]> Mar 31, 2015 2:04:13 PM Mark Schildhauer Revised version: DataONE ontology to describe Carbon Flux measurements in the MsTMIP and LTER Use Cases. Collaborative work of: Margaret O'Brien, Sophie Hou, Chase LeCroy, and Mark Schildhauer SophieHou This ontology was generated from an ontology revision in WebProtege http://webprotege.nceas.ucsb.edu clecroy guest mobb ontology work in progress for DataONE MSTMip/LTER Carbon cycling use cases system ontology to start modeling primary production measurements margaret 2014-11-13 definition_Source Schildhauer Schildhauer, pers comm, 05Feb2015 Definition Source "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 defintion 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. example_Of_Usage "example_Of_Usage" is an OWL annotation property to record examples of how the concept or property should be used. O'Brien, pers comm, 2015-02-19 O'Brien, pers comm, 2015-02-19 "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. Margaret O'Brien, orcid.org/0000-0002-1693-8322 Example of Usage presentation_Label O'Brien, 2015-02-16 Carbon Flux This field may be deprecated. Presentation Label Margaret O'Brien, orcid.org/0000-0002-1693-8322 "presentation_Label" is an OWL "Annotation property" that contains a label suitable for presentation to general audiences, such as with graph bubbles. Usually this will be the same as "rdfs:label", and it should initially be auto-populated with the contents of the "rdfs:label" field, if that property is not empty. But in special cases, an application might prefer differentiating the "presentation:label" from the default "rdfs:label", in which case it can be customized. Title case capitalization is acceptable. "presentation_Label" is an OWL "Annotation property" that contains a label suitable for presentation to general audiences, such as with graph bubbles. Title case capitalization is acceptable. definition_Contributor defintion_Contributor Contributor Margaret O'Brien, orcid.org/0000-0002-1693-8322, Shild "contributor" is an OWL "Annotation property" that names the person contributing the content, so s/he can be contacted, especially during development. 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. O'Brien, pers comm. 2015-02-15 Margaret O'Brien, orcid.org/0000-0002-1693-8322 description_Source Schildhauer, pers comm, 05Feb2015 Description Source Schildauer "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 rdfs:label Margaret O'Brien, orcid.org/0000-0002-1693-8322 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 Carbon_Flux_NASA, definition_Source, rdfs:label rdfs:label is an instance of rdf:Property that may be used to provide a human-readable version of a resource's name O'Brien, 2015-02-19 examples definition Schildhauer, O'Brien Definition "definition" is an OWL "Annotation property" that contains a concise, often abstract, but ideally precise natural language "description" of the concept to which it is attached (or annotated). In scientific contexts, the "definition" Annotation property is preferred over a "description" Annotation property, because "description" is typically a more verbose, less prescriptive natural language explication of the concept to which it is attached (or applied, or annotated). Schildhauer, pers comm, Feb 9, 2015, description "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 Description Schildhauer, pers comm, 05Feb2014 Schildhauer has_Related_Synonym mobb has_Exact_Synonym Margaret O'Brien, 2015-03-18 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. ad hoc! 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. has_Exact_Synonym mobb has_Exact_Synonym is an OWL annotation property that holds an alternate name or lexical variant of an owl class. 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. 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. has_Related_Synonym Margaret O'Brien, 2015-03-18 ad hoc Total_Living_Biomass_MOV Total carbon content of the living biomass (leaves+roots+wood) http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Net_Longwave_Radiation_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Incident longwave radiation minus simulated outgoing longwave radiation (positive into grnd) Total_Soil_Wetness_MOV Vertically integrated soil moisture divided by maximum allowable soil moisture above wilting point http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Absorbed_Fraction_Incoming_PAR_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Absorbed fraction incoming photosyntetically active radiation http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Near_Surface_Air_Temperature_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Near surface air temperature Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Near_Surface_CO2_Concentration_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Near surface dry air CO2 mole fraction Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Total_Respiration_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Total respiration (TotalResp=AutoResp+heteroResp, always positive) Leaf_Area_Index_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Area of leaves per area ground Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Surface_Pressure_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Surface pressure http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Near_Surface_Specific_Humidity_MOV Near surface specific humidity Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 MsTMIP_Measurement mob Parent class for all MsTMIP variables Average_Layer_Soil_Moisture_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Soil water content in each soil layer, including liquid, vapor and ice Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Average_Layer_Soil_Temperature_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Average soil temperature in each soil layer Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Size_Of_Each_Carbon_Pool_MOV Total size of each carbon pool vertically integrated over the entire soil column http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Surface_Runoff_MOV Runoff from the landsurface and/or subsurface stormflow Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Soil_Layer_Top_Depth_MOV Depth from soil surface to top of soil layer Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Near_Surface_Module_Of_The_Wind_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Near surface wind magnitude Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Soil_Layer_Node_Depth_MOV Depth from soil surface to layer prognostic variables; typically center of soil layer Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Snow_Water_Equivalent_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Total water mass of snow pack, including ice and liquid water MsTMIP_Driver_Variable Dissolved_Organic_Carbon_Carbon_Pool TO DO, Margaret TO DO, Margaret Longwave_Albedo_MOV Longwave Albedo Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Measurement "measurement." The Columbia Electronic Encyclopedia®. 2013. Columbia University Press 20 Feb. 2015 http-encyclopedia2.thefreedictionary.com/Measurement Chase LeCroy, orcid.org/0000-0002-1338-9436 A determination of the magnitude of a quantity by comparison with a standard for that quantity. Total_Soil_Carbon_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Total soil and litter carbon content vertically integrated over the enire soil column Autotrophic_Respiration_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Autotrophic respiration rate (always positive) Rainfall_Rate_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Rainfall rate Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Gross_Primary_Productivity_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 MsTMIP Output: Rate of photosynthesis (always positive) mob Name_Of_Each_Carbon_Pool_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Name of each carbon pool (i.e., "wood," or "Coarse Woody Debris") Soil_Layer_Bottom_Depth_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Depth from soil surface to bottom of soil layer http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Heterotrophic_Respiration_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Heterotrophic respiration rate (always positive) http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 MsTMIP_Output_Variable Net_Shortwave_Radiation_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Incident shortwave radiation minus simulated outgoing shortwave radiation (positive into grnd) Active_Layer_Thickness_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Thaw depth; depth to zero centigrade isotherm in permafrost LIDAR_Method LIDAR 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]. A LIDAR_Method for NPP is a methodology to predict the net primary production (NPP) from ground and LiDAR data mob, 2015-03-25 Total_Snow_Depth_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Total snow depth Fire_Emissions_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Flux of carbon due to fires (always positive) http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Surface_Incident_Longwave_Radiation_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Surface incident longwave radiation Sensible_Heat_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Sensible heat flux into the boundary layer (positive into atmosphere) Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Net_Ecosystem_Exchange_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Net Ecosystem Exchange (NEE=HeteroResp+AutoResp-GPP, positive into atmosphere) Surface_Incident_Shortwave_Radiation_MOV http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Surface incident shortwave radiation MsTMIP_Simulation 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) adapted from wikipedia, Simulation Above_Ground_Woody_Biomass_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Total above ground wood biomass http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Subsurface_Runoff_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Gravity soil water drainage and/or soil water lateral flow http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Shortwave_Albedo_MOV Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Shortwave albedo Net_Primary_Productivity_MOV Net Primary Productivity (NPP=GPP-AutoResp, positive into plants) Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Total_Evaporation_MOV Sum of all evaporation sources (positive into atmosphere) http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Latent_Heat_MOV Latent heat flux into the boundary layer (positive into atmosphere) Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25 ANPP Chase LeCroy, orcid.org/0000-0002-1338-9436 Gross primary production (GPP) minus autotrophic respiration (AR) over one year. 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 Above_Ground_Woody_Biomass_Carbon_Pool Litton, C.M. et al. Carbon allocation in forest ecosystems. Global Change Biology. V 13 I 10. pp. 2089 - 2109. July 2007. The mass of any or all woody organic components within an ecosystem. Chase LeCroy, orcid.org/0000-0002-1338-9436 Annual_Net_Primary_Productivity 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 Chase LeCroy, orcid.org/0000-0002-1338-9436 Gross primary production (GPP) minus autotrophic respiration (AR) over one year. BIOME-BGC_Mstmip_Version1_Modeled_Method 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. http-www.ntsg.umt.edu/project/biome-bgc Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/mstmipdata/ Contacts: Weile Wang (weile.wang CLASS-CTEMNplus_Mstmip_Version1_Modeled_Method http-www.cccma.ec.gc.ca/ctem/ Chung-Yi Hou, orcid.org/0000-0002-8087-1775 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. http-nacp.ornl.gov/mstmipdata/ Contacts: Altaf Arain (arainm CLM4VIC_MstmipVersion1_Modeled_Method Incorporating parameterizations from the Variable Infiltration Capacity (VIC) land surface model into CLM. http-nacp.ornl.gov/mstmipdata/ Contacts: Maoyi Huang (maoyi.huang http-www.cesm.ucar.edu/working_groups/Land/Presentations/2012/huang.pdf Chung-Yi Hou, orcid.org/0000-0002-8087-1775 CLM_Mstmip_Version1_Modeled_Method Chung-Yi Hou, orcid.org/0000-0002-8087-1775 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. http-nacp.ornl.gov/mstmipdata/ Contacts: Daniel J. Hayes (hayesdj http-www.cesm.ucar.edu/models/ccsm4.0/clm/ Carbon_Cycle_Components 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). "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 Chase LeCroy, orcid.org/0000-0002-1338-9436 DLEM_Mstmip_Version1_Modeled_Method 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. https-scisoc.confex.com/crops/2013am/webprogram/Paper78258.html Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/mstmipdata/ Contacts: Hanqin Tian (tianhan Field_Method 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. GPP 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 Chase LeCroy, orcid.org/0000-0002-1338-9436 The sum of gross carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time. GTEC_Mstmip_Version1_Modeled_Method Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-www.esd.ornl.gov/~wmp/GTEC/pgtec.html 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. http-nacp.ornl.gov/mstmipdata/ Contacts: Daniel Ricciuto (ricciutodm ISAM_Mstmip_Version1_Modeled_Method http-climate.atmos.uiuc.edu/isam2/descript.html 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. Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/mstmipdata/ Contacts: Atul Jain (jain1 LPJ-wsl_Mstmip_Version1_Modeled_Method http-digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1132&context=nasapub LPJ-wsl is a dynamic global vegetation model that simulates coupled biogeography and biogeochemical responses to climate, CO2, and disturbance (Sitch et al., 2003). Chung-Yi Hou, orcid.org/0000-0002-8087-1775 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. Modeled_Method 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. NPP Gross primary production (GPP) minus autotrophic respiration (AR). Chase LeCroy, orcid.org/0000-0002-1338-9436 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 Net_Primary_Productivity 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 Gross primary production (GPP) minus autotrophic respiration (AR). Chase LeCroy, orcid.org/0000-0002-1338-9436 ORCHIDEE-LSCE_MstmipVersion1_Modeled_Method 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 http-nacp.ornl.gov/mstmipdata/ Contacts: Shushi Peng (Shushi.Peng@lsce.ipsl.fr) Gwena‰lle Berthier (Gwenaelle.Berthier http-unfccc.int/adaptation/nairobi_work_programme/knowledge_resources_and_publications/items/7382.php Chung-Yi Hou, orcid.org/0000-0002-8087-1775 Net_Primary_Production_Carbon_Flux Gross primary production (GPP) minus autotrophic respiration (AR) per unit ground or water area and time. 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 Chase LeCroy, orcid.org/0000-0002-1338-9436 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 Soil_Carbon_Pool Chase LeCroy, orcid.org/0000-0002-1338-9436 "soil." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/soil 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. Carbon_Flux Litton, C.M. et al. Carbon allocation in forest ecosystems. Global Change Biology. V 13 I 10. pp. 2089 - 2109. July 2007. unknown. The rate at which a mass of carbon moves to or from a particular component of the ecosystem per unit time. 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 Chase LeCroy, orcid.org/0000-0002-1338-9436 Plankton_Carbon_Pool 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. Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998. Chase LeCroy, orcid.org/0000-0002-1338-9436 Carbon_Pool 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). Carbon Pools are amounts of carbon in the system. dimensions are mass Carbon per area (eg, kg per m2 (can these be moles?) {contributor, citation unkknown} 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). Carbon Pools are amounts of carbon in the system. diimensions are mass Carbon per area (eg, kg per m2 (can these be moles?) O'Brien, pers comm. 2015-02-20 Chase LeCroy, orcid.org/0000-0002-1338-9436 "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 A reservoir with the capacity to store and release carbon, such as soil, terrestrial vegetation, the ocean, and the atmosphere {contributed by margaret, from Gross_Primary_Production_Carbon_Flux The sum of gross carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time. Chase LeCroy, orcid.org/0000-0002-1338-9436 primary production before the autotrphs' own respiration is subtracted. also called photosynthetic rate, or carbon fixation rate. Synonyms: GPP 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 Method A regular and systematic way of accomplishing something, characteristic of a particular discipline or field of knowledge. 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 "method." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/method Chase LeCroy, orcid.org/0000-0002-1338-9436 Peak_Biomass_Harvest_Method Fahey and Knapp, 2007, p33 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). Fahey and Knapp, 2007, p33 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 Eddy_Covariance_Method add these synonyms (near? exact?): also known as eddy correlation and eddy flux 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 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. http-en.wikipedia.org/wiki/Eddy_covariance http-en.wikipedia.org/wiki/Eddy_covariance Total_Living_Carbon_Pool Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998. The mass of carbon contained within all living organisms or a designated group of living organisms in a designated area. Chase LeCroy, orcid.org/0000-0002-1338-9436 Heterotrophic_Respiration_Carbon_Flux The respiration rate of heterotrophic organisms (animals and microbes) summed per unit ground or water area and time. Chase LeCroy, orcid.org/0000-0002-1338-9436 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 Leaf_Carbon_Pool Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998. The mass of carbon contained within flattened photosynthetic structures emerging laterally from a main axis or stem and possessing true vascular tissue. leaves Chase LeCroy, orcid.org/0000-0002-1338-9436 Carbon14_Uptake_Method O'Brien, pers comm 2015-02-15 Fahey and Knapp, 2007 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. Benthic_Algae_Carbon_Pool Chase LeCroy, orcid.org/0000-0002-1338-9436 Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998. The mass of carbon present in algae on the seafloor. Net_Ecosystem_Exchange_Carbon_Flux 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 The magnitude of carbon sources and sinks is defined as the vertical exchange of CO2 between the surface (land or ocean) and the atmosphere. Chase LeCroy, orcid.org/0000-0002-1338-9436 NEE Grass_Carbon_Pool "grass." Collins English Dictionary – Complete and Unabridged. 1991, 1994, 1998, 2000, 2003. HarperCollins Publishers 24 Feb. 2015 http-www.thefreedictionary.com/grass 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. Chase LeCroy, orcid.org/0000-0002-1338-9436 Primary_Production_Carbon_Flux Chase LeCroy, orcid.org/0000-0002-1338-9436 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 The process of carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time. 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. Dissolved_Organic_Carbon_Flux 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. Wangersky, P.J. Dissolved organic carbon methods: a critical review. Marine Chemistry. V 41 I 1-3. pp. 61-74. 1993. DOC flux Chase LeCroy, orcid.org/0000-0002-1338-9436 Oxygen_Evolution_LightDark_Method 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.) Allometric_Method Chase LeCroy, orcid.org/0000-0002-1338-9436 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. Begon, M., Harper, J.L., Townsend, C.R. Ecology: Individuals, Populations, and Communities. Third Edition. Blackwell Science. 1996. A method determining the relationship between a physical or physiological property of an organism relative to the size of the organism. O'Brien, pers comm, 2014-10-15 Wood_Carbon_Pool "wood." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/wood 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. Chase LeCroy, orcid.org/0000-0002-1338-9436 Leaf_Litter_Carbon_Pool leaf decomposition synonyms from LTER searched terms (mob, 2015-03-24) The mass of carbon contained in the partly decomposed remains of plants on the surface and in the upper layers of the soil. Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998. leaves Chase LeCroy, orcid.org/0000-0002-1338-9436 Respiration_Carbon_Flux CO2 produced by organisms and emitted to the environment per unit ground or water area and time. Chase LeCroy, orcid.org/0000-0002-1338-9436 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 Fire_Carbon_Flux The mass of carbon released from burning vegetation per unit time. Johnson, E.A. and Miyanishi, K. Forest Fires: Behavior and Ecological Effects. Academic Press. 2001 Chase LeCroy Fire Carbon Flux is a measure of carbon released into the atmosphere due to fire (MPS, 2015) Autotrophic_Respiration_Carbon_Flux 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 Chase LeCroy, orcid.org/0000-0002-1338-9436 The sum of respiration (CO2 production) by all living parts of primary producers per unit ground or water area and time. SIB3-JPL_MstmipVersion1_Modeled_Method Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-biocycle.atmos.colostate.edu/research/models/sib3/ 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. http-nacp.ornl.gov/mstmipdata/ Contacts: Nicholas C. Parazoo (nicholas.c.parazoo SIBCASA_MstmipVersion1_Modeled_Method 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. http-biocycle.atmos.colostate.edu/Documents/SiB/Schaefer_2008_J._Geophys._Res.pdf Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/mstmipdata/ Contacts: Kevin Schaefer (kevin.schaefer TEM6_MstmipVersion1_Modeled_Method 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). http-ecosystems.mbl.edu/TEM/ Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/mstmipdata/ Contacts: Dan Hayes (hayesdj TRIPLEX-GHG_MstmipVersion1_Modeled_Method http-www.researchgate.net/publication/260724890_Modelling_methane_emissions_from_natural_wetlands_TRIPLEX-GHG_model_integration_sensitivity_analysis_and_calibration Chung-Yi Hou, orcid.org/0000-0002-8087-1775 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. http-nacp.ornl.gov/mstmipdata/ Contacts: Changhui Peng (peng.changhui VEGAS2.1_MstmipVersion1_Modeled_Method The VEgetation-Global Atmosphere-Soil Model (VEGAS) http-www.ldeo.columbia.edu/~biasutti/Workshop/ppts/Zeng.pdf Chung-Yi Hou, orcid.org/0000-0002-8087-1775 http-nacp.ornl.gov/mstmipdata/ Contacts: Ning Zeng (zeng VISIT_MstmipVersion1_Modeled_Method http-www.fluxdata.org/DataInfo/AsilomarPresentations/090210_asilomar_aito.pdf Chung-Yi Hou, orcid.org/0000-0002-8087-1775 VISIT:
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Century NIES = National Institute for Environmental Studies, Japan http-nacp.ornl.gov/mstmipdata/ Contacts: Akihiko Ito (z060507