Garbe-Schonberg, D., & Lea, D. W. (2014). Global dissolution effects on planktonic foraminiferal Mg/Ca ratios controlled by the calcite-saturation state of bottom waters. Paleoceanography, 29, 127-142. doi:10.1002/2013PA002492
7. Jump up ? Dee, S., Emile-Geay, J., Evans, M. N., Allam, A., Steig, E. J., & Thompson, D. M. (2015). PRYSM: An open-source framework for PRoxy System Modeling, with applications to oxygen-isotope systems. Journal of Advances in Modeling Earth Systems, 7, 1220-1247. doi:10.1002/2015MS000447

Defined in: The LiPD Ontology

ProxySystemModel

In the Evans et al. (2013) framework, this is the combination of sensor, archive and observation models . "A generalized proxy system model encapuslates a simplified representation of prior physical, chemical, biological, and/or geological understanding of the ways in which environmental variation ultimately results in the observations used to retrieve paleoclimatic information."

Defined in: The LiPD Ontology

Publication

A document that serves as reference for a Dataset or its components

Defined in: The LiPD Ontology

publicationYear

Answers the question: What year was the Publication issued?

Defined in: The LiPD Ontology

publishedIn

Answers the question: In which Publication was the Dataset or Compilation issued?

Defined in: The LiPD Ontology

R

Radiocarbon

Defined in: The Proxy Observation Type Ontology

radiocarbonAge

Defined in: The Inferred Variable Ontology

Radioisotope

Defined in: The Proxy Observation Type Ontology

Reflectance

Defined in: The Proxy Observation Type Ontology

relevantQuote

Answers the question: Which part of the publication describes the Calibration or Interpretation?

Defined in: The LiPD Ontology

reportedIn

Answers the question: In which EnsembleTable, DistributionTable, and/or SummaryTable is the Uncertainty reported?

Defined in: The LiPD Ontology

Resistivity

Defined in: The Proxy Observation Type Ontology

Resolution

Refers to the time difference between two adjacent values of a Variable.

Defined in: The LiPD Ontology

Rock

Defined in: The Proxy Sensor Ontology

RockHammer

Defined in: The Instrument Ontology

S

salinity

Defined in: The Inferred Variable Ontology

SandFraction

Defined in: The Proxy Observation Type Ontology

sclerosponge

Defined in: The Proxy Archive Ontology

scope

Answers the question: how would you classify the Interpretation? Examples include Isotope, Climate…

Defined in: The LiPD Ontology

seasonality

Answers the question: To which part of the year is the Interpretation or ProxySensor restricted to? Acceptable answers may be "MJJA", "growing season",or [5,6,7,8]

Defined in: The LiPD Ontology

seaSurfaceTemperature

The temperature close to the ocean's surface

Defined in: The Inferred Variable Ontology

SecondaryIonMassSpectrometer

Defined in: The Instrument Ontology

sensorGenus

Answers the question: What is the Genus of the Organic ProxySensor?

Defined in: The LiPD Ontology

sensorSpecies

Answers the question: What is the species of the Organic ProxySensor?

Defined in: The LiPD Ontology

SHRIMP

Defined in: The Instrument Ontology

Si

Defined in: The Proxy Observation Type Ontology

SiltFraction

Defined in: The Proxy Observation Type Ontology

SIMS

Defined in: The Instrument Ontology

Snow

Defined in: The Proxy Sensor Ontology

SoftwareCode

A script that describes the model, in any programming language (e.g., Excel, Matlab, Python, R)

Defined in: The LiPD Ontology

southernAnnularMode

Defined in: The Inferred Variable Ontology

southernOscillationIndex

Defined in: The Inferred Variable Ontology

Spectral

Defined in: The Proxy Observation Type Ontology

Spectrometer

Defined in: The Instrument Ontology

Spectroscope

Defined in: The Instrument Ontology

speleothem

Defined in: The Proxy Archive Ontology

Sr/Ca

Defined in: The Proxy Observation Type Ontology

StableCarbonIsotope

Carbon in nature exists in oxidized (i.e., CO2 and carbonates), elemental (i.e., graphite and diamond), and reduced (i.e., methane and organic matter]) forms. Carbon has two stable isotopes: the light isotope 12C (abundance: 98.9%, mass: 12.000000 amu) and the heavy isotope 13C (abundance: 1.1%, mass: 13.003355 amu). Since the mass of 13C is higher than the mass of 12C, the carbon isotopes are fractionated by chemical and biological processes. In general, 12C is strongly partitioned into organic matter (reduced form) while the heavy isotope is concentrated in the oxidized forms of carbon.

Defined in: The Proxy Observation Type Ontology

StableHydrogenIsotope

Defined in: The Proxy Observation Type Ontology

StableIsotope

Defined in: The Proxy Observation Type Ontology

StableNitrogenIsotope

Defined in: The Proxy Observation Type Ontology

StableOxygenIsotope

Defined in: The Proxy Observation Type Ontology

StableSulfurIsotope

Defined in: The Proxy Observation Type Ontology

standard

Answers the question: Reference material against which the MeasuredVariable is reported?

Defined in: The LiPD Ontology

SummaryTable

A DataTable that contains summary information for the Variable and is output from a Model.

Defined in: The LiPD Ontology

summaryTableGeneratedByModel

Answers the question: In which SummaryTable can the statistics on the Model Output be found?

Defined in: The LiPD Ontology

surfaceAirTemperature

Defined in: The Inferred Variable Ontology

T

takenAtDepth

Answers the question: At which depth in the ProxyArchive is the Variable measured or inferred?

Defined in: The LiPD Ontology

Temperature

Thermodynamic property allowing to quantitatively measure how warm or cold a material, fluid is.

Defined in: The Inferred Variable Ontology

TEX86

The use of TEX86 (TetraEther indeX of 86 carbons) as a tool to reconstruct past sea surface temperature variability is based on the relative cyclization of isoprenoidal glycerol dialkyl glycerol tetra ethers (GDGTs) produced by marine archaea. TEX86 is defined as [1]: TEX_{86}=\frac{GDGT-2+GDGT-3+Cren'}{GDGT-1+GDGT-2+GDGT-3+Cren'} where GDGTs 1-3 indicate compounds containing 1-3 cyclopentyl moieties, respectively, and Cren' denotes the regioisomer of crenarchaeol, a diagnostic biomarker for the Thaumarchaeota, the primary producers of GDGTs in the marine realm. By definition, values of the TEX86 index are comprised between 0 and 1. Experimental evidence suggests that archaea produce GDGTs with more rings warmer waters, a response observed in cultures of hyperthermophile archaea [2] [3] and mesocosm experiments with natural seawater containing heterogenous archaeal population [4] [5]. References [1] Schouten, S., Hopmans, E. C., Schefuß, E., & Sinninghe Damsté, J. S. (2002). Distributional variations in marine crenarchaeotal membrane lipids: a new organic proxy for reconstructing ancient sea water temperatures? . Earth and Planetary Science Letters, 204, 265-274. [2] de Rosa, M., Esposito, E., Gambacorta, A., Nicolaus, B., & Bu'Lock, J. (1980). Effects of temperature on ether lipid composition of Caldariella acidophilia. Phytochemistry, 19, 827-831. [3] Uda, I., Sugai, A., Itoh, Y., & Itoh, T. (2001). Variation in molecular species of polar liipds from Thermoplasma acidophilum depends on growth temperature. Lipids, 36, 103-105. [4] Wuchter, C., Schouten, S., Coolen, M. J. L., & Sinninghe Damsté, J. S. (2004). Temperature-dependent variation in the distribution of tetraether membrane lipids of marine Crenarchaeota: implications for TEX86 paleothermometry. Paleoceanography, 19, PA4028. doi:10.1029/2004PA001041 [5]Schouten, S., Forster, A., Panato, E., & Sinninghe Damsté, J. S. (2007). Towards the calibration of the TEX86 paleothermometer on ancient greenhouse worlds. Organic Geochemistry. doi:10.1016/j.orggeochem.2007.05.014

Defined in: The Proxy Observation Type Ontology

Time

Defined in: The Inferred Variable Ontology

title

Answers the question: What is the title of the Publication?

Defined in: The LiPD Ontology

TraceElement

Defined in: The Proxy Observation Type Ontology

Tree

Defined in: The Proxy Sensor Ontology

U

U-Th

Defined in: The Proxy Observation Type Ontology

Uk37

The C37 alkenone unsaturation index ( U_{37}^{k'} ) is a firmly established tool for past sea surface temperatures reconstruction and is based on the relative abundance of di- (C37:2) and tri- (C37:3) unsaturated ketones with 37 carbon atoms. The index varies between 0 and 1, thus it may saturate in the temperature extremes as it becomes more challenging to determine since C37:3 and C37:2 alkenones approach their detection limits. Since alkenones come exclusively from a few species of haptophyte algae which require sunlight, alkenone thermometry offers the advantage of direct estimate of near-surface ocean temperatures. The ubiquitous presence of alkenone-synthesizing organisms (most commonly the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanic through the world's ocean and the rapidity and high-precision of the alkenone analyses had made U_{37}^{k'} a valuable proxy for paleoceanographic reconstructions. However, the U_{37}^{k'} proxy is subject to non-temperature effects, such as lateral transport through oceanic currents (Ohkouchi et al. (2002)) and preferential post-depositional oxidation of C37:3 compared to C37:2 [1] [2]. Furthermore, changes in the seasonality of the proxy (i.e., which part of the seasonal cycle the proxy is recording) may bias the inferred temperatures toward winter or summer conditions [3]. Finally in oceanic regions where the photic zone extends below the surface mixed layer, the sedimentary signal may not strictly represent sea surface temperatures but rather a composite temperature of the mixed layer and the thermocline [4][5]. References [1] Hoefs, M. J. L., Versteegh, G. J. M., Rijpstra, W. I. C., de Leeuw, J. W., & Damsté, J. S. S. (1998). Postdepositional oxic degradation of alkenones: Implications for the measurement of palaeo sea surface temperatures. Paleoceanography, 13(1), 42-49. doi:10.1029/97pa02893 [2] Ohkouchi, N., Eglinton, T. I., Keigwin, L. D., & Hayes, J. M. (2002). Spatial and temporal offsets between proxy records in a sediment drift. Science, 298(5596), 1224-1227. doi:10.1126/science.1075287 [3] Herfort, L., Schouten, S., Boon, J. P., & Sinninghe Damsté, J. S. (2006). Application of the TEX86 temperature proxy in the southern North Sea. Organic Geochemistry, 37, 1715-1726. [4] Müller, P. J., Kirst, G., Ruhland, G., von Storch, I., & Rosell-Melé, A. (1998). Calibration of the alkenone paleotemperature index U_{37}^{k'} based on core-tops from the eastern South Atlantic and the global ocean (60°N-60°S). Geochimica et cosmochimica acta, 62, 1757-1772. [5] Prahl, F. G., Mix, A. C., & Sparrow, M. A. (2006). Alkenone paleothermometry: biological lessons from amrine sediment records off Western South America. Geochimica and Cosmochimica Acta, 70, 101-117.

Defined in: The Proxy Observation Type Ontology

Uk37Prime

The currently accepted U37kprime (Prahl and Wakeman, 1987) varies positively with temperature, and is defines as C(37:2)/(C(37:2)+C(37:3), where C(37:2) represents the quantity of the di-unsaturated ketone and C(37:3) the quantity of the tri-unsaturated form. Herbet, T.D., 2003, Alkenone paleotemperature determinations in Treatise on Geochemistry, Volume 6, pp 391-432

Defined in: The Proxy Observation Type Ontology

Uncertainty

A state of incomplete knowledge that results from a lack of information or from different modeling choices. Uncertainty may come from many sources, from imprecision in the data to ambigously defined concepts or terminology. Uncertainty can be represented by quantitative measures (e.g., probability density function) or by qualitative statements (e.g., reflecting the judgement of a team of experts). Sensu IPCC AR5

Defined in: The LiPD Ontology

uncertaintyLevel

Answers the question: What parameter of the error distribution is the Uncertainty value referring to? Examples include 1-sigma, 2-sigma, 95% confidence bounds

Defined in: The LiPD Ontology

UncertaintyModel

A Model quantifiying the Uncertainty

Defined in: The LiPD Ontology

V

Variable

Quantities that may change from value to value. They are usually represented as column of values in a data table

Defined in: The LiPD Ontology

Vegetation

Defined in: The Proxy Sensor Ontology

volume

Answers the question: In which volume of the Publication does the reference to the Datatset appear?

Defined in: The LiPD Ontology

W

Watershed

Defined in: The Proxy Sensor Ontology

WavelengthDispersiveSpectrometer

Defined in: The Instrument Ontology

Wood

The field of dendroclimatology and, to some extent, the field of dendrochronology have played an important role in generating climate reconstructions of the past millennium [1] [2] [3] [4]. In regions with large seasonal variations, trees produce rings of varying color depending on the species. In most cases, the rings shift from a lighter, low density early wood of spring and early summer to a darker, denser band of late wood at the end of the growing season. The growing season generally occurs during the summer month and its length depends on the species, latitude, and altitude. Therefore, trees hold perhaps the greatest potential for reconstructing past terrestrial climates at annual or even sub-annual resolution.

The following observations can be made on the wood archive:

• Tree ring width
• Wood density
• Stables isotopes
1. ? Mann, M. E., Bradley, R. S., & Hughes, M. K. (1998). Global-scale temperature patterns and climate forcing over the past six centuries. Nature, 392(6678), 779-787. doi:10.1038/33859
2. ? Mann, M. E., Bradley, R. S., & Hughes, M. K. (1999). Northern Hemipshere temperatures during the past millennium: Inferences, Uncertainties, and Limitations. Geophysical Research Letters, 26(6), 759.
3. ? Moberg, A., Sonechkin, D. M., Holmgren, K., Datsenko, N. M., & Karlen, W. (2005). Highly variable Northern Hemisphere temperatures reconstructed from low- and high-resolution proxy data. Nature, 433(7026), 613-617. doi:10.1038/nature03265
4. ? Mann, M. E., Zhang, Z., Rutherford, S., Bradley, R., Hughes, M. K., Shindell, D. T., . . . Ni, F. (2009). Global signatures and dynamical origins of the Little Ice Age and Medieval Climate Anomaly. Science, 326, 1256-1260. dos: 10.1126/science.1177303

Defined in: The Proxy Archive Ontology

X

X-RayDiffraction

Defined in: The Proxy Observation Type Ontology

X-rayFluorescence

Defined in: The Proxy Observation Type Ontology

Y

year

Defined in: The Inferred Variable Ontology

Z

ZeissPetrographicMicroscope

Defined in: The Instrument Ontology

Zn/Ca

Defined in: The Proxy Observation Type Ontology