The Linked Earth Ontology aims to provide a common vocabulary for annotating paleoclimatology data
Give credit to the original author of the resource
Answers the question: Who wrote (i.e., created) the resource, such as a Publication?
author
Provides calibration information, especially useful for legacy datasets where the raw measurements may not be available and for comparison of datasets. If both raw and calibrated data are present, calibratedWith and calibratedFrom should link to the same Calibration instance
Answers the question: What calibration process was used to relate the InferredVariable to the MeasuredVariable?
calibrated via
Relationship needed to link to a Publication desribing the calibration being applied to the dataset
Answers the question: In what Reference(s) is the Calibration described/justified?
calibration references
Subproperty of modeledBy. The subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
Answers the question: What is the ChronModel for the ChronData or ProxySystem under consideration?
chron modeled by
Describe the geographical coordinates for the provenance of the ProxyArchive where the dataset was collected from
Answers the question: Where (in the world) was the data in the Dataset collected? Refers to the location of the ProxyArchive
collected from
Allows distinction between contributor to a resource and the author
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 LinkedMember may contribute a previously-published dataset that he/she may not have authored
contributor
"Subproperty of foundinTable to Link the Model to its outputs"
Answers the question: In which DistributionTable is the Model output found?
found in distribution table
"Subproperty of foundinTable to link the Model to its outputs"
Answers the question: In which EnsembleTable is the Model output found?
found in ensemble table
Subproperty of foundinTable to link the Data to the Variables
Answers the question: In which MeasurementTable are the Variables found?
found in measurement table
Subproperty of foundinTable to link the Model to its outputs
Answers the question: In which SummaryTable can the statistics on the Model Output be found?
found in summary table
Allows to link the data to the csv table and the models to its output
Answers the question: In which DataTable can the information/data be found?
found in table
Links a dataset to its source of funding
Answers the question: What was the Funding source for the Dataset?
funded by
Links a Model to its SoftwareCode.
Answers the question: What SoftwareCode was used to generate the Model output?
has code
Property added to link the proxySystem to the IntegrationTime class
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
has integration time
Links the MeasuredVariable to its ProxySystem. For instance, Mg/Ca measurements on foraminiferal shells have ProxySystem: MarineSediment.Foraminifera.Mg/Ca
Answers the question: What is the ProxySystem associated with this MeasuredVariable?
has proxy system
Needed to link a Variable to Resolution
Answers the question: What is the Resolution of the Variable?
has resolution
Links to the Uncertainty class
Answers the question: What is the Uncertainty associated with the Variable, Model, or Instrument?
has uncertainty
Subproperty of includesData. The subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
Answers the question: Which ChronData are included in the Dataset?
includes chron data
Links Dataset to Data
Answers the question: Which Data are included in the Dataset?
includes data
Answers the question: Which PaleoData are included in the Dataset?
includes paleo data
Links DataTable to Variable
Answers the question: Which Variables are included in the DataTable?
includes variable
Provides a link between the Measured and Inferred Variables. For instance, SST is inferred from Mg/Ca measurements
Answers the question: From which MeasuredVariable(s) is (are) the InferredVariable inferred from?
inferred from
Links the InferredVariable values to their type. For instance, the value of 29.1 degC is of type SST. This is important to normalize the variations in VariableNames (e.g. SST, sst, sea-surface temp)
Answers the question: What type of InferredVariable does the InferredVariable belongs to?
inferred variable type
Links an interpretation to a reference citation (can be the same as the calibrationReferences for a Dataset)
Answers the question: In which Publication(s) is the Interpretation substantiated?
interpretation references
Links the Variable to its Interpretation
Answers the question: What is the Variable's Interpretation?
interpreted as
Links the MeasuredVariable to the Instrument responsible for its creation
Answers the question: Which Instrument was used to produce the MeasuredVariable?
measured by
Links the MeasuredVariable to the ProxyArchive. Refers to the specific archive (i.e. the specific coral head, lake sediment...) and a specific Variable since ProxyArchive provides a link to the ProxySensor. In some instances, two MeasuredVariables on the same PhysicalSample may have different ProxyArchive page. This would be the case for measurements on various species of foraminifera in a MarineSediment
Answers the question: On which ProxyArchive was the MeasuredVariable measured?
measured on
Links a Model to its Publication. Note: calibrationReferences and modelReferences in the Calibration may not need to be the same. For instance, the calibration data and one mathematical formulation can be provided in one Publication (answering the calibrationReferences) but a different mathematical Model may be applied in another Publication (answering the modelReferences)
Answers the question: In which Publication is the model described/applied?
model references
Links Data or ProxySystem to Model
Answers the question: What is the Model for the Data or ProxySystem under consideration?
modeled by
Subclass of modeledBy, pertaining to paleoenvironmental information
Answers the question: What is the PaleoModel for the PaleoData or ProxySytem under consideration?
paleo modeled by
Links the dataset to the compilation
Answer the question: Which compilation does a dataset belong to?
part of compilation
Links the source of Funding to the PI (a Person)
Answers the question: Who was the lead on the source of Funding for the Dataset?
principal investigator
Links ProxySystemModel to ProxyArchiveModel
Answers the question: Which ProxyArchiveModel is used in the ProxySystemModel?
proxy archive model
Links ProxySystem to ProxyArchive
Answers the question: Which ProxyArchive underlies this ProxySystem?
proxy archive type
Links ProxySystemModel to ProxyObservationModel
Answers the question: Which ProxyObservationModel is used in the ProxySystemModel?
proxy observation model
The need to link a measured variable or a proxy system to the proxy observation type being measured.
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
proxy observation type
Links ProxySystemModel to ProxySensorModel
Answers the question: Which ProxySensorModel is used in the ProxySystemModel?
proxy sensor model
Links ProxySensor to ProxyArchive
Answers the question: Which ProxySensor underlies this ProxySystem?
proxy sensor type
Links the resource to its Publication
Answers the question: In which Publication was the Dataset or Compilation issued?
published in
Links the uncertainty to the model output
Answers the question: In which EnsembleTable, DistributionTable, and/or SummaryTable is the Uncertainty reported?
reported in
Provides depth information. Can link to the depth Variable in the DataTable
Answers the question: At which depth in the ProxyArchive is the Variable measured or inferred?
taken at depth
Separate between journal and book publication
Answers the question: In which book was the resource published?
book
Separate compilation date from the publication year. An example is LR04 (datsetdate in 2004) but published in 2005
Answers the question: At what date was the Compilation created?
compilation date
Needed to state the version associated to a compilation, which may not be the same as the datasets it contains
Answers the question: What is the version of the Compilation?
compilation version
The need for providing appropriate credit to the datasets
Sentence indicating how a dataset should be cited
dataset citation
Separate dataset date from the publication year. An example is LR04 (datsetdate in 2004) but published in 2005
Answers the question: At what date was the Dataset created?
dataset date
Property needed to let other scientists know about the usage and attribution terms of the uploaded dataset
License associated to a dataset
dataset license
Allows to update a dataset if Data/Models are added and keep track of the various versions
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).
dataset version
This property may be used to provide further details on instrument descriptions, uncertainty description,etc.
Answers the question: What additional details would you give about the resource?
description
Answers the "of what" question for an Interpretation. For intance, sea surface in sea surface temperature.
detail
Allow to store contact information
Answers the question: What is the email address of the Person?
email
Allows to provide the equation as part of the metadata
Answers the question: What is the mathematical formulation of the Model?
equation
Provides information about the Agency funding the study
Answers the question: Which entity was the Dataset fundedBy?
funding agency
Provides information about the country the agency is from
Answers the question: Which nation funded the Dataset?
funding country
Provides information about the grant number
Answers the question: What is the unique identifier associated with the Funding for the Dataset?
grant number
Links the Variable metadata to the values stored in the csv file
Answers the question: In which column of the csv file can the Variable be found?
has column number
Allows to link to a resource using a digital object identifier
Answers the question: What is the digital object identifier associated with the resource?
has DOI
Allows to store the execution command of a script
Answers the question: What is the command to run the script or the code?
has execution command
Provides information about the operating system version in which the software code was exceuted?
Answers the question: In which environment is the script meant to be run in?
has execution environment
Links a DataTable with its appropriate csv file
Answers the question: What is the name of the csv file in which the Variable values are stored?
has file name
Needed to properly described physical samples
IGSN identifier associated to a physical sample
has IGSN
Link to the ISBN: Identifier used commonly to refer to publications
Answers the question: What is the international book number of the Publication?
has ISBN
8-digit code used to identify publications
Answers the question: What is the International Standard Serial Number of the Publication?
has ISSN
Allows to point to the original source of a resource
Answers the question: What is the universal resource locator to a resource?
has link
property relevant to facilitate queries, as in most cases the ocntents of a csv file are not directly represented
Answers the question: What is the maximum value of the Variable?
has max value
Answers the question: What is the mean value of the Variable?
has mean value
Answers the question: What is the median value of the Variable?
has median value
Answers the question: What is the minimum value of the Variable?
has min value
Useful for coding around the missing values
Answers the question: How are the missing values of the Variable identified in the DataTable?
has missing value
Allows to rank the environmental variable controlling the interpretation. For instance, the d18O of coral aragonite responds to both temperature and the d18O of seawater (closely linked to salinity). Depending on the locale and/or timescale, one variable may dominate over the other.
Answers the question: What is the importance of the ClimateInterpretation or IsotopeInterpretation?
has rank
Links the units and the values of the Variable
Answers the question: In what unit of measure is (are) the Variable(s) expressed?
has units
Useful if there is only a single value rather than a vector of numbers. Often the case for analytical uncertainty or uncertainty reported as a RMSE
Answers the question: What are the numerical values of the Variable, Uncertainty, and Model outputs?
has value
LiPD assigns a unique identifier (TSid) to each table column described in a LiPD file. Allows to assign a unique identifier to each series, facilitating data citation and recognition This allows someone to change every piece of metadata about column or dataset, including its names (both dataset and variable) and still get back to the right spot. It’s fundamental to working with LiPD data.
Answers the question: What is the unique identifier for the Variable?
has variable ID
Link to a particular laboratory. Provides circumstantial information about the measurement technique and how it was applied. Allows to give some information about the actual location of the sample
Answers the question: In which laboratory/repository is the Instrument/PhysicalSample located?
housed at
Answer is only positive or negative. Useful metadata when the calibration equation is not readily available. Also applies to InferredVariable to faciliate the search in database
Answers the question: Is the InferredVariable value increasing or decreasing as the value of the MeasuredVariable is increasing?
interpretation direction
Added to allow data analysis. Is the interpretation relevant to these coordinates? Does putting a colored dot on the map here make sense?
Answers the question: Does the Interpretation describe local variability, or far-field variability that may not reflect local conditions?
is local
Part of standard metadata for Publications
Answers the question: In what issue of the journal can the resource be found?
issue
Answers the question: What is the name of the journal in which the resource can be found?
journal
Allows to describe methods.
Answers the question: How is the information obtained from the resource?
method
Answers the question: How is the resource called?
name
Allows to add notes to specific cells in the DataTable
Answers the question: What additional information would you give about the Variable or DataTable ?
notes
LinkedEarth uses ORCID number for membership
Answers the question: What is the persistent digital identifier of the Person?
orcid number
Answers the question: In what pages of the Publication can the reference to the resource be found?
pages
Provides the user with information about the software
Answers the question: In which language was the software code written in?
programmed in
Answers the question: What year was the Publication issued?
publication year
Often it's useful to put a quote from the paper that describes the interpretation
Answers the question: Which part of the publication describes the Calibration or Interpretation?
relevant quote
Seasonality is critical to properly related measuredVariable and innferredVariable, as the former only senses part of the range of the latter.
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]
seasonality
Scientific Name of the organic ProxySensor
Answers the question: What is the Genus of the Organic ProxySensor?
sensor genus
Answers the question: What is the species of the Organic ProxySensor
sensor species
Crucial for isotopic measurements (for instance, d18O measurements (VSMOW vs VPDB))
Answers the question: Reference material against which the MeasuredVariable is reported?
standard
Answers the question: What is the title of the Publication?
title
Allows to properly make use of the reported Uncertainty values
Answers the question: What parameter of the error distribution is the Uncertainty value referring to? Examples include 1-sigma, 2-sigma, 95% confidence bounds
uncertainty level
Answers the question: In which volume of the Publication does the reference to the Datatset appear?
volume
Make the model behing the calibration explicit
Metadata about how the variable was calibrated to reflect an environmental variable
Calibration model
Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
The data, metadata, and Model that describe the set of Variables used to relate depth/position to time (chronological information)
Crhon data
DataTable containing Variables pertaining to chronological information
Chron data table
Model used to derive a time (or age) axis from the ChronDataModel
Chron model
Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components. Agreed that the ProxySystem concept applies to both Chron and PaleoData
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])
Chron proxy system
Encodes what Data/Metadata gathering effort/scientific project led to the curation of the Datasets. Examples: PAGES2k, Iso2k, LR04, OC3, MARGO
A curated aggregation of datasets
Compilation
Needed to describe the paleoenvironmental and/or chronological data comprising the dataset as opposed to the Publication, Funding and Location information
An aggregation of DataTables and Models with their supporting paleoenvironmental and/or chronological information
Data
Connects to the csv file where the data values are stored
A set of Variables organized in columns
Data table
Fundamental unit at which we think about paleoclimate data. Also tends to correspond to the scope of the study
A structured collection of related information, including -but not limited to -measured and/or modelled geograhical, chronological, and environmental data
Dataset
Added to allow outputs from Bayesian model (especially Bchron) to be saved as part of a dataset. Required to encode irregular probability distributions
DataTable containing the probability distribution of a single value of a Variable. Output of a Model
Distribution table
Added to allow outputs from Bayesian model to be saved as part of a dataset
DataTable constaining many possible series of how the Variable is modeled. Output of a Model
Ensemble table
Allows to associate a grant number following U.S. federal regulation
Source of monetary support underlying the collection/creation/analysis/curation of the Dataset
Funding
See InferredVariable Ontology for concept description.
A Variable that is inferred from one or more MeasuredVariable (s)
Inferred variable
Encode the Genus and Species metadata
An inorganic substrate sensing enviromental changes. Examples: karst, snow, watershed, ice sheet, rock, etc.
Inorganic proxy sensor
Needed to categorize types of instruments used for taking the different measurements. See Instrument Ontology for concept description.
A tool used to produce MeasuredVariables
Instrument
Soilwater mixing above speleothems: Although the sample might only represent 5 years of calcification, it can record 30 years of water mixing.
The time it takes for the ProxySensor to imprint environmental information on the ProxyArchive. It may be further qualified with time periods and units
Integration time
Used to describe the interpretation of the Variable. For instance, radiocarbon is interpreted to represent age
A suite of metadata that describes which phenomena drove variability in this Variable (e.g. environmental drivers).
Interpretation
Gives information about where the ProxyArchive comes from.
The geographic data and metadata for the dataset
Location
Subclass of Variables. Allows to make the disctinction between raw measurements (e.g., tree ring width, oxygen isotopes, trace elements) and the variables being reconstructed (e.g., moisture, temperature)
Variables that are measured by an Instrument. MeasuredVariables are ssn: Observations. They represent the values of a certain type of ProxyObservations
Measured variable
Subclass of DataTable. Allows InferredVariables (despite the name) for practical purposes
DataTable that contains the Variables (both measured and inferred)
Measurement table
Allows to describe models whose outputs are stored in the Dataset. One example of is Bchron for age modeling
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
Model
Subclass of Publication.Allows to clearly mark datasets not generated as part of a peer-reviewed publication.
A publication that has not undergone a formal review process; for instance, a Dataset attached to a dissertation.
Non peer reviewed publication
Subclass of ProxySensor. Makes the distinction between organic and inorganic. See the ProxySensor ontology for concepts
Biologically-mediated ProxySensor. Examples include: foraminifera, trees, mollusks, polyps
Organic proxy sensor
The Data pertaining to past environmental variability
Paleo data
DataTable containing PaleoData Variables
PaleoData table
Model used to derive an environmental axis from the PaleoDataModel
Paleo model
Gives a formal definition of climate proxy following the Evans et al. (2013) framework. Subclass of ProxySystem, pertaining to climate information
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.
Paleo proxy system
Subclass of Publication.Allows to clearly mark datasets generated as part of a peer-reviewed publication.
A Publication that has undergone a formal peer-review process
Peer reviewed publication
The researcher, author on a publication.
An individual who has participated directly or indirectly in the authoring of any resources on the LinkedEarth wiki
Person
Used to differentiate between the concept of a ProxyArchive and its physical (real) manifestation
The actual sample on which the measurements are made. For instance, the lake core analyzed in the lab is the physical sample. Physical samples belong to an Proxy Archive type
Physical sample
"See ProxyArchive ontology for details about the concept. We adopted the Evans et al. (2013) framework since this is the only published definition of what is most commonly referred to as ""proxy"" in the paleoclimate community"
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
Proxy archive
We adopted the Evans et al. (2013) framework since this is the only published definition of what is most commonly referred to as ""proxy"" in the paleoclimate community"
A Model of how the ProxySensor either creates or emplaces the signal into the ProxyArchive. Sensu Evans et al. (2013)
Proxy archive model
See ProxyObservation ontology for details about the concept. We adopted the Evans et al. (2013) framework since this is the only published definition of what is most commonly referred to as ""proxy"" in the paleoclimate community
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)
Proxy observation
We adopted the Evans et al. (2013) framework since this is the only published definition of what is most commonly referred to as ""proxy"" in the paleoclimate community
The Model of how ProxyObservations are made on the archive. Sensu Evans et al. (2013)
Proxy observation model
See ProxySensor ontology for details about the concept. We adopted the Evans et al. (2013) framework since this is the only published definition of what is most commonly referred to as ""proxy"" in the paleoclimate community
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.
Proxy sensor
One component of the ProxySystemModel
A Model of the ProxySensor. Sensu Evans et al. (2013)
Proxy sensor model
We adopted the Evans et al. (2013) framework since this is the only published definition of what is most commonly referred to as "proxy" in the paleoclimate community
Climate monitoring prior to the instrumental era are necessarily indirect. This indirect assessment is made on proxies. According to Evans et al. (2013), a proxy system is comprised of three components: - A ProxySensor - A ProxyArchive - A ProxyObservation
Proxy system
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."
Proxy system model
Can be used to credit the contributor of the dataset as well as linking toward the conclusions of the study and relevant methods
A document that serves as reference for a Dataset or its components
Publication
Class added to describe the annual resolution of the archives
Refers to the distance (physical or temporal) between each point on the archive. May or May not be related to sampling. Value with units
Resolution
Added to allow for a link towards the code if on a public repository like GitHub
A script that describes the model, in any programming language (e.g., Excel, Matlab, Python, R)
Software code
Allows to represent a summary of basic statistics such as median, mean, standard deviation, and various quantiles from the output of the Model
A DataTable that contains summary information for the Variable and is output from a Model.
Summary table
To allow to describe the uncertainty on a Variable or a Model, would it be a single number (e.g., the uncertainty on the measurements are 0.1 per mil, one sigma confidence level, or reportedIn an EnsembleTable and/or SummaryTable)
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
Uncertainty
Allows description of how uncertainty was calculated
A Model quantifiying the Uncertainty
Uncertainty model
Basic definition of the values in the columns of the csv file
Quantities that may change from value to value. They are usually represented as column of values in a data table
Variable
The class ssn:Observation provides the structure to represent a single observation. An observation is a situation that describes an observed feature, an observed property, a sensor and method of sensing used and a value observed for the property: that is, an observation describes a single value attributed to a single property by a particular sensor. Observations of multiple features or multiple properties of the one feature should be represented as either compound properties, features and values or as multiple observations, grouped in some appropriate structure.
The Linked Earth Ontology