The Ecosystems Ontology
type: Ontology
contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
date: Mar 31, 2015 2:04:13 PM
contributor: Margaret O'Brien, orcid.org/0000-0002-1693-8322
contributor: Mark Schildhauer, orcid.org/0000-0003-0632-7576
comment: Revised version: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases. Collaborative work of: Margaret O'Brien, Sophie Hou, Chase LeCroy, and Mark Schildhauer
contributor: SophieHou, orcid.org/0000-0002-8087-1775
comment: This ontology was generated from an ontology revision in WebProtege http://odo.nceas.ucsb.edu
comment: ontology in progress for DataONE MSTMip/LTER Carbon cycling use cases
contributor: system
imports: skos-owl1-dl.rdf
imports: ENVO import.owl
imports: UO import.owl

definition_Contributor
type: AnnotationProperty
definition_Contributor: Margaret O'Brien, orcid.org/0000-0002-1693-8322, Shild
definition_Source: O'Brien, pers comm. 2015-02-15
example_Of_Usage: Margaret O'Brien, orcid.org/0000-0002-1693-8322
description: The "contributor" Annotation Property" is to record the name of the those contributing to the resource. If there is any potential ambiguity, an identifier should be added, including the system to which it belongs.
definition: "contributor" is an OWL "Annotation property" that names the person contributing the content, so s/he can be contacted, especially during development.
type: NamedIndividual

definition_Source
type: AnnotationProperty
definition_Contributor: Schildhauer, orcid.org/0000-0003-0632-7576
definition: "definitionSource" is the Annotation property that can be used to provide the reference source or Authority for the "definition" (of interest), as an ISBN,DOI, bibliographic citation, etc. to the source of the "definition" contained in an associated "definition" Annotation property that is attached (annotated) to the concept. Ideally a definition Source is structured in a well-known and accepted format, that provides an unambiguous pointer to a source reference, but often even some accurate indication of a reference source is better than nothing at all.
definition_Source: Schildhauer, pers comm, 05Feb2015, orcid.org/0000-0003-0632-7576
type: NamedIndividual

description
type: AnnotationProperty
definition: "description" is an OWL "Annotation property" that contains a a more verbose, less prescriptive natural language explication of the concept to which it is attached (or applied, or annotated) in contrast to a "definition" Annotation property. Use the "definition" Annotation property for scientific concepts when possible, as opposed to the "description" Annotation property
definition_Source: Schildhauer, pers comm, 05Feb2014, orcid.org/0000-000300632-7576
definition_Contributor: Schildhauer, orcid.org/0000-0003-0632-7576
type: NamedIndividual

description_Source
type: AnnotationProperty
description_Source: Schildhauer, pers comm, 05Feb2015, orcid.org/0000-0003-0632-7576
definition_Contributor: Schildhauer, orcid.org/0000-0003-0632-7576
definition: "description_Source" is the Annotation property that can be used to provide the reference source or Authority, as an ISBN,DOI, bibliographic citation, etc. to the source of the "description" contained in an associated "description" Annotation property that is attached (annotated) to some concept. Ideally a descriptionSource is structured in a well-known and accepted format, that provides an unambiguous pointer to a source reference, but often even some accurate indication of a reference source is better than nothing at all. As description Annotation properties are often not as rigorous, and hence looser and more verbose than definition Annotation properties, these fields may be more readily used for informal pedagogical advice and direction rather than being proscriptive
type: NamedIndividual

has_Exact_Synonym
type: AnnotationProperty
description: The DataONE carbon flux ontology uses synonyms for terms that may not be well defined. But we know that they are used, and refer to an owl class. I.e., a concept can have a synonym, but a concept should not be a synonym.
definition_Source: ad hoc
description_Source: Margaret O'Brien, 2015-03-18
definition_Contributor: mobb
definition: has_Exact_Synonym is an OWL annotation property that holds an alternate name or lexical variant of an owl class.
comment: We are not planning to use has_Broad_Synonym or has_Narrow_Synonym at this time. although other ontologies do. the concepts of "broad" and "narrow" imply relationships that could be better described with the class hierarchy.
type: NamedIndividual

example_Of_Usage
type: AnnotationProperty
description_Source: O'Brien, pers comm, 2015-02-19
definition: "example_Of_Usage" is an OWL annotation property to record examples of how the concept or property should be used.
description: "example_Of_Usage" is for providing examples. It should contain actual sample strings for the resource it applies to. longer, text descriptions of good practice for the resource belong in the "description" annotation.
definition_Source: O'Brien, pers comm, 2015-02-19
definition_Contributor: Margaret O'Brien, orcid.org/0000-0002-1693-8322
type: NamedIndividual

has_Related_Synonym
type: AnnotationProperty
definition: has_Related_Synonym is an owl annotation property to hold a term that is not an owl class, but is a primary term found in the literature but is not necessarily correct.
description: The DataONE carbon flux ontology uses synonyms for terms that may not be well defined. But we know that they are used, and refer to an owl class. I.e., a concept can have a synonym, but a concept should not be a synonym.
definition_Source: ad hoc!
definition_Contributor: mobb
description_Source: Margaret O'Brien, 2015-03-18
type: NamedIndividual

rdfs:label
type: AnnotationProperty
definition_Contributor: Margaret O'Brien, orcid.org/0000-0002-1693-8322
example_Of_Usage: Carbon_Flux_NASA, definition_Source, rdfs:label
description: rdfs:label is a built in annotation property, and W3C does not give guidelines beyond the definition. In the DataONe Carbon Flux ontology, we use rdfs:label for a human-readable version of the resource's name, but adhere to a particular pattern. Our goal is that content of rdfs:label are not broken into individual terms arbitrarily. 1. Our practice is to separate individual words in the rdfs:label with underscores, but maintain capitalization consistent with the conventions of the resources type (e.g., camel case for properties, capitalized words for classes, capitalized abbreviations and acronyms). 2. include namespace in the label, if resource is imported. See example_Of_Usage, presentation_Label
description_Source: O'Brien, 2015-02-19
definition: rdfs:label is an instance of rdf:Property that may be used to provide a human-readable version of a resource's name
definition_Source: ch label
type: NamedIndividual

has State
type: ObjectProperty
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: Describes the physical state of a substance
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

has Location
type: ObjectProperty
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: Defines where a class exists or takes place
type: NamedIndividual

has Result
type: ObjectProperty

has Input
type: ObjectProperty

has Output
type: ObjectProperty

Carbon Cycle Components
type: Class
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: "carbon cycle." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/carbon+cycle
definition: The parts that make up the combined processes that cycle carbon, (including photosynthesis, decomposition, and respiration) between its major reservoirs (the atmosphere, oceans, and living organisms).
type: NamedIndividual

Carbon Flux
type: Class
subclass of: Carbon Cycle Components
definition: The rate at which a mass of carbon moves to or from a particular component of the ecosystem per unit time.
description_Source: unknown.
definition_Source: Litton, C.M. et al. Carbon allocation in forest ecosystems. Global Change Biology. V 13 I 10. pp. 2089 - 2109. July 2007.
description: Carbon fluxes are the movement of Carbon from one place (Source) to another (Sink). Carbon fluxes all have dimensions of {mass or amount of} Carbon per area (or volume) per time biochemically-oriented projects use moles (e.g., for Stoichiometry) rather than kg to quantify the amount of Carbon, whereas Climate-oriented projects use kg
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Dissolved Organic Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Class
    intersection of: Restriction
      on property: RO_0000086
      some values from: Dissolved State
    intersection of: Restriction
      on property: ENVO_01001309
      all values from: Organic Carbon
subclass of: Carbon Flux
definition: The rate at which a mass of dissolved organic carbon moves to or from a particular component of an ecosystem per unit time. Dissolved organic cabon is defined as the fraction of organic matter which is neither excluded nor adsorbed by the filter used to remove particulate organic carbon, and which is not volatile enough to be lost by the acidification and purging technique used to remove inorganic carbon.
has_Exact_Synonym: DOC flux
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Wangersky, P.J. Dissolved organic carbon methods: a critical review. Marine Chemistry. V 41 I 1-3. pp. 61-74. 1993.
type: NamedIndividual

Fire Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: ENVO_01001309
    some values from: Carbon Dioxide
  intersection of: Restriction
    on property: ENVO_01001309
    some values from: Carbon Monoxide
subclass of: Carbon Flux
alternative label: Fire Emissions
description: Fire Carbon Flux is a measure of carbon released into the atmosphere due to fire (MPS, 2015)
definition_Source: Johnson, E.A. and Miyanishi, K. Forest Fires: Behavior and Ecological Effects. Academic Press. 2001
definition: The mass of carbon released from burning vegetation per unit time.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Net Ecosystem Exchange Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: ENVO_01001309
    some values from: Class
      union of: Carbon Dioxide
      union of: Organic Carbon
subclass of: Carbon Flux
alternative label: NEE
alternative label: Net Ecosystem Exchange
definition: The magnitude of carbon sources and sinks is defined as the vertical exchange of CO2 between the surface (land or ocean) and the atmosphere.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Hayes, D.J. et al. Reconciling estimates of the contemporary North American carbon balance among terrestrial biosphere models, atmospheric inversions, and a new approach for estimating net ecosystem exchange from inventory-based data. Global Change Biology. V 8, i 4. pp. 1282-1299. April 2012. DOI: 10.1111/j.1365-2486.2011.02627.x
type: NamedIndividual

Primary Production Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: has Input
    some values from: Class
      union of: Carbon Dioxide
      union of: Inorganic Carbon
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: has Output
    some values from: Class
      union of: Carbohydrate
      union of: Organic Carbon
subclass of: Carbon Flux
alternative label: Primary production
alternative label: Primary productivity
definition_Source: Inferred from: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
comment: http-en.wikipedia.org/wiki/Primary_production Gross primary production (GPP) is the amount of chemical energy as biomass that primary producers create in a given length of time. (GPP is sometimes confused with Gross Primary productivity, which is the rate at which photosynthesis or chemosynthesis occurs.) For most purposes (including this one) the two can be the same. It's most practical to measure production over a given time interval and area, and that amounts to an areal rate.
definition: The process of carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Respiration Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: has Input
    some values from: Class
      union of: Carbohydrate
      union of: Organic Carbon
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: has Output
    some values from: Class
      union of: Carbon Dioxide
      union of: CHEBI_33582
subclass of: Carbon Flux
alternative label: Respiration
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: CO2 produced by organisms and emitted to the environment per unit ground or water area and time. Equivalent to the sum of autotrophic and heterotrophic respiration.
definition: CO2 produced by organisms and emitted to the environment per unit ground or water area and time.
definition_Source: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
alternative label: Total Respiration
type: NamedIndividual

Autotrophic Respiration Carbon Flux
type: Class
subclass of: Respiration Carbon Flux
disjoint with: Heterotrophic Respiration Carbon Flux
alternative label: Autotrophic Respiration
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The sum of respiration (CO2 production) by all living parts of primary producers per unit ground or water area and time.
definition_Source: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
type: NamedIndividual

Heterotrophic Respiration Carbon Flux
type: Class
subclass of: Respiration Carbon Flux
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
alternative label: Heterotrophic Respiration
definition: The respiration rate of heterotrophic organisms (animals and microbes) summed per unit ground or water area and time.
type: NamedIndividual

Gross Primary Production Carbon Flux
type: Class
subclass of: Primary Production Carbon Flux
disjoint with: Net Primary Production Carbon Flux
alternative label: Gross Primary Productivity
comment: Primary production before the autotrophs' own respiration is subtracted. Also called photosynthetic rate, or carbon fixation rate.
definition_Source: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
definition: The sum of gross carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time.
alternative label: Gross Primary Production
comment: primary production before the autotrphs' own respiration is subtracted. also called photosynthetic rate, or carbon fixation rate. Synonyms: GPP
alternative label: GPP
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Net Primary Production Carbon Flux
type: Class
subclass of: Primary Production Carbon Flux
alternative label: Net Primary Production
alternative label: NPP
definition_Source: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
alternative label: Net Primary Productivity
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: Gross primary production (GPP) minus autotrophic respiration (AR) per unit ground or water area and time.
comment: the amount of primary production available for export (ie, gross, minus losses, like the autotrophs' own respiration, or other loss (exudation) not used by the carbon-fixing organism itself) = gross primary production - autotrophic respiration synonyms: NPP
type: NamedIndividual

Carbon Pool
type: Class
subclass of: Carbon Cycle Components
description_Source: O'Brien, pers comm. 2015-02-20
definition_Source: "carbon pool." McGraw-Hill Dictionary of Scientific & Technical Terms, 6E. 2003. The McGraw-Hill Companies, Inc. 20 Feb. 2015 http-encyclopedia2.thefreedictionary.com/carbon+pool
description: Carbon Pools are reservoirs in the system with the capacity to exchange carbon. Usually scientists are interested in the size of pools, and the movement of carbon between pools. The dimensions of a carbon pool are likely to be mass or moles Carbon per area or volume (eg, kg per m2).
alternative label: Name of Each Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: A reservoir with the capacity to store and release carbon, such as soil, terrestrial vegetation, the ocean, and the atmosphere {contributed by margaret, from
description: Carbon Pools are reservoirs in the system with the capacity to exchange. Usually scientists are interested in the size of carbon pools, and the movement of carbon between pools. Carbon pools can vary widely in scale, from an ecosystem to an species functional level. The dimensions are likely to be mass or moles Carbon per area (eg, kg per m2).
type: NamedIndividual

Soil Carbon Pool
type: Class
equivalent class: Class
  intersection of: Inorganic Carbon Pool
  intersection of: Restriction
    on property: has Location
    all values from: ENVO_00001998
equivalent class: Class
  intersection of: Organic Carbon Pool
  intersection of: Restriction
    on property: has Location
    all values from: ENVO_00001998
subclass of: Organic Carbon Pool
subclass of: Inorganic Carbon Pool
alternative label: Total Soil Carbon
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: "soil." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company. 24 Feb. 2015 http-www.thefreedictionary.com/soil
definition: The mass of carbon contained within the top layer of the earth's surface in which plants can grow, consisting of rock and mineral particles mixed with decaying organic matter and having the capability of retaining water.
type: NamedIndividual

Plankton Carbon Pool
type: Class
subclass of: Biomass Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998.
definition: The mass of carbon contained in free-floating organisms of the sea and fresh water that for the most part move passively with the water currents and consist mostly of microorganisms and small plants and animals.
type: NamedIndividual

Leaf Carbon Pool
type: Class
subclass of: Biomass Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The mass of carbon contained within flattened photosynthetic structures emerging laterally from a main axis or stem and possessing true vascular tissue.
comment: 'leaf carbon pool' and 'leaf litter carbon pool' also had associated with them the concepts 'leaves' and 'leaf decomposition' as related terms. These latter two concepts have been removed at this time as too general (leaves) or too processual (leaf decomposition as opposed to 'leaf decompositional pool'). Might consider adding these back in as skos:alLabel.
has_Related_Synonym: leaves
definition_Source: Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998.
type: NamedIndividual

Benthic Algae Carbon Pool
type: Class
equivalent class: Class
  intersection of: Biomass Carbon Pool
  intersection of: Restriction
    on property: has Location
    all values from: ENVO_01000321
subclass of: Biomass Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The mass of carbon present in algae on the seafloor.
definition_Source: Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998.
type: NamedIndividual

Grass Carbon Pool
type: Class
subclass of: Biomass Carbon Pool
definition: The mass of carbon contained within monocotyledonous plants of the family Poaceae, having jointed stems sheathed by long, narrow leaves, flowers in spikes, and seedlike fruits.
definition_Source: "grass." Collins English Dictionary – Complete and Unabridged. 1991, 1994, 1998, 2000, 2003. HarperCollins Publishers 24 Feb. 2015 http-www.thefreedictionary.com/grass
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Wood Carbon Pool
type: Class
subclass of: Biomass Carbon Pool
definition_Source: "wood." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/wood
definition: The mass of carbon contained in the tough, fibrous substance lying beneath the bark of trees and shrubs, consisting of the vascular tissue known as xylem and composed chiefly of cellulose and lignin.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Leaf Litter Carbon Pool
type: Class
subclass of: Organic Carbon Pool
definition_Source: Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998.
has_Related_Synonym: leaf decomposition
comment: synonyms from LTER searched terms (mob, 2015-03-24)
has_Related_Synonym: leaves
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The mass of carbon contained in the partly decomposed remains of plants on the surface and in the upper layers of the soil.
type: NamedIndividual

Dissolved Organic Carbon Pool
type: Class
equivalent class: Class
  intersection of: Organic Carbon Pool
  intersection of: Restriction
    on property: has State
    all values from: Dissolved State
subclass of: Organic Carbon Pool
disjoint with: Particulate Organic Carbon Pool
definition_Source: Fiedler, S. et al. 2008. Particulate organic carbon (POC) in relation to other pore water carbon fractions in drained and rewetted fens in Southern Germany. Biogeosciences, 5, 1615–1623, 2008.
alternative label: DOC
definition: The pool of organic carbon made up of particles smaller than 0.45 um.
alternative label: Total Dissolved Organic Carbon
type: NamedIndividual

Annual Net Primary Productivity Flux
type: Class
equivalent class: Class
  intersection of: Net Primary Production Carbon Flux
  intersection of: Restriction
    on property: ENVO_2100001
    some values from: UO_0000036
subclass of: Net Primary Production Carbon Flux
definition: Gross primary production (GPP) minus autotrophic respiration (AR) over one year.
alternative label: Annual Net Primary Production
alternative label: Annual Net Primary Productivity
definition_Source: Chapin, F.J. et al. Reconciling Carbon-cycle Concepts, Terminology, and Methods. Ecosystems. V 9 I 7. pp. 1041-1050. 2006. DOI: 10.1007/s10021-005-0105-7
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
alternative label: ANPP
type: NamedIndividual

Measurement
type: Class
subclass of: Carbon Cycle Components
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: "measurement." The Columbia Electronic Encyclopedia®. 2013. Columbia University Press 20 Feb. 2015 http-encyclopedia2.thefreedictionary.com/Measurement
definition: A determination of the magnitude of a quantity by comparison with a standard for that quantity.
type: NamedIndividual

MsTMIP_Measurement
type: Class
subclass of: Measurement
definition_Contributor: mob
definition: Parent class for all MsTMIP variables
type: NamedIndividual

MsTMIP_Driver_Variable
type: Class
subclass of: MsTMIP_Measurement

MsTMIP_Output_Variable
type: Class
subclass of: MsTMIP_Measurement

Total_Living_Biomass_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Total carbon content of the living biomass (leaves+roots+wood)
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Net_Longwave_Radiation_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Incident longwave radiation minus simulated outgoing longwave radiation (positive into grnd)
type: NamedIndividual

Total_Soil_Wetness_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Vertically integrated soil moisture divided by maximum allowable soil moisture above wilting point
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Near_Surface_CO2_Concentration_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Near surface dry air CO2 mole fraction
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Total_Respiration_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Total respiration (TotalResp=AutoResp+heteroResp, always positive)
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Absorbed_Fraction_Incoming_PAR_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Absorbed fraction incoming photosyntetically active radiation
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Near_Surface_Air_Temperature_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Near surface air temperature
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Leaf_Area_Index_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Area of leaves per area ground
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Surface_Pressure_MOV
type: Class
label: Near_Surface_Specific_Humidity_MOV
subclass of: MsTMIP_Output_Variable
definition: Near surface specific humidity
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Surface pressure
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Average_Layer_Soil_Moisture_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Soil water content in each soil layer, including liquid, vapor and ice
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Average_Layer_Soil_Temperature_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Average soil temperature in each soil layer
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Surface_Runoff_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Runoff from the landsurface and/or subsurface stormflow
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Soil_Layer_Top_Depth_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Depth from soil surface to top of soil layer
type: NamedIndividual

Near_Surface_Module_Of_The_Wind_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Near surface wind magnitude
type: NamedIndividual

Size_Of_Each_Carbon_Pool_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Total size of each carbon pool vertically integrated over the entire soil column
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Soil_Layer_Node_Depth_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Depth from soil surface to layer prognostic variables; typically center of soil layer
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Snow_Water_Equivalent_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Total water mass of snow pack, including ice and liquid water
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Total_Soil_Carbon_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Total soil and litter carbon content vertically integrated over the enire soil column
type: NamedIndividual

Autotrophic_Respiration_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Autotrophic respiration rate (always positive)
type: NamedIndividual

Rainfall_Rate_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Rainfall rate
type: NamedIndividual

Longwave_Albedo_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Longwave Albedo
type: NamedIndividual

Gross_Primary_Productivity_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: mob
definition: MsTMIP Output: Rate of photosynthesis (always positive)
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Name_Of_Each_Carbon_Pool_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Name of each carbon pool (i.e., "wood," or "Coarse Woody Debris")
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Soil_Layer_Bottom_Depth_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Depth from soil surface to bottom of soil layer
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Heterotrophic_Respiration_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Heterotrophic respiration rate (always positive)
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Active_Layer_Thickness_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Thaw depth; depth to zero centigrade isotherm in permafrost
type: NamedIndividual

Net_Shortwave_Radiation_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Incident shortwave radiation minus simulated outgoing shortwave radiation (positive into grnd)
type: NamedIndividual

Total_Snow_Depth_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Total snow depth
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Fire_Emissions_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Flux of carbon due to fires (always positive)
type: NamedIndividual

Surface_Incident_Longwave_Radiation_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Surface incident longwave radiation
type: NamedIndividual

Above_Ground_Woody_Biomass_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Total above ground wood biomass
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Subsurface_Runoff_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Gravity soil water drainage and/or soil water lateral flow
type: NamedIndividual

Sensible_Heat_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Sensible heat flux into the boundary layer (positive into atmosphere)
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Net_Ecosystem_Exchange_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Net Ecosystem Exchange (NEE=HeteroResp+AutoResp-GPP, positive into atmosphere)
type: NamedIndividual

Shortwave_Albedo_MOV
type: Class
label: Net_Primary_Productivity_MOV
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Shortwave albedo
definition: Net Primary Productivity (NPP=GPP-AutoResp, positive into plants)
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Surface_Incident_Shortwave_Radiation_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition: Surface incident shortwave radiation
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Total_Evaporation_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
definition: Sum of all evaporation sources (positive into atmosphere)
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
type: NamedIndividual

Latent_Heat_MOV
type: Class
subclass of: MsTMIP_Output_Variable
definition: Latent heat flux into the boundary layer (positive into atmosphere)
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
type: NamedIndividual

Method
type: Class
definition_Source: "method." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/method
comment: The methods that can be used for measurements. I don't think its the place of this ontology to model all the differences and assumptions between methods. Reasons: 1. That would get very complicated and is probably out of scope. 2. we should assume some level of knowledge of the user. People using pprod data should know enough to evaluate basic diifferences between methods. eg, an ecologist ought to know that "allometrics" are an average for a species or population, not a community. or an oceanographer ought to know the difference between light-dark O2 and light-dark C14 inclubations. So if you want "community NPP", and you see the method used was allometric -- you'd know you had to understand the community composition to know if prod of one or a few groups is enough. if you wanted "community NPP",in ocean data, you would know that O2 light-dark was OK, but that C14 update might actually be GPP
definition: A regular and systematic way of accomplishing something, characteristic of a particular discipline or field of knowledge.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Field Method
type: Class
subclass of: Method
definition: strawman definition from margaret: a Field_Method is a method for determining a component of primary production that involves observations or measurements of the real world. A field method may have steps which could be considered 'modeling' (such as development of an allometric model of tree growth based on height), but measurements "in the field" (eg, of trees) are always involved. compare to Modeled_Method.
type: NamedIndividual

Modeled Method
type: Class
subclass of: Method
definition: strawman definition from Margaret a Modeled_Method (is Simulated_Method better?) uses only data obtained from some source. It does not directly measure any real phenomenon.
type: NamedIndividual

Peak Biomass Harvest Method
type: Class
subclass of: Field Method
description: The "Peak Standing Biomass Harvest" method is recommended for grasslands that meet the following criteria: 1) there is little carryover of living biomass from previous years due to distinct dormant season or fire during the dormant season or the previous year's biomass can be easily recognized and separated from the current year's biomass (living and dead) 2) the growing season is sufficiently short or plant material is of such low quality that decomposition of biomass produced can be ignored 3) consumption of plants by herbivores is minimal (i.e., large grazers are absent and small vertebrates and invertebrates can be ignored).
definition_Source: Fahey and Knapp, 2007, p33
definition: Peak_Biomass_Harvest_Method is an estimate of above ground NPP based on the above ground biomass harvested once, usually near the end of the growing season, at or just after the time of peak biomass
description_Source: Fahey and Knapp, 2007, p33
type: NamedIndividual

Eddy Covariance Method
type: Class
subclass of: Field Method
description_Source: http-en.wikipedia.org/wiki/Eddy_covariance
comment: add these synonyms (near? exact?): also known as eddy correlation and eddy flux
description: It is frequently used to estimate momentum, heat, water vapor, carbon dioxide and methane fluxes. The technique is mathematically complex, and requires significant care in setting up and processing data. To date, there is no uniform terminology or a single methodology for the Eddy Covariance technique. The technique has additionally proven applicable under water to the benthic zone for measuring oxygen fluxes between seafloor and overlying water.[6] In these environments, the technique is generally known as the eddy correlation technique, or just eddy correlation. For CO2.... tbd
definition_Source: http-en.wikipedia.org/wiki/Eddy_covariance
definition: The eddy covariance method is an atmospheric measurement technique to measure and calculate vertical turbulent fluxes within atmospheric boundary layers, and analyzes high-frequency wind and scalar atmospheric data series, to yield exchange rates (fluxes) of trace gasses.
type: NamedIndividual

Carbon14 Uptake Method
type: Class
subclass of: Field Method
description_Source: O'Brien, pers comm 2015-02-15 Fahey and Knapp, 2007
description: A C14 uptake method is typically used in aquatic environments, for microscopic autotrophs (phytoplankton). C14 is a radioactive tracer added as bicarbonate, and its concentration determined in the plankton after removed by filtration. Measurement scales tend to be small (hours and liters) relative to the scales of other field methods. Photosynthetic and heterotrophic activity are tightly coupled in planktonic systems (Fahey and Knapp, 2007). If the incubation is short enough, the result will be GPP (gross), because presumably, no labeled c14 was recycled (or respired) by the cells. Sometimes researchers conduct "light-dark bottle", but the dark bottle tells you something different than in o2 light-dark. It gives you dark CO2 uptake, so subtract this from light CO2 uptake if you want autotrophic GPP.

Oxygen Evolution LightDark Method
type: Class
subclass of: Field Method
definition: The stoichiometry of phtotsynthesis is well known. So you can measure O2 evolution, and back calculate to CO2 use. usually, there is a "iight bottle" and "dark bottle". O2 evolution in the Light bottle is the net result, or sum, of all processes (GPP, Autotrophic resp, and probably some heterotrophic respiration too, because heterotrophs are hard to exclude). So Light bottle = NPP. Dark bottle is respiration, probably total, eg, autotrophs + heterotrophs. So light + dark = GPP (or about as close as you can get with a field measurement, and assume that heterotrophs aren't respiring much.)
type: NamedIndividual

Allometric Method
type: Class
subclass of: Field Method
definition_Source: Begon, M., Harper, J.L., Townsend, C.R. Ecology: Individuals, Populations, and Communities. Third Edition. Blackwell Science. 1996.
definition_Source: O'Brien, pers comm, 2014-10-15
description: an allometric method is usually accomplished with a combination of measurements that are tailored to the organism, e.g, size, growth rate, carbon content, plus some loss terms. SBC's dataset 21 has a good example of an allometric method for kelp.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: A method determining the relationship between a physical or physiological property of an organism relative to the size of the organism.
type: NamedIndividual

LIDAR Method
type: Class
subclass of: Field Method
definition_Contributor: mob, 2015-03-25
alternative label: LIDAR
definition: A LIDAR_Method for NPP is a methodology to predict the net primary production (NPP) from ground and LiDAR data
definition_Source: Available from: https-www.researchgate.net/publication/233137060_Use_of_ground_and_LiDAR_data_to_model_the_NPP_of_a_Mediterranean_pine_forest [accessed Mar 25, 2015].
type: NamedIndividual

MsTMIP_Simulation
type: Class
subclass of: Modeled Method
definition: Simulation is the imitation of the operation of a real-world process or system over time. (wikipedia). A MsTMIP Simulation is a simulation carried out by the MsTMIP project (margaret)
definition_Source: adapted from wikipedia, Simulation
type: NamedIndividual

BIOME-BGC_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
description_Source: http-www.ntsg.umt.edu/project/biome-bgc
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Weile Wang (weile.wang@gmail.com) citations: 1. thornton et al. (2002) modeling and measuring the effects of disburbance history and climate on carbon and water budgets in evergreen needleleaf forests. agriculture and forest meteorology, 113, 185-222.
description: Biome-BGC is an ecosystem process model that estimates storage and flux of carbon, nitrogen and water. Biome-BGC is a computer program that estimates fluxes and storage of energy, water, carbon, and nitrogen for the vegetation and soil components of terrestrial ecosystems. We call it a process model because its algorithms represent physical and biological processes that control fluxes of energy and mass. The model uses a daily time-step. This means that each flux is estimated for a one-day period. Between days, the program updates its memory of the mass stored in different components of the vegetation, litter, and soil. Weather is the most important control on vegetation processes. Flux estimates in Biome-BGC depend strongly on daily weather conditions. Model behavior over time depends on the history of these weather conditions, the climate.

CLASS-CTEMNplus_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Altaf Arain (arainm@mcmaster.ca) citations: 1. s. huang, m. a. arain, v. arora, f. yuan, j. brodeur, m. peichl, 2011. analysis of nitrogen controls on carbon and water exchanges in a conifer forest using the class-ctemn+ model, ecological modeling, 222(20–22): 3743–3760, http-dx.doi.org/10.1016/j.ecolmodel.2011.09.008.
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description_Source: http-www.cccma.ec.gc.ca/ctem/
description: The Canadian Terrestrial Ecosystem Model (CTEM) is designed to serve as the terrestrial carbon cycle component in the coupled Canadian Centre for Climate Modelling and Analysis (CCCma) atmosphere-ocean general circulation model (GCM). CTEM is a dynamic vegetation model that is able to grow vegetation from bare ground and provides time-varying vegetation structural attributes (e.g., leaf area index (LAI), vegetation height, rooting depth and distribution, and canopy mass) to the land surface scheme it is coupled with. Other than simulating vegetation biomass and its structural attributes CTEM also simulates amount of carbon in its dead pools (litter and soil organic matter), and thus is able to provide net fluxes of CO2 between the land and the atmosphere. This documentation provides a brief description of CTEM 1.0/1.1 and the manner in which CTEM is coupled to Canadian Land Surface Scheme (CLASS, version 2.7) [Verseghy et al. 1993; Verseghy, 1991]. Coupled CLASS 2.7/CTEM 1.0 are implemented in CCCma's coupled carbon climate model.

CLM4VIC_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
description: Incorporating parameterizations from the Variable Infiltration Capacity (VIC) land surface model into CLM.
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Maoyi Huang (maoyi.huang@pnnl.gov) citations: 1. li, h., m. huang, m. s. wigmosta, et al. 2011, evaluating runoff simulations from the community land model 4.0 using observations from flux towers and a mountainous watershed, j. geophys. res., 116, d24120, doi:10.1029/2011jd016276.
description_Source: http-www.cesm.ucar.edu/working_groups/Land/Presentations/2012/huang.pdf
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775

CLM_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
description: The Community Land Model version 4.0 (CLM4.0) is the land model used in the CCSM4.0. CLM4.0 is the latest in a series of land models developed through the CCSM project.
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Daniel J. Hayes (hayesdj@ornl.gov) citations: 1. mao, jiafu, peter e. thornton, xiaoying shi, maosheng zhao, wilfred m. post, 2012: remote sensing evaluation of clm4 gpp for the period 2000–09. j. climate, 25, 5327–5342. doi: http-dx.doi.org/10.1175/jcli-d-11-00401.1 2. shi, x., mao j., thornton p. e., hoffman f. o. r. r. e. s. t. m., & post w. m. (2011). the impact of climate, co2, nitrogen deposition and land use change on simulated contemporary global river flow. geophysical research letters. 38(8). doi: 10.1029/2011gl046773 3. mao, jiafu; shi, xiaoying; thornton, peter e.; hoffman, forrest m.; zhu, zaichun; myneni, ranga b. 2013. "global latitudinal-asymmetric vegetation growth trends and their driving mechanisms: 1982–2009." remote sens. 5, no. 3: 1484-1497.
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description_Source: http-www.cesm.ucar.edu/models/ccsm4.0/clm/

DLEM_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: The Dynamic Land Ecosystem Model (DLEM) represents the state-of-the-art in terrestrial ecosystem modeling, which couples biophysical, hydrological, major biogeochemical processes (C, N, and P cycling) including trace gases emissions such as CO2, N2O, CH4 , vegetation dynamics, disturbances including natural and anthropogenic aspects (e.g. land-use/land-cover change, intensive management on crops and forests, wild fire, insect and disease etc.) , and works at multiple scales in time from daily to yearly and space from meters to kilometers, from region to globe across Earth’s land surface and in adjacent ocean regions.
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Hanqin Tian (tianhan@auburn.edu) citations: 1. tian, h., x. xu, c. lu, m. liu, w. ren, g. chen, j. melillo, and j. liu (2011), net exchanges of co2, ch4, and n2o between china's terrestrial ecosystems and the atmosphere and their contributions to global climate warming, j. geophys. res., 116, g02011, doi:10.1029/2010jg001393. 2. tian, hq, g. chen, c. zhang, m. liu, g. sun, a. chappelka, w. ren, x. xu, c. lu, s. pan, h. chen, d. hui, s. mcnulty, g. lockaby and e. vance. 2012. century-scale response of ecosystem carbon storage to multifactorial global change in the southern united states. ecosystems 15(4): 674-694, doi: 10.1007/s10021-012-9539-x
description_Source: https-scisoc.confex.com/crops/2013am/webprogram/Paper78258.html

GTEC_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Daniel Ricciuto (ricciutodm@ornl.gov)
definition_Source: http-www.esd.ornl.gov/~wmp/GTEC/pgtec.html
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: GTEC = Global Terrestrial Ecosystem Carbon Model GTEC - global model contains 21,600 1 degree terrestrial cells. The carbon dynamics of each vegetated land cell (1.0 degree latitude X 1.0 degree longitude resolution) is described by a mechanistic soil-plant-atmosphere model (LoTEC) of ecosystem carbon storage and CO2 and H2O flux. Each grid cell is assigned to one of 15 ecosystem types and one of 105 soil types.

ISAM_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: Integrated Assessment Modeling (IAM) is a new important research methodology for examining the complex interactions among physical, and human systems. Rather than actually using many of the multi-dimensional and complicated expert models, IAM build on the knowledge achieved by each individual scientific discipline. The uses of such tools need to explicitly recognize and address the existence of considerable uncertainty and scientific debate surrounding climate issues. Our existing Integrated Science Assessment Model (ISAM) for assessment of climate change (Jain et al., 1994) consists of coupled modules for representation of the carbon cycle, effects of greenhouse gas emissions and aerosols on atmospheric composition, effects on global temperatures using an energy balance model, and processes affecting sea level change. This model has been used to estimate the relation between the time-dependent rate of greenhouse gas emissions and quantitative features of climate global temperature, the rate of temperature change, and sea level that are thought to be indicators of human impact on climate and ecosystems (Wigley et al., 1998). This model has also been applied to studies of Global Warming Potential (GWP, Wuebbles, et al., 1995), and the Economic-Damage Index (EDI, Hammitt et al., 1996) concepts.
description_Source: http-climate.atmos.uiuc.edu/isam2/descript.html
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Atul Jain (jain1@illinois.edu)

LPJ-wsl_Mstmip_Version1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
description_Source: http-digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1132&context=nasapub
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Benjamin Poulter (benjamin.poulter@lsce.ipsl.fr) Citations: 1. Sitch S, Smith B, Prentice IC, Arneth A, Bondeau A, Cramer W, Kaplan J, Levis S, Lucht, W, Sykes M, Thonicke K, Venevsky S 2003. Evaluation of ecosystem dynamics, plant geography and terrestrial carbon cycling in the LPJ Dynamic Vegetation Model. Global Change Biology 9: 161–185. 2. Bondeau A, Smith PC, Zaehle S, Schaphoff S, Lucht W, Cramer W, Gerten D, Lotze-Campen H, Müller C, Reichstein M & Smith B (2007) Modelling the role of agriculture for the 20th century global terrestrial carbon balance. Gl Ch Biol 13:679-706, 3. Poulter, B, L Aragao, U Heyder, Gumpenberger, M, F Langerwisch, A Rammig, K Thonicke and W Cramer. 2010. Net biome production of the Amazon Basin in the 21st century. Global Change Biology, 16(7):2062-2075.
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: LPJ-wsl is a dynamic global vegetation model that simulates coupled biogeography and biogeochemical responses to climate, CO2, and disturbance (Sitch et al., 2003).

ORCHIDEE-LSCE_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Shushi Peng (Shushi.Peng@lsce.ipsl.fr) Gwena‰lle Berthier (Gwenaelle.Berthier@lsce.ipsl.fr) citations: 1. krinner, g., viovy, n., noblet-ducoudre, n. de, ogee, j., polcher, j., friedlingstein, p., ciais, p., sitch, s., and prentice, i. c (2005). a dynamic global vegetation model for studies of the coupled atmosphere-biosphere system. global biogeochem. cycles, 19, gb1015.
description_Source: http-unfccc.int/adaptation/nairobi_work_programme/knowledge_resources_and_publications/items/7382.php
description: The ORCHIDEE dynamic global vegetation model represents the land surface features of the IPSL coupled atmosphere-ocean-vegetation model. ORCHIDEE has been developed using first order ecophysiological principles to represent both natural ecosystem and managed land carbon, water, and energy dynamics across multiple spatial (site to globe) and temporal (sub-daily to centennial) scales. lsce = Laboratoire des Sciences du Climat et l'Environnement

SIB3-JPL_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
description_Source: http-biocycle.atmos.colostate.edu/research/models/sib3/
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: The Simple Biosphere (SiB) Model was originally developed by Piers Sellers in the mid-1980’s as an internally-consistent module to surface-atmosphere exchanges of radiation, heat, moisture, and momentum over land. It was extended in the mid-1990’s by a team of interdisciplinary scientists to include mechanistic linkages to photosynthesis, stomatal physiology, and satellite remote sensing. Since that time it has been extended to include improved treatment of carbon cycling, soils, snow, hydrology, stable isotopes, phenology, and crops.
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Nicholas C. Parazoo (nicholas.c.parazoo@jpl.nasa.gov) citations: 1. baker, i. t., l. prihodko, a. s. denning, m. goulden, s. miller, and h. r. da rocha (2008), seasonal drought stress in the amazon: reconciling models and observations, j. geophys. res., 113(g1), g00b01.

SIBCASA_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Kevin Schaefer (kevin.schaefer@nsidc.org) citations: 1. schaefer, k., g. j. collatz, p. tans, a. s. denning, i. baker, j. berry, l. prihodko, n. suits, and a. philpott (2008), combined simple biosphere/carnegie-ames-stanford approach terrestrial carbon cycle model, j. geophys. res., 113, g03034, doi:10.1029/2007jg000603. 2. schaefer, k., t. zhang, a. g. slater, l. lu, a. etringer, and i. baker (2009), improving simulated soil temperatures and soil freeze/thaw at high-latitude regions in the simple biosphere/carnegie-ames-stanford approach model, j. geophys. res., 114, f02021, doi:10.1029/2008jf001125.
description: We combine the photosynthesis and biophysical calculations in the Simple Biosphere model, Version 2.5 (SiB2.5) with the biogeochemistry from the Carnegie-Ames-Stanford Approach (CASA) model to create SiBCASA, a hybrid capable of estimating terrestrial carbon fluxes and biomass from diurnal to decadal timescales.
description_Source: http-biocycle.atmos.colostate.edu/Documents/SiB/Schaefer_2008_J._Geophys._Res.pdf

TEM6_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Dan Hayes (hayesdj@ornl.gov) citations: 1. hayes, d.j., a.d. mcguire, d.w. kicklighter, k.r. gurney, t.j. burnside, and j.m. melillo (2011), is the northern high latitude land-based co2 sink weakening? global biogeochemical cycles, 25(3), gb3018, doi:10.1029/2010gb003813.
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: The Terrestrial Ecosystem Model (TEM) is a process-based ecosystem model that describes carbon, nitrogen and water dynamics of plants and soils for terrestrial ecosystems of the globe. The TEM uses spatially referenced information on climate, elevation, soils and vegetation as well as soil- and vegetation-specific parameters to make estimates of important carbon, nitrogen and water fluxes and pool sizes of terrestrial ecosystems. The TEM normally operates on a monthly time step and at a 0.5 degrees latitude/longitude spatial resolution, but the model has been applied at finer spatial resolutions (down to 1 hectare).
description_Source: http-ecosystems.mbl.edu/TEM/

TRIPLEX-GHG_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Changhui Peng (peng.changhui@uqam.ca) citations: 1. peng, c.h., zhu, q.a and h. chen, 2011. integrating greenhouse gas emission processes into a dynamic global vegetation model: triplex-ghg model development and testing, in: procceding of isem 2011 conference, pp76 2. peng et al (2013), in preparation
description_Source: http-www.researchgate.net/publication/260724890_Modelling_methane_emissions_from_natural_wetlands_TRIPLEX-GHG_model_integration_sensitivity_analysis_and_calibration
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: TRIPLEX-GHG is a process-based model framework used to quantify terrestrial ecosystem greenhouse gas dynamics by incorporating both ecological drivers and biogeochemical processes. TRIPLEX-GHG was developed from the Integrated Biosphere Simulator (IBIS), a dynamic global vegetation model, coupled with a new methane (CH4) biogeochemistry module (incorporating CH4 production, oxidation, and transportation processes) and a water table module to investigate CH4 emission processes that occur in natural wetlands.

VEGAS2.1_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
description_Source: http-www.ldeo.columbia.edu/~biasutti/Workshop/ppts/Zeng.pdf
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Ning Zeng (zeng@atmos.umd.edu)
description: The VEgetation-Global Atmosphere-Soil Model (VEGAS)
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775

VISIT_MstmipVersion1_Modeled_Method
type: Class
subclass of: MsTMIP_Simulation
definition_Contributor: Chung-Yi Hou, orcid.org/0000-0002-8087-1775
description: VISIT: Vegetation Integrative Simulator for Trace gases by A.Ito (NIES) => ecophysiological, biogeochemical model: cf. Biome‐BGC, Century NIES = National Institute for Environmental Studies, Japan
description_Source: http-www.fluxdata.org/DataInfo/AsilomarPresentations/090210_asilomar_aito.pdf
definition_Source: http-nacp.ornl.gov/mstmipdata/ Contacts: Akihiko Ito (z060507@gmail.com) citations: 1. ito, a. (2010), changing ecophysiological processes and carbon budget in east asian ecosystems under near-future changes in climate: implications for long-term monitoring from a process-based model, j.plant res., 123, 577-588, doi:10.1007/s10265-009-0305-x. 2. ito, a. (2008), the regional carbon budget of east asia simulated with a terrestrial ecosystem model and validated using asiaflux data, agricultural and forest meteorology, 148(5), 738-747, doi:10.1016/j.agrformet.2007.12.007.

Areal Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Class
    intersection of: Restriction
      on property: has Output
      some values from: Class
        union of: Organic Carbon
        union of: Inorganic Carbon
    intersection of: Restriction
      on property: ENVO_2100001
      some values from: UO_0000047
subclass of: Carbon Flux
definition: A flux of carbon per unit area.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Carbon Dioxide Diffusion Flux
type: Class
equivalent class: Class
  intersection of: Dissolution Carbon Flux
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Carbon Dioxide
subclass of: Dissolution Carbon Flux
alternative label: Carbon Dioxide Diffusion
definition: The process by which carbon dioxide in the atmosphere moves across a phase boundary and into the ocean. This is a major sink of atmospheric carbon dioxide. Dissolved carbon dioxide subsequently reacts to form carbonic acid, bicarbonate ions, and carbonate ions, leading to ocean acidification.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Bicarbonate Pool
type: Class
equivalent class: Class
  intersection of: Inorganic Carbon Pool
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Bicarbonate
subclass of: Inorganic Carbon Pool
definition_Source: http://purl.obolibrary.org/obo/CHEBI_17544
definition: The pool of carbon oxoanions that are the result of the removal of a proton from carbonic acid.
alternative label: HCO3 Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Carbon Dioxide Pool
type: Class
equivalent class: Class
  intersection of: Inorganic Carbon Pool
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Carbon Dioxide
subclass of: Inorganic Carbon Pool
alternative label: CO2 Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The pool of carbon dioxide within a carbon cycle.
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436

Carbonate Pool
type: Class
equivalent class: Class
  intersection of: Inorganic Carbon Pool
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Carbonate
subclass of: Inorganic Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
alternative label: CO3 Pool
definition: The pool of carbon oxoanions that have formula CO3.
definition_Source: http://purl.obolibrary.org/obo/CHEBI_41609

Methane Pool
type: Class
equivalent class: Class
  intersection of: Inorganic Carbon Pool
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Methane
subclass of: Inorganic Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: A one-carbon compound in which the carbon is attached by single bonds to four hydrogen atoms. It is a colourless, odourless, non-toxic but flammable gas (b.p. -161degreeC).
alternative label: CH4 Pool
definition_Source: http://purl.obolibrary.org/obo/CHEBI_16183
type: NamedIndividual

Atmospheric Carbon Dioxide Pool
type: Class
equivalent class: Class
  intersection of: Carbon Dioxide Pool
  intersection of: Restriction
    on property: has State
    all values from: Gas State
alternative label: Atmospheric CO2 Pool
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: Gas phase carbon dioxide molecules in the air surrounding Earth. A principle contributor to climate change and the main source of carbon used by photoautotrophs to store energy during primary production.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Dissolved Carbon Dioxide Pool
type: Class
equivalent class: Class
  intersection of: Carbon Dioxide Pool
  intersection of: Restriction
    on property: has State
    all values from: Dissolved State
alternative label: Dissolved CO2 Pool
definition: Carbon dioxide that has passed from the gas phase into the dissolved phase, with the the ocean begin the largest component of this pool. This process contributes to acidification by forming carbonic acid with water molecules.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

CO2 Enrichment Method
type: Class
subclass of: Field Method
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: A method of artificially raising the atmospheric CO2 concentration in field plots in order to study effects on the ecosystem.
type: NamedIndividual

Aboveground Net Primary Productivity Flux
type: Class
equivalent class: Class
  intersection of: Net Primary Production Carbon Flux
  intersection of: Restriction
    on property: has Location
    all values from: Class
      complement of: ENVO_00001998
subclass of: Net Primary Production Carbon Flux
alternative label: Aboveground Net Primary Productivity
alternative label: Aboveground Net Primary Production
definition: Gross primary productivity (GPP) minus autotrophic respiration (AR) in plant segments other than the roots, e.g. leaves and shoots.
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Organism
type: Class
subclass of: Carbon Cycle Components
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: An individual form of life, such as a bacterium, protist, fungus, plant, or animal, composed of a single cell or a complex of cells in which organelles or organs work together to carry out the various processes of life.
definition_Source: "organism." American Heritage® Dictionary of the English Language, Fifth Edition. (2011). Houghton Mifflin Harcourt Publishing Company. 23 June 2015. http-www.thefreedictionary.com/soil

Single-Celled Organism
type: Class
subclass of: Organism
disjoint with: Multi-Celled Organism
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: An organism composed entirely of a single cellular unit.
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436

Multi-Celled Organism
type: Class
subclass of: Organism
definition_Source: "organism." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Jun. 2015 http://www.thefreedictionary.com/organism
definition: An individual form of life composed of a complex of cells in which organelles or organs work together to carry out the various processes of life.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

Microbe
type: Class
subclass of: Single-Celled Organism
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Adapted from: "microbe." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company. 24 June 2015. http-www.thefreedictionary.com/soil
definition: A minute life form, such as a bacterium or phytoplankton.

Functional Level
type: Class
subclass of: Carbon Cycle Components
comment: This class and all subclasses should be incorporated into ENVO.
definition_Contributor: Margaret O'Brien
definition: Functional levels defined here: http://www.physicalgeography.net/fundamentals/9d.html maybe others.
type: NamedIndividual

Ecosystem Functional Level
type: Class
subclass of: Functional Level
definition: Ecosystems are dynamic entities composed of the biological community and the abiotic environment.
definition_Source: http://www.physicalgeography.net/fundamentals/9d.html
comment: This class should be incorporated into ENVO.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Community Functional Level
type: Class
subclass of: Functional Level
comment: This class should be incorporated into ENVO.
definition_Source: http://ecoinformatics.org/oboe/oboe.1.0/oboe-ecology.owl#EcologicalCommunity
definition: In ecology, a community is an assemblage of two or more populations of different species occupying the same geographical area. (wikipedia) An ecological unit composed of a group of organisms or a population of different species occupying a particular area, usually interacting with each other and their environment. (biology-online.org)
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Population Functional Level
type: Class
subclass of: Functional Level
definition_Source: http://www.physicalgeography.net/fundamentals/9d.html
comment: This class should be incorporated into ENVO.
definition: A population comprises all the individuals of a given species in a specific area or region at a certain time.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Species Functional Level
type: Class
subclass of: Functional Level
definition: A group of interbreeding organisms that do not ordinarily breed with members of other groups.
definition_Source: http://www.physicalgeography.net/fundamentals/9d.html
comment: This class should be incorporated into ENVO.
definition_Contributor: Margaret O'brien
type: NamedIndividual

Physical State
type: Class
definition_Source: Adapted from: "Physical state." The American Heritage® Dictionary of Student Science, Second Edition. 2014. Houghton Mifflin Harcourt Publishing Company 24 Jun. 2015 http://www.thefreedictionary.com/Physical+stat
definition: One of the principal conditions in which matter exists; traditionally divided into three states—solid, liquid, and gas.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

Gas State
type: Class
subclass of: Physical State
disjoint with: Liquid State
disjoint with: Solid State
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: "gas." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Jun. 2015 http://www.thefreedictionary.com/gas
alternative label: Gas
definition: The state of matter distinguished from the solid and liquid states by relatively low density and viscosity, relatively great expansion and contraction with changes in pressure and temperature, the ability to diffuse readily, and the spontaneous tendency to become distributed uniformly throughout any container.

Liquid State
type: Class
subclass of: Physical State
disjoint with: Solid State
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The state of matter in which a substance exhibits a characteristic readiness to flow and little or no tendency to disperse, and is amorphous but has a fixed volume and is difficult to compress.
definition_Source: "liquid." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Jun. 2015 http://www.thefreedictionary.com/liquid
alternative label: Liquid

Solid State
type: Class
subclass of: Physical State
definition_Source: "solid." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Jun. 2015 http://www.thefreedictionary.com/solid
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: A substance having a definite shape and volume; one that is neither liquid nor gaseous.
alternative label: Solid

Dissolution Carbon Flux
type: Class
equivalent class: Class
  intersection of: Carbon Flux
  intersection of: Restriction
    on property: has Result
    some values from: Dissolved State
subclass of: Carbon Flux
definition: The process by which carbon dissolves, moving from one pool to another. For example, the dissolution of atmospheric carbon dioxide into the ocean or the dissolution of organic carbon into dissolved organic carbon.
alternative label: Carbon Dissolution
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
type: NamedIndividual

Dissolved State
type: Class
subclass of: Physical State
alternative label: In Solution
definition: A homogeneous mixture of two or more substances, which may be solids, liquids, gases, or a combination of these.
definition_Source: "solution." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Jun. 2015 http://www.thefreedictionary.com/solution
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
alternative label: Dissolved

Carbon Dioxide
type: Class
subclass of: Inorganic Carbon
definition_Source: carbon dioxide. (n.d.) American Heritage® Dictionary of the English Language, Fifth Edition. (2011). Retrieved June 23 2015 from http://www.thefreedictionary.com/carbon+dioxide
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: A colorless, odorless, incombustible gas, CO2, that is formed during respiration, combustion, and organic decomposition, is an essential component in photosynthesis, and is used in food refrigeration, carbonated beverages, inert atmospheres, fire extinguishers, and aerosols.
alternative label: CO2

Methane
type: Class
subclass of: Organic Carbon
definition: An odorless, colorless, flammable gas, CH4, the major constituent of natural gas, that is used as a fuel and is an important source of hydrogen and a wide variety of organic compounds.
definition_Source: "methane." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 23 Jun. 2015 http://www.thefreedictionary.com/methane
alternative label: CH4
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

Carbonate
type: Class
subclass of: Inorganic Carbon
definition: Carbon oxoanions that have formula CO3.
definition_Source: http://purl.obolibrary.org/obo/CHEBI_41609
alternative label: CO3
type: NamedIndividual

Bicarbonate
type: Class
subclass of: Inorganic Carbon
definition: Carbon oxoanions resulting from the removal of a proton from carbonic acid.
alternative label: HCO3
definition_Source: http://purl.obolibrary.org/obo/CHEBI_17544
type: NamedIndividual

Carbohydrate
type: Class
subclass of: Organic Carbon
alternative label: Fixed Carbon
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: http://purl.obolibrary.org/obo/CHEBI_16646
alternative label: CnH2nOn
definition: Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
type: NamedIndividual

Carbon Monoxide
type: Class
subclass of: Inorganic Carbon
definition_Source: carbon monoxide. (n.d.) American Heritage® Dictionary of the English Language, Fifth Edition. (2011). Retrieved June 23 2015 from http://www.thefreedictionary.com/carbon+monoxide
alternative label: CO
definition: A colorless, odorless, highly poisonous gas, CO, formed by the incomplete combustion of carbon or a carbonaceous material, such as gasoline.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

Organic Carbon
type: Class
subclass of: CHEBI_50860
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Source: Adapted from: U.S. EPA. 2002. Methods for the Determination of Total Organic Carbon (TOC) in Soils and Sediments. U.S. Environmental Protection Agency, Ecological Risk Assessment Support Center.
definition: Carbon derived initially from primary production or from the decomposition of biological materials, ranging from freshly deposited litter to highly decomposed forms such as humus.

Organic Carbon Pool
type: Class
equivalent class: Class
  intersection of: Organic Carbon Pool
  intersection of: Restriction
    on property: RO_0001000
    some values from: Primary Production Carbon Flux
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Organic Carbon
subclass of: Carbon Pool
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
alternative label: Total Organic Carbon
definition: The pool of all forms of organic carbon in a carbon cycle.
alternative label: Fixed Carbon Pool
alternative label: Fixed Carbon
alternative label: TOC

Aboveground Woody Biomass Carbon Pool
type: Class
equivalent class: Class
  intersection of: Wood Carbon Pool
  intersection of: Restriction
    on property: has Location
    all values from: Class
      complement of: ENVO_00001998
subclass of: Wood Carbon Pool
definition_Source: "wood." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/wood
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The total sum of the mass of carbon contained in the tough, fibrous substance lying beneath the bark of trees and shrubs, consisting of the vascular tissue known as xylem and composed chiefly of cellulose and lignin.

Particulate Organic Carbon Pool
type: Class
equivalent class: Class
  intersection of: Organic Carbon Pool
  intersection of: Restriction
    on property: has State
    all values from: Solid State
subclass of: Organic Carbon Pool
alternative label: Total Particulate Organic Carbon
definition: The pool of organic carbon made up of particles larger than 0.45 um.
alternative label: POC
definition_Source: Fiedler, S. et al. 2008. Particulate organic carbon (POC) in relation to other pore water carbon fractions in drained and rewetted fens in Southern Germany. Biogeosciences, 5, 1615–1623, 2008.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-943

Inorganic Carbon
type: Class
subclass of: CHEBI_24835
definition: Carbon derived from non-living or geologic parent material sources. Importantly, inorganic carbon can be derived from biological processes like exhalation of carbon dioxide during aerobic metabolism or the deposition of carbonate to form shells.
definition_Source: Adapted from: U.S. EPA. 2002. Methods for the Determination of Total Organic Carbon (TOC) in Soils and Sediments. U.S. Environmental Protection Agency, Ecological Risk Assessment Support Center.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

Inorganic Carbon Pool
type: Class
equivalent class: Class
  intersection of: Carbon Pool
  intersection of: Restriction
    on property: ENVO_01001309
    all values from: Inorganic Carbon
subclass of: Carbon Pool
alternative label: Total Inorganic Carbon
alternative label: TIC
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The pool of all forms of inorganic carbon in a carbon cycle.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

Carbon Pool Size
type: Class
comment: MsTMIP variable #22
alternative label: Size of Each Carbon Pool
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: Total mass of carbon per meter squared in each pool.
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436

Biomass Carbon Pool
type: Class
subclass of: Organic Carbon Pool
definition_Source: Chase LeCroy, orcid.org/0000-0002-1338-9436
definition: The mass of all carbon contained within live organisms for a defined space and time.
definition_Contributor: Chase LeCroy, orcid.org/0000-0002-1338-9436

ECSO Leaf Decomposition
type: Class
subclass of: Concept
deprecated: true
comment: this concept is used for "related term' to "leaf litter carbon pool' and should not have class status. Possibly re-use as skos:altLabel {MPS, 28APR15}

ECSO Leaves
type: Class
subclass of: Concept
deprecated: true
comment: this concept was used as a related term for 'leaf carbon pool' and does not merit class status (although we coud leave it here as a SKOS concept if we want all potential "labels" to show up in our class hierarchy that is now a "class/concept" hierarchy due to importing SKOS-dl {MPS, 28APR15}

Concept
type: Class
definition: An idea or notion; a unit of thought
type: NamedIndividual