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
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
Elizabeth Olson, http://orcid.org/0000-0001-8622-9698
Mark Schildhauer, http://orcid.org/0000-0003-0632-7576
Margaret O'Brien, http://orcid.org/0000-0002-1693-8322
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'.
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'.
A coral reef environment is determined by a particular coral reef
S determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
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
A relation between a continuant and a process, in which the continuant is somehow involved in the process
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.
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'.
this parent cell derives into this cell (cell division); this parent nucleus derives into this nucleus (nuclear division)
A relation between two distinct material entities, the old entity and the new 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
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
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
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.
The relationship between a fraction and the number above the line
The relationship between a fraction and the number below the line (or divisor)
related
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
expanse, surface area
Area
the extent of a 2-dimensional surface enclosed within a boundary
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
counting, numeration, enumeration, reckoning, tally
Count
the total number counted
radiant emittance, radiant exitance
Irradiance
Irradiance is the radiant flux (power) received by a surface per unit area.
Confirm: to follow the pattern, 'length' could be a subclass and the parent class (OBOE) more general ("linear"). Is this justified? or necessary?
Length
The linear extent in space from one end to the other; the longest dimension of something that is fixed in place
Mass
the property of a body that causes it to have weight in a gravitational field
Confirm: meaning of term (same concept as density)? See ArealDensity, ArealMassDensity. These need better definitions before ECSO can use them
MassDensity
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
MassSpecificCount
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)
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.
ratio
Proportion
the quotient obtained when the magnitude of a part is divided by the magnitude of the whole
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.
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.
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.
VolumePerVolume
Confirm: same concept as Density?
VolumetricDensity
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.
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
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-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-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-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-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.
http-nacp.ornl.gov/mstmipdata/ Contacts: Daniel Ricciuto (ricciutodm@ornl.gov)
GTEC = Global Terrestrial Ecosystem Carbon Model GTEC - global model contains 21,600 1 degree terrestrial cells. The carbon dynamics of each vegetated land cell (1.0 degree latitude X 1.0 degree longitude resolution) is described by a mechanistic soil-plant-atmosphere model (LoTEC) of ecosystem carbon storage and CO2 and H2O flux. Each grid cell is assigned to one of 15 ecosystem types and one of 105 soil types.
http-nacp.ornl.gov/mstmipdata/ Contacts: 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-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-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-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-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-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-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-nacp.ornl.gov/mstmipdata/ Contacts: Ning Zeng (zeng@atmos.umd.edu)
The VEgetation-Global Atmosphere-Soil Model (VEGAS)
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
The pool of carbon oxoanions that have formula CO3.
atmospheric carbon dioxide that has been converted into organic carbon compounds, usually by plants and algae via photosynthesis
unicellular, single-celled, single cell, monad
An organism that consists of only one cell
multi-cellular organism; whole organism
animal
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.
microorganism
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.
phase, state, state of matter
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.
air is a gas mixture with various pure gases
gaseous state
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.
crystalline solids include metals and ice
solid state
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.
metal alloys are dissolved solid solutions
dissolution, dissolved state
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.
CHEBI:41526, CHEBI:3282, CHEBI:13281, CHEBI:23013
A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas.
https://en.wikipedia.org/wiki/Total_organic_carbon and https://en.wikipedia.org/wiki/Organic_compound
A system that has the capacity to store or release carbon that is either of a biologic origin or can be found or incorporated into a living organism.
"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 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 also decomposes relatively quickly (years to decades) and provides an important source of energy for soil microorganisms. It also plays an important role in maintaining soil structure and providing soil nutrients. Plant residues and particulate organic carbon are often referred to as ‘labile carbon’ because they cycle in the soil relatively quickly.
A system that has the capacity to store or release carbon, in the form of pieces of plant debris 0.053–2 mm in size.
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.
Made this class a sibling of CHEBI class 'inorganic molecular entity' because CHEBI says that an 'inorganic molecular entity' contains no carbon, and we didn't want to contradict that.
https://en.wikipedia.org/wiki/Inorganic_compound and https://en.wikipedia.org/wiki/Total_inorganic_carbon
A system that has the capacity to store or release carbon that is either of a non-biologic origin or cannot be found or incorporated into a living organism. The inorganic carbon species include carbon dioxide, carbonic acid, biocarbonate anion, and carbonate.
A system that has the capacity to store or release carbon, via processes inherient to the condition of death (the cessation of all biological functions that sustain a living organism).
a tall perennial woody plant having a main trunk and branches forming a distinct elevated crown; includes both gymnosperms and angiosperms
In botany, a tree is a perennial plant with an elongated stem, or trunk, supporting branches and leaves in most species.
Adapted from https://en.wikipedia.org/wiki/Soil_carbon
numerator is carbon, denominator is a volume or weight of soil.
Margaret O'Brien, orcid.org/0000-0002-1693-8322
Plant Ontology (PO:0025161)
A portion of organism substance that is or was part of a plant, the whole or part thereof.
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
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.
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).
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)
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.
Adapted from https://en.wikipedia.org/wiki/Seaweed and Dawes, Cl J. 1978. Marine Botany, John Wiley and Sons., p 113
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.
the length of a straight line passing through the center of a circle and connecting two points on the circumference
PATO:0001648 http://www.ontobee.org/ontology/PATO?iri=http://purl.obolibrary.org/obo/PATO_0001648
the size of something as given by the distance around it
Perimeter of a circle
The circumference (from Latin circumferentia, meaning "carrying around") of a closed curve or circular object is the linear distance around its edge. The circumference of a circle is of special importance in geometry and trigonometry. Informally "circumference" may also refer to the edge itself rather than to the length of the edge. Circumference is a special case of perimeter: the perimeter is the length around any closed figure, but conventionally "perimeter" is typically used in reference to a polygon while "circumference" typically refers to a continuously differentiable curve.
the vertical dimension of extension; distance from the base of something to the top
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)
the strength of a solution (i.e. number of molecules of a substance in a given volume)
A concentration measurement describes a mixture of two entities, usually expressed as 'concentration of [entity 1] in [entity 2].'
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.
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".
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.
deepness
the perpendicular measurement downward from a surface
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.
Concentration may be expressed per volume of water (e.g., for phytoplankton), or per some measure of plant material.
http://www.thefreedictionary.com/rate https://en.wikipedia.org/wiki/Rate_(mathematics)#Temporal
A rate measurement is a quantity measured with respect to a second measured quantitiy. In temporal rates, the denominator (second quantity) is time.
Amount of carbon in some material. measurements will be a ratio where the numerator is Carbon (in mass or amount) and denominator is [mass or amount] of the material the Carbon is mixed with. Various units are used, eg, gram/gram,gram/volume, percent.
Alkalinity is the name given to the quantitative capacity of an aqueous solution to neutralize an acid.
https://en.wikipedia.org/wiki/Alkalinity accessed 2017-07-08
the distance between the top and bottom or front and back surfaces of something
this class is general enough to be in oboe. but it could be a child of PATO concentration.
In chemistry, the mass concentration is defined as the mass of a constituent divided by the volume of the mixture.
SOM Percent soil organic matter in mineral soil (by compustion at 550 c) number https://pasta.lternet.edu/package/metadata/eml/knb-lter-and/3142/7
Soil carbon includes both inorganic carbon as carbonate minerals, and as soil organic matter present in soil
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.
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)
the only growth was some salt grass
growing, maturation, development
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
Tree height is the vertical distance between the base of the tree and the highest sprig at the top of the tree. The base of the tree is measured for both height and girth as being the elevation at which the pith of the tree intersects the ground surface beneath, or "where the acorn sprouted."
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.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
the majority of tree growth occurs in late spring and early summer
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.
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.
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "biomass".
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.
the amount per unit size (i.e. the total mass of living matter in a given unit area)
Deliberately did not use the OBOE characteristic ArealDensity, because that one seemed to be specific to physics.
Biomass, in ecology, is the mass of living biological organisms per unit area 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.
of or in or along or relating to a line; involving or having a single dimension
one-dimensional
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.
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.
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.
ash_content
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).
Adapted from https://en.wikipedia.org/wiki/Bicarbonate
CO3_CO2calc_output CO3, CO2calc output (micromol/kgSW) Concentration of carbonate ion https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/75/1
Concentration of bicarbonate in freshwater serves a crucial biochemical role in the physiological pH buffering system. Bicarbonate is an intermediate form in the deprotonation of carbonic acid.
bacteria. Dictionary.com. Dictionary.com Unabridged. Random House, Inc. http://www.dictionary.com/browse/bacteria (accessed: June 30, 2016).
single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission; important as pathogens and for biochemical properties; taxonomy is difficult; often considered to be plants
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
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.
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.
Defined by the Plant Ontology as a plant structure (PO:0005679) which is a whole organism. PO label is 'whole plant'
soil profile, soil profiles
This is a grouping class, analogous to 'lake layer' and 'marine layer'
A layer which is part of soil. Soil generally consists of visually and texturally distinct layers.
In environments containing permafrost, the active layer is the top layer of soil that thaws during the summer and freezes again during the autumn.
Concentration of carbon in soil, which could include all forms (eg, inorganic carbon, carbonate minerals, and as soil organic matter). Soil carbon plays a key role in the carbon cycle, and thus it is important in global climate models.
adapted from https://en.wikipedia.org/wiki/Soil_organic_matter, 2017-07-08
Organic content consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms. SOM exerts numerous positive effects on soil physical and chemical properties, as well as the soil’s capacity to provide regulatory ecosystem services.[1] Particularly, the presence of SOM is regarded as being critical for soil function and soil quality.[2]
Soil organic content proportion is the fractional amount of all organic matter components of soil, relative to a measurement of the total.
since light can be either a wave or a particle, is it a material entity? for ECSO purposes, yes.
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.
This is a "foster parent" class, for holding MTs that are not quite done. It is intended to be removed.
sunlight
Sunlight is a portion of the electromagnetic radiation given off by the Sun, in particular infrared, visible, and ultraviolet light.
momentum transfer
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).
Adapted from http://www.madsci.org/posts/archives/2000-09/970201967.Es.r.html
AshWeight ash weight Soil Ash Weight gram https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1115/1
Mass of the ash remaining from comustion of a dried sample, thus the inorganic content.
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 is a process in which nitrogen (N2) in the atmosphere is converted into ammonia (NH3). Atmospheric nitrogen or molecular dinitrogen (N2) is relatively inert: it does not easily react with other chemicals to form new compounds. The fixation process frees nitrogen atoms from their triply bonded diatomic form, N≡N, to be used in other ways.
Adapted from https://en.wikipedia.org/wiki/Bulk_density
Dry Bulk density (g/cm3) Dry bulk density gramsPerCubicCentimeter www.supersites.net.au/knb/metacat/lloyd.301.8/html
mass density numerator and denominator same entity
Soil bulk density is a property used in reference to mineral components (soil, gravel) defined as the mass of many particles of the material divided by the total volume they occupy.
water content, moisture
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.
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.
Area is the quantity that expresses the extent of a two-dimensional figure or shape, or planar lamina, in the plane. Surface area is its analog on the two-dimensional surface of a three-dimensional object.
Ai rate Net Assimilation Rate microMolesPerMetersSquaredPerSecond urn:node:LTER
Confirm: Not sure what to do with these. in our corpus, there is only only one dataset with this measurement (https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1150/1) It seems like it is a Specific production rate, but we have not decided how to model these combinations of existing measurement types
the rate of increase of dry weight per unit of leaf area
Net_Carbon_Production rate Periphyton Net carbon production milligramsPerGramPerHour https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1107/3
Adapted from https://en.wikipedia.org/wiki/Carbon_respiration
Net_Respiration rate Periphyton Net carbon respiration milligramsPerGramPerHour urn:node:LTER
Carbon respiration (also called carbon emissions and carbon releases) is used in combination with carbon fixation to gauge carbon flux (as CO2) between atmospheric carbon and the global carbon cycle.
CO3_CO2calc_output CO3, CO2calc output (micromol/kgSW) Concentration of carbonate ion, micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram urn:node:LTER
Concentration of bicarbonate in sea water serves a crucial biochemical role in the physiological pH buffering system. Bicarbonate is an intermediate form in the deprotonation of carbonic acid.
Adapted from https://en.wikipedia.org/wiki/Vegetation
coupledvegCchange coupledvegCchange coupled vegetation Carbon change dimensionless (coupled/uncoupled) urn:node:LTER
Change in carbon percentage of vegetation, which are assemblages of plant species and the ground cover they provide.
coupledsoilCchange coupledsoilCchange coupled soil Carbon change dimensionless (coupled/uncoupled) urn:node:LTER
Soil carbon change percentage includes change of both inorganic carbon as carbonate minerals, and as soil organic matter.
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
The rate, or speed, at which the number of organisms in a population increases.
Adapted from https://en.wikipedia.org/wiki/Primary_production
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
Net primary production is the synthesis of organic compounds from atmospheric or aqueous carbon dioxide accountig for losses to processes such as cellular respiration. Biomass flux is the change in biomass over a given area over time. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through chemosynthesis, which uses the oxidation or reduction of inorganic chemical compounds as its source of energy.
Evap Daily evapottranspiration in mm millimeter peggym.110159.2
Height of transpiration is the process of water movement through a plant and its evaporation from aerial parts, such as leaves, stems and flowers. Water is necessary for plants but only a small amount of water taken up by the roots is used for growth and metabolism.
Count count dimensionless doi:10.5063/AA/gtg488d.4.1
Counting is the action of finding the number of elements of a finite set of objects. The traditional way of counting consists of continually increasing a (mental or spoken) counter by a unit for every element of the set, in some order, while marking (or displacing) those elements to avoid visiting the same element more than once, until no unmarked elements are left; if the counter was set to one after the first object, the value after visiting the final object gives the desired number of elements. The related term enumeration refers to uniquely identifying the elements of a finite (combinatorial) set or infinite set by assigning a number to each element.
Percent_N Percent Nitrogen dimensionless urn:node:KNB
Adapted from https://en.wikipedia.org/wiki/Biomass_(ecology)
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
Biomass excluding non-plants per unit area at a given time.
Stem/branch/foliage biomass Stem/branch/foliage biomass kilogram cmchiu.135.2
salmonBM2005 Salmon Biomass 05 Salmon Biomass in 2005 kilogramsPerSquareMeter df35b.159.6
Biomass excluding plants per unit area at a given time.
basSpawnBM2004 Basin Spawner Biomass 2004 Basin spawner biomass in 2004 in metric tons tonne df35b.159.6
Adapted from http://www.biology-online.org/dictionary/Dry_mass
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
The dry mass of a biomass sample or of an object when completely dried (lacks or excluding water).
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
The potential temperature of a parcel of fluid at pressure is the temperature that the parcel would acquire if adiabatically brought to a standard reference pressure, usually 1000 millibars.
Adapted from https://en.wikipedia.org/wiki/Precipitation
WaterLevel water level water level centimetersPerDay https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1098/3
Rate of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity.
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
Concentration of soil salinity, the salt content in the soil; the process of increasing the salt content is known as salinization. Salts occur naturally within soils and water. Salination can be caused by natural processes such as mineral weathering or by the gradual withdrawal of an ocean. It can also come about through artificial processes such as irrigation.
Adapted from https://en.wikipedia.org/wiki/Density
col_4144 CephalopVol biomass milliliterPerThousandCubicMeter https://pasta.lternet.edu/package/metadata/eml/knb-lter-pal/212/1
Confirm: This class may be deprecated, or transformed somehow for use in population measurements. For now, only one dataset in the corpus uses it, for a common representation of abundance, for groups of organisms. (https://pasta.lternet.edu/package/metadata/eml/knb-lter-pal/212/1)
The density, or more precisely, the volumetric mass density of biomass per unit volume.
There could be a subclass for a material's areal density that measuresCharacterstic only ArealDensity
The quantity, amount, weight, etc or things in a given area or space, ie, where the numerator and denominator are different entities. If the numerator and denominator are the same entity, then this would be a measurement of material density (of a 2-dimensional object), eg, as in physics.
OBSERVATION animal density of Cymatogaster aggregata numberPerMeterSquared https://pasta.lternet.edu/package/metadata/eml/ecotrends/5556/2
Number of non-plant material entities (i.e. animals, fungi) per unit area at a given time
AESPRA Plant density Aeschynomene pratensis numberPerMeterSquared taxa:Aeschynomene_pratensis
Number of plant material entities (i.e. trees, plant parts) per unit area at a given time
roadDens_BUFR Density of roads within the buffer. Derived using methods of Pechenick et al. 2014 (km^-1) dimensionless cgries.16.1
Number of built feature entities (i.e. roads, bridges) per unit area at a given time
Adapted from http://www.biology-online.org/dictionary/Litter
avg/m2 mean litterfall gramsPerSquareMeter https://pasta.lternet.edu/package/metadata/eml/knb-lter-hfr/8/18
Mass of undecomposed biomass material found on the forest floor per unit area at a given time.
Adapted from https://en.wikipedia.org/wiki/Tide
Mean_Higher_High_Water Mean higher-high water based on historic station datum meter https://pasta.lternet.edu/package/metadata/eml/knb-lter-gce/249/33
Height of tides, which are the rise and fall of sea levels caused by the combined effects of the gravitational forces exerted by the Moon and the Sun and the rotation of the Earth.
Adapted from https://en.wikipedia.org/wiki/Sea_level
Mean Sea Level Mean Monthly Sea Level Mean Monthly Sea Level meter https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1059/3
Height of sea level, which is generally used to refer to mean sea level (MSL), an average level for the surface of one or more of Earth's oceans from which heights such as elevations may be measured.
Adapted from https://en.wikipedia.org/wiki/Water
Evap Daily evapottranspiration in mm millimeter peggym.110155.3
Height of water, which is a transparent fluid which forms the world's streams, lakes, oceans and rain, and is the major constituent of the fluids of organisms.
Wave_Height Wave-height in meters df35d.398.6
The wave height of a surface wave is the difference between the elevations of a crest and a neighbouring trough.
Body_Length Body Length (mm) millimeter doi:10.5063/AA/nceas.919.3
Length of an entity that is not a plant (i.e. body length of a specimen)
Adapyed from http://www.biology-online.org/dictionary/Dry_mass
Dry_m2 Dry Mass Dry mass density derived from estimates of density or percent cover and laboratory estimates of taxa dry mass. gramPerMeterSquared https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/49/8
The dry matter of a sample or of an object when completely dried (lacks or excluding water) per area
Pressure is the force applied perpendicular to the surface of an object per unit area over which that force is distributed. Gauge pressure is the pressure relative to the ambient pressure.
Adapted from https://en.wikipedia.org/wiki/Seawater
Pressure [db] pressure center of the pressure averaging interval decibar https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/1009/6
Pressure of seawater, or salt water, which is water from a sea or ocean. On average, seawater in the world's oceans has a salinity of about 3.5% (35 g/L, or 599 mM). This means that every kilogram (roughly one litre by volume) of seawater has approximately 35 grams (1.2 oz) of dissolved salts (predominantly sodium (Na+) and chloride (Cl−) ions).
Adapted from https://en.wikipedia.org/wiki/Plant_cover
OBSERVATION plant cover of Dasyochloa pulchella (low woollygrass) percent https://pasta.lternet.edu/package/metadata/eml/ecotrends/15283/2
The abundances of plant species are often measured by plant cover, i.e. the relative area covered by different plant species in a small plot. Plant cover is not biased by the size and distributions of individuals, and is an important and often measured characteristic of the composition of plant communities. Plant cover data may be used to classify the studied plant community into a vegetation type, to test different ecological hypothesis on plant abundance, and in gradient studies, where the effects of different environmental gradients on the abundance of specific plant species are investigated. The most common way to measure plant cover in herbal plant communities, is to make a visual assessment of the relative area covered by the different species in a small plot (see quadrat).
Adapted from https://en.wikipedia.org/wiki/Canopy_(biology)
%CC Percentage canopy cover of a single plot, calculated with a supervisd classification with maximum likelihood classifier(IDRISI GIS) on the area of an experimental burn plot dimensionless judithk.173.7
Percentage cover of canopy, which is the aboveground portion of a plant community or crop, formed by the collection of individual plant crowns
A name is a term used for identification. Names can identify a class or category of things, or a single thing, either uniquely, or within a given context. A personal name identifies, not necessarily uniquely, a specific individual human. The name of a specific entity is sometimes called a proper name (although that term has a philosophical meaning also) and is, when consisting of only one word, a proper noun. Other nouns are sometimes called "common names" or (obsolete) "general names". A name can be given to a person, place, or thing; for example, parents can give their child a name or a scientist can give an element a name.
N1 Proportion of individuals sampled who were in the naupliar 1 stage number ark:/90135/q13j39xf/4/mrt-eml.xml
A data sample is a set of data collected and/or selected from a statistical population about entities by a defined procedure.
Adapted from https://en.wikipedia.org/wiki/Area https://en.wikipedia.org/wiki/Quadrat
PCT_WETLAND_BUFR Percent of buffer area as Wetlands (Woody + Herbaceous) squareKilometers cgries.16.1
An area, such as a quadrat sample, can be used to measure the percentage cover of an entity, such as a certain species
units typical for this kind of measurement are milligramsPerGramPerHour e.g, see these attributes and dataset: GrossProductionPerMass rate Periphyton Gross Production per Mass https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1107/3
OBSERVATION plant cover of Carex percent https://pasta.lternet.edu/package/metadata/eml/ecotrends/2645/2
Percentage of plant cover, which is the relative area covered by different plant species in a small plot. Plant cover is not biased by the size and distributions of individuals, and is an important and often measured characteristic of the composition of plant communities.
The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume.
density density of animals density of animals per liter numberPerLiter https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/79/4
The density, or more precisely, the volumetric mass density, of a substance is a characteristic, such as mass or count, per unit volume.
density number per liter number per liter summed over sex and stage and volumetrically integrated over the water column numberPerLiter https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/37/11
The density, or more precisely, the volumetric count density of entities per unit volume.
Adapted from https://en.wikipedia.org/wiki/Biomass https://en.wikipedia.org/wiki/Concentration
total_biomass total biomass of taxon total biomass of taxon milligramPerLiter https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/79/4
Abundance of a constituent divided by the total volume of a mixture, or concentration, of biomass, which is organic matter derived from living, or recently living organisms
waterdepth depth below water surface in meter meter cgries.23.1
Depth of water, which is a transparent fluid which forms the world's streams, lakes, oceans and rain, and is the major constituent of the fluids of organisms.
Adapted from https://en.wikipedia.org/wiki/Snow
Mean snow depth Irkutsk - boulder Snow & Ice data Snow depth in cm at Irkutsk Weather station Snow depth in cm at Irkutsk station in the National Snow and Ice Data Center's Historical Soviet Daily Snow Depth - version 2.0 centimeter doi:10.5063/AA/nceas.290.8
Depth of snow, which is precipitation in the form of flakes of crystalline water ice that falls from clouds
Adapted from https://en.wikipedia.org/wiki/Lake
depth_ned lake depth lake depth derived from National Elevation Dataset meter ben.1.1
Depth of a lake, which is an area of variable size filled with water, localized in a basin, that is surrounded by land, apart from any river or other outlet that serves to feed or drain the lake.
Adapted from https://en.wikipedia.org/wiki/Soil
depth Depth range of layer centimeter www.supersites.net.au/knb/metacat/supersite.182.10/html
Depth of soil, which is a mixture of minerals, organic matter, gases, liquids, and countless organisms that together support life on Earth.
The disc is mounted on a pole or line, and lowered slowly down in the water. The depth at which the disk is no longer visible is taken as a measure of the transparency of the water. This measure is known as the Secchi depth and is related to water turbidity.
Adapted from https://en.wikipedia.org/wiki/Plant_litter
LITTER Letter depth centimeter https://pasta.lternet.edu/package/metadata/eml/knb-lter-and/3142/7
The depth of dead plant material, such as leaves, bark, needles, and twigs, that have fallen to the ground. This detritus or dead organic material and its constituent nutrients are added to the top layer of soil, commonly known as the litter layer or O horizon ("O" for "organic").
Adapted from https://en.wikipedia.org/wiki/Primary_production#Gross_primary_production_and_net_primary_production
NPP net primary productivity Net primary productivity milligramsPerGramPerHour https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1087/3
Carbon in the numerator (weight or moles) and measured weight (in weight or moles) in both the numerator and denominator
Net primary production (NPP) flux that relative to another mass (or other measurement of amount, eg, leaf area, plant wet weight) that primary producers create in a given length of time over a given area Net primary production flux is the rate at which all the plants in an ecosystem produce net useful chemical energy, in this case, relative to another mass (usually of the same plant)
Adapted from https://en.wikipedia.org/wiki/Stream
Logger 1 (tide gauge) Dc (m) Logger 1 (tide gauge) Dc (m) Depth of water (in m) above creek bottom relative to the tide gauge meter https://pasta.lternet.edu/package/metadata/eml/knb-lter-pie/161/3
Depth of a stream, which is a body of water with a current, confined within a bed and banks.
Adapted from https://en.wikipedia.org/wiki/Groundwater
SBAS3_BR_80 readings (mm). actual water level below ground surface millimeter judithk.1716.4
Depth of groundwater (or ground water), which is the water present beneath Earth's surface in soil pore spaces and in the fractures of rock formations. A unit of rock or an unconsolidated deposit is called an aquifer when it can yield a usable quantity of water. The depth at which soil pore spaces or fractures and voids in rock become completely saturated with water is called the water table.
G1 G1 Ground heat flux wattPerMeterSquared knb-lter-arc.20005.1
Ground heat flux is the process where heat energy is transferred from the Earth’s surface to the subsurface of the Earth via conduction. It is an important component of the Earth’s surface energy budget. Ground heat flux can be presented by the amount of heat transmitted per unit of area per unit of time.
LE LE Latent heat flux wattPerMeterSquared knb-lter-arc.20005.1
Latent heat flux is the flux of heat from the Earth's surface to the atmosphere that is associated with evaporation of water at the surface and subsequent condensation of water vapor in the troposphere. It is an important component of Earth's surface energy budget. Latent heat flux is commonly measured with the Bowen ratio technique, or by eddy covariance.
Adapted from https://en.wikipedia.org/wiki/Tree_crown_measurement
Crown length (m) Crown length meter www.supersites.net.au/knb/metacat/lloyd.628.7/html
Height of the crown of a tree, which consists of the mass of foliage and branches growing outward from the trunk of the tree. The average crown spread is the average horizontal width of the crown, taken from dripline to dripline as one moves around the crown.
h1 Stem 1 height meter www.supersites.net.au/knb/metacat/supersite.116.9/html
Height of a physical entity that is a plant or part of a plant (i.e. tree trunk height)
Rain Total daily rainfall in mm millimeter peggym.110130.3
Height of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity. The main forms of precipitation include drizzle, rain, sleet, snow, graupel and hail. Precipitation occurs when a portion of the atmosphere becomes saturated with water vapor, so that the water condenses and "precipitates".
Adapted from https://en.wikipedia.org/wiki/Carbon_dioxide
fCO2_CO2calc_input fCO2, measured (microatm) Fugosity of CO2 (measured), in saturated air at equilibrium with water in microatmospheres (CO2calc input) microatmosphere https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/75/1
Pressure of carbon dioxide gas, which is composed of a carbon atom covalently double bonded to two oxygen atoms.
Adapted from https://en.wikipedia.org/wiki/Temperature
Ta Air Temperature celsius ark:/90135/q17s7kq7/1/mrt-eml.xml
Objective comparative measure of hot or cold of air
T00 water temperature, from primary sensor ITS-90, based on International Temperature Scale of 1990 celsius https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/1009/6
Objective comparative measure of hot or cold of water in sea
T00 water temperature, from primary sensor ITS-90, based on International Temperature Scale of 1990 celsius https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/1007/6
Objective comparative measure of hot or cold of water
temperature temperature celsius doi:10.5063/AA/Jinyuntang.15.5
Objective comparative measure of hot or cold of peat
avg_grndt average ground temperature celsius https://pasta.lternet.edu/package/metadata/eml/knb-lter-hfr/68/21
Objective comparative measure of hot or cold of ground
s_temp soil temperature at 10 cm depth celsius https://pasta.lternet.edu/package/metadata/eml/knb-lter-hfr/130/13
Objective comparative measure of hot or cold of soil
meanT_1m Seasonal (June to October) mean temperature for the 1 meter stratum celsius df35d.362.10
Objective comparative measure of hot or cold of water in lake
GrossProductionPerMass rate Periphyton Gross Production per Mass milligramsPerGramPerHour https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1107/3
Carbon in the numerator (weight or moles) and measured weight (in weight or moles) in both the numerator and denominator. For example, carbon or some other material can be in the numerator.
Gross primary production (GPP) flux that relative to another mass (or other measurement of amount, eg, leaf area, plant wet weight) that primary producers create in a given length of time over a given area
Adapted from https://en.wikipedia.org/wiki/Velocity
Wind speed Wind speed metersPerSecond peggym.109987.2
Wind measurements are usually reported in two parts: speed and direction. Velocity is direction-aware, so would be a combined form of these (the OBOE observation). A measurement of a wind vector would be wind velocity, and would need a new class.
The speed of wind is the rate of change of its position with respect to a frame of reference, and is a function of time.
XVEL velocity water velocity in x direction centimetersPerSecond https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1135/1
The velocity of water is the rate of change of its position with respect to a frame of reference, and is a function of time.
E_Vel_02_5m_bin E_Vel_02.5m_bin adcp, east velocity, 02.5m up from bottom, westward values are negative meterPerSecond https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/2005/15
The velocity of sea water is the rate of change of its position with respect to a frame of reference, and is a function of time.
Total_Precipitation Volume Volume of total precipitation in bucket milliliter https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1067/3
Volume of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity
TrWidth Transect width Width of transect, typically 300m (150m on each side and in front of vessel) meter jstocking.3.4
Width of a physical abiotic entity (i.e. width of a stream)
mass is a property of a physical body. It is a measure of an object's resistance to acceleration (a change in its state of motion) when a force is applied. It also determines the strength of its mutual gravitational attraction to other bodies. In the theory of relativity a related concept is the mass–energy content of a system. The SI unit of mass is the kilogram (kg).
Adapted from https://en.wikipedia.org/wiki/Chlorophyll
The concentration of chlorophyll, which are related green pigments found in cyanobacteria and the chloroplasts of algae and plants. to do: delete extra string.
The addition of grams in the denominator makes it a specific flux (i.e. gC/(g DW * t * m^2))
Flux where the units of the numerator include mass and units of the denominator include mass (or some other measurement of 'amount', eg leaf area) in addition to flux units of area and time
Ecosystem respiration flux is the respiration occurring by the living organisms in a specific ecosystem over a given area, relative to some other measure of those organisms.
Adapted from https://en.wikipedia.org/wiki/Ecosystem_respiration
Net_Respiration rate Periphyton Net carbon respiration milligramsPerGramPerHour https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1107/3
https://en.wikipedia.org/wiki/Periphyton, 2017-07-08
periphyton is a complex mixture of algae, cyanobacteria, heterotrophic microbes, and detritus that is attached to submerged surfaces in most aquatic ecosystems.
https://en.wikipedia.org/wiki/Soil_organic_matter, 2017-07-08
"organic content" is the organic matter component of another entity, e.g., soil.
Organic matter in soil consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms.
SOM exerts numerous positive effects on soil physical and chemical properties, as well as the soil’s capacity to provide regulatory ecosystem services.[1] Particularly, the presence of SOM is regarded as being critical for soil function and soil quality.[2]]
[Soil organic content ] is a measurement of the total organic components of soil, measured as mass.
https://en.wikipedia.org/wiki/Calcium_carbonate, 2017-07-08
Calcium carbonate is a chemical compound with the formula CaCO₃. It is a common substance found in rocks as the minerals calcite and aragonite and is the main component of pearls and the shells of marine organisms, snails, and eggs.
adapted from https://en.wikipedia.org/wiki/Calcium_carbonate#Occurrence
Calcium Carbonate is found in both geologic and biologic settings and constitutes an enormous carbon reservoir. Concentrations are measured in water (both fresh and saline), soil, rock and biological fluids.
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}
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}
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).
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.
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).
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.
oxygen
ChEBI:C00007; WebElements:O
chebi_ontology
oxygen atom
A chalcogen that has formula O
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.
Snow is an environmental material which is primarily composed of flakes of crystalline water ice. [database_cross_reference: Wikipedia:Snow]
An entity that has temporal parts and that happens, unfolds or develops through time.
a certain PDF file that exists in different and in several hard drives
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
Consisting entirely of single-bonded carbon and hydrogen atoms and lacking functional groups.
molecular entities
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
atom is a chemical entity
chemical entity
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
inorganic compounds, inorganic entity, inorganic molecular entities, inorganics
A molecular entity that contains no carbon.
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.
nitrogen atom
carbon atom is a carbon group element atom
carbon group element, carbon group elements, group IV elements
group 15 elements
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
chalcogen
Any p-block element belonging to the group 16 family of the periodic table.
carbon group element atom is a p-block element atom
Any main group element atom belonging to the p-block of the periodic table.
carbon group molecular entities, carbon group molecular entity
The stable isotope of oxygen with relative atomic mass 17.999160 and 0.205 atom percent natural abundance.
carbon-13 atom, carbon, isotope of mass 14
Uses in science: used in carbon dating and as a tracer in biochemistry.
a long-lived naturally occurring radioactive carbon isotope of mass 14 (6 protons and 8 neutrons)
carbon-13 atom, carbon, isotope of mass 13
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.
natural, stable isotope of carbon with a nucleus containing 6 protons and 7 neutrons.
carbon-12 atom
the most common natural carbon isotope, of mass 12. It is the basis for the accepted scale of atomic mass units.
organic compounds, organic entity, organic molecular entities
CHEBI:25700, CHEBI:33244
Any molecular entity that contains carbon.
one-carbon compounds
An organic molecular entity containing a single carbon atom (C1).
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]
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.
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
An organic material primarily composed of a portion of plant root.
leaf litter; litterfall; tree litter; soil litter; duff
[database_cross_reference: Adapted from Wikipedia:Plant_litter]
Leaf litter is dead plant material, such as leaves, bark, needles, and twigs, that has fallen to the ground.
ground
Land is a planetary surface that is not covered by liquid. [database_cross_reference: Adpated from Wikipedia:Planetary_surface]
land
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]
wind
atmospheric wind
A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria.
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]
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.
respiration
ecosystem-wide respiration
A process which consists of all respiration processes instantiated in an ecosystem.
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]
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method that reliably tends to produce (approximately) truthful statements.
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
An information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A data item that is a recording of the output of an assay.
concentration
[database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/concentration]
quality
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.
decreased mass equivalentClass : mass and ( decreased_in_magnitude_relative_to some normal)
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.
decreased weight equivalentClass : weight and ( decreased_in_magnitude_relative_to some normal)
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Weight
scalar_slim; attribute_slim
A physical quality inhering in a bearer that has mass near a gravitational body.
database_cross_reference: PATOC:GVG
time
A quality in which events occur in sequence.
viability (of living things) capable of normal growth and development
relational physical quality
[database_cross_reference: PATOC:GVG]
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.
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
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
monadic quality of an object; monadic quality of continuant
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.
period
decreased duration equivalentClass : duration and ( decreased_in_magnitude_relative_to some normal)
database_cross_reference: PATOC:mellybelly
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.
not showing characteristics of life especially the capacity to sustain life; no longer exerting force or having energy or heat
damaged by decay; hence unsound and useless
database_cross_reference: IUPAC:IUPAC
A concentration quality inhering in a bearer by virtue of the bearer's catalytic activity divided by the volume of the system.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Molar_volume
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.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Molar_mass
molar mass
A physical quality that inheres in a homogeneous substance containing 6.02 x 1023 atoms or molecules.
2-D size
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.
3D size
3-D extent
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
[database_cross_reference: wordreference.com:wordreference.com]
scalar_slim; attribute_slim; mpath_slim
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid.
value_slim; mpath_slim
A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid.
[database_cross_reference: PATOC:CJM]
A quality that inheres in an entire organism or part of an organism.
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
distance
george gkoutos
unit.ontology
unit_group_slim
linear unit
A unit which is a standard measure of the distance between two points.
temperature derived unit
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
[database_cross_reference: NIST:NIST]
unit_slim
centimeter
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
mm; micrometre
millimeter
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
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.
mass density unit
A unit which is a standard measure of the influence exerted by some mass.
mass per unit area unit
areal density unit
A density unit which is a standard measure of the mass exerting an influence on a given area.
force per unit area
A unit which is a standard measure of the force applied to a given area.
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
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]
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.
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]. [
density unit
linear density unit
A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object.
dimensionless unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
percent
A dimensionless ratio unit which denotes numbers as fractions of 100.
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
fraction
A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator).
millimeters of mercury; mmHg
[database_cross_reference: url:en.wiktionary.org/wiki/mmHg]
A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
carbon cycling
Can be used to track CO2 uptake during plant photosynthesis
carbonyl sulfide
A one-carbon compound in which the carbon atom is attached to an oxygen and a sulfur atom via double bonds.
protium atom
The stable isotope of hydrogen with relative atomic mass 1.007825 and a natural abundance of 99.9885 atom percent (from Greek πρωτοσ, first).
tritium atom
The radioactive isotope of hydrogen with relative atomic mass 3.016049 and half-life of 12.33 years (from Greek τριτοσ, third).
oxygen-16 atom
The stable isotope of oxygen with relative atomic mass 15.994914. The most abundant (99.76 atom percent) isotope of naturally occurring oxygen.
oxygen-17 atom
The stable isotope of oxygen with relative atomic mass 16.999131. The least abundant (0.038 atom percent) isotope of naturally occurring oxygen.
nitrogen-14 atom
The stable isotope of nitrogen with relative atomic mass 14.003074. The most abundant (99.63 atom percent) isotope of naturally occurring nitrogen.
n-alkane
branched chain alkane
n-Hentriacontane
n-Nonacosane
n-Heptacosane
The long-chain (C27–C35) n-alkanes are a main component of the epicuticular waxes of higher plants.
long-chain n-alkanes
n-Pentacosane
n-Hexacosane
n-Octacosane
n-Triacontane
n-Dotriacontane
n-Tritriacontane
n-Tetratriacontane
n-Pentatriacontane
N-alkanes C23 - C25 dominated by submerged aquatic macrophtyes.
mid-chain n-alkanes
N-alkanes C17 - C21 dominated by aquatic algae.
short-chain n-alkanes
n-Tricosane
n-Tetracosane
n-Henicosane
n-icosane
n-Nonadecane
n-Octadecane
n-Heptadecane
refactory organic material
organic compounds (woody debris made of lignin and cellulose) have very high TOC:TN ratios and are highly resistant to degradation
Elizabeth Olson, https://orcid.org/0000-0001-8622-9698
labile organic carbon
organic matter with low TOC:TN ratios (e.g. phytoplankton) that breaks down easily
Normallized Difference Vegetation Index
A graphical indicator used to analyze remote sensing measurements to determine the density of green on an area of land. Calculated from the distinct colors (wavelengths) of visible and near-infrared sunlight reflected by plants on the surface the NDVI is calculated using the equation: the visible and near-infrared radiation minus visible radiation divided by near-infrared radiation plus visible radiation.
Water Content
The total amount of water (unfrozen water + ice) contained in soil or rock
cryoturbation
the mixing of materials from various horizons of the soil down to the bedrock due to freezing and thawing in permafrost soils
Thawing Index
the cumulative number of degree-days when air temperatures are above zero degrees Celsius
Thaw Consolidation Ratio
A dimensionless ratio of the rate of thaw to the rate of consolidation of the thawing soil, which is considered to be a measure of the relative rates of generation and expulsion of excess pore fluids during thaw
n-factor
the number of H+ ions replaced by 1 mole of acid in a reaction
permafrost layer
permafrost active layer
The top layer of ground subject to annual thawing and freezing in areas underlain by permafrost
permafrost relict active layer
A layer of ground, now perennially frozen, lying immediately below the modern active layer. Itsthickness indicatesthe greater annual depth of thawthat occurred during a previous, warmer climatic period
permafrost active layer failure
A general term referring to several forms of slope failures or failure mechanisms commonly occurring in areas underlain by permafrost
adfreeze
The process by which two objects are bonded together by ice formed between them during the freezing of water.
Typically, alassesare large depressions ranging from 0.5 to more than 100 km2 in area and from 5 to 20 m in depth. In the early stagesof formation, a shallow « 2 m) circular "alas lake" forms in a steep-sideddepression. Enlargementand ultimate drainage of a number of such lakes produce low interalas plateaus (termed "mezhalasye" in Russian). Ultimately, the plateaus disappear and mass wasting produces gentle side slopes. The term is of Yakut origin. REFERENCES: Czudek and Demek, 1970;Soloviev,1973
alas
A depression found in thermokarst terrain, produced by thawing of extensive areas of very thick and exceedingly ice-rich permafrost.
A characteristic pattern of small streams in areas underlain by ice wedges. The course of the stream channel is controlled by the pattern of the wedges, with the beads (pools) occurring at the junctions of the wedges. When the intervening channels are dry, they may be called "beaded channels."
beaded stream
A stream characterized by narrow reaches linking pools or small lakes
block field
A surficial layer of angular shattered rocks formed in either modern or Pleistocene periglacial environments.
A collapse scar is not a depression but is marked by vegetation different from the wetland that did not contain permafrost. Irregular topography (hence thermokarst terrains may be present on the peatland as a whole but the collapse scars are only part of that thermokarst terrain, marked by the absence of permafrost, and by vegetation different from that on both the previously unfrozen peatlandsand the remnant permafrost peat landforms. REFERENCE: Zoltai, 1971.
collapse scar
That portion of a peatland where the whole or part of a paisa or peat plateau has thawed and collapsed to the level of the surrounding peatland
wedge
composite wedge
A wedge showing evidence of both primary and secondary filling
WASHBURN, AL., 1979. Geocryology. Edward Arnold, London, 406 p.
creep of frozen ground
The slow deformation that results from long-term application of a stress too small to produce failure in the frozen material.
soil creep
is the slow downward progression of rock and soil down a low grade slope; it can also refer to slow deformation of such materials as a result of prolonged pressure and stress.
cryofront
The boundary between cryotic and noncryotic ground as indicated by the position of the O°C isotherm in the ground
cryogenesis
The combination of thermophysical, physico-chemical and physicomechanical processes occurring in freezing, frozen and thawing earth materials.
permafrost process
aquitard
a bed of low permeability along an aquifer
cryogenic aquiclude
A layer of ground which, because of its frozen state, has a low enough permeability to act as a confining bed for an underlying aquifer.
Cryogenic Temperature
In international materials science, this term refers to temperatures generally below -sooe, but usually to temperatures within a few degrees of absolute zero (-273°C). In the Russian permafrost literature, this term refers to temperatures below O°C.
cryopeg
A layer of unfrozen ground that is perennially cryotic (forming part of the permafrost), in which freezing is prevented by freezing-point depression due to the dissolved-solids content or the pore water
basal cryopeg
forms the basal portion of the permafrost
isolated cryopeg
entirely surrounded by perennially frozen ground
marine cryopeg
Found in coastal or subsea perennially frozen ground.
cryoplanation terrace
A step-like or table-like bench cut in bedrock in cold climate regions
Degree Day
A measure of the departure of the mean temperature for a day from a given reference (or base) temperature.
degree of saturation
The total degree of saturation of frozen soil isthe ratio of the volume of ice and unfrozen water in the soil pores to the volume of the pores.
Depth of Thaw
The minimum distance between the ground surface and frozen groundat any time during the thawing season
Depth of Zero Annual Amplitude
The distance from the ground surface downward to the level beneath which there is practically no annual fluctuation in ground temperature
A slope failure in which the thawed or thawing active layerand vegetation mat detach from the underlying frozen material
detachment failure
sedimentary feature
dilation crack
A tensile fracture in a frozen material due to surface extension caused by doming.
drunken forest
Trees leaning in random directions in a permafrostregion
freezeback
The cumulative number of degree-days below O°C for a given time period.
Freezing Index
BOYD, D.w., 1973. Normal freezing and thawing degree-daysfor Canada: 1931-1960. Environment Canada, Atmospheric EnvironmentService, Downsview, Ontario, Publication CLI 4-73, 38 p. BOYD, D.W., 1979. Degree days: The different types. National Research Council Canada, Division of Building Research, Ottawa, Building Research Note No. 138, 8 p.
Approximate Freezing Index
calculated from the mean monthly air temperatures for a specific station without making corrections for positive degree-days (above DoC) in spring and fall
HARRIS, S.A, 1981. "Climatic relationshipsof permafrost zones in areas of low winter snow-cover." Arctic, Vol. 36, No.1, pp. 64-70.
calculated by adding all the negative mean daily air temperatures (DC) for a specific station during a calendar year
Total Annual Freezing Index
HUSCHKE, RE. (Editor), 1959. Glossary of Meteorology. American Meteorological Society, 638 p.
Seasonal Freezing Index
calculated as the arithmetic sum of all the negative and positive mean daily air temperatures (DC) for a specific station during the time period between the highest point in the fall and the lowest point the next spring on the cumulative degree-day time curve
Design Freezing Index
calculated by taking the average of the seasonal freezing indices for the three coldest winters in the most recent 30 years of record. If data for 30 years are not available, then the index is based on the coldest winter in the latest lO-year period of record
Freezing Point Depression
The number of degrees by which the freezing point of an earth material is depressed below 0oC
Freezing Pressure
The positive (heaving) pressure developedat ice-water interfaces in a soil as it freezes
seasonal frost
The occurrenceof ground temperatures below O°C for only part of the year
JOHNSTON, G.H. (Editor), 1981. Permafrost: Engineering Design and Construction. John Wiley & Sons, Canada Ltd.,Toronto, 540 p.
frost action
The process of alternate freezing and thawing of moisture in soil, rock and other materials, and the resulting effects on materials and on structures placed on, or in, the ground.
permafrost feature
A feature associated with permafrost (soil at or below the freezing point of water (0C or 32F) for two or more years).
THORN, C.E., 1976. "A model of stoney earth circle development, Schefferville, Quebec." Association of American Geographers, Proceedings, Vol. 8, pp. 19-23.
frost blister
A seasonal frost mound produced through doming of seasonally frozen ground by a subsurface accumulation of water under high hydraulic potential during progressive freezing of the active layer.
A more or less symmetrical zone of frozen ground formed around a buried chilled pipeline or beneath or around a structure maintained at temperatures below 0 oC.
MULLER, S.W., 1943. Permafrost or permanently frozen ground and related engineering problems. U.S. Engineers Office, Strategic Engineering Study,Special Report No. 62, 136p. (Reprinted in 1947, J.w. Edwards, Ann Arbor, Michigan, 231 p.)
frost bulb
A small mound of fresh soil material, formed by frost action
JOHNSTON, G.H. (Editor), 1981. Permafrost: Engineering Design and Construction. John Wiley & Sons, Canada Ltd.,Toronto, 540 p
frost boil
frost heave
The upward or outward movement of the ground surface (or objects on, or in, the ground) caused by the formation of ice in the soil
frost jacking
Cumulative upward displacement of objects embedded in the ground, caused by frost action
van EVERDINGEN, R.o., 1978. "Frost mounds at Bear Rock, near Fort Norman, N.W.I., 1975-1976." Canadian JournalofEarth Sciences, Vol. 15,No.2, pp. 263-276.
frost mound
Any mound-shaped landform produced by ground freezing combined with groundwater movement or the migration of soil moisture.
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
Amount
measure, quantity, total, sum
AmountOfSubstanceMass
bulk
the vertical force exerted by a mass as a result of gravity
AmountOfSubstanceWeight
AmountOfSubstanceWeightFlux
Confirm: still looking for a definition of this...
the space between two lines or planes that intersect; the inclination of one line to another; measured in degrees or radians
Angle
Confirm: same concept as mass flow rate? https://en.wikipedia.org/wiki/Mass_flow_rate
ArealMassDensityRate
electrical capacity, capacity
Capacitance
Capacitance is the ability of a body to store an electrical charge.
CatalyticActivity
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
electric charge
the quantity of unbalanced electricity in a body (either positive or negative)
Charge
a material's capacity to conduct electricity; measured as the reciprocal of electrical resistance
Conductivity of an electrolyte solution is a measure of its ability to conduct electricity.
specific conductance
Conductivity
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.
DoseEquivalent
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?
Energy
a thermodynamic quantity equivalent to the capacity of a physical system to do work
free energy
Force
A force is any interaction that, when unopposed, will change the motion of an object.
Frequency
Frequency is the number of occurrences of a repeating event per unit time.
illumination
Illuminance is the total luminous flux incident on a surface, per unit area.
Illuminance
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
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
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.
MagneticFieldStrength
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
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.
magnetic flux density. A vector quantity measuring the strength and direction of the magnetic field around a magnet or an electric current. Magnetic flux density is equal to magnetic field strength times the magnetic permeability in the region in which the field exists. Magnetic flux density - Dictionary.com
MagneticFluxDensity
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.
Power
Radiance is the radiant flux emitted, reflected, transmitted or received by a surface, per unit solid angle per unit projected area
Radiance
RadionucleotideActivity
Confirm: term definition
impedance
any mechanical force that tends to retard or oppose motion
Resistance
Resistivity
material's opposition to the flow of electric current; measured in ohms
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
energy density
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.
SpecificEnergy
SpecificVolume
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.
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.
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
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.
Temperature
Confirm: appropriate definition for term?
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
VolumetricMassDensityRate
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.
WaveNumber
wave number, wavenumber
Confirm: no object property 'standardFor' found in OBOE.1.2 (usesStandard?)
standardFor
"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).
The rate at which a mass of dissolved organic carbon moves to or from a particular component of an ecosystem per unit time. Dissolved organic cabon is defined as the fraction of organic matter which is neither excluded nor adsorbed by the filter used to remove particulate organic carbon, and which is not volatile enough to be lost by the acidification and purging technique used to remove inorganic carbon.
Wangersky, P.J. Dissolved organic carbon methods: a critical review. Marine Chemistry. V 41 I 1-3. pp. 61-74. 1993.
The mass of carbon released from burning vegetation per unit time.
Johnson, E.A. and Miyanishi, K. Forest Fires: Behavior and Ecological Effects. Academic Press. 2001
Fire Carbon Flux is a measure of carbon released into the atmosphere due to fire (MPS, 2015)
Hayes, D.J. et al. Reconciling estimates of the contemporary North American carbon balance among terrestrial biosphere models, atmospheric inversions, and a new approach for estimating net ecosystem exchange from inventory-based data. Global Change Biology. V 8, i 4. pp. 1282-1299. April 2012. DOI: 10.1111/j.1365-2486.2011.02627.x
The magnitude of carbon sources and sinks is defined as the vertical exchange of CO2 between the surface (land or ocean) and the atmosphere.
The process of carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time.
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.
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
CO2 produced by organisms and emitted to the environment per unit ground or water area and time.
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. Equivalent to the sum of autotrophic and heterotrophic respiration.
The sum of respiration (CO2 production) by all living parts of primary producers per unit ground or water area and time.
The respiration rate of heterotrophic organisms (animals and microbes) summed per unit ground or water area and time.
Primary production before the autotrophs' own respiration is subtracted. Also called photosynthetic rate, or carbon fixation rate.
primary production before the autotrphs' own respiration is subtracted. also called photosynthetic rate, or carbon fixation rate. Synonyms: GPP
The sum of gross carbon fixation by autotrophic carbon-fixing tissues per unit ground or water area and time.
Gross primary production (GPP) minus autotrophic respiration (AR) per unit ground or water area and time.
the amount of primary production available for export (ie, gross, minus losses, like the autotrophs' own respiration, or other loss (exudation) not used by the carbon-fixing organism itself) = gross primary production - autotrophic respiration synonyms: NPP
"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
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 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
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).
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.
"soil." American Heritage® Dictionary of the English Language, Fifth Edition. 2011. Houghton Mifflin Harcourt Publishing Company 24 Feb. 2015 http-www.thefreedictionary.com/soil
The mass of carbon contained 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.
The mass of carbon contained within flattened photosynthetic structures emerging laterally from a main axis or stem and possessing true vascular tissue.
'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.
The mass of carbon present in algae on the seafloor.
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." Collins English Dictionary – Complete and Unabridged. 1991, 1994, 1998, 2000, 2003. HarperCollins Publishers 24 Feb. 2015 http-www.thefreedictionary.com/grass
The mass of carbon contained 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.
synonyms from LTER searched terms (mob, 2015-03-24)
The mass of carbon contained in the partly decomposed remains of plants on the surface and in the upper layers of the soil.
A system that has the capacity to store or release carbon, in the form of the organic matter that is able to pass through a filter (filters generally range in size between 0.7 and 0.22 um)
Gross primary production (GPP) minus autotrophic respiration (AR) over one year.
Biomass is organic matter derived from living organisms.
http-nacp.ornl.gov/MsTMIP_variables.shtml, accessed 2015-03-25
Total carbon content of the living biomass (leaves+roots+wood)
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.
Incident longwave radiation minus simulated outgoing longwave radiation (positive into grnd)
Vertically integrated soil moisture divided by maximum allowable soil moisture above wilting point
Water content or moisture content is the quantity of water contained in a material.
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.
Near Surface Carbon Dioxide Concentration MOV
Near surface dry air CO2 mole fraction (micromoles per mole)
Total respiration (TotalResp=AutoResp+heteroResp, always positive)
Ecosystem respiration is the sum of all respiration occurring by the living organisms in a specific ecosystem.
Absorbed fraction incoming photosyntetically active radiation
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.
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.
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.
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.
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.
Average soil temperature in each soil layer
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.
Runoff from the landsurface and/or subsurface stormflow
Depth from soil surface to top 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.
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.
Total size of each carbon pool vertically integrated over the entire soil column
Depth from soil surface to layer prognostic variables; typically center of soil layer
Total water mass of snow pack, including ice and liquid water
Total soil and litter carbon content vertically integrated over the enire soil column
Soil carbon includes both inorganic carbon as carbonate minerals, and as soil organic matter.
Autotrophic respiration rate (always positive)
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).
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.
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.
MsTMIP Output: Rate of photosynthesis (always positive)
Gross Primary productivity is the rate at which photosynthesis or chemosynthesis occurs.
Name of each carbon pool (i.e., "wood," or "Coarse Woody Debris")
Depth from soil surface to bottom of soil layer
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 rate (always positive)
Thaw depth; depth to zero centigrade isotherm in permafrost
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.
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.
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)
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.
Gravity soil water drainage and/or soil water lateral flow
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.
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.
Sensible heat flux into the boundary layer (positive into atmosphere)
Net Ecosystem Exchange (NEE=HeteroResp+AutoResp-GPP, positive into atmosphere)
Surface Incident Shortwave Radiation MOV
Sum of all evaporation sources (positive into atmosphere)
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.
Latent heat flux into the boundary layer (positive into atmosphere)
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.
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.
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.
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
add these synonyms (near? exact?): also known as eddy correlation and eddy flux
It is frequently used to estimate momentum, heat, water vapor, carbon dioxide and methane fluxes. The technique is mathematically complex, and requires significant care in setting up and processing data. To date, there is no uniform terminology or a single methodology for the Eddy Covariance technique. The technique has additionally proven applicable under water to the benthic zone for measuring oxygen fluxes between seafloor and overlying water.[6] In these environments, the technique is generally known as the eddy correlation technique, or just eddy correlation. For CO2.... tbd
The eddy covariance method is an atmospheric measurement technique to measure and calculate vertical turbulent fluxes within atmospheric boundary layers, and analyzes high-frequency wind and scalar atmospheric data series, to yield exchange rates (fluxes) of trace gasses.
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.)
A method determining the relationship between a physical or physiological property of an organism relative to the size of the organism.
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.
Available from: https-www.researchgate.net/publication/233137060_Use_of_ground_and_LiDAR_data_to_model_the_NPP_of_a_Mediterranean_pine_forest [accessed Mar 25, 2015].
A LIDAR_Method for NPP is a methodology to predict the net primary production (NPP) from ground and LiDAR data
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)
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.
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 e.g., into the ocean, which 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.
The pool of carbon oxoanions resulting from the removal of a proton from carbonic acid.
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).
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.
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.
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
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.
This class and all subclasses should be incorporated into ENVO.
This class should be incorporated into ENVO.
a system formed by the interaction of a community of organisms with their physical environment
Ecosystems are dynamic entities composed of the biological community and the abiotic environment.
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)
A population comprises all the individuals of a given species in a specific area or region at a certain time.
a group of organisms of the same species inhabiting a given area
It seems like this class could be related to ENVO's anatomical entity, as in "Organism has part 'anatomical entity" '
An organism is a single individual.
A group of interbreeding organisms that do not ordinarily breed with members of other groups.
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.
Describes the physical state of a substance
Defines where a class exists or takes place
The rate at which carbon dissolves, moving from one pool to another.
carbonic anhydride, CO2
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).
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).
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.
carbonate ion
CHEBI:22863, CHEBI:40961, CHEBI:5589, CHEBI:13363
Acid carbonate, Bicarbonate, hydrogen carbonate
Carbon oxoanions resulting from the removal of a proton from carbonic acid.
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.
saccharide
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.
photosynthetic or plant constituent of plankton; mainly unicellular algae
Adapted from https://en.wikipedia.org/wiki/Phytoplankton, http://oceanservice.noaa.gov/facts/phyto.html
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.
the act of conducting a controlled test or investigation
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.
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.
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/Flux, Bird, R. Byron; Stewart, Warren E.; Lightfoot, Edwin N. (1960). Transport Phenomena. Wiley. ISBN 0-471-07392-X.
Flow Measurement Type
Chlorophyll a is a specific form of chlorophyll used in oxygenic photosynthesis.
Concentration of carbon dioxide in fresh water, a naturally occurring chemical compound is composed of a carbon atom covalently double bonded to two oxygen atoms
CO2_CO2calc_output CO2, CO2calc output (micromol/kgSW) Concentraiton of CO2,; micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram urn:node:LTER
mob: this probably should be in OBOE, and is a synomym of AmountOfSubstanceConcentration.
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.
A number of entities taken together as a unit because members share a common characteristic or relation
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.
EquivalentTo: concentration and measurementFor only Observation and ofEntity only CO2
Concentration of carbon dioxide, a naturally occurring chemical compound is composed of a carbon atom covalently double bonded to two oxygen atoms
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.
Grassland Above Ground Net Primary Production Carbon Flux
Adapted from ECSO_00000021 (Net Primary Production Carbon FLux) and ECSO_00000301 (Above Ground Net Primary Production Carbon Flux)
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.
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.
Oceanic Total Inorganic Carbon Concentration
DIC_Meas Dissolved inorganic carbon concentration, measured microMolesPerLiter https://pasta.lternet.edu/package/metadata/eml/knb-lter-gce/22/20
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.
The total inorganic carbon or dissolved inorganic carbon (DIC) is the sum of inorganic carbon species in a solution in sea water. 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.
The rate at which a Carbon Dioxide (CO2) moves to or from a particular component of the ecosystem per unit time.
ECSO_00000011 (Carbon Flux), adapted for CO2
CO3_CO2calc_output CO3, CO2calc output (micromol/kgSW) Concentration of carbonate ion, micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/75/1
Concentration of bicarbonate serves a crucial biochemical role in the physiological pH buffering system. Bicarbonate is an intermediate form in the deprotonation of carbonic acid.
total inorganic carbon, CT, dissolved inorganic carbon
tic total inorganic carbon total inorganic carbon milligramPerLiter ben.1.1
Class to hold measurements for concentration for any form of inorganic C.. three main ones, carbonate, bicarbonate and co2 (also carbonic acid, but they might add that into the co2) 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. The class for 'Oceanic ...' should be a subclass of this one. Right now, we have separate classes for 'total', as in the sum of all forms - this is a different concept than "any" form. also note: parent is incomplete; there are probably 8 leafs, only 6 at the moment.
Determination of total dissolved inorganic carbon in water, expressed as moles of carbon per kilogram of water; this method is suitable for the assay of aquatic levels of total dissolved inorganic carbon (1800-2300 micromol/kg)
Aquatic Inorganic Carbon Concentration, all forms
Marine Macroalgae Net Primary Production 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.
adapted from ECSO_00000021 (Net Primary Production Carbon FLux)
This class probably could be a child of "carbon dioxide diffusion flux", especially since definition of the parent is based on the ocean. But contributor is not confident saying that it always is diffusion.
ECSO_00000200, Areal Carbon Flux, adapted for the ocean.
A flux of carbon across the surface of the ocean, per unit area.
Distance around the tree, often a specified, average distance from the ground, eg 4.5 ft (or average person's 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.
AFDW
Ash-free dry weight is used as an index for percent organic carbon in the quantified substrate.
any of a group of green pigments found in photosynthetic organisms; there are four naturally occurring forms
Chlorophyll is a term used for several closely related green pigments found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived from the Greek words chloros ("green") and phyllon ("leaf"). Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to absorb energy from light. Chlorophyll absorbs light most strongly in the blue portion of the electromagnetic spectrum, followed by the red portion. Conversely, it is a poor absorber of green and near-green portions of the spectrum which it reflects, hence the green color of chlorophyll-containing tissues.
not imported with ENVO import of chemical entity.
Pheophytin or phaeophytin (abbreviated Pheo) is a chemical compound that serves as the first electron carrier intermediate in the electron transfer pathway of photosystem II (PS II) in plants, and the photosynthetic reaction center (RC P870) found in purple bacteria. In both PS II and RC P870, light drives electrons from the reaction center through pheophytin, which then passes the electrons to a quinone (QA) in RC P870 and RC P680. The overall mechanisms, roles, and purposes of the pheophytin molecules in the two transport chains are analogous to each other.
Adapted from https://en.wikipedia.org/wiki/Carbonate
Concentration of carbonate, which is a salt of carbonic acid characterized by the presence of the carbonate ion, CO3 2- (one carbon atom, three oxygen atoms negative 2 charge)
HCO3_CO2calc_output HCO3, CO2calc output (micromol/kgSW) Concentration of bicarbonate ion micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/75/1
Concentration of carbonate, which is a salt of carbonic acid characterized by the presence of the carbonate ion, CO2−3
primitive chlorophyll-containing mainly aquatic eukaryotic organisms lacking true stems and roots and leaves
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.
Concentration of dissolved organic carbon (DOC) within aquatic systems
Adapted from https://en.wikipedia.org/wiki/Dissolved_organic_carbon
Concentration of carbon in particulate form that is too large to pass through a filter in aquatic environments
Adapted from https://en.wikipedia.org/wiki/Total_organic_carbon#Measurement
Concentration of CO2 in the earth's atmosphere
ECSO_00000011 (Carbon Flux), adapted for Methane
The rate at which Methane moves to or from a particular component of the ecosystem per unit area, time.
the degree of hotness or coldness of a body or environment (corresponding to its molecular activity)
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.
mass transport, mass transfer
Mass Flux
The rate at which a mass or amount of carbon moves to or from a particular component of the ecosystem per unit time.
Carbon fluxes are the movement of Carbon from one place (Source) to another (Sink). Carbon fluxes all have dimensions of {mass or amount of} Carbon per area (or volume) per time. Biochemically-oriented projects use moles (e.g., for Stoichiometry) rather than kg to quantify the amount of Carbon, whereas Climate-oriented projects use kg. 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.'
Litton, C.M. et al. Carbon allocation in forest ecosystems. Global Change Biology. V 13 I 10. pp. 2089 - 2109. July 2007.
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 transport, energy transfer, radiative flux, radiative flux density, radiation flux, irradiance, radiant exitance, radiant emittance, energy transfer
Energy Flux
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.
The total amount or weight, or energy content, of (a portion of) organisms existing in a specific area at a particular time below a ground surface.
Adapted from http://www.biology-online.org/dictionary/Standing_crop
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
plant materials and animal waste used as fuel
Adapted from http://www.extension.umn.edu/agriculture/nutrient-management/nitrogen/understanding-nitrogen-in-soils/
Ammonium (NH4) is the form of ammonia (NH3) typically found in water (aquatic environments, soil porewater). It is a postively charged cation. Ammonium is a source of nitrogen for plants, algae and phytoplankton.
MIN_N Concentration ammoniom after incubaton at 40 deg C for 7 days (dry weight basis) dimensionless https://pasta.lternet.edu/package/metadata/eml/knb-lter-and/3142/7 NH4, ammonium, concentration of ammonium https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/10/21
Aquatic Total Organic Carbon Concentration
Concentration of material derived from decaying vegetation, bacterial growth, and metabolic activities of living organisms or chemicals
toc total organic carbon total organic carbon milligramPerLiter urn:node:GLEON
Concentration is the abundance of a constituent divided by the total volume of a mixture. Several types of mathematical description can be distinguished: mass concentration, molar concentration, number concentration, and volume concentration. The term concentration can be applied to any kind of chemical mixture, but most frequently it refers to solutes and solvents in solutions. The molar (amount) concentration has variants such as normal concentration and osmotic concentration.
The total inorganic carbon or dissolved inorganic carbon (DIC) is the sum of inorganic carbon species in a solution in freshwater. 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.
Freshwater Total Inorganic Carbon Concentration
dic dissolved inorganic carbon dissolved inorganic carbon milligramPerLiter urn:node:GLEON
doc dissolved organic carbon dissolved organic carbon milligramPerLiter s_DOC surface stream organic carbon milligramsPerLiter w_DOC shallow riparian groundwater organic urn:node:GLEON
Concentration of dissolved organic carbon (DOC) , which is a broad classification for organic molecules of varied origin and composition within aquatic systems. The "dissolved" fraction of organic carbon is an operational classification. Many researchers use the term "dissolved" for compounds below 0.45 micrometers, but 0.22 micrometers is also common, saving colloidal for higher concentrations. A practical definition of dissolved typically used in marine chemistry is all substances that pass through a GF/F filter.
Concentration of carbonate in sea water, which is a salt of carbonic acid characterized by the presence of the carbonate ion, CO2−3
HCO3_CO2calc_output HCO3, CO2calc output (micromol/kgSW) Concentration of bicarbonate ion micromol per kilogram seawater (CO2calc output) milliMolesPerKilogram urn:node:LTER
total_c Total carbon Percentage urn:node:TERN
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
Concentration of total organic carbon (TOC) is the concentration of amount of carbon found in an organic compound
Adapted from https://en.wikipedia.org/wiki/Total_organic_carbon
Concentration of carbon dioxide in sea water, a naturally occurring chemical compound is composed of a carbon atom covalently double bonded to two oxygen atoms
The total amount or weight, or energy content, of (a portion of) organisms existing in a specific area at a particular time. In plants, the standing crop pertains to the amount of plant material harvested by normal procedures, and may not necessarily include the entire plant.
C_to_N Ratio of Carbon to Nitrogen dimensionless urn:node:LTER
Carbon-to-nitrogen ratio is a ratio of the mass of carbon to the mass of nitrogen in a substance. It can, amongst other things, be used in analysing sediments and compost. A useful application for C/N ratios is as a proxy for paleoclimate research, having different uses whether the sediment cores are terrestrial-based or marine-based. Carbon-to-nitrogen ratios are an indicator for nitrogen limitation of plants and other organisms and can identify whether molecules found in the sediment under study come from land-based or algal plants. Further, they can distinguish between different land-based plants, depending on the type of photosynthesis they undergo.
Adapted from http://www.greenfacts.org/glossary/wxyz/wet-weight.htm
The biomass 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.
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
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
An isotopic signature is a ratio of non-radiogenic 'stable isotopes', stable radiogenic isotopes, or unstable radioactive isotopes of particular elements in an investigated material. The ratios of isotopes in a sample material are measured by isotope ratio mass spectrometry. The atomic mass of different isotopes affect their chemical kinetic behavior, leading to natural isotope separation processes. For example, different sources and sinks of methane have different affinity for the 12C and 13C isotopes, which allows distinguishing between different sources by the 13C/12C ratio in methane in the air.
Adapted from https://en.wikipedia.org/wiki/Biomass
wtC Carbon Weight Weight of carbon in sample dimensionless df35b.161.4
Total soil nitrogen (mg/kg) Total soil nitrogen (mg/kg) milligramsPerKilogram urn:node:LTER
total amount of nitrogen (usually mass) per volume of soil
http://www.biology-online.org/dictionary/Area http://www.biology-online.org/dictionary/Sample https://en.wikipedia.org/wiki/Quadrat
fert_area measurement area of the experimental unit : m² for fertilization manipulation squareMeter doi:10.5063/AA/nceas.347.3
a selected subset of a population over the extent of a surface; a sample may be random or nonrandom; representative or nonrepresentative
DryWeight dry weight X Dry Weight gram https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1115/1
The weight of dry biomass matter when completely dried (lacks or excluding water).
LAI Leaf Area Index number www.supersites.net.au/knb/metacat/supersite.377.4/html
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 (LAI = leaf area / ground area, m2 / m2) in broadleaf canopies.
An identifier is a name that identifies (that is, labels the identity of) either a unique object or a unique class of objects, where the "object" or class may be an idea, physical [countable] object (or class thereof), or physical [noncountable] substance (or class thereof). The abbreviation ID often refers to identity, identification (the process of identifying), or an identifier (that is, an instance of identification). An identifier may be a word, number, letter, symbol, or any combination of those.
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
pH of water is based on a numeric scale used to specify the acidity or basicity of an aqueous solution. It is approximately the negative of the logarithm to base 10 of the molar concentration, measured in units of moles per liter, of hydrogen ions. More precisely it is the negative of the logarithm to base 10 of the activity of the hydrogen ion. Solutions with a pH less than 7 are acidic and solutions with a pH greater than 7 are basic. Pure water is neutral, being neither an acid nor a base. Contrary to popular belief, the pH value can be less than 0 or greater than 14 for very strong acids and bases respectively.
Number density is an intensive quantity used to describe the degree of concentration of countable objects in a given physical space.
LeafNum density Number of Thalassia testudinum Leaves Per Short Shoot leafnumberPerShortShoot https://pasta.lternet.edu/package/metadata/eml/knb-lter-fce/1130/2
Confirm: if OBOE class ArealDensity is for physical (material) measuements, then we need a different characteristics for this class, eg, analogous to biomass_density.
Water vapor, water vapour or aqueous vapor, is the gaseous phase of water. It is one state of water within the hydrosphere. Water vapor can be produced from the evaporation or boiling of liquid water or from the sublimation of ice. Unlike other forms of water, water vapor is invisible. Under typical atmospheric conditions, water vapor is continuously generated by evaporation and removed by condensation. It is lighter than air and triggers convection currents that can lead to clouds.
Humidity in % Humidity in % dimensionless peggym.109987.2
Salinity salinity Composite salinity PSU (practical salinity unit) doi:10.6073/AA/knb-lter-fce.39.5
Salinity is the saltiness or dissolved salt content of a body of water (see also soil salinity). Salinity is an important factor in determining many aspects of the chemistry of natural waters and of biological processes within it, and is a thermodynamic state variable that, along with temperature and pressure, governs physical characteristics like the density and heat capacity of the water.
Soil 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.
1 Difference/Dry weight proportion of water in soil sample dimensionless judithk.1264.2
Woody N Pool Woody N Pool Woody N Pool gramsPerSquareMeter https://pasta.lternet.edu/package/metadata/eml/knb-lter-bnz/344/16
Mass of nitrogen in biomass per unit area at a given time.
Adapted from http://www.biology-online.org/dictionary/Biomass
The total mass per area of all carbon in living material in a specific area, habitat, or region.
Woody C Pool Woody C Pool Woody C Pool gramsPerSquareMeter https://pasta.lternet.edu/package/metadata/eml/knb-lter-bnz/344/16
Adapted from https://en.wikipedia.org/wiki/Time
Interval of time representing duration of observation
Atmospheric pressure, sometimes also called barometric pressure, is the pressure exerted by the weight of air in the atmosphere of Earth (or that of another planet). In most circumstances atmospheric pressure is closely approximated by the hydrostatic pressure caused by the weight of air above the measurement point.
Pa Air Pressure pascal ark:/90135/q17s7kq7/1/mrt-eml.xml
Adapted from https://en.wikipedia.org/wiki/Counting
N_OBSERVED number of observations actually observed in a sample number https://pasta.lternet.edu/package/metadata/eml/ecotrends/3114/2
Counting entities within a sample is the action of finding the number of elements of a finite set of entities constrained within a sample.
Average number of live pupae per mature tree based on average number of pupae per square meter (surface area excavated) and assuming that pupae are found around each mopane tree to a radius of 1.25m (calculation made on sheet 3: Hole specs and density calcs). dimensionless judithk.1287.1
Counting entities is the action of finding the number of elements of a finite set of entities.
CC (%) Percentage crown cover Percentage www.supersites.net.au/knb/metacat/lloyd.635.9/html
Crown cover is the proportion of a stand covered by the crowns of live trees.
cal_sp_ls Average biomass (mg C m-3) of calanoid copepodites and adults during Spring (March-May) in the low salinity zone (0.5-10 ppt) dimensionless doi:10.5063/AA/nceas.958.8
Adapted from https://en.wikipedia.org/wiki/Sea
Bot_ Depth [m] Bot. Depth [m] depth to the bottom at this station, column required by ODV meter https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/1009/6
Depth in a sea, which is a large body of salt water that is surrounded in whole or in part by land.
Active_Layer (cm) Active_Layer (cm) Active layer depth for the day of the measurement (in cm) centimeter https://pasta.lternet.edu/package/metadata/eml/knb-lter-bnz/190/20
In environments containing permafrost, the active layer is the top layer of soil that thaws during the summer and freezes again during the autumn. In all climates, whether they contain permafrost or not, the temperature in the lower levels of the soil will remain more stable than that at the surface, where the influence of the ambient temperature is greatest.
Adapted from https://en.wikipedia.org/wiki/Active_layer
Diameter of the crown of a tree, which consists of the mass of foliage and branches growing outward from the trunk of the tree. The average crown spread is the average horizontal width of the crown, taken from dripline to dripline as one moves around the crown.
ActualCrown Actual crown diameter centimeter judithk.1060.2
Diameter of the canopy, which is the aboveground portion of a plant community or crop, formed by the collection of individual plant crowns
Canopy_diam1 First diagonal of the canopy diameter meter judithk.1000.13
A tag number provides an alphanumeric string of characters to refer to an entity. A TagNumber is typically used to uniquely identify an entity such as a sample or an individual specimen such as a tree or a rock sample.
Adapted from OBOE definition of tag number
binary indication of an instance of something occurring (i.e. presence - yes, no)
Height of the canopy, which is the aboveground portion of a plant community or crop, formed by the collection of individual plant crowns
Canopy cover The furthest distance of the canopy reach from the base of the tree (m). meter judithk.1256.3
Adapted from http://medical-dictionary.thefreedictionary.com/dry+mass
Weight1dry weight of soil sample after drying in an oven for 24 hours. dimensionless judithk.1264.2
Weight of soil dried at 105 °C until no further water loss takes place
Concentration of oxygen, which is a chemical element that is a member of the chalcogen group on the periodic table and is a highly reactive nonmetal and oxidizing agent that readily forms oxides with most elements as well as other compounds
Free oxygen also occurs in solution in the world's water bodies. The increased solubility of O2 at lower temperatures has important implications for ocean life, as polar oceans support a much higher density of life due to their higher oxygen content. Water polluted with plant nutrients such as nitrates or phosphates may stimulate growth of algae by a process called eutrophication and the decay of these organisms and other biomaterials may reduce the O2 content in eutrophic water bodies. Scientists assess this aspect of water quality by measuring the water's biochemical oxygen demand, or the amount of O2 needed to restore it to a normal concentration.
Adapted from https://en.wikipedia.org/wiki/Pheophytin
Concentration of pheophytin, which is chemical compound that serves as the first electron carrier intermediate in the electron transfer pathway of photosystem II (PS II) in plants, and the photosynthetic reaction center (RC P870) found in purple bacteria
Structurally, phaeophytin is a chlorophyll molecule without the central magnesium ion. https://en.wikipedia.org/wiki/Pheophytin
Margaret O'Brien, orcid.org/0000-0002-1693-8322, Shild
"contributor" is an OWL "Annotation property" that names the person contributing the content, so s/he can be contacted, especially during development.
The "contributor" Annotation Property" is to record the name of the those contributing to the resource. If there is any potential ambiguity, an identifier should be added, including the system to which it belongs.
"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, pers comm, 05Feb2015, orcid.org/0000-0003-0632-7576
"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, 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
has_Exact_Synonym is an OWL annotation property that holds an alternate name or lexical variant of an owl class.
The DataONE carbon flux ontology uses synonyms for terms that may not be well defined. But we know that they are used, and refer to an owl class. I.e., a concept can have a synonym, but a concept should not be a synonym.
We are not planning to use has_Broad_Synonym or has_Narrow_Synonym at this time. although other ontologies do. the concepts of "broad" and "narrow" imply relationships that could be better described with the class hierarchy.
"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.
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.
Lipid
'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).
A monoatomic or polyatomic species having one or more elementary charges of the electron.
anions
arsenate, arsenate anions, arsenate ions
benzoate anion
A monocarboxylic acid anion obtained by deprotonation of the carboxy group of any benzoic acid.
hydroxybenzoates
Any benzoate derivative carrying a single carboxylate group and at least one hydroxy substituent.
inorganic anions
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
A molecular entity having a net electric charge.
monohydroxybenzoates
A hydroxybenzoate carrying a single hydroxy substituent at unspecified position.
organic anions
organic ions
A macromolecule composed of units connected by carboxylic ester (-O-CO-) linkages.
polyester, polyesters
A cyclitol carboxylic acid anion that is conjugate base of quinic acid.
CHEBI:2845, CHEBI:22630
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.
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
Arsenate, ARSENATE, Arsenate ion, AsO43−
An arsenate ion resulting from the removal of three protons from arsenic acid.
CHEBI:15061, CHEBI:26595
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.
p-block element atom is an atom
CHEBI:22671, CHEBI:23907
element, elements
polyatomic anions
An anion consisting of more than one atom.
heteroorganic entities, organoelement compounds
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
p-block element atom is a main group element atom
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
main group element
pnictogen oxoanion, pnictogen oxoanions
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
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
metal atom is an atom
main group compounds, main group molecular entities
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.
p-block compounds, p-block molecular entities, p-block molecular entitiy
A main group molecular entity that contains one or more atoms of a p-block element.
chromium oxoanion, chromium oxoanions, oxoanions of chromium
transition metal oxoanion, transition metal oxoanions, transition element oxoanions
oxoacid anions, oxoanions
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
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.
CHEBI:4859, CHEBI:23960
Ester, esters
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
a monocarboxylate, Carboxylate, Monocarboxylate, monocarboxylates, monocarboxylic acid anions
CHEBI:3407, CHEBI:13657, CHEBI:25382
arsenic oxoanion, arsenic oxoanions, oxoanions of arsenic
hydroxy monocarboxylic acid anions, hydroxymonocarboxylic acid anion, hydroxymonocarboxylic acid anions
Any monocarboxylic acid anion carrying at least one hydroxy substituent.
cyclitol carboxylic acid anions
An ion consisting of more than one atom.
polyatomic ions
inorganic ions
The stable isotope of nitrogen with relative atomic mass 15.000109. The least abundant (0.368 atom percent) isotope of naturally occurring nitrogen.
quinolinemonocarboxylates
A monocarboxylic acid anion that is the monoanion obtained by the deprotonation of the carboxy group attached to the quinoline skeleton
A polymer composed of repeating hydroxyalkanoyl units.
PHAs, poly(hydroxyalkanoate)s, polyhydroxyalkanoate, polyhydroxyalkanoates
A polymer composed of repeating hydroxybutyryl units.
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
organic acids
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
A layer in a water mass, itself composed primarily of water.
ecosystem-wide photosynthesis
A process which consists of all photosynthesis processes instantiated in an ecosystem.
photosynthesis
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
sensitivity
disposition_slim; attribute_slim; relational_slim
A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation.
PATO:0001631; PATO:0001032
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
attribute_slim; disposition_slim
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
value_slim; disposition_slim
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
high temperature; hot
A temperature which is relatively high.
value_slim
A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base.
[database_cross_reference: chemicool:chemicool]
An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions.
An medium acidity quality inhering in a solution by virtue of the bearer's a low concentration of H+ ions.
[database_cross_reference: WordNet:WordNet]
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.
scalar_slim; attribute_slim; disposition_slim
disposition_slim; value_slim
A quality inhering in a bearer by virtue of the bearer's dependence on oxygen.
A quality inhering in a bearer by virtue of the bearer's independence on oxygen.
A pressure which is relatively high.
high pressure
[database_cross_reference: PATO:GVG]
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.
relational_slim; value_slim
exposed; exits through
extruding from
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.
[database_cross_reference: PATOC:nc]
[database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Osmolarity]
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
A osmolarity which is relatively high.
high osmolarity
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
radioactivity
A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate.
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
[database_cross_reference: biology-online:biology-online]
A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions).
ice has quality some frozen
relational molecular quality
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
A quality that has a value that is increased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
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
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.
inferior epigastric vein tributary_of external iliac vein; Deschutes River tributary_of Columbia River
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
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
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.
desert has_condition some arid
rdfs:label is a built in annotation property, and W3C does not give guidelines beyond the definition. In the DataONe Carbon Flux ontology, we use rdfs:label for a human-readable version of the resource's name, but adhere to a particular pattern. Our goal is that content of rdfs:label are not broken into individual terms arbitrarily. 1. Our practice is to separate individual words in the rdfs:label with underscores, but maintain capitalization consistent with the conventions of the resources type (e.g., camel case for properties, capitalized words for classes, capitalized abbreviations and acronyms). 2. include namespace in the label, if resource is imported. See example_Of_Usage, presentation_Label
Carbon_Flux_NASA, definition_Source, rdfs:label
rdfs:label is an instance of rdf:Property that may be used to provide a human-readable version of a resource's name