The Linked Earth LiPD Ontology
type: Ontology
version IRI: http://linked.earth/ontology/core/1.2.0
comment: The Linked Earth LiPD Ontology aims to provide a common vocabulary for annotating paleoclimatology data
preferred namespace prefix: le
version info: 1.2.0
contributor: http://w3id.org/people/dgarijo
contributor: http://www.isi.edu/~gil/
contributor: http://www.isi.edu/~varunr/
creator: http://earth.usc.edu/~khider/
creator: http://orcid.org/0000-0001-5920-4751
creator: http://www.cefns.nau.edu/~npm4/
license: http://creativecommons.org/licenses/by/2.0/

author
type: ObjectProperty
sub property of: creator
sub property of: author
domain: Class
  union of: Compilation
  union of: Dataset
  union of: Publication
range: Person
example: 2013PA002534
rationale: Give credit to the original author of the resource
comment: Answers the question: Who wrote (i.e., created) the resource, such as a Publication?

calibrated via
type: ObjectProperty
domain: Inferred variable
range: Calibration model
rationale: Provides calibration information, especially useful for legacy datasets where the raw measurements may not be available and for comparison of datasets.
comment: Answers the question: What calibration process was used to relate the InferredVariable to the MeasuredVariable?

calibration references
type: ObjectProperty
sub property of: references
domain: Calibration model
range: Publication
rationale: Relationship needed to link to a Publication desribing the calibration being applied to the dataset
comment: Answers the question: In what Reference(s) is the Calibration described/justified?

chron modeled by
type: ObjectProperty
sub property of: modeled by
domain: Class
  union of: Chron data
  union of: Chron proxy system
range: Chron model
rationale: Subproperty of modeledBy. The subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: Answers the question: What is the ChronModel for the ChronData or ProxySystem under consideration?

collected from
type: ObjectProperty
sub property of: contentLocation
domain: Dataset
range: Location
example: MD982181.Khider.2014
rationale: Describe the geographical coordinates for the provenance of the ProxyArchive where the dataset was collected from
comment: Answers the question: Where (in the world) was the data in the Dataset collected? Refers to the location of the ProxyArchive

contributor
type: ObjectProperty
sub property of: contributor
domain: Dataset
range: Person
example: MD982181.Khider.2014
rationale: Allows distinction between contributor to a resource and the author
comment: 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

distribution table generated by Model
type: ObjectProperty
sub property of: generated by model
type: FunctionalProperty
domain: Distribution table
range: Class
  union of: Chron model
  union of: Paleo model
example: ODP1098B1 2.ChronData1.Model1
rationale: "Subproperty of foundinTable to Link the Model to its outputs"
comment: Answers the question: In which DistributionTable is the Model output found?

ensemble table generated by model
type: ObjectProperty
sub property of: generated by model
type: FunctionalProperty
domain: Ensemble table
range: Class
  union of: Chron model
  union of: Paleo model
rationale: ODP1098B1 2.ChronData1.Model1
rationale: "Subproperty of foundinTable to link the Model to its outputs"
comment: Answers the question: In which EnsembleTable is the Model output found?

found in measurement table
type: ObjectProperty
sub property of: found in table
domain: Data
range: Measurement table
example: MD982181.Khider.2014.PaleoData1
rationale: Subproperty of foundinTable to link the Data to the Variables
comment: Answers the question: In which MeasurementTable are the Variables found?

found in table
type: ObjectProperty
domain: Class
  union of: Data
  union of: Variable
range: Data table
rationale: Allows to link the data to the csv table and the models to its output
comment: Answers the question: In which DataTable can the information/data be found?

funded by
type: ObjectProperty
sub property of: funder
domain: Class
  union of: Compilation
  union of: Dataset
range: Funding
example: MD982181.Khider.2014
rationale: Links a dataset to its source of funding
comment: Answers the question: What was the Funding source for the Dataset?

generated by model
type: ObjectProperty
sub property of: wasDerivedFrom
domain: Data table
range: Model
rationale: Needed to link the model to the data tables it generates
comment: Answers the question: which model was used to generated this data table?

has code
type: ObjectProperty
type: FunctionalProperty
domain: Model
range: Software code
rationale: Links a Model to its SoftwareCode.
comment: Answers the question: What SoftwareCode was used to generate the Model output?

has integration time
type: ObjectProperty
domain: Proxy sensor
range: Integration time
rationale: Property added to link the proxySystem to the IntegrationTime class
comment: 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 proxy system
type: ObjectProperty
domain: Measured variable
range: Proxy system
rationale: Links the MeasuredVariable to its ProxySystem. For instance, Mg/Ca measurements on foraminiferal shells have ProxySystem: MarineSediment.Foraminifera.Mg/Ca
comment: Answers the question: What is the ProxySystem associated with this MeasuredVariable?

has resolution
type: ObjectProperty
domain: Variable
range: Resolution
example: http://wiki.linked.earth/MD982181.Khider.2014.paleo1measurement1.mgcarub.ICPAES
rationale: Needed to link a Variable to Resolution
comment: Answers the question: What is the Resolution of the Variable?

has uncertainty
type: ObjectProperty
domain: Class
  union of: Instrument
  union of: Model
  union of: Variable
range: Uncertainty
rationale: Links to the Uncertainty class
comment: Answers the question: What is the Uncertainty associated with the Variable, Model, or Instrument?

includes chron data
type: ObjectProperty
sub property of: includes data
domain: Dataset
range: Chron data
example: MD982181.Khider.2014
rationale: Subproperty of includesData. The subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: Answers the question: Which ChronData are included in the Dataset?

includes data
type: ObjectProperty
domain: Dataset
range: Data
rationale: Links Dataset to Data
comment: Answers the question: Which Data are included in the Dataset?

includes paleo data
type: ObjectProperty
sub property of: includes data
domain: Dataset
range: Paleo data
example: MD982181.Khider.2014
rationale: Subproperty of includesData. The subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: Answers the question: Which PaleoData are included in the Dataset?

includes variable
type: ObjectProperty
domain: Data table
range: Variable
example: MD982181.Khider.2014.paleo1measurement2
rationale: Links DataTable to Variable
comment: Answers the question: Which Variables are included in the DataTable?

inferred from
type: ObjectProperty
domain: Inferred variable
range: Measured variable
rationale: Provides a link between the Measured and Inferred Variables. For instance, SST is inferred from Mg/Ca measurements
comment: Answers the question: From which MeasuredVariable(s) is (are) the InferredVariable inferred from?

inferred variable type
type: ObjectProperty
domain: Inferred variable
range: Inferred variable
rationale: 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)
comment: Answers the question: What type of InferredVariable does the InferredVariable belongs to?

interpretation references
type: ObjectProperty
sub property of: references
domain: Interpretation
range: Publication
rationale: Links an interpretation to a reference citation (can be the same as the calibrationReferences for a Dataset)
comment: Answers the question: In which Publication(s) is the Interpretation substantiated?

interpreted as
type: ObjectProperty
domain: Variable
range: Interpretation
rationale: Links the Variable to its Interpretation
comment: Answers the question: What is the Variable's Interpretation?

measured by
type: ObjectProperty
sub property of: observedBy
domain: Measured variable
range: Instrument
rationale: Links the MeasuredVariable to the Instrument responsible for its creation
comment: Answers the question: Which Instrument was used to produce the MeasuredVariable?

measured on
type: ObjectProperty
sub property of: topObjectProperty
domain: Measured variable
range: Physical sample
rationale: 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
comment: Answers the question: On which PhysicalSample was the MeasuredVariable measured?

model references
type: ObjectProperty
sub property of: references
domain: Model
range: Publication
rationale: 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)
comment: Answers the question: In which Publication is the model described/applied?

modeled by
type: ObjectProperty
domain: Class
  union of: Compilation
  union of: Data
  union of: Proxy system
range: Model
rationale: Links Data, Compilation or ProxySystem to Model
comment: Answers the question: What is the Model for the Data, Compilation or ProxySystem under consideration?

paleo modeled by
type: ObjectProperty
sub property of: modeled by
domain: Class
  union of: Paleo data
  union of: Proxy system
range: Paleo model
rationale: Subclass of modeledBy, pertaining to paleoenvironmental information
comment: Answers the question: What is the PaleoModel for the PaleoData or ProxySytem under consideration?

part of compilation
type: ObjectProperty
sub property of: isPartOf
sub property of: includedInDataCatalog
domain: Dataset
range: Compilation
rationale: Links the dataset to the compilation
comment: Answer the question: Which compilation does a dataset belong to?

principal investigator
type: ObjectProperty
domain: Funding
range: Person
example: MD982181.Khider.2014.Funding1
rationale: Links the source of Funding to the PI (a Person)
comment: Answers the question: Who was the lead on the source of Funding for the Dataset?

proxy archive model
type: ObjectProperty
domain: Proxy system model
range: Proxy archive model
rationale: Links ProxySystemModel to ProxyArchiveModel
comment: Answers the question: Which ProxyArchiveModel is used in the ProxySystemModel?

proxy archive type
type: ObjectProperty
domain: Proxy system
range: Proxy archive
example: Ca
rationale: Links ProxySystem to ProxyArchive
comment: Answers the question: Which ProxyArchive underlies this ProxySystem?

proxy observation model
type: ObjectProperty
domain: Proxy system model
range: Proxy observation model
rationale: Links ProxySystemModel to ProxyObservationModel
comment: Answers the question: Which ProxyObservationModel is used in the ProxySystemModel?

proxy observation type
type: ObjectProperty
domain: Class
  union of: Measured variable
  union of: Proxy system
range: Proxy observation
example: Ca
rationale: The need to link a measured variable or a proxy system to the proxy observation type being measured.
comment: 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 sensor model
type: ObjectProperty
domain: Proxy system model
range: Proxy sensor model
rationale: Links ProxySystemModel to ProxySensorModel
comment: Answers the question: Which ProxySensorModel is used in the ProxySystemModel?

proxy sensor type
type: ObjectProperty
domain: Proxy system
range: Proxy sensor
example: Ca
rationale: Links ProxySensor to ProxyArchive
comment: Answers the question: Which ProxySensor underlies this ProxySystem?

published in
type: ObjectProperty
domain: Dataset
range: Publication
example: MD982181.Khider.2014
rationale: Links the resource to its Publication
comment: Answers the question: In which Publication was the Dataset or Compilation issued?

reported in
type: ObjectProperty
domain: Uncertainty
range: Class
  union of: Data table
  union of: Variable
rationale: Links the uncertainty to the model output
comment: Answers the question: In which EnsembleTable, DistributionTable, and/or SummaryTable is the Uncertainty reported?

summary table generated by model
type: ObjectProperty
sub property of: generated by model
type: FunctionalProperty
domain: Summary table
range: Class
  union of: Chron model
  union of: Paleo model
example: MD982181.Khider.2014.PaleoData1.Model1
rationale: Subproperty of foundinTable to link the Model to its outputs
comment: Answers the question: In which SummaryTable can the statistics on the Model Output be found?

taken at depth
type: ObjectProperty
domain: Variable
range: Variable
rationale: Provides depth information. Can link to the depth Variable in the DataTable
comment: Answers the question: At which depth in the ProxyArchive is the Variable measured or inferred?

book
type: DatatypeProperty
domain: Publication
range: string
rationale: Separate between journal and book publication
comment: Answers the question: In which book was the resource published?

compilation citation
type: DatatypeProperty
sub property of: bibliographicCitation
sub property of: citation
domain: Compilation
range: string
rationale: Data property needed to specify how to cite compilations, in order to provide appropriate credit to all contributors
comment: Answers the question: How should someone cite the compilation?

compilation date
type: DatatypeProperty
sub property of: created
sub property of: dateCreated
domain: Compilation
range: dateTime
rationale: Separate compilation date from the publication year. An example is LR04 (datsetdate in 2004) but published in 2005
comment: Answers the question: At what date was the Compilation created?

compilation version
type: DatatypeProperty
sub property of: version
domain: Compilation
range: string
rationale: Needed to state the version associated to a compilation, which may not be the same as the datasets it contains
comment: Answers the question: What is the version of the Compilation?

dataset citation
type: DatatypeProperty
sub property of: bibliographicCitation
sub property of: citation
domain: Dataset
range: Literal
rationale: The need for providing appropriate credit to the datasets
comment: Sentence indicating how a dataset should be cited

dataset date
type: DatatypeProperty
sub property of: created
sub property of: dateCreated
type: FunctionalProperty
domain: Dataset
range: dateTime
example: http://wiki.linked.earth/MD982181.Khider.2014
rationale: Separate dataset date from the publication year. An example is LR04 (datsetdate in 2004) but published in 2005
comment: Answers the question: At what date was the Dataset created?

dataset license
type: DatatypeProperty
sub property of: license
domain: Dataset
range: anyURI
rationale: Property needed to let other scientists know about the usage and attribution terms of the uploaded dataset
comment: License associated to a dataset

dataset version
type: DatatypeProperty
sub property of: version
type: FunctionalProperty
domain: Dataset
range: string
example: MD982181.Khider.2014
rationale: Allows to update a dataset if Data/Models are added and keep track of the various versions
comment: 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).

description
type: DatatypeProperty
domain: Thing
range: string
rationale: This property may be used to provide further details on instrument descriptions, uncertainty description,etc.
comment: Answers the question: What additional details would you give about the resource?

detail
type: DatatypeProperty
domain: Interpretation
range: string
comment: Answers the "of what" question for an Interpretation. For intance, sea surface in sea surface temperature.

email
type: DatatypeProperty
domain: Person
range: string
example: D. Khider
rationale: Allow to store contact information
comment: Answers the question: What is the email address of the Person?

equation
type: DatatypeProperty
domain: Model
range: string
example: Ca-g.rub.Calibration
rationale: Allows to provide the equation as part of the metadata
comment: Answers the question: What is the mathematical formulation of the Model?

funding agency
type: DatatypeProperty
type: FunctionalProperty
domain: Funding
range: string
example: MD982181.Khider.2014.Funding1
rationale: Provides information about the Agency funding the study
comment: Answers the question: Which entity was the Dataset fundedBy?

funding country
type: DatatypeProperty
type: FunctionalProperty
domain: Funding
range: string
rationale: MD982181.Khider.2014.Funding1
rationale: Provides information about the country the agency is from
comment: Answers the question: Which nation funded the Dataset?

grant number
type: DatatypeProperty
domain: Funding
range: string
example: MD982181.Khider.2014.Funding1
rationale: Provides information about the grant number
comment: Answers the question: What is the unique identifier associated with the Funding for the Dataset?

has column number
type: DatatypeProperty
domain: Variable
range: integer
rationale: Links the Variable metadata to the values stored in the csv file
comment: Answers the question: In which column of the csv file can the Variable be found?

has DOI
type: DatatypeProperty
sub property of: identifier
type: FunctionalProperty
domain: Class
  union of: Dataset
  union of: Publication
  union of: Software code
range: string
example: 2013PA002534
rationale: Allows to link to a resource using a digital object identifier
comment: Answers the question: What is the digital object identifier associated with the resource?

has execution command
type: DatatypeProperty
domain: Software code
range: string
rationale: Allows to store the execution command of a script
comment: Answers the question: What is the command to run the script or the code?

has execution environment
type: DatatypeProperty
domain: Software code
range: string
rationale: Provides information about the operating system version in which the software code was exceuted?
comment: Answers the question: In which environment is the script meant to be run in?

has file name
type: DatatypeProperty
type: FunctionalProperty
domain: Data table
range: string
example: MD982181.Khider.2014.paleo1measurement2
rationale: Links a DataTable with its appropriate csv file
comment: Answers the question: What is the name of the csv file in which the Variable values are stored?

has IGSN
type: DatatypeProperty
sub property of: identifier
domain: Physical sample
range: string
rationale: Needed to properly described physical samples
comment: IGSN identifier associated to a physical sample

has ISBN
type: DatatypeProperty
sub property of: identifier
domain: Publication
range: string
rationale: Link to the ISBN: Identifier used commonly to refer to publications
comment: Answers the question: What is the international book number of the Publication?

has ISSN
type: DatatypeProperty
sub property of: identifier
domain: Publication
range: string
rationale: 8-digit code used to identify publications
comment: Answers the question: What is the International Standard Serial Number of the Publication?

has link
type: DatatypeProperty
domain: Thing
range: anyURI
example: 2013PA002534
rationale: Allows to point to the original source of a resource
comment: Answers the question: What is the universal resource locator to a resource?

has max value
type: DatatypeProperty
domain: Variable
range: float
rationale: property relevant to facilitate queries, as in most cases the contents of a csv file are not directly represented
comment: Answers the question: What is the maximum value of the Variable?

has mean value
type: DatatypeProperty
domain: Variable
range: float
rationale: property relevant to facilitate queries, as in most cases the contents of a csv file are not directly represented
comment: Answers the question: What is the mean value of the Variable?

has median value
type: DatatypeProperty
domain: Variable
range: float
rationale: property relevant to facilitate queries, as in most cases the contents of a csv file are not directly represented
comment: Answers the question: What is the median value of the Variable?

has min value
type: DatatypeProperty
domain: Variable
range: float
rationale: property relevant to facilitate queries, as in most cases the contents of a csv file are not directly represented
comment: Answers the question: What is the minimum value of the Variable?

has missing value
type: DatatypeProperty
type: FunctionalProperty
domain: Class
  union of: Uncertainty
  union of: Variable
range: string
property disjoint with: has value
rationale: Useful for coding around the missing values
comment: Answers the question: How are the missing values of the Variable identified in the DataTable?

has rank
type: DatatypeProperty
type: FunctionalProperty
domain: Interpretation
range: int
rationale: 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.
comment: Answers the question: What is the importance of the Interpretation?

has units
type: DatatypeProperty
type: FunctionalProperty
domain: Class
  union of: Measured variable
  union of: Resolution
  union of: Uncertainty
  union of: Variable
range: string
rationale: Links the units and the values of the Variable
comment: Answers the question: In what unit of measure is (are) the Variable(s) expressed?

has value
type: DatatypeProperty
domain: Class
  union of: Model
  union of: Uncertainty
  union of: Variable
range: string
rationale: 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
comment: Answers the question: What are the numerical values of the Variable, Uncertainty, and Model outputs?

has variable ID
type: DatatypeProperty
sub property of: identifier
domain: Variable
range: string
rationale: 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.
comment: Answers the question: What is the unique identifier for the Variable?

housed at
type: DatatypeProperty
domain: Class
  union of: Instrument
  union of: Physical sample
range: string
rationale: 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
comment: Answers the question: In which laboratory/repository is the Instrument/PhysicalSample located?

interpretation direction
type: DatatypeProperty
type: FunctionalProperty
domain: Interpretation
range: string
rationale: 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
comment: Answers the question: Is the InferredVariable value increasing or decreasing as the value of the MeasuredVariable is increasing?

is local
type: DatatypeProperty
type: FunctionalProperty
domain: Interpretation
range: string
rationale: Added to allow data analysis. Is the interpretation relevant to these coordinates? Does putting a colored dot on the map here make sense?
comment: Answers the question: Does the Interpretation describe local variability, or far-field variability that may not reflect local conditions?

issue
type: DatatypeProperty
type: FunctionalProperty
domain: Publication
range: int
example: 2013PA002534
rationale: Part of standard metadata for Publications
comment: Answers the question: In what issue of the journal can the resource be found?

journal
type: DatatypeProperty
domain: Publication
range: string
example: 2013PA002534
rationale: Part of standard metadata for Publications
comment: Answers the question: What is the name of the journal in which the resource can be found?

method
type: DatatypeProperty
domain: Class
  union of: Measured variable
  union of: Model
  union of: Physical sample
range: string
example: A7.Sun.2005.paleo1measurement1.d18og
rationale: Allows to describe methods.
comment: Answers the question: How is the information obtained from the resource?

name
type: DatatypeProperty
sub property of: name
domain: Thing
range: string
example: Ca-g.rub
comment: Answers the question: How is the resource called?

notes
type: DatatypeProperty
domain: Class
  union of: Data table
  union of: Dataset
  union of: Model
  union of: Variable
range: string
example: A7.Sun.2005.chron1measurement1
rationale: Allows to add notes to specific cells in the DataTable
comment: Answers the question: What additional information would you give about the Variable or DataTable ?

orcid number
type: DatatypeProperty
sub property of: identifier
type: FunctionalProperty
domain: Person
range: string
example: D. Khider
rationale: LinkedEarth uses ORCID number for membership
comment: Answers the question: What is the persistent digital identifier of the Person?

pages
type: DatatypeProperty
type: FunctionalProperty
domain: Publication
range: string
example: 2013PA002534
rationale: Part of standard metadata for Publications
comment: Answers the question: In what pages of the Publication can the reference to the resource be found?

programmed in
type: DatatypeProperty
sub property of: hasImplementationLanguage
domain: Software code
range: string
example: Pyleoclim
rationale: Provides the user with information about the software
comment: Answers the question: In which language was the software code written in?

publication year
type: DatatypeProperty
sub property of: created
sub property of: dateCreated
type: FunctionalProperty
domain: Publication
range: int
example: 2013PA002534
rationale: Part of standard metadata for Publications
comment: Answers the question: What year was the Publication issued?

relevant quote
type: DatatypeProperty
sub property of: description
range: string
example: Ocean2kHR 119.d18O.ClimateInterpretation
rationale: Often it's useful to put a quote from the paper that describes the interpretation
comment: Answers the question: Which part of the publication describes the Calibration or Interpretation?

scope
type: DatatypeProperty
domain: Interpretation
range: string
rationale: Allows to separate the various types of interpretation
comment: Answers the question: how would you classify the Interpretation? Examples include Isotope, Climate…

seasonality
type: DatatypeProperty
domain: Class
  union of: Interpretation
  union of: Proxy sensor
range: string
example: Ocean2kHR 119.d18O.ClimateInterpretation
rationale: Seasonality is critical to properly related measuredVariable and innferredVariable, as the former only senses part of the range of the latter.
comment: 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]

sensor genus
type: DatatypeProperty
domain: Organic proxy sensor
range: string
example: Globigerinoides ruber
rationale: Scientific Name of the organic ProxySensor
comment: Answers the question: What is the Genus of the Organic ProxySensor?

sensor species
type: DatatypeProperty
domain: Organic proxy sensor
range: string
example: Globigerinoides ruber
rationale: Scientific Name of the organic ProxySensor
comment: Answers the question: What is the species of the Organic ProxySensor?

standard
type: DatatypeProperty
domain: Measured variable
range: string
rationale: Crucial for isotopic measurements (for instance, d18O measurements (VSMOW vs VPDB))
comment: Answers the question: Reference material against which the MeasuredVariable is reported?

title
type: DatatypeProperty
sub property of: title
domain: Publication
range: string
example: 98PA00070
rationale: Part of standard metadata for Publications
comment: Answers the question: What is the title of the Publication?

uncertainty level
type: DatatypeProperty
domain: Uncertainty
range: string
rationale: Allows to properly make use of the reported Uncertainty values
comment: Answers the question: What parameter of the error distribution is the Uncertainty value referring to? Examples include 1-sigma, 2-sigma, 95% confidence bounds

volume
type: DatatypeProperty
type: FunctionalProperty
domain: Publication
range: string
example: 98PA00070
rationale: Part of standard metadata for Publications
comment: Answers the question: In which volume of the Publication does the reference to the Datatset appear?

Calibration model
type: Class
subclass of: Model
rationale: Make the model behind the calibration explicit
comment: Metadata about how the variable was calibrated to reflect an environmental variable

Chron data
type: Class
subclass of: Data
example: MD982181.Khider.2014.ChronData1
rationale: Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: The data, metadata, and Model that describe the set of Variables used to relate depth/position to time (chronological information)

Chron data table
type: Class
subclass of: Data table
disjoint with: PaleoData table
example: MD982181.Khider.2014.chron1measurement1
rationale: Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: DataTable containing Variables pertaining to chronological information

Chron model
type: Class
subclass of: Model
example: MD982181.Khider.2014.ChronData1.Model1
rationale: Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: Model used to derive a time (or age) axis from the ChronDataModel

Chron proxy system
type: Class
subclass of: Proxy system
rationale: 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
comment: 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])

Compilation
type: Class
subclass of: DataCatalog
rationale: Encodes what Data/Metadata gathering effort/scientific project led to the curation of the Datasets. Examples: PAGES2k, Iso2k, LR04, OC3, MARGO
comment: A curated aggregation of datasets

Data
type: Class
rationale: Needed to describe the paleoenvironmental and/or chronological data comprising the dataset as opposed to the Publication, Funding and Location information
comment: An aggregation of DataTables and Models with their supporting paleoenvironmental and/or chronological information

Data table
type: Class
rationale: Connects to the csv file where the data values are stored
comment: A set of Variables organized in columns

Dataset
type: Class
subclass of: Dataset
rationale: Fundamental unit at which we think about paleoclimate data. Also tends to correspond to the scope of the study
comment: A structured collection of related information, including -but not limited to -measured and/or modelled geograhical, chronological, and environmental data

Distribution table
type: Class
subclass of: Data table
example: ODP1098B12.Chron1.Model1.distributionTable.1
rationale: Added to allow outputs from Bayesian model (especially Bchron) to be saved as part of a dataset. Required to encode irregular probability distributions
comment: DataTable containing the probability distribution of a single value of a Variable. Output of a Model

Ensemble table
type: Class
subclass of: Data table
example: ODP1098B12.Chron1.Model1.EnsembleTable
rationale: Added to allow outputs from Bayesian model to be saved as part of a dataset
comment: DataTable constaining many possible series of how the Variable is modeled. Output of a Model

Funding
type: Class
example: http://wiki.linked.earth/MD982181.Khider.2014.Funding1
rationale: Allows to associate a grant number following U.S. federal regulation
comment: Source of monetary support underlying the collection/creation/analysis/curation of the Dataset

Inferred variable
type: Class
subclass of: Variable
disjoint with: Measured variable
rationale: See InferredVariable Ontology for concept description.
comment: A Variable that is inferred from one or more MeasuredVariable (s)

Inorganic proxy sensor
type: Class
subclass of: Proxy sensor
disjoint with: Organic proxy sensor
rationale: Encode the Genus and Species metadata
comment: An inorganic substrate sensing enviromental changes. Examples: karst, snow, watershed, ice sheet, rock, etc.

Instrument
type: Class
rationale: Needed to categorize types of instruments used for taking the different measurements. See Instrument Ontology for concept description.
comment: A tool used to produce MeasuredVariables

Integration time
type: Class
rationale: Soilwater mixing above speleothems: Although the sample might only represent 5 years of calcification, it can record 30 years of water mixing.
comment: The time it takes for the ProxySensor to imprint environmental information on the ProxyArchive. It may be further qualified with time periods and units

Interpretation
type: Class
rationale: Used to describe the interpretation of the Variable. For instance, radiocarbon is interpreted to represent age
comment: A suite of metadata that describes which phenomena drove variability in this Variable (e.g. environmental drivers).

Location
type: Class
subclass of: Place
subclass of: Feature
subclass of: SpatialThing
example: MD982181.Khider.2014.Location
rationale: Gives information about where the ProxyArchive comes from.
comment: The geographic data and metadata for the dataset

Measured variable
type: Class
subclass of: Class
  intersection of: Variable
  intersection of: Observation
rationale: 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)
comment: Variables that are measured by an Instrument. MeasuredVariables are ssn: Observations. They represent the values of a certain type of ProxyObservations

Measurement table
type: Class
subclass of: Data table
example: MD982181.Khider.2014.paleo1measurement1
rationale: Subclass of DataTable. Allows InferredVariables (despite the name) for practical purposes
comment: DataTable that contains the Variables (both measured and inferred)

Model
type: Class
example: MD982181.Khider.2014.PaleoData1.Model1
rationale: Allows to describe models whose outputs are stored in the Dataset. One example of is Bchron for age modeling
comment: 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

Non peer reviewed publication
type: Class
subclass of: Publication
disjoint with: Peer reviewed publication
rationale: Subclass of Publication.Allows to clearly mark datasets not generated as part of a peer-reviewed publication.
comment: A publication that has not undergone a formal review process; for instance, a Dataset attached to a dissertation.

Organic proxy sensor
type: Class
subclass of: Proxy sensor
example: Globigerinoides ruber
rationale: Subclass of ProxySensor. Makes the distinction between organic and inorganic. See the ProxySensor ontology for concepts
comment: Biologically-mediated ProxySensor. Examples include: foraminifera, trees, mollusks, polyps

Paleo data
type: Class
subclass of: Data
example: MD982181.Khider.2014.PaleoData1
rationale: Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: The Data pertaining to past environmental variability

PaleoData table
type: Class
subclass of: Data table
example: MD982181.Khider.2014.paleo1measurement1
rationale: Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: DataTable containing PaleoData Variables

Paleo model
type: Class
subclass of: Model
example: MD982181.Khider.2014.PaleoData1.Model1
rationale: Subdivision between chronological and paleoenvironmental information reflects the fact that Datasets are fundamentally characterized by two distinct components
comment: Model used to derive an environmental axis from the PaleoDataModel

Paleo proxy system
type: Class
subclass of: Proxy system
rationale: Gives a formal definition of climate proxy following the Evans et al. (2013) framework. Subclass of ProxySystem, pertaining to climate information
comment: 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.

Peer reviewed publication
type: Class
subclass of: Publication
example: 2013PA002534
rationale: Subclass of Publication.Allows to clearly mark datasets generated as part of a peer-reviewed publication.
comment: A Publication that has undergone a formal peer-review process

Person
type: Class
equivalent class: Person
example: D. Khider
rationale: The researcher, author on a publication.
comment: An individual who has participated directly or indirectly in the authoring of any resources on the LinkedEarth wiki

Physical sample
type: Class
example: MD98-2181
rationale: Used to differentiate between the concept of a ProxyArchive and its physical (real) manifestation
comment: The actual sample on which the measurements are made. For instance, the lake core analyzed in the lab is the physical sample.

Proxy archive
type: Class
rationale: "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"
comment: 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 model
type: Class
subclass of: Model
rationale: 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"
comment: A Model of how the ProxySensor either creates or emplaces the signal into the ProxyArchive. Sensu Evans et al. (2013)

Proxy observation
type: Class
example: D18O
rationale: 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
comment: 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 model
type: Class
subclass of: Model
rationale: 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
comment: The Model of how ProxyObservations are made on the archive. Sensu Evans et al. (2013)

Proxy sensor
type: Class
example: Cibicidoides mundulus
rationale: 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
comment: 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 model
type: Class
subclass of: Model
rationale: One component of the ProxySystemModel
comment: A Model of the ProxySensor. Sensu Evans et al. (2013)

Proxy system
type: Class
example: Ca
rationale: 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
comment: 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, δ18O, 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". "O…

Proxy system model
type: Class
subclass of: Model
rationale: 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
comment: 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."

Publication
type: Class
example: 2012GC004293
rationale: Can be used to credit the contributor of the dataset as well as linking toward the conclusions of the study and relevant methods
comment: A document that serves as reference for a Dataset or its components

Resolution
type: Class
rationale: Class added to describe the annual resolution of the archives
comment: Refers to the time difference between two adjacent values of a Variable.

Software code
type: Class
subclass of: Software
example: Pyleoclim
rationale: Added to allow for a link towards the code if on a public repository like GitHub
comment: A script that describes the model, in any programming language (e.g., Excel, Matlab, Python, R)

Summary table
type: Class
subclass of: Data table
rationale: Allows to represent a summary of basic statistics such as median, mean, standard deviation, and various quantiles from the output of the Model
comment: A DataTable that contains summary information for the Variable and is output from a Model.

Uncertainty
type: Class
rationale: 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)
comment: 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 model
type: Class
subclass of: Model
rationale: Allows description of how uncertainty was calculated
comment: A Model quantifiying the Uncertainty

Variable
type: Class
rationale: Basic definition of the values in the columns of the csv file
comment: Quantities that may change from value to value. They are usually represented as column of values in a data table

Observation
type: Class
comment: 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.