This ontology was generated from an ontology revision in WebProtege http://odo.nceas.ucsb.edu
ontology in progress for DataONE MSTMip/LTER Carbon cycling use cases
Mar 31, 2015 2:04:13 PM
0.9
Chase LeCroy, http://orcid.org/0000-0002-1338-9436
Sara Lafia, http://orcid.org/0000-0002-5896-7295
The Ecosystems Ontology
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
SophieHou, http://orcid.org/0000-0002-8087-1775
Mark Schildhauer, http://orcid.org/0000-0003-0632-7576
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
system
Matthew B. Jones, http://orcid.org/0000-0003-0077-4738
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#measuresCharacteristic
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#measuresEntity
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#measuresUsingProtocol
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#measuresUsingStandard
has Result
has Input
has Output
http://purl.obolibrary.org/obo/BFO_0000050
this day is part of this year (occurrent parthood); my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity); my brain is part of my body (continuant parthood, two material entities)
part_of
A core relation that holds between a part and its whole
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
http://purl.obolibrary.org/obo/BFO_0000051
my body has part my brain (continuant parthood, two material entities); this year has part this day (occurrent parthood); my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
has_part
A core relation that holds between a whole and its part
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
http://purl.obolibrary.org/obo/RO_0002473
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
Confirm: changed to 'composed primarily of' and inherited from RO
X composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
http://purl.obolibrary.org/obo/ENVO_2100001
habitat determined by some population
http://purl.obolibrary.org/obo/RO_0000086
this apple has quality this red color
has_quality
A relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
http://purl.obolibrary.org/obo/RO_0001000
this cell derives from this parent cell (cell division); this nucleus derives from this parent nucleus (nuclear division)
A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
http://purl.obolibrary.org/obo/RO_0001025
my brain is located in my head; this rat is located in this cage
located_in
A relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical
http://purl.obolibrary.org/obo/RO_0000056
this input material (or this output material) participates in this process; this blood clot participates in this blood coagulation; this investigator participates in this investigation
Confirm: That import of RO IRI is correct (not allowed to change IRI)
participates in
A relation between a continuant and a process, in which the continuant is somehow involved in the process
https://www.w3.org/2009/08/skos-reference/skos.html#related
related
https://www.w3.org/2009/08/skos-reference/skos.html#relatedMatch
relatedMatch
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
density
AmountOfSubstanceConcentration
the strength of a solution; number of molecules of a substance in a given volume
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
expanse, surface area
Area
the extent of a 2-dimensional surface enclosed within a boundary
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Area_density
area density, surface density, superficial density
ArealDensity
The area density of a two-dimensional object is calculated as the mass per unit area.
Confirm: how is this different from ArealDensity?
ArealMassDensity
https://en.wikipedia.org/wiki/Irradiance
radiant emittance, radiant exitance
Irradiance
Irradiance is the radiant flux (power) received by a surface per unit area.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
Length
The linear extent in space from one end to the other; the longest dimension of something that is fixed in place
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
Mass
the property of a body that causes it to have weight in a gravitational field
Confirm: meaning of term (same concept as density)?
MassDensity
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Mass_flux
MassFlux
Mass flux is the rate of mass flow per unit area, perfectly overlapping with the momentum density, the momentum per unit volume.
Confirm: meaning of term
MassPerMass
Confirm: meaning of term
MassSpecificCount
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Molality
molal concentration
Molality
Molality is a measure of the concentration of a solute in a solution in terms of amount of substance in a specified amount of mass of the solvent.
a language unit by which a person or thing is known (WordNet)
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Pressure
Pressure
Pressure (symbol: p or P) is the force applied perpendicular to the surface of an object per unit area over which that force is distributed.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
ratio
Proportion
the quotient obtained when the magnitude of a part is divided by the magnitude of the whole
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Speed
Speed
The speed of an object is the magnitude of its velocity or the rate of change of its position; it is thus a scalar quantity.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Temperature
Temperature
A temperature is an objective comparative measure of hot or cold. It is measured by a thermometer, which may work through the bulk behavior of a thermometric material, detection of thermal radiation, or particle kinetic energy.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Time
Time
Time is the indefinite continued progress of existence and events that occur in apparently irreversible succession from the past through the present to the future. Time is a component quantity of various measurements used to sequence events, to compare the duration of events or the intervals between them, and to quantify rates of change of quantities in material reality or in the conscious experience.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Volume
Volume
Volume is the quantity of three-dimensional space enclosed by a closed surface, for example, the space that a substance (solid, liquid, gas, or plasma) or shape occupies or contains.
Confirm: meaning of term
VolumePerVolume
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Volumetric_flow_rate
volume flow rate, rate of fluid flow or volume velocity
Confirm: similar to volumetric flow rate?
VolumetricRate
The volumetric flow rate is the volume of fluid which passes per unit time
Confirm: structure of Entity (with subclass of 'continuant' and 'occurrent' from BFO) or 'continuant' and 'occurrent > process' from ENVO)?
foot
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.
O'Brien, pers comm 2015-02-15
Fahey and Knapp, 2007
Carbon14 Uptake Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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
BIOME-BGC_Mstmip_Version1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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-www.cccma.ec.gc.ca/ctem/
CLASS-CTEMNplus_Mstmip_Version1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
Incorporating parameterizations from the Variable Infiltration
Capacity (VIC) land surface model into CLM.
http-www.cesm.ucar.edu/working_groups/Land/Presentations/2012/huang.pdf
CLM4VIC_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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-www.cesm.ucar.edu/models/ccsm4.0/clm/
CLM_Mstmip_Version1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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
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
DLEM_Mstmip_Version1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/mstmipdata/
Contacts:
Daniel Ricciuto (ricciutodm@ornl.gov)
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.
GTEC_Mstmip_Version1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/mstmipdata/
Contacts:
Atul Jain (jain1@illinois.edu)
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.
http-climate.atmos.uiuc.edu/isam2/descript.html
ISAM_Mstmip_Version1_Modeled_Method
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.
LPJ-wsl is a dynamic global vegetation model that simulates
coupled biogeography and biogeochemical responses to climate,
CO2, and disturbance (Sitch et al., 2003).
http-digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1132&context=nasapub
LPJ-wsl_Mstmip_Version1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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-unfccc.int/adaptation/nairobi_work_programme/knowledge_resources_and_publications/items/7382.php
ORCHIDEE-LSCE_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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-biocycle.atmos.colostate.edu/research/models/sib3/
SIB3-JPL_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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
SIBCASA_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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/
TEM6_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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
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-www.researchgate.net/publication/260724890_Modelling_methane_emissions_from_natural_wetlands_TRIPLEX-GHG_model_integration_sensitivity_analysis_and_calibration
TRIPLEX-GHG_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/mstmipdata/
Contacts:
Ning Zeng (zeng@atmos.umd.edu)
The VEgetation-Global Atmosphere-Soil Model (VEGAS)
http-www.ldeo.columbia.edu/~biasutti/Workshop/ppts/Zeng.pdf
VEGAS2.1_MstmipVersion1_Modeled_Method
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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
http-www.fluxdata.org/DataInfo/AsilomarPresentations/090210_asilomar_aito.pdf
VISIT_MstmipVersion1_Modeled_Method
Carbon Dioxide Pool
Chase LeCroy, orcid.org/0000-0002-1338-9436
http://purl.obolibrary.org/obo/CHEBI_41609
The pool of carbon oxoanions that have formula CO3.
Carbonate Pool
Fixed Carbon Pool
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Unicellular_organism
unicellular, single-celled, single cell, monad
Single-Celled Organism
An organism that consists of only one cell
https://en.wikipedia.org/wiki/Multicellular_organism
Sara Lafia, http://orcid.org/0000-0002-5896-7295
multi-cellular organism; whole organism
animal
Multi-Celled Organism
An organism that consist of more than one cell
Microorganisms are very diverse and include all bacteria, archaea and most protozoa. This group also contains some species of fungi, algae, and certain microscopic animals, such as rotifers.
https://en.wikipedia.org/wiki/Microorganism
microorganism
Microbe
Sara Lafia, http://orcid.org/0000-0002-5896-7295
A state of matter is one of the distinct forms that matter takes on. Four states of matter are observable in everyday life: solid, liquid, gas, and plasma. Historically, the distinction is made based on qualitative differences in properties.
https://en.wikipedia.org/wiki/State_of_matter
phase, state, state of matter
Physical State
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Gas is one of the four fundamental states of matter. A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or compound molecules made from a variety of atoms (e.g. carbon dioxide). What distinguishes a gas from liquids and solids is the vast separation of the individual gas particles.
https://en.wikipedia.org/wiki/Gas
air is a gas mixture with various pure gases
gaseous state
Gas
Sara Lafia, http://orcid.org/0000-0002-5896-7295
A liquid is a nearly incompressible fluid that conforms to the shape of its container but retains a (nearly) constant volume independent of pressure. As such, it is one of the four fundamental states of matter and is the only state with a definite volume but no fixed shape. A liquid is made up of tiny vibrating particles of matter, such as atoms, held together by intermolecular bonds.
https://en.wikipedia.org/wiki/Liquid
water is the most abundant liquid on Earth
liquid state, liquified
Liquid
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Solid is one of the four fundamental states of matter. It is characterized by structural rigidity and resistance to changes of shape or volume. Unlike a liquid, a solid object does not flow to take on the shape of its container, nor does it expand to fill the entire volume available to it like a gas does. The atoms in a solid are tightly bound to each other, either in a regular geometric lattice or irregularly.
https://en.wikipedia.org/wiki/Solid
crystalline solids include metals and ice
solid state
Solid
Sara Lafia, http://orcid.org/0000-0002-5896-7295
The dissolution of gases, liquids, or solids into a liquid or other solvent is a process by which these original states become solutes (dissolved components), forming a solution of the gas, liquid, or solid in the original solvent. Solid solutions are the result of dissolution of one solid into another.
https://en.wikipedia.org/wiki/Dissolution_(chemistry)
metal alloys are dissolved solid solutions
dissolution, dissolved state
Dissolved
http://purl.obolibrary.org/obo/CHEBI_16183
methyl hydride, CH4, marsh gas
CHEBI:16183
Methane
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. −161°C).
http://purl.obolibrary.org/obo/CHEBI_17245
Carbon monoxide is a colorless, odorless, and tasteless gas that is slightly less dense than air. It is toxic to hemoglobic animals (including humans) when encountered in concentrations above about 35 ppm, although it is also produced in normal animal metabolism in low quantities, and is thought to have some normal biological functions. In the atmosphere, it is spatially variable and short lived, having a role in the formation of ground-level ozone.
CO
CHEBI:41526, CHEBI:3282, CHEBI:13281, CHEBI:23013
CHEBI:17245
Carbon Monoxide
A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas.
Organic Carbon
Organic Carbon Pool
Chase LeCroy, orcid.org/0000-0002-1338-9436
"wood." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/wood
Aboveground Woody Biomass Carbon Pool
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
Inorganic carbon is carbon extracted from ores and minerals, as opposed to organic carbon found in nature through plants and living things. Some examples of inorganic carbon are carbon oxides such as carbon monoxide and carbon dioxide; polyatomic ions, cyanide, cyanate, thiocyanate, carbonate and carbide in carbon.
http://chemwiki.ucdavis.edu/Core/Inorganic_Chemistry/Descriptive_Chemistry/Elements_Organized_by_Block/2_p-Block_Elements/Group_14%3A_The_Carbon_Family/Chemistry_of_Carbon
Confirm: CHEBI description of 'inorganic molecular entity' as a 'molecular entity that contains no carbon' contradicts inorganic carbon as subclass?
Inorganic Carbon
Inorganic Carbon Pool
Total Living Biomass Carbon Pool
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
ECSO_00000501
Tree
In botany, a tree is a perennial plant with an elongated stem, or trunk, supporting branches and leaves in most species. Wikipedia
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Plant Ontology (PO:0025161)
Plant Ontology, accession:
PO:0025161
plant material
A portion of organism substance that is or was part of a plant, the whole or part thereof.
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
https://en.wikipedia.org/wiki/Phytoplankton,
http://oceanservice.noaa.gov/facts/phyto.html
phytoplankton
The autotrophic components of the plankton community and a key factor of oceans, seas and freshwater basin ecosystems. Microscopic, but when present in high enough numbers, some varieties may be produce colored patches on the water surface. From Greek, 'phyto' = plant and 'planktos' = wanderer.
Adapted from oceanservice.noaa.gov/facts/phyto.html, https://en.wikipedia.org/wiki/Phytoplankton
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://www.thefreedictionary.com/Scientific+experiment
Experiment
A test under controlled conditions that is made to demonstrate a known truth, examine the validity of a hypothesis, or determine the efficacy of something previously untried.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Morrison, M. L., W.M. Block, M. D Strickland, B. A. Collier, M. J. Peterson. 2008 Wildlife Study Design. Springer Science & Business Media,
(via google books, sect 2.4.1, p 42)
and cited therein:
FIsher. R. A. 1925. Statistical Methods for Research Workers. Oliver and Boyd, London.
Hurlbert, S. H. 1984. Pseudoreplication and the design of ecolgical field experments. Ecol Monogr. 54:187-211
http://everything2.com/title/Manipulative+experiment
also see the below, from everything2.com
A manipulative experiment is one in which the experimenter manipulates the system of study in order to attempt to uncover causal relationships. Such experiments can either be rigidly or loosely controlled. In the former case, investigator may create an artificial system in a laboratory setting and control all confounding variables so as to eliminate ambiguity in the interpretation of results. In the latter case, the investigator may simply modify one or two variables of interest in order to determine how the natural system will respond. The statistical methods used to analyse the data are generally of the analysis of variance type, but there are exceptions (especially in the case of loosely controlled manipulations). Two examples follow, one where rigid control was exercised, and one where loose control was used.
Manipulative experiment
Observation of an ecological system of interest under specific, controllable circumstances in an effort to evaluate system response. Fundamentally, manipulative or comarative experments (Hurlbert 1984) require 1) random allocation of treatments (ncluding controls) to experimental units from the population under study and 2) replication of each tratment over several experimental units (Fisher 1925).
Margaret O'Brien, orcid.org/0000-0002-1693-8322
https://en.wikipedia.org/wiki/Natural_experiment
Also could use:
Term loosely used to apply to the study of any naturally occurring differences among groups.
W. Paul Vogt, Dianne C. Gardner, Lynne M. Haeffele. 2012. When to Use What Research Design Guilford Press (p 62 via google books)
Natural experiment
A natural experiment is an empirical study in which individuals (or clusters of individuals) exposed to the experimental and control conditions are determined by nature or by other factors outside the control of the investigators, yet the process governing the exposures arguably resembles random assignment.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Adapted from
https://en.wikipedia.org/wiki/Seaweed
and
Dawes, Cl J. 1978. Marine Botany, John Wiley and Sons., p 113
Macroalgae
An operational term for photosynthetic, nonvascular plants that contain chlorophyll a nad have simple reproductive structures, and that are visible to the unaided eye. Includes some members of the red, brown, and green algae, taxonomic groups which do not have a common multicellular ancestor. Some tuft-forming cyanobacteria or diatoms are sometimes considered macroalgae.
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
PATO:0001334
diameter
the length of a straight line passing through the center of a circle and connecting two points on the circumference
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
Sara Lafia, http://orcid.org/0000-0002-5896-7295
PATO:0001648
http://www.ontobee.org/ontology/PATO?iri=http://purl.obolibrary.org/obo/PATO_0001648
WordNet
perimeter
circumference
the size of something as given by the distance around it
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
www.thefreedictionary.com/height
height
PATO:0000119
the measurement from base of something to top, or to a fixed point.
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "concentration". (via https://en.wikipedia.org/wiki/Concentration#cite_note-goldbook-1)
https://en.wikipedia.org/wiki/Concentration
the strength of a solution (i.e. number of molecules of a substance in a given volume)
WordNet
A concentration measurement describes a mixture of two entities, usually expressed as 'concentration of [entity 1] in [entity 2].'
Confirm: concentration a subclass of proportion?
Note: see list of issues, text file called ECSO_notes_issues.txt
PATO concentration_of explicitly says mixture of one substance with another.
superclasses (measuresEntity, measuresCharacterstic) deliberately left off this class because mixtures can be quite variable. See children.
added a child of concentration-of, called 'molar concentration', and put the equivalence class there. alternative could be that 'molar concentration' is a synonym of AmountOfSubstanceConcentration in OBOE.
concentration_MeasurementType
PATO:0000033, concentration of
Concentration is the abundance of a constituent divided by the total volume of a mixture. The term concentration can be applied to any kind of chemical mixture, but most frequently it refers to solutes and solvents in solutions.
Several types of mathematical description can be distinguished: mass concentration, molar concentration, number concentration, and volume concentration.
https://en.wikipedia.org/wiki/Biomass_(ecology)
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "biomass".
biomass_MeasurementType
From Wikipedia:
Biomass, in ecology, is the mass of living biological organisms in a given area or ecosystem at a given time. Biomass can refer to species biomass, which is the mass of one or more species, or to community biomass, which is the mass of all species in the community. It can include microorganisms, plants or animals.
Use in ECSO:
There are many methods and usages of biomass measurements. This ECSO class is for a group of measurements where only the mass of the material was recorded. Pertinent area and datetime components are implicit (or in the protocol). The mass can be expressed as an average, or as the total mass in the community.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
https://en.wikipedia.org/wiki/Flux, Bird, R. Byron; Stewart, Warren E.; Lightfoot, Edwin N. (1960). Transport Phenomena. Wiley. ISBN 0-471-07392-X.
The study of transport phenomena concerns the exchange of mass, energy, and momentum between observed and studied systems. Fundamental analyses in all three subfields are often grounded in the simple principle that the sum total of the quantities being studied must be conserved by the system and its environment.
https://en.wikipedia.org/wiki/Transport_phenomena
flow
flux_MeasurementType
the rate of transfer of a substance or energy across a given surface
In transport phenomena (heat transfer, mass transfer and fluid dynamics), flux is defined as the rate of flow of a property per unit area, which has the dimensions [quantity]·[time]−1·[area]−1.[Bird et al, 1960] The area is of the surface the property is flowing "through" or "across". For example, the magnitude of a river's current, i.e. the amount of water that flows through a cross-section of the river each second, or the amount of sunlight that lands on a patch of ground each second, are kinds of flux.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
http://www.merriam-webster.com/dictionary/depth, accessed 2016-06-27
deepness
depth
the perpendicular measurement downward from a surface
Margaret O'Brien, orcid.org/0000-0002-1693-8322
ECSO_00000011 (Carbon Flux), adapted for (a) CO2 and (b) a manipulated experiment
'Soil heterotrophic respiration under manipulated conditions'
The respiration rate of heterotrophic organisms (animals and microbes) summed per unit area and time, occuring in soil, and during a experiment in which some condition has been manipulated or altered to understand its effect.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
Moisture refers to the presence of a liquid, especially water, often in trace amounts. Moisture also refers to the amount of water vapour present in the air. There are many ways to measure moisture in products, such as different wave measurement (light and audio), electromagnetic fields, capacitive methods, and the more traditional weighing and drying technique.
https://en.wikipedia.org/wiki/Moisture
wet, wetness
Confirm: dimensionless measurement (percentage) g/g
Is this a concentration or a proportion?
smh_l soil moisture high profile, litter layer at 1.25 volt
Soil Moisture
wetness caused by water
Confirm: different from other term definitions?
http://purl.obolibrary.org/obo/PATO_0000146
temperature_518
http://www.thefreedictionary.com/rate
https://en.wikipedia.org/wiki/Rate_(mathematics)#Temporal
temporal_rate_MeasurementType
A rate measurement is a quantity measured with respect to a second measured quantitiy. In temporal rates, the denominator (second quantity) is time.
added by margaret, to get the mstimips out of the way for now. however, groups of measurements should have multiple parent classes, like this class. E.g. see, Autotrophic_respiration_MOV, Total_respiration_MOV, etc.
Confirm: is this class still needed?
MsTMIP_output_variable
Total_Soil_Carbon_concentration
total amount of carbon (usually mass) per volume of soil
Sara Lafia, http://orcid.org/0000-0002-5896-7295
CO2_CO2calc_output CO2, CO2calc output (micromol/kgSW) Concentraiton of CO2,; micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram
urn:node:LTER
'Freshwater Carbon Dioxide Concentration'
http://www.merriam-webster.com/dictionary/thickness
thickness
the distance between the top and bottom or front and back surfaces of something
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Molar_concentration
amount_of_substance_concentration
mob:
this probably should be in OBOE, and is a synomym of AmountOfSubstanceConcentration.
molar concentration
Molar concentration, also called molarity, amount concentration or substance concentration, is a measure of the concentration of a solute in a solution, or of any chemical species, in terms of amount of substance in a given volume.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
http://www.biology-online.org/dictionary/Group
grouping
group
A number of entities taken together as a unit because members share a common characteristic or relation
ecosystem component entity
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Humidity is the amount of water vapor in the air. Water vapor is the gaseous state of water. Specific humidity is a ratio of the water vapor content of the mixture to the total air content on a mass basis.
https://en.wikipedia.org/wiki/Humidity
Near_Surface_Specific_Humidity_MOV
Near surface specific humidity
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Mass_concentration_(chemistry)
this class is general enough to be in oboe. but it could be a child of PATO concentration.
mass concentration
In chemistry, the mass concentration is defined as the mass of a constituent divided by the volume of the mixture.
EquivalentTo: concentration and measurementFor only Observation and ofEntity only CO2
CO2 Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Soil_carbon
Total_Soil_Carbon
Soil carbon includes both inorganic carbon as carbonate minerals, and as soil organic matter.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Adapted from ECSO_00000018, Heterotrophic Respiration Carbon Flux
Soil_Heterotrophic_Respiration_Carbon_Flux
The respiration rate of heterotrophic organisms (animals and microbes) summed per unit area and time, and occuring in soil.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Adapted form ECSO_00000021 (Net Primary Production Carbon FLux) and ECSO_00000301 (Above Ground Net Primary Production Carbon Flux)
Grassland Above Ground NPP Carbon Flux
Gross primary productivity (GPP) minus autotrophic respiration (AR) in a GRASSLAND of plant segments other than the roots, e.g. leaves and shoots.
Often abbreviated to ANPP, and in grasslands, measured by peak biomass.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Adapted from
https://en.wikipedia.org/wiki/Primary_production
From Moigis and Gocke, 2003, 10.1093/plankt/fbg089
The primary production of phytoplankton has been estimated for decades by the 14C (Steemann-Nielsen, 1952) and O2 (Gaarder and Gran, 1927) methods.
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 (or volume), and that amounts to an areal (or volumetric) rate.
Phytoplankton Primary Production Carbon Flux
The process of carbon fixation by autotrophic phytoplankton per unit area or volume and time. May occur in aquatic environments of all types.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
The total inorganic carbon or dissolved inorganic carbon (DIC) is the sum of inorganic carbon species in a solution. The inorganic carbon species include carbon dioxide, carbonic acid, bicarbonate anion, and carbonate.[1] It is customary to express carbon dioxide and carbonic acid simultaneously as CO2* . CT is a key parameter when making measurements related to the pH of natural aqueous systems,[2] and carbon dioxide flux estimates.
This might be a subclass of CO2 concentration (rather than it's sibling). Margaret needs to talk to her local CO2 system experts.
generally, CO2 that enters the ocean dissociates into bicarbonate, carbonate, (and some stays as CO2). but not sure what people in that domain call the total. (or if this is actually what they would search for! will confirm that, too, this week.
Oceanic total inorganic carbon concentration
Margaret O'Brien, orcid.org/0000-0002-1693-8322
ECSO_00000011 (Carbon Flux), adapted for CO2
CO2 Carbon Flux
The rate at which a Carbon Dioxide (CO2) moves to or from a particular component of the ecosystem per unit time.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
ECSO_00000011 (Carbon Flux), adapted for (a) CO2 and (b) a manipulated experiment
Confirm: we should remove "manipulated conditions". That was an experiment. In reality, the 'experiment' would probably be an additional protocol.
CO2 flux under manipulated conditions
The rate at which a Carbon Dioxide (CO2) moves to or from a particular component of the ecosystem per unit time, during a experiment in which some condition has been manipulated or altered to understand its effect.
Bicarbonate Concentration
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Determination of total dissolved inorganic carbon in sea water, expressed as moles of carbon per kilogram of sea water; this method is suitable for the assay of oceanic levels of total dissolved inorganic carbon (1800-2300 micromol/kg)
http://cdiac.ornl.gov/ftp/cdiac74/sop02.pdf
total inorganic carbon, CT, TIC, dissolved inorganic carbon
This class is an analog to "Oceanic total inorganic Carbon", for any aquatic environment.
The class for 'Oceanic ...' should be a subclass of this one.
This might be a subclass of CO2 concentration (rather than it's sibling). Margaret needs to talk to her local CO2 system experts.
generally, CO2 that enters water dissociates into bicarbonate, carbonate, (and some stays as CO2). but not sure what people in that domain call the total.
Aquatic total inorganic carbon concentration
Margaret O'Brien, orcid.org/0000-0002-1693-8322
adapted from:
http://www.bbc.co.uk/bitesize/higher/biology/control_regulation/growth/revision/1/
http://www.biology-online.org/dictionary/Growth
Google (no ref to src material)
WordNet
the only growth was some salt grass
growing, maturation, development
Growth
The process of increasing in physical size, mass or number, gradually and irreversibly. the process of developing or maturing. the increase in number and spread of small or microscopic organisms.
potential synonyms: development, maturation, growing, germination, sprouting; blooming, expansion, extension, development, progress, advance, advancement
Margaret O'Brien, orcid.org/0000-0002-1693-8322
https://en.wikipedia.org/wiki/Tree_height_measurement
Tree Height
Height of a tree, by various methods.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
adapted from ECSO_00000021 (Net Primary Production Carbon FLux)
Marine Macroalgae NPP Carbon Flux
Gross primary production (GPP) minus autotrophic respiration (AR) by marine macroalgae. Usually expressed per unit area (substrate or water surface) and time. Marine macroalgae occur in oceanic or estuarine environments.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
ECSO_00000200, Areal Carbon Flux, adapted for the ocean.
Oceanic CO2 Carbon Flux
A flux of carbon across the surface of the ocean, per unit area.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://www.fs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb5202838.pdf
Tree Diameter
Diameter of a tree. Often measured at a specified, average distance from the ground, eg 4.5 ft (or average person's breast height). May be measured as circumference, then divided by pi.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://www.fs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb5202838.pdf
Tree Circumference
Girth. Distance around the tree, often a specified, average distance from the ground, eg 4.5 ft (or average person's breast height).
http://purl.obolibrary.org/obo/envo.owl
process
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://www.fia.fs.fed.us/library/fact-sheets/p3-factsheets/tree-growth.pdf
https://en.wikipedia.org/wiki/Tree_measurement
http://texastreeid.tamu.edu/content/howTreesGrow/
the majority of tree growth occurs in late spring and early summer
Tree growth
Tree growth is computed from sequential measurements of a tree that often depend on the species and its form. Measurements include (but are not limited to) height, circumference and diamater, eg, diameter at breast height, or DBH.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
http://www.greenfacts.org/glossary/wxyz/wet-weight.htm
wet_weight
The plant, animal, or other material containing the chemical of interest is not dried to remove water. The amount of the chemical found in subsequent analysis is expressed as the weight of chemical divided by the total weight, including any water present, of the material which once contained it.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://www.fs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb5202838.pdf
DBH Tree diameter at breast height
Domain protocol for measuring the diameter of a tree. Measured at a specified, average distance from the ground, eg 4.5 ft (or average person's breast height). May be measured as circumference, then divided by pi.
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "biomass".
https://en.wikipedia.org/wiki/Biomass_(ecology)
biomass_density
Biomass, in ecology, is the mass of living biological organisms in a given area or ecosystem at a given time. Biomass can refer to species biomass, which is the mass of one or more species, or to community biomass, which is the mass of all species in the community. It can include microorganisms, plants or animals.[4]
Use in ECSO: The mass expressed as mass per unit area.
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "biomass".
https://en.wikipedia.org/wiki/Biomass_(ecology)
the amount per unit size (i.e. the total mass of living matter in a given unit area)
WordNet
Use in ECSO: mass per area.
biomass_density_MeasurementType
Biomass, in ecology, is the mass of living biological organisms in a given area or ecosystem at a given time. Biomass can refer to species biomass, which is the mass of one or more species, or to community biomass, which is the mass of all species in the community. It can include microorganisms, plants or animals.
biomass density
https://www.reference.com/science/linear-measurement-c0842dc7f571f781
of or in or along or relating to a line; involving or having a single dimension
WordNet
one-dimensional
linear_MeasurementType
A linear measurement assigns a numerical value for the length of an object or between objects. Units of linear measure include inch, foot, meter, kilometer and mile. Linear measurements have one dimension, whereas square measurements have two dimensions and cubic measurements have three.
http://www.ontobee.org/ontology/PATO?iri=http://purl.obolibrary.org/obo/PATO_0002390
radius
A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter
This class is a grouping for all protocols that measure the biomass of something. These might include total weight of (e.g.) a sample of grass or fish, or total carbon in a sample, where the size of the sample is not part of the observation. Hence, unit should be a mass unit only.
Biomass Method
Sara Lafia, http://orcid.org/0000-0002-5896-7295
http://medical-dictionary.thefreedictionary.com/dry+mass
Confirm: appropriate definition?
dry_weight
the weight of biological material dried at 105 °C until no further water loss takes place. Because water content varies considerably between individuals, dry weight is the most commonly used method of assessing weight in plants and animals.
http://umbs.lsa.umich.edu/research/variable/ash-free-dry-weight.htm
ash_content
syn = ash_content
ash_weight
https://en.wikipedia.org/wiki/Fluorescence
Fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation.
https://en.wikipedia.org/wiki/Rate_(mathematics)
rate unit
units for rates, where a rate is the ratio between two related quantities.[1]
The most common type of rate is "per unit of time", such as speed, heart rate and flux. Ratios that have a non-time denominator include exchange rates, literacy rates and electric field (in volts/meter).
see flux_MeasurementType
flux unit
Units for flux measurements should have a quantity in the numerator and time and area in the denominator. A flux is the rate of transfer of a substance or energy across a given surface
temporal rate unit
Rate units with a denominator in time units.
not imported with ENVO import of chemical entity.
chlorophyll
http://purl.obolibrary.org/obo/CHEBI_28966
chloroplyll-a
phaeophytin
pheophytin
http://purl.obolibrary.org/obo/CHEBI_8108
Carbonate Concentration
Freshwater Carbonate Concentration
Freshwater Bicarbonate Concentration
bacteria. Dictionary.com. Dictionary.com Unabridged. Random House, Inc. http://www.dictionary.com/browse/bacteria (accessed: June 30, 2016).
bacterium
Bacteria
a very large group of microorganisms comprising one of the three domains of living organisms. They are prokaryotic, unicellular, and either free-living in soil or water or parasites of plants or animals See also prokaryote
http://serc.carleton.edu/microbelife/research_methods/biogeochemical/organic_carbon.html
DOC
DOM
dissolved organic material
dissolved organic carbon
Dissolved organic carbon (DOC) is defined as the organic matter that is able to pass through a filter (filters generally range in size between 0.7 and 0.22 um). See particulate organic carbon.
http://www.ecologydictionary.org/PARTICULATE_ORGANIC_MATTER_(POM)
POC
POM
particulate organic matter
particulate organic carbon
Particulate organic carbon (POC), or particulate organic matter (POM) is that organic matter suspended in water, and that is not able to pass through a filter (filters generally range in size between 0.7 and 0.22 um). Usually plant or animal origin.
Plant Ontology, PO:0000003
whole plant
plant
Defined by the Plant Ontology as a plant structure (PO:0005679) which is a whole organism. PO label is 'whole plant'
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Soil_horizon#Layers
soil profile, soil profiles
This is a grouping class, analogous to 'lake layer' and 'marine layer'
soil layer
A layer which is part of soil. Soil generally consists of visually and texturally distinct layers.
https://en.wikipedia.org/wiki/Active_layer
soil active layer
In environments containing permafrost, the active layer is the top layer of soil that thaws during the summer and freezes again during the autumn.
numerator is carbon, denominator is a volume or weight of soil.
total soil carbon concentration
Aquatic dissolved organic carbon (DOC)
Aquatic particulate organic carbon (POC)
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Electromagnetic_radiation
Confirm: wave-particle duality; if particle, then measured material
electromagnetic radiation
Electromagnetic radiation is the radiant energy released by certain electromagnetic processes. Visible light is one type of electromagnetic radiation; other familiar forms are invisible to the human eye, such as radio waves, infrared light and X-rays.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Name of carbon pool (indicating composition by measured entities)
other_measurementType
https://en.wikipedia.org/wiki/Carbon_cycle
Sara Lafia, http://orcid.org/0000-0002-5896-7295
ratio, dimensionless quantity
proportion_measurementType
https://en.wikipedia.org/wiki/Dimensionless_quantity
the quotient obtained when the magnitude of a part is divided by the magnitude of the whole
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Sunlight
sunlight
solar radiation
Sunlight is a portion of the electromagnetic radiation given off by the Sun, in particular infrared, visible, and ultraviolet light.
https://en.wikipedia.org/wiki/Temperature#Temperature_measurement
the degree of hotness or coldness of a body or environment (corresponding to its molecular activity)
WordNet
temperature_measurementType
Temperature is measured with thermometers that may be calibrated to a variety of temperature scales. Most scientists measure temperature using the Celsius scale and thermodynamic temperature using the Kelvin scale, which is the Celsius scale offset so that its null point is 0K = −273.15°C, or absolute zero. The basic unit of temperature in the International System of Units (SI) is the kelvin. It has the symbol K.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Transport_phenomena#Momentum_transfer
momentum transfer
Momentum Flux
In momentum transfer, the fluid is treated as a continuous distribution of matter. The study of momentum transfer, or fluid mechanics can be divided into two branches: fluid statics (fluids at rest), and fluid dynamics (fluids in motion).
Sara Lafia, http://orcid.org/0000-0002-5896-7295
AshWeight ash weight Soil Ash Weight gram
https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1115/1
Biomass Ash Weight
n_fixation nitrogen fixation rate nitrogen fixation rate as integrated photic zone rates micromolPerLiterPerHour
https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/299/1
Nitrogen Fixation Rate
Soil Bulk Density
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Density Water density kilogramPerCubicMeter
https://pasta.lternet.edu/package/metadata/eml/knb-lter-gce/74/33
Water Density
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Water_content#Measurement
water content, moisture
Volumetric Water Content Method
Water content can be directly measured using a known volume of the material, and a drying oven. Volumetric water content is calculated via the volume of water and the masses of water sample before and after drying in the oven. For materials that change in volume with water content, such as coal, the water content is expressed in terms of the mass of water per unit mass of the moist specimen.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Total_organic_carbon#Combustion
High Temperature Combustion
In a combustion analyzer, half of the sample is injected into a chamber where it is acidified, usually with phosphoric acid, to turn all of the inorganic carbon into carbon dioxide. This is then sent to a detector for measurement. The other half of the sample is injected into a combustion chamber which is raised to between 600–700 °C, some even up to 1200 °C. Here, all the carbon reacts with oxygen, forming carbon dioxide. It's then flushed into a cooling chamber, and finally into the detector. Usually, the detector used is a non-dispersive infrared spectrophotometer. By finding the total inorganic carbon and subtracting it from the total carbon content, the amount of organic carbon is determined.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Biomass
biomass
Biomass is organic matter derived from living, or recently living organisms. Biomass can be used as a source of energy and it most often refers to plants or plant-based materials which are not used for food or feed.
Temporal Rate
Sara Lafia, http://orcid.org/0000-0002-5896-7295
dic dissolved inorganic carbon dissolved inorganic carbon milligramPerLiter
urn:node:GLEON
Dissolved Inorganic Carbon Flux
Sara Lafia, http://orcid.org/0000-0002-5896-7295
toc total organic carbon total organic carbon milligramPerLiter
urn:node:GLEON
Aquatic Total Organic Carbon
temp_addedClassesCorpusF
Concentration
Flux
Sara Lafia, http://orcid.org/0000-0002-5896-7295
dic dissolved inorganic carbon dissolved inorganic carbon milligramPerLiter
urn:node:GLEON
Freshwater total inorganic carbon concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Ai rate Net Assimilation Rate microMolesPerMetersSquaredPerSecond
urn:node:LTER
Net Assimilation Rate
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Carbon Litter Nutrient Concentration
c_conc carbon concentration (mg/g) litter nutrient concentration; To reduce the number of samples analyzed for total carbon, nitrogen and phosphorus, ground samples were pooled by species, water depth and collection date prior to chemical analysis. When possible, five litter bag samples were combined to make 1 sample for nutrient analysis. Water depths were stratified into 30-cm intervals: i.e. 0 cm = unflooded, 1- 30 cm = shallow, 31-60 cm = medium, 60-90 cm = deep sites, and >90cm.
doi:10.5063/AA/duc_merp.88.6
Sara Lafia, http://orcid.org/0000-0002-5896-7295
doc dissolved organic carbon dissolved organic carbon milligramPerLiter
s_DOC surface stream organic carbon milligramsPerLiter
w_DOC shallow riparian groundwater organic
urn:node:GLEON
Dissolved Organic Carbon Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
HCO3_CO2calc_output HCO3, CO2calc output (micromol/kgSW) Concentration of bicarbonate ion micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram
urn:node:LTER
Oceanic Carbonate Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
total_c Total carbon Percentage
urn:node:TERN
Percentage Carbon
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Net_Carbon_Production rate Periphyton Net carbon production milligramsPerGramPerHour
urn:node:LTER
Net Carbon Production Rate
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Net_Respiration rate Periphyton Net carbon respiration milligramsPerGramPerHour
urn:node:LTER
Net Carbon Respiration Rate
Sara Lafia, http://orcid.org/0000-0002-5896-7295
POC [umol/l] particulate organic carbon concentration of POC from CHN analysis micromolePerLiter
s_extOC surface soil extractable organic Carbon in mg per kg dry
urn:node:LTER
Organic Carbon Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
CO3_CO2calc_output CO3, CO2calc output (micromol/kgSW) Concentration of carbonate ion, micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram
urn:node:LTER
Oceanic Bicarbonate Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
CO2_CO2calc_output CO2, CO2calc output (micromol/kgSW) Concentraiton of CO2,; micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram
urn:node:LTER
Oceanic Carbon Dioxide Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
coupledvegCchange coupledvegCchange coupled vegetation Carbon change dimensionless
(coupled/uncoupled)
urn:node:LTER
Vegetation carbon change
Sara Lafia, http://orcid.org/0000-0002-5896-7295
coupledsoilCchange coupledsoilCchange coupled soil Carbon change dimensionless
(coupled/uncoupled)
urn:node:LTER
Soil Carbon Change
Sara Lafia, http://orcid.org/0000-0002-5896-7295
agb "agb" is the standing above ground biomass of each measured stem, given by the formula: AGB = 0.0673 x (ρD²H) 0.976 kilogram
www.supersites.net.au/knb/metacat/tucker.17.15/html
Aboveground Standing Biomass
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Growth_rate_carbon Growth rate, carbon The seasonal growth rate of M. pyrifera carbon mass (day-1). This variable is calculated as the growth rate necessary to explain the observed change in biomass during each period, given the initial biomass and the independently measured loss rates (see Section I.B Equation 1). Growth rates for all days in each season are averaged. reciprocalDay
urn:node:LTER
Growth Rate
Sara Lafia, http://orcid.org/0000-0002-5896-7295
"biomass flux"
npp Net primary production (g m-2 yr-1) dimensionless
this is one that needs the NPP in plant weight, not carbon.
doi:10.5063/AA/nceas.347.3
Biomass Net Primary Production
Sara Lafia, http://orcid.org/0000-0002-5896-7295
C_to_N Ratio of Carbon to Nitrogen dimensionless
urn:node:LTER
Carbon to Nitrogen Ratio
Sara Lafia, http://orcid.org/0000-0002-5896-7295
biomass Biomass Wet weight (kg) of kelp canopy in the pixel (900 meter squared) kilogram
https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/54/6
Biomass Wet Weight
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Plant_Biomass Plant biomass calculated from shoot height and flowering status, based on curve fits of allometric data collected for each site, marsh zone and species gram
https://pasta.lternet.edu/package/metadata/eml/knb-lter-gce/281/32
Plant Biomass
Column 4 tree numbers tree numbers mole
can't possibly be count in moles. but could be an id of the tree that was measured. abstract says they calculate carbon storage - method says trees were counted.
urn:node:TFRI
Count
Sara Lafia, http://orcid.org/0000-0002-5896-7295
carbonStableIsotopeRatio Carbon SI ratio Carbon stable isotope ratio of the bulk sample in standard delta units relative to VPDB to the nearest 0.1 Ratio
urn:node:GOA
Carbon Stable Isotope Ratio
Sara Lafia, http://orcid.org/0000-0002-5896-7295
wtC Carbon Weight Weight of carbon in sample dimensionless
urn:node:GOA
Weight of Carbon in Sample
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Total soil nitrogen (mg/kg) Total soil nitrogen (mg/kg) milligramsPerKilogram
urn:node:LTER
Total Soil Nitrogen Concentration
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Percent_N Percent Nitrogen dimensionless
urn:node:KNB
Percentage Nitrogen
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Percent_ Phosphorus % Phosphorus dimensionless
urn:node:KNB
Percentage Phosphorus
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Browse biomass (g DM_m-1) Browse biomass (g DM.m-1) dimensionless
judithk.109849.2
Preferred biomass (g DM_m-1) Preferred biomass (g DM.m-1) dimensionless
judithk.109849.2
Plant Material Biomass Density
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Stem/branch/foliage biomass
Stem/branch/foliage biomass kilogram
cmchiu.135.2
Plant Material Biomass
Sara Lafia, http://orcid.org/0000-0002-5896-7295
salmonBM2005 Salmon Biomass 05 Salmon Biomass in 2005 kilogramsPerSquareMeter
df35b.159.6
Non-Plant Material Biomass Density
Sara Lafia, http://orcid.org/0000-0002-5896-7295
basSpawnBM2004 Basin Spawner Biomass 2004 Basin spawner biomass in 2004 in metric tons tonne
df35b.159.6
Non-Plant Material Biomass
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Column 12 Halodule Biomass (g AFDW) of Halodule leaves and rhizomes dimensionless
(where AFDW is ash-free dry weight)
doi:10.5063/AA/hstuar01.6.3
Biomass Ash Free Dry Weight
Sara Lafia, http://orcid.org/0000-0002-5896-7295
DryWeight dry weight X Dry Weight gram
https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1115/1
Biomass Dry Weight
Sara Lafia, http://orcid.org/0000-0002-5896-7295
deltaD Dynamic height measured in meters meter
df35b.21.6
Dynamic Height
Sara Lafia, http://orcid.org/0000-0002-5896-7295
LAI Leaf Area Index number
www.supersites.net.au/knb/metacat/supersite.377.4/html
Leaf Area Index
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Loss_on_ignition
Loss on ignition
Loss on ignition is a test used in inorganic analytical chemistry, particularly in the analysis of minerals. It consists of strongly heating ("igniting") a sample of the material at a specified temperature, allowing volatile substances to escape, until its mass ceases to change. This may be done in air, or in some other reactive or inert atmosphere.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
pH_tot_insitu in situ pH, Total scale seaFET pH, Total scale (CO2calc input) dimensionless
https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/6004/1
Water pH
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Number_density
LeafNum density Number of Thalassia testudinum Leaves Per Short Shoot leafnumberPerShortShoot
https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1130/2
Count Density
Number density is an intensive quantity used to describe the degree of concentration of countable objects in physical space: three-dimensional volume number density, two-dimensional area number density, or one-dimensional line number density.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
potemp00 potential temperature from first sensor pair Temperature after the effects of compression have been removed. Defined as the temperature of a parcel of water at the sea surface after it has been raised adiabatically from some depth in the ocean celsius
https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/1009/6
Potential Temperature
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Precipitation Rate
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Confirm: sibling to soil moisture (air moisture)
Relative Humidity
Humidity in % Humidity in % dimensionless
peggym.109987.2
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Salinity salinity Composite salinity PSU (practical salinity unit)
doi:10.6073/AA/knb-lter-fce.39.5
Water Salinity
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Soil_Salinity_Porewater Porewater salinity calculated from soil sample dry weight and salinity of supernatant after resuspension in water dimensionless
https://pasta.lternet.edu/package/metadata/eml/knb-lter-gce/433/8
Soil Porewater Salinity
Sara Lafia, http://orcid.org/0000-0002-5896-7295
col_4144 CephalopVol biomass milliliterPerThousandCubicMeter
https://pasta.lternet.edu/package/metadata/eml/knb-lter-pal/212/1
Biomass Volume Fraction
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Water_content Percent of wet soil mass made up of water percent
https://pasta.lternet.edu/package/metadata/eml/knb-lter-gce/572/2
Soil Water Content
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}
true
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}
true
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Leaf_area_index
LAI
Leaf Area Index
Leaf area index (LAI) is a dimensionless quantity that characterizes plant canopies. It is defined as the one-sided green leaf area per unit ground surface area in broadleaf canopies. LAI ranges from 0 (bare ground) to over 10 (dense conifer forests).
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Photosynthetically_active_radiation
photosynthetically active radiation
PAR
Photosynthetically active radiation, often abbreviated PAR, designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis. This spectral region corresponds more or less with the range of light visible to the human eye.
[database_cross_reference: Wikipedia:Wikipedia]
degree Fahrenheit
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Infrared
infrared
Infrared (IR) is invisible radiant energy, electromagnetic radiation with longer wavelengths than those of visible light, extending from the nominal red edge of the visible spectrum at 700 nanometers (frequency 430 THz) to 1 mm (300 GHz).
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Ocean#Ocean_surface
sea surface
ocean surface
The ocean surface meets Earth's planetary boundary layer and troposphere, a range view which varies depending on the assumed surface elevation.
http://purl.obolibrary.org/obo/CHEBI_25805
oxygen
ChEBI:C00007; WebElements:O
chebi_ontology
oxygen atom
A chalcogen that has formula O
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Ultraviolet
ultraviolet
Ultraviolet (UV) light is an electromagnetic radiation with a wavelength from 10 nm (30 PHz) to 380 nm (750 THz), shorter than that of visible light but longer than X-rays. UV radiation is present in sunlight.
http://purl.obolibrary.org/obo/ENVO_01000406
snow
Snow is an environmental material which is primarily composed of flakes of crystalline water ice. [database_cross_reference: Wikipedia:Snow]
http://purl.obolibrary.org/obo/envo.owl
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
Confirm: move out of 'Physical State'
http://purl.obolibrary.org/obo/CHEBI_23367
molecular entities
CHEBI:23367
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
http://purl.obolibrary.org/obo/CHEBI_24431
atom is a chemical entity
chemical entity
CHEBI:24431
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
http://purl.obolibrary.org/obo/CHEBI_24835
inorganic compounds, inorganic entity, inorganic molecular entities, inorganics
CHEBI:24835
A molecular entity that contains no carbon.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
http://purl.obolibrary.org/obo/CHEBI_25555
Nitrogen is a chemical element with symbol N and atomic number 7. It is the lightest pnictogen and at room temperature, it is a transparent, odorless diatomic gas.
https://en.wikipedia.org/wiki/Nitrogen
CHEBI:25555
nitrogen atom
http://purl.obolibrary.org/obo/CHEBI_27594
carbon atom is a carbon group element atom
carbon group element, carbon group elements, group IV elements
CHEBI:33306
carbon atom
http://purl.obolibrary.org/obo/CHEBI_33300
group 15 elements
CHEBI:33300
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
http://purl.obolibrary.org/obo/CHEBI_33303
chalcogen
Any p-block element belonging to the group 16 family of the periodic table.
http://purl.obolibrary.org/obo/CHEBI_33560
carbon group element atom is a p-block element atom
CHEBI:33560
Any main group element atom belonging to the p-block of the periodic table.
http://purl.obolibrary.org/obo/CHEBI_33582
carbon group molecular entities, carbon group molecular entity
CHEBI:33582
http://purl.obolibrary.org/obo/CHEBI_36927
carbon-13 atom, carbon, isotope of mass 14
CHEBI:36927
Uses in science:
used in carbon dating and as a tracer in biochemistry.
carbon-14
a long-lived naturally occurring radioactive carbon isotope of mass 14 (6 protons and 8 neutrons)
CHEBI, wikipedia (accessed 2016-06-30)
http://purl.obolibrary.org/obo/CHEBI_36928
carbon-13 atom, carbon, isotope of mass 13
CHEBI:36928
Uses in science:
Due to differential uptake in plants as well as marine carbonates of 13C, it is possible to use these isotopic signature in earth science. In aqueous geochemistry, by analyzing the δ13C value of surface and ground waters the source of the water can be identified. This is because atmospheric, carbonate, and plant derived δ13C values all differ with respect to Pee Dee Belemnite (PDB) standard. In biology, the ratio of carbon-13 and carbon-12 isotopes in plant tissues is different depending on the type of plant photosynthesis and this can be used, for example, to determine which types of plants were consumed by animals.
carbon-13
natural, stable isotope of carbon with a nucleus containing 6 protons and 7 neutrons.
CHEBI, wikipedia (accessed 2016-06-30)
http://purl.obolibrary.org/obo/CHEBI_36931
carbon-12 atom
CHEBI:36931
carbon-12
the most common natural carbon isotope, of mass 12. It is the basis for the accepted scale of atomic mass units.
http://purl.obolibrary.org/obo/CHEBI_50860
organic compounds, organic entity, organic molecular entities
CHEBI:25700, CHEBI:33244
Any molecular entity that contains carbon.
CHEBI:50860
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://purl.obolibrary.org/obo/ENVO_00001998
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. [database_cross_reference: Adapted from Wikipedia:Soil]
Margaret O'Brien, orcid.org/0000-0002-1693-8322
adapted from http://animals.about.com/od/habitat-facts/fl/aquatic-biome.htm
http://www.ucmp.berkeley.edu/exhibits/biomes/aquatic.php
LTER:41
note: ENVO also references LTER:41
The aquatic biome includes the habitats around the world that are dominated by water. Three-dimensional environments classified based on characteristics such as depth, tidal flow, temperature, and proximity to landmasses, salinty of their water.
Organic matter or organic material, natural organic matter refers to the large pool of carbon-based compounds found within natural and engineered, terrestrial and aquatic environments.
https://en.wikipedia.org/wiki/Organic_matter
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://purl.obolibrary.org/obo/ENVO_01000177
A grassland biome is a terrestrial biome which includes, across its entire spatial extent, an unbroken layer of grasses (Gramineae), sedges (Cyperaceae) or rushes (Juncaceae).
water_ice, frost
Sara Lafia, http://orcid.org/0000-0002-5896-7295
http://purl.obolibrary.org/obo/ENVO_01000635
ground
Land is a planetary surface that is not covered by liquid. [database_cross_reference: Adpated from Wikipedia:Planetary_surface]
land
http://purl.obolibrary.org/obo/ENVO_01000786
conflagration, wildfire
fire
A fire is a process whereby rapid and exothermic oxidation of a material through a combustion process releases heat, light, and other products. [database_cross_reference: http://www.eionet.europa.eu/gemet/concept?cp=3212][database_cross_reference: https://en.wikipedia.org/wiki/Fire]
http://purl.obolibrary.org/obo/ENVO_01000793
wind
atmospheric wind
A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria.
http://purl.obolibrary.org/obo/ENVO_01000830
rainfall, rain, rainwater
water-based rainfall
A hydrological precipitation process in which atmospheric water vapour condenses to form droplets of liquid water massive enough to fall to a planetary surface due to the planet's gravity. [database_cross_reference: https://en.wikipedia.org/wiki/Rain]
http://purl.obolibrary.org/obo/ENVO_01001305
http://purl.obolibrary.org/obo/ENVO_02500000
From ENVO: Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical.
environmental system process
http://purl.obolibrary.org/obo/ENVO_02500007
photosynthesis
ecosystem-wide photosynthesis
A process which consists of all photosynthesis processes instantiated in an ecosystem.
respiration
ecosystem-wide respiration
A process which consists of all respiration processes instantiated in an ecosystem.
http://purl.obolibrary.org/obo/ENVO_02500008
http://purl.obolibrary.org/obo/ENVO_02500034
vaporization, vaporisation
evaporation
Evaporation is a form of vaporisation which occurs when a portion of the surface layer of a liquid in contact with a gaseous material, which is not saturated with the evaporating substance, vaporises. [database_cross_reference: Adapted from Wikipedia:Evaporation]
http://purl.obolibrary.org/obo/PATO_0000033
concentration
[database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/concentration]
quality
PATO:0000033
scalar_slim; attribute_slim; relational_slim
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
http://purl.obolibrary.org/obo/PATO_0000125
decreased mass equivalentClass : mass and ( decreased_in_magnitude_relative_to some normal)
PATOC:GVG
quality
PATO:0000125
relational_slim; scalar_slim; attribute_slim
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
http://purl.obolibrary.org/obo/PATO_0000128
decreased weight equivalentClass : weight and ( decreased_in_magnitude_relative_to some normal)
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Weight
quality
PATO:0000128
scalar_slim; attribute_slim
Confirm: subclass of
force
weight
A physical quality inhering in a bearer that has mass near a gravitational body.
http://purl.obolibrary.org/obo/PATO_0000165
database_cross_reference: PATOC:GVG
quality
PATO:0000165
scalar_slim; attribute_slim
time
A quality in which events occur in sequence.
http://purl.obolibrary.org/obo/PATO_0001018
relational physical quality
PATO:0002079
[database_cross_reference: PATOC:GVG]
quality
PATO:0001018
attribute_slim
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
http://purl.obolibrary.org/obo/PATO_0001025
[database_cross_reference: PATOC:GVG]
quality
PATO:0001025
attribute_slim
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
http://purl.obolibrary.org/obo/PATO_0001241
quality of an object; quality of a single physical entity; quality of continuant; monadic quality of a continuant; multiply inhering quality of a physical entity ; quality of a continuant
PATO:0001238; PATO:0001237
[database_cross_reference: PATOC:GVG]
monadic quality of an object; monadic quality of continuant
quality
PATO:0001241
A quality which inheres in a continuant.
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
http://purl.obolibrary.org/obo/PATO_0001305
high temperature; hot
PATO:0000678
quality
PATO:0001305
value_slim
A temperature which is relatively high.
[database_cross_reference: PATOC:GVG]
http://purl.obolibrary.org/obo/PATO_0001309
period
decreased duration equivalentClass : duration and ( decreased_in_magnitude_relative_to some normal)
time
PATO:0000081
database_cross_reference: PATOC:mellybelly
quality
PATO:0001309
hpo_slim; attribute_slim
Confirm: subclass
process quality
physial quality of a process
duration
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
http://purl.obolibrary.org/obo/PATO_0001674
database_cross_reference: IUPAC:IUPAC
quality
PATO:0001674
scalar_slim; attribute_slim; relational_slim
catalytic (activity) concentration
A concentration quality inhering in a bearer by virtue of the bearer's catalytic activity divided by the volume of the system.
http://purl.obolibrary.org/obo/PATO_0001680
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Molar_volume
quality
PATO:0001680
scalar_slim; attribute_slim
molar volume
A volume quality inhering in a homogeneous substance containing 6.02 x 1023 atoms or molecules by virtue of the amount of 3-dimensional space it occupies.
http://purl.obolibrary.org/obo/PATO_0001681
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Molar_mass
quality
PATO:0001681
scalar_slim; attribute_slim
molar mass
A physical quality that inheres in a homogeneous substance containing 6.02 x 1023 atoms or molecules.
http://purl.obolibrary.org/obo/PATO_0001709
2-D size
database_cross_reference: PATOC:GVG
quality
PATO:0001709
attribute_slim
Confirm: subclass of
morphology
size
2-D extent
A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
http://purl.obolibrary.org/obo/PATO_0001710
3D size
quality
PATO:0001710
attribute_slim
Confirm: subclass of
morphology
size
3-D extent
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
http://purl.obolibrary.org/obo/PATO_0001985
ice has quality some frozen
distance
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000001
unit_group_slim
length unit
A unit which is a standard measure of the distance between two points.
temperature derived unit
george gkoutos
UO:0000126
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000005
unit_group_slim
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
kelvin
cm; centimetre
george gkoutos
[database_cross_reference: NIST:NIST]
unit.ontology
UO:0000015
unit_slim
centimeter
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
mm; micrometre
george gkoutos
[database_cross_reference: NIST:NIST]
unit.ontology
UO:0000016
unit_slim
millimeter
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
[database_cross_reference: NIST:NIST]
degree Celsius
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000182
unit_group_slim
mass density unit
A unit which is a standard measure of the influence exerted by some mass.
mass per unit area unit
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000054
unit_group_slim
area density unit
A density unit which is a standard measure of the mass exerting an influence on a given area.
kilogram per square metre; kg/m^[2]
george gkoutos
[database_cross_reference: NIST:NIST]
unit.ontology
UO:0000086
An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared.
unit_slim
kilogram per square meter
force per unit area
george gkoutos
[database_cross_reference: NIST:NIST]
unit.ontology
UO:0000109
unit_group_slim
pressure unit
A unit which is a standard measure of the force applied to a given area.
Pa
george gkoutos
[database_cross_reference: NIST:NIST]
unit.ontology
UO:0000110
unit_slim
pascal
A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2].
mass volume percentage
volume percentage
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000166
unit_group_slim
parts per notation unit
A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance.
ppth; 10^[-3]
[database_cross_reference: UOC:GVG]
unit.ontology
UO:0000168
unit_slim
parts per thousand
A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same.
10^[-6]; ppm
george gkoutos
[database_cross_reference: UOC:GVG]
unit.ontology
UO:0000169
unit_slim
parts per million
A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]. [
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000182
unit_group_slim
density unit
A unit which is a standard measure of the influence exerted by some mass.
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000183
unit_group_slim
linear density unit
A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object.
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000186
unit_group_slim
dimensionless unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
%
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000187
unit_group_slim
percent
A dimensionless ratio unit which denotes numbers as fractions of 100.
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000190
unit_group_slim
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
ratio
george gkoutos
[database_cross_reference: Wikipedia:Wikipedia]
unit.ontology
UO:0000191
unit_group_slim
fraction
A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator).
millimeters of mercury; mmHg
george gkoutos
[database_cross_reference: url:en.wiktionary.org/wiki/mmHg]
unit.ontology
UO:0000272
A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
unit_slim
millimetres of mercury
http://purl.obolibrary.org/obo/ENVO_02500010
carbon cycling
Fire Emissions
NEE
Net Ecosystem Exchange
Primary production
Primary productivity
Total Respiration
Autotrophic Respiration
Heterotrophic Respiration
GPP
Gross Primary Production
Gross Primary Productivity
NPP
Net Primary Production
Net Primary Productivity
Name of Each Carbon Pool
Total Soil Carbon
ANPP
Annual Net Primary Production
Annual Net Primary Productivity
LIDAR
CO2
CO3
HCO3
AFDW
Alga
Mass Flux
Energy Flux
WordNet
how much there is or how many there are of something that you can quantify; the relative magnitude of something with reference to a criterion
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Amount
measure, quantity, total, sum
AmountOfSubstanceMass
WordNet
Sara Lafia, http://orcid.org/0000-0002-5896-7295
the property of a body that causes it to have weight in a gravitational field
bulk
WordNet
Sara Lafia, http://orcid.org/0000-0002-5896-7295
the vertical force exerted by a mass as a result of gravity
AmountOfSubstanceWeight
AmountOfSubstanceWeightFlux
Confirm: not Mass Flux?
WordNet
the space between two lines or planes that intersect; the inclination of one line to another; measured in degrees or radians
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Angle
Confirm: same concept as mass flow rate?
https://en.wikipedia.org/wiki/Mass_flow_rate
ArealMassDensityRate
electrical capacity, capacity
Capacitance
https://en.wikipedia.org/wiki/Capacitance
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Capacitance is the ability of a body to store an electrical charge.
CatalyticActivity
Sara Lafia, http://orcid.org/0000-0002-5896-7295
contact action, catalysis
Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst
https://en.wikipedia.org/wiki/Catalysis
electric charge
the quantity of unbalanced electricity in a body (either positive or negative)
WordNet
Charge
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Sara Lafia, http://orcid.org/0000-0002-5896-7295
a material's capacity to conduct electricity; measured as the reciprocal of electrical resistance
WordNet
https://en.wikipedia.org/wiki/Conductivity_(electrolytic)
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Conductivity of an electrolyte solution is a measure of its ability to conduct electricity.
specific conductance
Conductivity
counting, numeration, enumeration, reckoning, tally
the total number counted
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
Count
WordNet
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Current
electric current, flow
a flow of electricity through a conductor
CurrentDensity
Current density is the electric current per unit area of cross section. It is defined as a vector whose magnitude is the electric current per cross-sectional area at a given point in space.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Current_density
https://en.wikipedia.org/wiki/Equivalent_dose
DoseEquivalent
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Equivalent dose represents the stochastic health effects (probability of cancer induction and genetic damage), of low levels of ionizing radiation on the human body.
Confirm: is this the appropriate definition for the concept?
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
Energy
a thermodynamic quantity equivalent to the capacity of a physical system to do work
free energy
https://en.wikipedia.org/wiki/Force
A force is any interaction that, when unopposed, will change the motion of an object.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Force
Frequency is the number of occurrences of a repeating event per unit time.
Frequency
https://en.wikipedia.org/wiki/Frequency
frequence
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Illuminance is the total luminous flux incident on a surface, per unit area.
illumination
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Illuminance
https://en.wikipedia.org/wiki/Illuminance
https://en.wikipedia.org/wiki/Inductance
Sara Lafia, http://orcid.org/0000-0002-5896-7295
induction
Inductance
Inductance is the property of an electrical conductor by which a change in current through it induces an electromotive force in both the conductor itself[1] and in any nearby conductors by mutual inductance.
maturation, life cycle
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Luminance
luminosity, brightness, brightness level
Luminance is a photometric measure of the luminous intensity per unit area of light travelling in a given direction. It describes the amount of light that passes through, is emitted or reflected from a particular area, and falls within a given solid angle. The SI unit for luminance is candela per square metre (cd/m2).
Luminance
Sara Lafia, http://orcid.org/0000-0002-5896-7295
brightness, brightness level, luminance, luminousness, light
Luminosity
Luminosity is the total amount of energy emitted by a star, galaxy, or other astronomical object per unit time. It is related to the brightness, which is the luminosity of an object in a given spectral region.
https://en.wikipedia.org/wiki/Luminosity
MagneticFieldStrength
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Magnetic_field
A magnetic field is the magnetic effect of electric currents and magnetic materials. The magnetic field at any given point is specified by both a direction and a magnitude (or strength); as such it is a vector field.
MagneticFlux
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Magnetic_flux
The magnetic flux through a surface is the surface integral of the normal component of the magnetic field B passing through that surface. The SI unit of magnetic flux is the weber (Wb) (in derived units: volt-seconds), and the CGS unit is the maxwell.
MagneticFluxDensity
Confirm: same concept as magnetic field density?
photon_areal_density_rate
PhotonFluxDensity
Power is the rate of doing work. It is the amount of energy consumed per unit time. Having no direction, it is a scalar quantity. In the SI system, the unit of power is the joule per second (J/s), known as the watt. Another common and traditional measure is horsepower.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Power
https://en.wikipedia.org/wiki/Power_(physics)
Radiance is the radiant flux emitted, reflected, transmitted or received by a surface, per unit solid angle per unit projected area
https://en.wikipedia.org/wiki/Radiance
Radiance
Sara Lafia, http://orcid.org/0000-0002-5896-7295
RadionucleotideActivity
Confirm: term definition
Sara Lafia, http://orcid.org/0000-0002-5896-7295
WordNet
impedance
any mechanical force that tends to retard or oppose motion
Resistance
material's opposition to the flow of electric current; measured in ohms
WordNet
Resistivity
Sara Lafia, http://orcid.org/0000-0002-5896-7295
ohmic_resistance
specific_surface_area
Specific surface area is a property of solids defined as the total surface area of a material per unit of mass.
SpecificArea
Sara Lafia, http://orcid.org/0000-0002-5896-7295
https://en.wikipedia.org/wiki/Specific_surface_area
energy density
https://en.wikipedia.org/wiki/Specific_energy
Specific energy is energy per unit mass. It is used to quantify, for example, stored heat or other thermodynamic properties of substances such as specific internal energy, and specific enthalpy.
Sara Lafia, http://orcid.org/0000-0002-5896-7295
SpecificEnergy
Sara Lafia, http://orcid.org/0000-0002-5896-7295
SpecificVolume
https://en.wikipedia.org/wiki/Specific_volume
The specific volume of a substance is the ratio of the substance's volume to its mass. It is the reciprocal of density and an intrinsic property of matter as well.
https://en.wikipedia.org/wiki/Irradiance
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Spectral irradiance is the irradiance of a surface per unit frequency or wavelength, depending on whether the spectrum is taken as a function of frequency or of wavelength.
SpectralRadiance
https://en.wikipedia.org/wiki/Radiance
Sara Lafia, http://orcid.org/0000-0002-5896-7295
spectral radiance is the radiance of a surface per unit frequency or wavelength, depending on whether the spectrum is taken as a function of frequency or of wavelength
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Confirm: appropriate definition for term?
https://en.wikipedia.org/wiki/Hydraulic_conductivity#Transmissivity
The transmissivity is a measure of how much water can be transmitted horizontally, such as to a pumping well.
Transmissivity
Confirm: definition of term
VolumetricArea
Confirm: same concept as Density?
https://en.wikipedia.org/wiki/Density
VolumetricDensity
VolumetricMassDensity
The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ (the lower case Greek letter rho), although the Latin letter D can also be used.
VolumetricMassDensityRate
Confirm: definition of term
WaveNumber
Sara Lafia, http://orcid.org/0000-0002-5896-7295
wave number, wavenumber
https://en.wikipedia.org/wiki/Wavenumber
The wavenumber is the spatial frequency of a wave, either in cycles per unit distance or radians per unit distance. It can be envisaged as the number of waves that exist over a specified distance.
CategoricalStandard
Index
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#characteristicFor
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#entityRelated
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasBaseQualifier
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasContext
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasMeasurement
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasMember
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasNextQualifier
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasObservedRelation
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasQualifier
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasSourceUnit
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasTargetUnit
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasUnit
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasValue
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#measurementFor
http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#ofCharacteristic
ofEntity
Confirm: no object property 'standardFor' found in OBOE.1.2 (usesStandard?)
standardFor
http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#usesProtocol
http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#usesStandard
Carbon Cycle Component
"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
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).
Chase LeCroy, orcid.org/0000-0002-1338-9436
Wangersky, P.J. Dissolved organic carbon methods: a critical review. Marine Chemistry. V 41 I 1-3. pp. 61-74. 1993.
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.
Dissolved Organic Carbon Flux
DOC flux
Chase LeCroy, orcid.org/0000-0002-1338-9436
Johnson, E.A. and Miyanishi, K. Forest Fires: Behavior and Ecological Effects. Academic Press. 2001
The mass of carbon released from burning vegetation per unit time.
Fire Carbon Flux is a measure of carbon released into the atmosphere due to fire (MPS, 2015)
Fire Carbon Flux
Chase LeCroy, orcid.org/0000-0002-1338-9436
NEE
Net Ecosystem Exchange Carbon Flux
The magnitude of carbon sources and sinks is defined as the vertical exchange of CO2 between the surface (land or ocean) and the atmosphere.
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
Chase LeCroy, orcid.org/0000-0002-1338-9436
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 (or volume), and that amounts to an areal (or volumetric) rate.
Primary Production Carbon Flux
The process of carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time.
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
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
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
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.
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.
Heterotrophic 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
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
Gross Primary Production Carbon Flux
Primary production before the autotrophs' own respiration is subtracted.
Also called photosynthetic rate, or carbon fixation rate.
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
primary production before the autotrphs' own respiration is subtracted.
also called photosynthetic rate, or carbon fixation rate.
Synonyms: GPP
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.
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
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 Production Carbon Flux
Gross primary production (GPP) minus autotrophic respiration (AR) per unit ground or water area and time.
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
Chase LeCroy, orcid.org/0000-0002-1338-9436
O'Brien, pers comm. 2015-02-20
Carbon Pools are amounts of carbon in the system. measurements of carbon pools would have dimensions of mass Carbon per area (eg, kg per m2
(can these be moles? can they just be biomass?)
{contributor, citation unkknown, questions are magaret's}
Carbon Pool
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. measurements of carbon pools would have dimensions of mass Carbon per area (eg, kg per m2
A reservoir with the capacity to store and release carbon, such as soil, terrestrial vegetation, the ocean, and the atmosphere {contributed by margaret, from
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.
Chase LeCroy, orcid.org/0000-0002-1338-9436
Soil Carbon Pool
"soil." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/soil
Plankton 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 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.
leaves
The mass of carbon contained within flattened photosynthetic structures emerging laterally from a main axis or stem and possessing true vascular tissue.
Chase LeCroy, orcid.org/0000-0002-1338-9436
'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.
Leaf Carbon Pool
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.
Benthic Algae Carbon Pool
Chase LeCroy, orcid.org/0000-0002-1338-9436
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.
Grass Carbon Pool
Chase LeCroy, orcid.org/0000-0002-1338-9436
"grass." Collins English Dictionary – Complete and Unabridged. 1991, 1994, 1998, 2000, 2003. HarperCollins Publishers 24 Feb. 2015 http-www.thefreedictionary.com/grass
Chase LeCroy, orcid.org/0000-0002-1338-9436
"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.
Wood Carbon Pool
Purves, W.K. et al. Life, the science of biology. Sinauer Associates, Inc. 5th Edition. 1998.
Chase LeCroy, orcid.org/0000-0002-1338-9436
leaf decomposition
leaves
synonyms from LTER searched terms (mob, 2015-03-24)
Leaf Litter Carbon Pool
The mass of carbon contained in the partly decomposed remains of plants on the surface and in the upper layers of the soil.
Dissolved Organic Carbon Pool
TO DO, Margaret
TO DO, Margaret
Annual Net Primary Productivity Flux
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
Gross primary production (GPP) minus autotrophic respiration (AR) over one year.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Total carbon content of the living biomass (leaves+roots+wood)
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Biomass is organic matter derived from living organisms.
Total_Living_Biomass_MOV
https://en.wikipedia.org/wiki/Biomass
Net_Longwave_Radiation_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Incident longwave radiation minus simulated outgoing longwave radiation (positive into grnd)
https://en.wikipedia.org/wiki/Outgoing_longwave_radiation
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Outgoing Longwave Radiation (OLR) is the energy radiating from the Earth as infrared radiation at low energy to Space. OLR is electromagnetic radiation emitted from Earth and its atmosphere out to space in the form of thermal radiation. The flux of energy transported by outgoing longwave radiation is measured in W/m².
Total_Soil_Wetness_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
https://en.wikipedia.org/wiki/Water_content
Water content or moisture content is the quantity of water contained in a material.
Vertically integrated soil moisture divided by maximum allowable soil moisture above wilting point
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Near_Surface_CO2_Concentration_MOV
EquivalentTo: concentration and measurementFor only ofEntity only partOf only Air
Confirm: micromol/mol-1 is same measure of molarity as micromol/L
https://en.wikipedia.org/wiki/Carbon_dioxide
Carbon dioxide is a greenhouse gas, absorbing and emitting infrared radiation at its two infrared-active vibrational frequencies. This process causes carbon dioxide to warm the surface and lower atmosphere, while cooling the upper atmosphere.
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Near surface dry air CO2 mole fraction
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
https://en.wikipedia.org/wiki/Ecosystem_respiration
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Ecosystem respiration is the sum of all respiration occurring by the living organisms in a specific ecosystem.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Total_Respiration_MOV
Total respiration (TotalResp=AutoResp+heteroResp, always positive)
https://en.wikipedia.org/wiki/Photosynthetically_active_radiation
Absorbed fraction incoming photosyntetically active radiation
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Photosynthetically active radiation, often abbreviated PAR, designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis.
Absorbed_Fraction_Incoming_PAR_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Near surface air temperature
A temperature is an objective comparative measure of hot or cold. It is measured by a thermometer, which may work through the bulk behavior of a thermometric material, detection of thermal radiation, or particle kinetic energy.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Near_Surface_Air_Temperature_MOV
https://en.wikipedia.org/wiki/Temperature
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Leaf_Area_Index_MOV
https://en.wikipedia.org/wiki/Leaf_area_index
Area of leaves per area ground
Leaf area index is a dimensionless quantity that characterizes plant canopies. It is defined as the one-sided green leaf area per unit ground surface area (LAI = leaf area / ground area, m2 / m2) in broadleaf canopies.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Surface pressure
In atmospheric science, surface pressure is the atmospheric pressure at a location on Earth's surface. It is directly proportional to the mass of air over that location.
https://en.wikipedia.org/wiki/Surface_pressure
Surface_Pressure_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Average_Layer_Soil_Moisture_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
https://en.wikipedia.org/wiki/Water_content
Soil water content in each soil layer, including liquid, vapor and ice
Water content or moisture content is the quantity of water contained in a material... Water content is expressed as a ratio, which can range from 0 (completely dry) to the value of the materials' porosity at saturation. It can be given on a volumetric or mass (gravimetric) basis.
Average_Layer_Soil_Temperature_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Soil temperature depends on the ratio of the energy absorbed to that lost. Soil has a temperature range between -20 to 60 °C. Soil temperature regulates seed germination, plant and root growth and the availability of nutrients.
https://en.wikipedia.org/wiki/Soil#Temperature
Average soil temperature in each soil layer
Surface_Runoff_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Surface runoff is the flow of water that occurs when excess stormwater, meltwater, or other sources flows over the earth's surface. This might occur because soil is saturated to full capacity, because rain arrives more quickly than soil can absorb it, or because impervious areas send their runoff to surrounding soil that cannot absorb all of it.
overland flow
Runoff from the landsurface and/or subsurface stormflow
https://en.wikipedia.org/wiki/Surface_runoff
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
https://en.wikipedia.org/wiki/Soil
Soil is a mixture of minerals, organic matter, gases, liquids, and countless organisms that together support life on Earth. Soil is a natural body called the pedosphere.
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Near surface wind magnitude
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Near_Surface_Module_Of_The_Wind_MOV
https://en.wikipedia.org/wiki/Wind
Wind is the flow of gases on a large scale. On the surface of the Earth, wind consists of the bulk movement of air. Wind is caused by differences in the atmospheric pressure.
Size_Of_Each_Carbon_Pool_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Total size of each carbon pool vertically integrated over the entire soil column
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Depth from soil surface to layer prognostic variables; typically center of soil layer
Soil is a mixture of minerals, organic matter, gases, liquids, and countless organisms that together support life on Earth. Soil is a natural body called the pedosphere.
https://en.wikipedia.org/wiki/Soil
Soil_Layer_Node_Depth_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Snow_Water_Equivalent_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Total water mass of snow pack, including ice and liquid water
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Total soil and litter carbon content vertically integrated over the enire soil column
https://en.wikipedia.org/wiki/Soil_carbon
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Total_Soil_Carbon_MOV
Soil carbon includes both inorganic carbon as carbonate minerals, and as soil organic matter.
https://en.wikipedia.org/wiki/Autotroph
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Autotrophic respiration rate (always positive)
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Autotrophic_Respiration_MOV
An autotroph or producer, is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) from simple substances present in its surroundings, generally using energy from light (photosynthesis) or inorganic chemical reactions (chemosynthesis).
Rainfall_Rate_MOV
Rainfall rate
Rain is liquid water in the form of droplets that have condensed from atmospheric water vapor and then precipitated, heavy enough to fall under gravity. Rain is a major component of the water cycle and is responsible for depositing most of the fresh water on the Earth.
https://en.wikipedia.org/wiki/Rain
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Albedo or reflection coefficient, derived from Latin albedo "whiteness" (or reflected sunlight) in turn from albus "white", is the diffuse reflectivity or reflecting power of a surface.
Longwave Albedo
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
https://en.wikipedia.org/wiki/Albedo
Longwave_Albedo_MOV
https://en.wikipedia.org/wiki/Primary_production#GPP_and_NPP
MsTMIP Output: Rate of photosynthesis (always positive)
Gross_Primary_Productivity_MOV
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Gross Primary productivity is the rate at which photosynthesis or chemosynthesis occurs.
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")
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Soil is a mixture of minerals, organic matter, gases, liquids, and countless organisms that together support life on Earth. Soil is a natural body called the pedosphere.
https://en.wikipedia.org/wiki/Soil
Soil_Layer_Bottom_Depth_MOV
Depth from soil surface to bottom of soil layer
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
A heterotroph is an organism that cannot fix carbon and uses organic carbon for growth. Ninety-five percent or more of all types of living organisms are heterotrophic, including all animals and fungi and most bacteria and protists.
Heterotrophic_Respiration_MOV
https://en.wikipedia.org/wiki/Heterotroph
Heterotrophic respiration rate (always positive)
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Thaw depth; depth to zero centigrade isotherm in permafrost
https://en.wikipedia.org/wiki/Active_layer
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Active_Layer_Thickness_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
In environments containing permafrost, the active layer is the top layer of soil that thaws during the summer and freezes again during the autumn.
https://en.wikipedia.org/wiki/Shortwave_radiation
Incident shortwave radiation minus simulated outgoing shortwave radiation (positive into grnd)
Shortwave radiation (SW) is radiant energy with wavelengths in the visible (VIS), near-ultraviolet (UV), and near-infrared (NIR) spectra.
Net_Shortwave_Radiation_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Snow is precipitation in the form of flakes of crystalline water ice that falls from clouds. Since snow is composed of small ice particles, it is a granular material.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
https://en.wikipedia.org/wiki/Snow
Total_Snow_Depth_MOV
Total snow depth
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
https://en.wikipedia.org/wiki/Wildfire
Fire_Emissions_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
A wildfire or wildland fire is an uncontrolled fire in an area of combustible vegetation that occurs in the countryside (i.e., not in an urban area).
Flux of carbon due to fires (always positive)
Surface incident longwave radiation
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Surface_Incident_Longwave_Radiation_MOV
Biomass is organic matter derived from living, or recently living organisms. Biomass can be used as a source of energy and it most often refers to plants or plant-based materials which are not used for food or feed.
Total above ground wood biomass
https://en.wikipedia.org/wiki/Biomass
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Above_Ground_Woody_Biomass_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Water flows from areas where the water table is higher to areas where it is lower. This flow can be either surface runoff in rivers and streams, or subsurface runoff infiltrating rocks and soil. The amount of runoff reaching surface and groundwater can vary significantly, depending on rainfall, soil moisture, permeability, groundwater storage, evaporation, upstream use, and whether or not the ground is frozen. The movement of subsurface water is determined largely by the water gradient, type of substrate, and any barriers to flow.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Subsurface_Runoff_MOV
Gravity soil water drainage and/or soil water lateral flow
https://en.wikipedia.org/wiki/Subsurface_flow#Runoff
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
https://en.wikipedia.org/wiki/Sensible_heat
Sensible_Heat_MOV
Sensible heat is heat exchanged by a body or thermodynamic system that changes the temperature, and some macroscopic variables of the body, but leaves unchanged certain other macroscopic variables, such as volume or pressure.
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
https://en.wikipedia.org/wiki/Ecosystem_respiration
Ecosystem respiration is the sum of all respiration occurring by the living organisms in a specific ecosystem.
Net_Ecosystem_Exchange_MOV
Net Ecosystem Exchange (NEE=HeteroResp+AutoResp-GPP, positive into atmosphere)
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Net Primary Productivity (NPP=GPP-AutoResp, positive into plants)
Shortwave_Albedo_MOV
Shortwave albedo
https://en.wikipedia.org/wiki/Albedo
mob thinks NPP SKOS definition is in here by mistake. because abedo is reflected light flux. it also might be a proportion (mstimip's)
Net_Primary_Productivity_MOV
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Albedo or reflection coefficient, derived from Latin albedo "whiteness" (or reflected sunlight) in turn from albus "white", is the diffuse reflectivity or reflecting power of a surface.
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
Surface_Incident_Shortwave_Radiation_MOV
Surface incident shortwave radiation
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Evaporation is a type of vaporization of a liquid that occurs from the surface of a liquid into a gaseous phase that is not saturated with the evaporating substance.
Total_Evaporation_MOV
https://en.wikipedia.org/wiki/Evaporation
Sum of all evaporation sources (positive into atmosphere)
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
https://en.wikipedia.org/wiki/Latent_heat
Latent heat flux into the boundary layer (positive into atmosphere)
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Latent heat is energy released or absorbed, by a body or a thermodynamic system, during a constant-temperature process that is specified in some way. An example is latent heat of fusion for a phase change, melting, at a specified temperature and pressure.
Latent_Heat_MOV
Chung-Yi Hou, orcid.org/0000-0002-8087-1775
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.
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.
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).
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
Fahey and Knapp, 2007, p33
http://en.wikipedia.org/wiki/Eddy_covariance
add these synonyms (near? exact?): also known as eddy correlation and eddy flux
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.
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
Eddy Covariance Method
http-en.wikipedia.org/wiki/Eddy_covariance
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.)
Chase LeCroy, orcid.org/0000-0002-1338-9436
O'Brien, pers comm, 2014-10-15
Allometric Method
Begon, M., Harper, J.L., Townsend, C.R. Ecology: Individuals, Populations, and Communities. Third Edition. Blackwell Science. 1996.
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.
A method determining the relationship between a physical or physiological property of an organism relative to the size of the organism.
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].
LIDAR Method
A LIDAR_Method for NPP is a methodology to predict the net primary production (NPP) from ground and LiDAR data
mob, 2015-03-25
Huntzinger, D. N., Schwalm, C., Michalak, A. M., Schaefer, K., King, A. W., Wei, Y., … Zhu, Q. (2013). The North American Carbon Program Multi-Scale Synthesis and Terrestrial Model Intercomparison Project -Part 1: Overview and experimental design Supplementary Material. Geoscientific Model Development, 6, 2121–2133.
MsTMIP_Simulation
adapted from wikipedia, 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)
terrestrial biospheric models vary in complexity and the way in which they simulate canopy conductance (energy and water fluxes), simulate photosynthesis and respiration (carbon fluxes), allocate carbon between soil and above and belowground biomass (carbon pools), and model vegetation dynamics and disturbances; MsTMIP models formulate and parameterize energy, carbon, vegetation, and nitrogen process dynamics
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.
Chase LeCroy, orcid.org/0000-0002-1338-9436
Chase LeCroy, orcid.org/0000-0002-1338-9436
Carbon Dioxide Diffusion Flux
Chase LeCroy, orcid.org/0000-0002-1338-9436
The pool of carbon oxoanions resulting from the removal of a proton from carbonic acid.
Bicarbonate Pool
http://purl.obolibrary.org/obo/CHEBI_17544
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).
http://purl.obolibrary.org/obo/CHEBI_16183
Chase LeCroy, orcid.org/0000-0002-1338-9436
Methane Pool
Chase LeCroy, orcid.org/0000-0002-1338-9436
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.
Chase LeCroy, orcid.org/0000-0002-1338-9436
Atmospheric Carbon Dioxide Pool
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.
Chase LeCroy, orcid.org/0000-0002-1338-9436
Chase LeCroy, orcid.org/0000-0002-1338-9436
Dissolved Carbon Dioxide Pool
Chase LeCroy, orcid.org/0000-0002-1338-9436
CO2 Enrichment Method
Chase LeCroy, orcid.org/0000-0002-1338-9436
A method of artificially raising the atmospheric CO2 concentration in field plots in order to study effects on the ecosystem.
Aboveground Net Primary Production Carbon Flux
Chase LeCroy, orcid.org/0000-0002-1338-9436
Chase LeCroy, orcid.org/0000-0002-1338-9436
Gross primary productivity (GPP) minus autotrophic respiration (AR) in plant segments other than the roots, e.g. leaves and shoots.
Functional levels defined here:
http://www.physicalgeography.net/fundamentals/9d.html
maybe others.
Margaret O'Brien
This class and all subclasses should be incorporated into ENVO.
Functional Level
Chase LeCroy, orcid.org/0000-0002-1338-9436
This class should be incorporated into ENVO.
Ecosystem
Ecosystems are dynamic entities composed of the biological community and the abiotic environment.
http://www.physicalgeography.net/fundamentals/9d.html
Chase LeCroy, orcid.org/0000-0002-1338-9436
This class should be incorporated into ENVO.
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)
http://ecoinformatics.org/oboe/oboe.1.0/oboe-ecology.owl#EcologicalCommunity
Community
Chase LeCroy, orcid.org/0000-0002-1338-9436
http://www.physicalgeography.net/fundamentals/9d.html
A population comprises all the individuals of a given species in a specific area or region at a certain time.
Population
This class should be incorporated into ENVO.
Margaret O'brien
Organism
being
An organism is a single individual.
This class should be incorporated into ENVO.
Confirm: compare with ENVO (anatomical entity)
Do we really have any carbon cycle data for a single organism? (MOB)
http://www.physicalgeography.net/fundamentals/9d.html
Margaret O'brien
This class should be incorporated into ENVO.
Species
A group of interbreeding organisms that do not ordinarily breed with members of other groups.
Chase LeCroy, orcid.org/0000-0002-1338-9436
Chase LeCroy, orcid.org/0000-0002-1338-9436
has State
Describes the physical state of a substance
has Location
Chase LeCroy, orcid.org/0000-0002-1338-9436
Chase LeCroy, orcid.org/0000-0002-1338-9436
Defines where a class exists or takes place
Chase LeCroy, orcid.org/0000-0002-1338-9436
Dissolution Carbon Flux
Chase LeCroy, orcid.org/0000-0002-1338-9436
The rate at which carbon dissolves, moving from one pool to another.
https://en.wikipedia.org/wiki/Carbon_dioxide
CHEBI:48829, CHEBI:3283, CHEBI:13282, CHEBI:13283, CHEBI:13285, CHEBI:13284, CHEBI:23011
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://purl.obolibrary.org/obo/CHEBI_16526
carbonic anhydride, CO2
Carbon Dioxide
Carbon dioxide is a colorless and odorless gas vital to life on Earth. This naturally occurring chemical compound is composed of a carbon atom covalently double bonded to two oxygen atoms. Carbon dioxide exists in Earth's atmosphere as a trace gas at a concentration of about 0.04 percent (400 ppm) by volume. Natural sources include volcanoes, hot springs and geysers, and it is freed from carbonate rocks by dissolution in water and acids. Because carbon dioxide is soluble in water, it occurs naturally in groundwater, rivers and lakes, in ice caps and glaciers and also in seawater. It is present in deposits of petroleum and natural gas.
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by organisms that depend directly or indirectly on living or decaying plants for food, and taken up during photosynthesis (adapted from ChEBI).
Carbon oxoanions that have formula CO3.
http://purl.obolibrary.org/obo/CHEBI_41609
In chemistry, a carbonate is a salt of carbonic acid, characterized by the presence of the carbonate ion, CO2−3. The name may also mean an ester of carbonic acid, an organic compound containing the carbonate group.
CHEBI:41609
https://en.wikipedia.org/wiki/Carbonate
carbonate ion
Carbonate
https://en.wikipedia.org/wiki/Bicarbonate
Carbon oxoanions resulting from the removal of a proton from carbonic acid.
CHEBI:22863, CHEBI:40961, CHEBI:5589, CHEBI:13363
Bicarbonate
Acid carbonate, Bicarbonate, BICARBONATE ION, HCO3-, hydrogencarbonate
CHEBI:17544
http://purl.obolibrary.org/obo/CHEBI_17544
Bicarbonate is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula HCO−3. Bicarbonate serves a crucial biochemical role in the physiological pH buffering system.
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.
http://purl.obolibrary.org/obo/CHEBI_16646
Carbohydrate
saccharide, saccharides
CHEBI:16646
ash_free_dry_weight
Ash-free dry weight is used as an index for percent organic carbon in the quantified substrate.
http://www.dictionary.com/browse/algae, accessed 2016-06-30
Algae
any of numerous groups of chlorophyll-containing, mainly aquatic eukaryotic organisms ranging from microscopic single-celled forms to multicellular forms 100 feet (30 meters) or more long, distinguished from plants by the absence of true roots, stems, and leaves and by a lack of nonreproductive cells in the reproductive structures: classified into the six phyla Euglenophyta, Crysophyta, Pyrrophyta, Chlorophyta, Phaeophyta, and Rhodophyta.
mass transport, mass transfer
Chase LeCroy, http://orcid.org/0000-0002-1338-9436
Sara Lafia, http://orcid.org/0000-0002-5896-7295
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.
When a system contains two or more components whose concentration vary from point to point, there is a natural tendency for mass to be transferred, minimizing any concentration difference within the system. Mass Transfer in a system is governed by Fick's First Law: 'Diffusion flux from higher concentration to lower concentration is proportional to the gradient of the concentration of the substance and the diffusivity of the substance in the medium.'
Carbon Flux
https://en.wikipedia.org/wiki/Transport_phenomena#Mass_transfer
Litton, C.M. et al. Carbon allocation in forest ecosystems. Global Change Biology. V 13 I 10. pp. 2089 - 2109. July 2007.
The rate at which a mass of carbon moves to or from a particular component of the ecosystem per unit time.
Radiative Flux
All processes in engineering involve the transfer of energy. Some examples are the heating and cooling of process streams, phase changes, distillations, etc. The basic principle is the first law of thermodynamics. The net flux of energy through a system equals the conductivity times the rate of change of temperature with respect to position.
energy transfer
Sara Lafia, http://orcid.org/0000-0002-5896-7295
Radiative flux is the amount of power radiated through a given area in the form of photons or other elementary particles, typically measured in W/m2. Radiative flux also acts as a generalization of heat flux, which is equal to the radiative flux when restricted to the infrared spectrum. When radiative flux is incident on a surface, it is often called irradiance. Flux emitted from a surface may be called radiant exitance or radiant emittance.
energy transport, energy transfer, radiative flux, radiative flux density, radiation flux, irradiance, radiant exitance, radiant emittance
https://en.wikipedia.org/wiki/Transport_phenomena#Energy_transfer
definition_Contributor
O'Brien, pers comm. 2015-02-15
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.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
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_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 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.
Schildhauer, orcid.org/0000-0003-0632-7576
Schildhauer, pers comm, 05Feb2015, orcid.org/0000-0003-0632-7576
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
Schildhauer, orcid.org/0000-0003-0632-7576
Schildhauer, pers comm, 05Feb2014, orcid.org/0000-000300632-7576
"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
description_Source
Schildhauer, pers comm, 05Feb2015, orcid.org/0000-0003-0632-7576
Schildhauer, orcid.org/0000-0003-0632-7576
has_Related_Synonym
has_Exact_Synonym
mobb
ad hoc
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.
Margaret O'Brien, 2015-03-18
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.
O'Brien, pers comm, 2015-02-19
Margaret O'Brien, orcid.org/0000-0002-1693-8322
O'Brien, pers comm, 2015-02-19
"example_Of_Usage" is an OWL annotation property to record examples of how the concept or property should be used.
"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.
example_Of_Usage
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.
has_Exact_Synonym
ad hoc!
mobb
Margaret O'Brien, 2015-03-18
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_Related_Synonym
http://purl.obolibrary.org/obo/CHEBI_18059
Lipid
CHEBI:18059
CHEBI:25054, CHEBI:14517, CHEBI:6486
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
An anion is an ion with more electrons than protons, giving it a net negative charge (since electrons are negatively charged and protons are positively charged).
http://purl.obolibrary.org/obo/CHEBI_22563
https://en.wikipedia.org/wiki/Ion#Anions_and_cations
anions
A monoatomic or polyatomic species having one or more elementary charges of the electron.
CHEBI:22563
http://purl.obolibrary.org/obo/CHEBI_22629
CHEBI:22629
arsenate, arsenate anions, arsenate ions
CHEBI:22718
benzoate anion
http://purl.obolibrary.org/obo/CHEBI_22718
A monocarboxylic acid anion obtained by deprotonation of the carboxy group of any benzoic acid.
http://purl.obolibrary.org/obo/CHEBI_24675
hydroxybenzoates
CHEBI:24675
Any benzoate derivative carrying a single carboxylate group and at least one hydroxy substituent.
http://purl.obolibrary.org/obo/CHEBI_24834
CHEBI:24834
inorganic anions
CHEBI:24870
An ion is an atom or a molecule in which the total number of electrons is not equal to the total number of protons, giving the atom or molecule a net positive or negative electrical charge. Ions can be created, by either chemical or physical means, via ionization.
ions
https://en.wikipedia.org/wiki/Ion
A molecular entity having a net electric charge.
http://purl.obolibrary.org/obo/CHEBI_24870
http://purl.obolibrary.org/obo/CHEBI_25388
CHEBI:25388
monohydroxybenzoates
A hydroxybenzoate carrying a single hydroxy substituent at unspecified position.
http://purl.obolibrary.org/obo/CHEBI_25696
organic anions
CHEBI:25696
http://purl.obolibrary.org/obo/CHEBI_25699
organic ions
CHEBI:25699
CHEBI:26178
polyester, polyesters
A macromolecule composed of units connected by carboxylic ester (-O-CO-) linkages.
http://purl.obolibrary.org/obo/CHEBI_26178
http://purl.obolibrary.org/obo/CHEBI_26490
A cyclitol carboxylic acid anion that is conjugate base of quinic acid.
CHEBI:26490
http://purl.obolibrary.org/obo/CHEBI_27563
CHEBI:27563
CHEBI:2845, CHEBI:22630
https://en.wikipedia.org/wiki/Arsenic
Arsenic is a chemical element with symbol As and atomic number 33. Arsenic occurs in many minerals, usually in combination with sulfur and metals, but also as a pure elemental crystal. Arsenic is a metalloid.
CHEBI:29067
http://purl.obolibrary.org/obo/CHEBI_29067
a carboxylate, carboxylic acid anions, carboxylic anions
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
CHEBI:13626, CHEBI:13945, CHEBI:23026, CHEBI:58657
http://purl.obolibrary.org/obo/CHEBI_29125
CHEBI:29125
An arsenate ion resulting from the removal of three protons from arsenic acid.
Arsenate, ARSENATE, Arsenate ion, AsO43−
CHEBI:15061, CHEBI:26595
http://purl.obolibrary.org/obo/CHEBI_30762
CHEBI:30762
2-hydroxybenzoic acid ion(1−), o-hydroxybenzoate, sal, salicylate
A monohydroxybenzoate that is the conjugate base of salicylic acid.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
CHEBI:33250
http://purl.obolibrary.org/obo/CHEBI_33250
p-block element atom is an atom
CHEBI:22671, CHEBI:23907
element, elements
polyatomic anions
An anion consisting of more than one atom.
CHEBI:33273
http://purl.obolibrary.org/obo/CHEBI_33273
CHEBI:33285
heteroorganic entities, organoelement compounds
http://purl.obolibrary.org/obo/CHEBI_33285
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
CHEBI:33318
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
http://purl.obolibrary.org/obo/CHEBI_33318
p-block element atom is a main group element atom
main group element
CHEBI:33459
pnictogen oxoanion, pnictogen oxoanions
http://purl.obolibrary.org/obo/CHEBI_33459
CHEBI:33521
A metal is a material (an element, compound, or alloy) that is typically hard, opaque, shiny, and has good electrical and thermal conductivity. Metals are generally malleable — that is, they can be hammered or pressed permanently out of shape without breaking or cracking — as well as fusible (able to be fused or melted) and ductile (able to be drawn out into a thin wire). About 91 of the 118 elements in the periodic table are metals, the others are nonmetals or metalloids. Some elements appear in both metallic and non-metallic forms. Astrophysicists use the term "metal" to collectively describe all elements other than hydrogen and helium. In that sense, the metallicity of an object is the proportion of its matter made up of chemical elements other than hydrogen and helium. Many elements and compounds that are not normally classified as metals become metallic under high pressures; these are formed as metallic allotropes of non-metals.
elemental metal, elemental metals, metal element, metal elements, metals
http://purl.obolibrary.org/obo/CHEBI_33521
metal atom is an atom
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
main group compounds, main group molecular entities
CHEBI:33579
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
http://purl.obolibrary.org/obo/CHEBI_33579
p-block compounds, p-block molecular entities, p-block molecular entitiy
http://purl.obolibrary.org/obo/CHEBI_33675
CHEBI:33675
A main group molecular entity that contains one or more atoms of a p-block element.
chromium oxoanion, chromium oxoanions, oxoanions of chromium
http://purl.obolibrary.org/obo/CHEBI_35402
CHEBI:35402
http://purl.obolibrary.org/obo/CHEBI_35404
CHEBI:35404
CHEBI:35405
transition metal oxoanion, transition metal oxoanions, transition element oxoanions
http://purl.obolibrary.org/obo/CHEBI_35405
oxoacid anions, oxoanions
CHEBI:35406
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
http://purl.obolibrary.org/obo/CHEBI_35406
CHEBI:35701
A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
http://purl.obolibrary.org/obo/CHEBI_35701
CHEBI:4859, CHEBI:23960
Ester, esters
http://purl.obolibrary.org/obo/CHEBI_35757
a monocarboxylate, Carboxylate, Monocarboxylate, monocarboxylates, monocarboxylic acid anions
CHEBI:35757
CHEBI:3407, CHEBI:13657, CHEBI:25382
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
CHEBI:35776
http://purl.obolibrary.org/obo/CHEBI_35776
arsenic oxoanion, arsenic oxoanions, oxoanions of arsenic
hydroxy monocarboxylic acid anions, hydroxymonocarboxylic acid anion, hydroxymonocarboxylic acid anions
http://purl.obolibrary.org/obo/CHEBI_36059
Any monocarboxylic acid anion carrying at least one hydroxy substituent.
CHEBI:36059
cyclitol carboxylic acid anions
http://purl.obolibrary.org/obo/CHEBI_36125
CHEBI:36125
polyatomic ions
http://purl.obolibrary.org/obo/CHEBI_36358
An ion consisting of more than one atom.
CHEBI:36358
CHEBI:36914
inorganic ions
http://purl.obolibrary.org/obo/CHEBI_36914
quinolinemonocarboxylates
http://purl.obolibrary.org/obo/CHEBI_38773
A monocarboxylic acid anion that is the monoanion obtained by the deprotonation of the carboxy group attached to the quinoline skeleton
CHEBI:38773
http://purl.obolibrary.org/obo/CHEBI_53387
A polymer composed of repeating hydroxyalkanoyl units.
CHEBI:53387
PHAs, poly(hydroxyalkanoate)s, polyhydroxyalkanoate, polyhydroxyalkanoates
http://purl.obolibrary.org/obo/CHEBI_53388
A polymer composed of repeating hydroxybutyryl units.
CHEBI:53388
PHB, PHBs, poly(hydroxy butyrate), poly(hydroxy butyrate)s, poly(hydroxybutyrate)s, polyhydroxy butyrate, polyhydroxy butyrates, polyhydroxybutyrate, polyhydroxybutyrates
A quinolinemonocarboxylate that is the conjugate base of kynurenic acid
CHEBI:58454
http://purl.obolibrary.org/obo/CHEBI_58454
CHEBI:64708
An organic molecular entity containing a single carbon atom (C1).
http://purl.obolibrary.org/obo/CHEBI_64708
one-carbon compounds
organic acids
http://purl.obolibrary.org/obo/CHEBI_64709
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
CHEBI:64709
http://purl.obolibrary.org/obo/ENVO_00000015
Margaret O'Brien, orcid.org/0000-0002-1693-8322
http://purl.obolibrary.org/obo/ENVO_01000325
A layer in a water mass, itself composed primarily of water.
http://purl.obolibrary.org/obo/ENVO_2100007
rhizosphere determined by part of some soil
http://purl.obolibrary.org/obo/PATO_0000068
quality
PATO:0000068
attribute_slim
[database_cross_reference: PATOC:GVG]
quality
http://purl.obolibrary.org/obo/PATO_0000069
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
PATO:0000069
sensitivity
[database_cross_reference: PATOC:GVG]
quality
disposition_slim; attribute_slim; relational_slim
PATO:0000085
http://purl.obolibrary.org/obo/PATO_0000085
A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation.
attribute_slim
PATO:0000140
quality
PATO:0001631; PATO:0001032
http://purl.obolibrary.org/obo/PATO_0000140
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
relational spatial quality; location; placement
[database_cross_reference: PATOC:GVG]
attribute_slim; disposition_slim
http://purl.obolibrary.org/obo/PATO_0000274
PATO:0000274
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
quality
[database_cross_reference: PATOC:GVG]
[database_cross_reference: PATOC:GVG]
http://purl.obolibrary.org/obo/PATO_0000956
quality
value_slim; disposition_slim
PATO:0000956
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
http://purl.obolibrary.org/obo/PATO_0001428
scalar_slim; attribute_slim
PATO:0001428
[database_cross_reference: chemicool:chemicool]
A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base.
quality
value_slim
http://purl.obolibrary.org/obo/PATO_0001429
An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions.
[database_cross_reference: chemicool:chemicool]
PATO:0001429
quality
An medium acidity quality inhering in a solution by virtue of the bearer's a low concentration of H+ ions.
[database_cross_reference: chemicool:chemicool]
http://purl.obolibrary.org/obo/PATO_0001430
PATO:0001430
quality
value_slim
PATO:0001434
http://purl.obolibrary.org/obo/PATO_0001434
[database_cross_reference: WordNet:WordNet]
quality
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
A sensitivity quality inhering in a bearer by virtue of the bearer's dependence on oxygen.
PATO:0001454
http://purl.obolibrary.org/obo/PATO_0001454
quality
scalar_slim; attribute_slim; disposition_slim
[database_cross_reference: PATOC:GVG]
disposition_slim; value_slim
PATO:0001455
A quality inhering in a bearer by virtue of the bearer's dependence on oxygen.
quality
http://purl.obolibrary.org/obo/PATO_0001455
[database_cross_reference: PATOC:GVG]
A quality inhering in a bearer by virtue of the bearer's independence on oxygen.
[database_cross_reference: PATOC:GVG]
value_slim; disposition_slim
PATO:0001456
quality
http://purl.obolibrary.org/obo/PATO_0001456
PATO:0001576
quality
value_slim
high pressure
A pressure which is relatively high.
[database_cross_reference: PATO:GVG]
http://purl.obolibrary.org/obo/PATO_0001576
protruding ; relational protruding quality
A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary.
value_slim
PATO:0001644
PATO:0001598
[database_cross_reference: WordNet:WordNet]
quality
http://purl.obolibrary.org/obo/PATO_0001598
relational_slim; value_slim
quality
A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary and outwards in relation to the physical space occupied by another entity.
exposed; exits through
extruding from
http://purl.obolibrary.org/obo/PATO_0001646
PATO:0001646
[database_cross_reference: PATOC:nc]
scalar_slim; attribute_slim; relational_slim
PATO:0001655
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
[database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Osmolarity]
http://purl.obolibrary.org/obo/PATO_0001655
quality
relational_slim; value_slim
A osmolarity which is relatively high.
quality
[database_cross_reference: PATOC:GVG]
PATO:0001657
high osmolarity
http://purl.obolibrary.org/obo/PATO_0001657
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
PATO:0001739
http://purl.obolibrary.org/obo/PATO_0001739
[database_cross_reference: PATOC:GVG]
attribute_slim
quality
PATO:0001740
radioactivity
attribute_slim
http://purl.obolibrary.org/obo/PATO_0001740
A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate.
[database_cross_reference: PATOC:GVG]
quality
value_slim
PATO:0001741
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
[database_cross_reference: WordNet:WordNet]
quality
http://purl.obolibrary.org/obo/PATO_0001741
scalar_slim; attribute_slim; mpath_slim
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
PATO:0001822
quality
http://purl.obolibrary.org/obo/PATO_0001822
[database_cross_reference: wordreference.com:wordreference.com]
PATO:0001824
quality
value_slim; mpath_slim
A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid.
http://purl.obolibrary.org/obo/PATO_0001824
[database_cross_reference: PATOC:GVG]
pH
http://purl.obolibrary.org/obo/PATO_0001842
quality
[database_cross_reference: biology-online:biology-online]
A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions).
scalar_slim; attribute_slim
PATO:0001842
quality
[database_cross_reference: PATOC:CJM]
A quality that inheres in an entire organism or part of an organism.
PATO:0001995
http://purl.obolibrary.org/obo/PATO_0001995
PATO:0002061
[database_cross_reference: PATOC:GVG]
http://purl.obolibrary.org/obo/PATO_0002182
PATO:0002182
relational molecular quality
quality
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
PATO:0002300
A quality that has a value that is increased compared to normal or average.
[database_cross_reference: PATOC:GVG]
http://purl.obolibrary.org/obo/PATO_0002300
quality
A quality of an object that has a value that is increased compared to normal or average.
[database_cross_reference: PATOC:GVG]
quality
http://purl.obolibrary.org/obo/PATO_0002305
PATO:0002305
X surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
http://purl.obolibrary.org/obo/RO_0002219
http://purl.obolibrary.org/obo/RO_0002220
X adjacent to y if and only if x and y share a boundary.
The epidermis layer of a vertebrate is adjacent to the dermis.; The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.; A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.; The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
http://purl.obolibrary.org/obo/RO_0002376
inferior epigastric vein tributary_of external iliac vein; Deschutes River tributary_of Columbia River
X tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
tributary channel of; drains into; drains to
distributary channel of, branch of
http://purl.obolibrary.org/obo/RO_0002377
X distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
Deschutes River distributary_of Little Lava Lake
Experimental relation used in EnvO. A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.
http://purl.obolibrary.org/obo/envo#has_condition
desert has_condition some arid
http://purl.obolibrary.org/obo/envo#has_increased_levels_of
http://purl.obolibrary.org/obo/uo#is_unit_of
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
O'Brien, 2015-02-19
rdfs:label is an instance of rdf:Property that may be used to provide a human-readable version of a resource's name
Carbon_Flux_NASA, definition_Source, rdfs:label
Margaret O'Brien, orcid.org/0000-0002-1693-8322
rdfs:label
http://www.w3.org/2004/02/skos/core
An idea or notion; a unit of thought
Concept