A project to represent the knowledge about plankton ecology bloom processes etc, to be paired with AWI chlorophyll A satellite data compiled by Dr. Tillman, which Pier will analyze.

background

ontology

PCO

PATO

ECOCORE

ENVO

Diatom Phenology in the Southern Ocean: Mean Patterns, Trends and the Role of Climate Oscillations Associated with Tillman satellite chlorophyll data and the plankton bloom ontology classes.

Tilman data about: ice cover and chlorophyll

Instructions from pier here

Eduard Bauerfeind is a good source of publications on the subject.

Add sea ice controlled bloom as a subclass of algal bloom Janout et al 2016 paper for reference Include zooplankton bloom as causally downstream of a phytoplankton bloom also make a note to add ice associated communities Add sea ice primary production Needs coordination with ECOCORE. So I need to make terms for zooplankton and phytoplankton blooms, link to ECOCORE, link to chlorophyll A data.

The Janout et al 2016 paper is on sea ice retreat so hopefully ideas and terms from this can be connected to sea ice, and phytoplankton.

From this paper Chlorophyll a is common to all photosynthetic organisms. Furthermore, it is the most abundant photosynthetic pigment and it is relatively easy and rapid to quantify.

Influence of the physical environment on polar phytoplankton blooms: A case study in the Fram St publication from Mariana Soppa about phytoplankton time series and phenology sent by Tilman.

I will read chapter 3 of the modeling book to get some incites into how modelers deal with population and community growth and death dynamics, and I would like to generalize this to encoding some basic ecological population dynamics concepts into PCO. Perhaps I could make the population community growth events like plankton bloom have a more general superclass along the lines of a population bloom in PCO. Which may also fit in with concepts about overfishing and population collapse to get at the idea of fish stock collapse and restoration.

Ontology Ontologizing population blooms. Background ideas described here Describing lag phase, log phase/exponential phase, stationary phase, death phase, using the terms from the logistic growth equation in the definition.

ecological community

microbial community

'located in' some ecosystem ENVO:ecosystem

//Eddie's ORCID: http://orcid.org/0000-0002-2289-2949

A microbial community which is composed primarily of bacteria of the phylum Cyanobacteria.

is a 'microbial community'

'composed primarily of' some Cyanobacteria NCBITaxon:Cyanobacteria

'causal agent in' some 'photoautotrophy' ECOCORE:photoautotrophy

'participates in' some 'photoautotrophic biomass formation' ENVO:no purl yet

'has part' some 'chlorophyll' CHEBI:chlorophyll

'has related synonym' 'blue-green algae'

dbxref

A microbial community which is composed primarily of bacteria of the phylum Bacteroidetes.

is a 'microbial community'

'composed primarily of' some Bacteroidetes NCBITaxon:Bacteroidetes

dbxref

A microbial community which is composed primarily of bacteroidetes of the class Flavobacteriia.

is a 'bacteroidetes-dominated microbial community'

'composed primarily of' some Flavobacteriia NCBITaxon:Flavobacteriia

'has exact synonym' 'flavobacteriia-dominated microbial community'

'causal agent in' some 'aerobic respiration' GO:aerobic respiration

'causal agent in' some heterotrophy ECOCORE:heterotrophy

dbxref, [dbxref2](Brock Biology of Microorganisms ISBN 13: 9780321649638)

A microbial community which is composed primarily of bacteria of the phylum proteobacteria.

is a 'microbial community'

'composed primarily of' some Proteobacteria NCBITaxon:Proteobacteria

dbxref

A microbial community which is composed primarily of proteobacteria of the class Gammaproteobacteria.

is a 'proteobacteria-dominated microbial community'

'composed primarily of' some Gammaproteobacteria NCBITaxon:Gammaproteobacteria

dbxref

A microbial community which is composed primarily of gammaproteobacteria of the order Oceanospirillales.

is a 'gammaproteobacteria-dominated microbial community'

'composed primarily of' some Oceanospirillales NCBITaxon:Oceanospirillales

dbxref

A microbial community which is composed primarily of gammaproteobacteria of the genus Alteromonas.

is a 'gammaproteobacteria-dominated microbial community'

'composed primarily of' some Alteromonas NCBITaxon:Alteromonas

dbxref

A microbial community which is composed primarily of proteobacteria of the class Alphaproteobacteria.

is a 'proteobacteria-dominated microbial community'

'composed primarily of' some Alphaproteobacteria NCBITaxon:Alphaproteobacteria

dbxref

A microbial community which is composed primarily of Alphaproteobacteria of the family Pelagibacteraceae, which includes the SAR11 clade. 

is a 'alphaproteobacteria-dominated microbial community'

'composed primarily of' some Pelagibacteraceae NCBITaxon:Pelagibacteraceae

'has narrow synonym' 'sar11 dominated community'

dbxref1, dbxref2

ecological community

// previous label: ENVO:alga //to be ceded to PCO see pato issue 58

An ecological community which consists of any type of photosynthetic organism unicellular or multicellular, sessile or non-sessile, residing in a body of water, including but not limited to phytoplankton, plants, protists and or cyanobacteria.   

is a 'ecological community'

'located in' some 'water body' ENVO:water body

'causal agent in' some 'photoautotrophy' ECOCORE:photoautotrophy

'participates in' some 'photoautotrophic biomass formation' ENVO:no purl yet

'has part' some 'chlorophyll' CHEBI:chlorophyll

'has part' some 'algal metabolite' CHEBI:algal metabolite

'has exact synonym' 'alga'

'has exact synonym' 'algal community'

dbxref1, [dbxref2](doi: 10.3732/ajb.91.10.1481), dbxref2, dbxref3, dbxref4

An ecological community which consists of unicellular eukaryotic algae and or cyanobacteria, associated with illuminated benthic substrates.

comment:

Microphytobenthos have a subtle brownish or greenish appearance. They are usually found as single cells but may also occur as filamentous or colonial forms.

is a 'ecological community'

'has part' some (algae or 'cyanobacteria-dominated microbial community')

'causal agent in' some 'photoautotrophy' ECOCORE:photoautotrophy

'participates in' some 'photoautotrophic biomass formation' ENVO:no purl yet

'has part' some 'chlorophyll' CHEBI:chlorophyll

'adjacent to' some ('illuminated biosphere part' and 'marine sediment') ENVO:illuminated biosphere part, ENVO:marine sediment

'has exact synonym' 'microphytobenthos'

'has related synonym' 'benthic microalgae'

dbxref1, dbxref2

An ecological community which reside in a body of water and are unable to sustain directed movement to overcome displacement by physical forces such as currents.

is a 'ecological community'

'located in' some 'water body' ENVO:water body

'has exact synonym' 'plankton'

dbxref

An plankton community which is composed primarily of endosymbiotic alveolates of the order Syndiniales.

comment:

Syndiniales are found exclusively as endosymbionts of the tintinnid ciliates, crustaceans, fish, protozoa, algae, and other dinoflagellates. Many are thought to be parasites.

is a 'plankton community'

'composed primarily of' some Syndiniales NCBITaxon:Syndiniales

'causal agent in' some 'symbiosis, encompassing mutualism through parasitism'GO:symbiosis, encompassing mutualism through parasitism

dbxref1, dbxref2

A plankton community which is composed primarily of dinoflagellates.

is a 'plankton community'

'composed primarily of' some Alveolata NCBITaxon:Alveolata

'causal agent in' some autotrophy or (phagocytosis and autotrophy) ECOCORE:[phagocytosis](no purl yet), ECOCORE:autotrophy

editors note:

NCBITaxon does not contain the Phylum: Dinoflagellata of which this class should be composed primarily of.

dbxref1, dbxref2

A plankton community which is composed primarily of dinoflagellates of the class Dinophyceae.

is a 'dinoflagellate-dominated community'

'composed primarily of' some Dinophyceae NCBITaxon:Dinophyceae

dbxref1, dbxref2

A plankton community which consists of photosynthetic organisms. 

is a 'plankton community'

'causal agent in' some 'photoautotrophy' ECOCORE:photoautotrophy

'participates in' some 'photoautotrophic biomass formation' ENVO:no purl yet

'has part' some 'chlorophyll' CHEBI:chlorophyll

'has exact synonym' 'phytoplankton'

dbxref1, dbxref2

A phytoplankton community which is composed primarily of organisms of the phyla Bacillariophyta (also known as Ochrophyta).

is a 'phytoplankton community'

'composed primarily of' some Bacillariophyta NCBITaxon:Bacillariophyta

'has part' some 'silicic acid' CHEBI:silicic acid

dbxref1, dbxref2

A phytoplankton community which is composed primarily of organisms of the family Phaeocystaceae.

is a 'phytoplankton community'

'composed primarily of' some Phaeocystaceae NCBITaxon:Phaeocystaceae

dbxref

A plankton community which consists of heterotrophic organisms.

is a 'plankton community'

'has exact synonym' 'zooplankton'

'causal agent in' some heterotrophy ECOCORE:heterotrophy

population processes

//add axiom: 'occurs in' some ecosystem ENVO:ecosystem

A population process during which the reproductive rate of a population is of sufficient magnitude to approximately replace the same number of individuals lost from the population by emigration, death or predation. 

is a 'population process'

'has exact synonym' 'population maintenance process'

A process during which a population, having reached the carrying capacity of their environment, maintains a constant population size. 

The population's growth rate is equal to the population's death rate.

is a 'population process'

'has related synonym' 'stationary phase'

dbxref1, dbxref2, [dbxref3](ISBN-13: 978-0691123448)

A process during which a population is introduced into a new environment, or is subject to different environmental conditions, and in which individuals of the population must undergo physiological or behavioral changes in order for the population to realize its net potential reproduction rate within their new environment.

is a 'population process'

'has part' some 'population persistence process'

'has related synonym' 'lag phase'

dbxref1, dbxref2, [dbxref3](ISBN-13: 978-0691123448)

A process during which the size of a population decreases as the population's growth rate is lower than the death, predation, or emigration rate.

is a 'population process'

'has related synonym' 'death phase'

'has related synonym' 'decline phase'

dbxref1, dbxref2, [dbxref3](ISBN-13: 978-0691123448)

definition

A process that leads to a change in the number of individuals (positive or negative) in a population.

new definition:

A process that leads to an increase in the number of individuals in a population.

is a 'population process'

//existing term:exponential population growth

A population growth process that leads to an exponential increase in the number of individuals in a population.

new definition:

A population growth process during which the size of a population increases at a rate which is of a factor multiplicative of the size of the population. 

is a 'population growth'

'has related synonym' 'logarithmic population growth'

'has related synonym' 'exponential population growth'

'has related synonym' 'exponential phase

'has related synonym' 'log phase

dbxref1, dbxref2, [dbxref3](ISBN-13: 978-0691123448)

//existing PCO class. Perhaps add axiom? 'has quality' some 'carrying capacity' PCO:carrying capacity // carrying capacity class may be ported to ECOCORE

Transitions //based on the fact that their exists in NCIT the G1 to S Transition Process, I figure I can model the transitions between population growth processes as additional processes, (which will later come in handy for a bloom initiation process).

A population process during which the rate of growth of a population, previously becoming established in a new environment, transitions from not changing to a rate which is of a factor multiplicative of the size of the population.

is a 'population process'

'causally downstream of or within' some 'population establishment process'

'causally upstream of or within' some 'multiplicative population growth'

'has related synonym' 'lagged to exponential population growth transition'

'has related synonym' 'lag to exponential phase transition'

'has related synonym' 'lag to log phase transition'

A population process during which the growth rate of a population transitions from a rate which is of a factor multiplicative of the size of the population, to an fixed population growth rate, constrained by the carrying capacity of the environment.

is a 'population process'

'causally downstream of or within' some 'multiplicative population growth'

'causally upstream of or within' some 'carrying capacity saturation by a population'

'has related synonym' 'exponential to stationary population growth transition'

'has related synonym' 'exponential to stationary phase transition'

'has related synonym' 'log to stationary phase transition'

A population process during which a population undergoing a bloom achieves a maximum growth rate and or population size. 

is a 'multiplicative population growth to carrying capacity saturation transition'

'causally downstream of or within' some 'population bloom'

A population process during which the growth rate of a population transitions from being constrained by the carrying capacity of their environment to a decreasing growth rate.

is a 'population process'

'causally downstream of or within' some 'carrying capacity saturation by a population'

'causally upstream of or within' some 'population decline'

'has related synonym' 'stationary to declining population growth transition'

'has related synonym' 'stationary to death phase transition'

'has related synonym' 'stationary to decline phase transition'

A population process during which the rapid growth of a population undergoing a population bloom ceases, and the population size decreases due to death, predation, transport or displacement.

is a 'carrying capacity saturation to population decline transition'

'has part' some 'population decline'

ends some 'population bloom'

'causally downstream of or within' some 'population bloom'

A population process during which a population within an ecosystem undergo rapid growth, resulting in high abundances that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.

is a 'population process'

dbxref1, dbxref2

A population process during which the growth and reproduction rate of a population exceeds the rate of death, predation, and or transport, initiating a population bloom.

is a 'population establishment to multiplicative growth transition'

starts some 'population bloom'

'causally upstream of or within' some 'population bloom'

community processes

multi-organism process
  ecological community process

A multi-organism process that has as primary participant an ecological community. 

is a 'multi-organism process'

'occurs in' some ecosystem ENVO:ecosystem

'has participant' some 'ecological community'

A community process during which the reproductive rates of at least two of the populations within a community, are of sufficient magnitude to approximately replace the same number of individuals lost by emigration, death or predation. 

is a 'ecological community process'

'has part' some 'population persistence process'

'has exact synonym' 'community maintenance process'

A process during which at least two of the populations in a community, have reached the carrying capacity of their environment, and maintain a constant population size. 

is a 'ecological community process'

'has part' some 'carrying capacity saturation by a population'

dbxref1, dbxref2, [dbxref3](ISBN-13: 978-0691123448)

A process during which at least two of the populations in a community are introduced into a new environment, or are subject to different environmental conditions, and in which individuals must undergo physiological or behavioral changes in order for populations within the community to realize their net potential reproduction rate within their new environment.

is a 'ecological community process'

'has part' some 'community persistence process'

'has part' some 'population establishment process'

dbxref1 dbxref2 [dbxref3](ISBN-13: 978-0691123448)

A process during which the size of at least two of the populations in a community decrease as their growth rates are lower than the death, predation, or emigration rates.

is a 'ecological community process'

'has part' some 'population decline'

dbxref1, dbxref2 [dbxref3](ISBN-13: 978-0691123448)

A process that leads to an increase in the number of individuals in at least two of the populations in a community.

is a 'ecological community process'

'has part' some 'population growth'

A community growth process during which the size of at least two of the populations in a community increase at a rate which is of a factor multiplicative of the size of such populations. 

is a 'community growth'

'has part' some 'multiplicative population growth'

dbxref1, dbxref2, [dbxref3](ISBN-13: 978-0691123448)

Transitions

A community process during which the rate of growth of at least two of the community's populations, previously becoming established within a new environment, transition from a non-changing growth rate, to a rate which is of a factor multiplicative of the size of such populations.

is a 'ecological community process'

'has part' some 'population establishment to multiplicative growth transition'

'causally downstream of or within' some 'community establishment process'

'causally upstream of or within' some 'multiplicative community growth'

A community process during which the growth rate of at least two of the populations in a community, transition from growth rates of a factor multiplicative of the size of the community, to an fixed growth rate, constrained by the carrying capacity of the environment.

is a 'ecological community process'

'has part' some 'multiplicative population growth to carrying capacity saturation transition'

'causally downstream of or within' some 'multiplicative community growth'

'causally upstream of or within' some 'carrying capacity saturation by a community'

A community process during which at least two of the populations in a community undergoing a bloom, achieve a maximum growth rate and or size. 

is a 'multiplicative community growth to carrying capacity saturation transition'

'has part' some 'population bloom saturation'

'causally downstream of or within' some 'community bloom'

A community process during which at least two of the populations in a algal community undergoing a bloom, achieve a maximum growth rate and or size.   

is a 'community bloom saturation'

'causally downstream of or within' some 'algal bloom process'

A community process during which at least two of the populations in a plankton community undergoing a bloom, achieve a maximum growth rate and or size.  

Comment:

This could result from a plankton community reaching the carrying capacity of their environment or from a decrease in the carrying capacity due to a physical processes altering the environment such as an increasing of the mixed layer depth reducing light availability.

is a 'community bloom saturation'

'causally downstream of or within' some 'plankton bloom process' dbxref

A community process during which at least two of the populations in a phytoplankton community undergoing a bloom, achieve a maximum growth rate and or size.

is a 'plankton bloom saturation'

'causally downstream of or within' some 'phytoplankton bloom process'

A community process during which at least two of the populations in a zooplankton community undergoing a bloom, achieve a maximum growth rate and or size.

is a 'plankton bloom saturation'

'causally downstream of or within' some 'zooplankton bloom process'

A community process during which the growth rate of at least two of the populations in a community transition from being constrained by the carrying capacity of their environment to a decreasing growth rate.

is a 'ecological community process'

'has part' some 'carrying capacity saturation to population decline transition'

'causally downstream of or within' some 'carrying capacity saturation by a community'

'causally upstream of or within' some 'community decline'

bloom collapse

A community process during which the rapid growth of at least two of the populations in a community undergoing a community bloom cease, and the population's size decreases due to death, predation, transport or displacement.

is a 'carrying capacity saturation to community decline transition'

'has part' some 'community decline'

'has part' some 'population bloom collapse'

ends some 'community bloom'

'causally downstream of or within' some 'community bloom'

//cede from ENVO Existing definition:

A process during which the rapid growth of algal populations that result in an algal bloom ceases, and cell densities begin to fall due to death, predation, and transport.

A community process during which the rapid growth of at least two of the populations in a algal community undergoing a bloom cease, and cell densities begin to fall due to death, predation, and transport.

is a 'community bloom collapse'

ends some 'algal bloom process'

'causally downstream of or within' some 'algal bloom process'

A community process during which the rapid growth of at least two of the populations in a plankton community undergoing a bloom cease, and cell densities begin to fall due to death, predation, and transport.

is a 'community bloom collapse'

ends some 'plankton bloom process'

'causally downstream of or within' some 'plankton bloom process'

A community process during which the rapid growth of at least two of the populations in a phytoplankton community undergoing a bloom cease, and cell densities begin to fall due to death, predation, and transport.

is a 'plankton bloom collapse'

ends some 'phytoplankton bloom process'

'causally downstream of or within' some 'phytoplankton bloom process'

A community process during which the rapid growth of at least two of the populations in a zooplankton community undergoing a bloom cease, and cell densities begin to fall due to death, predation, and transport.

is a 'plankton bloom collapse'

ends some 'zooplankton bloom process'

'causally downstream of or within' some 'zooplankton bloom process'

bloom process classes

A process during which at least two of the populations in a community, within an ecosystem, undergo rapid growth, resulting in high population abundances that occur only periodically and briefly in that ecosystem, relative to their abundances through the majority of the planetary orbital period.

is a 'ecological community process'

'has part' some 'population bloom'

dbxref1, dbxref2

//To cede to PCO from ENVO

is a 'community bloom'

'has participant' some algae

'occurs in' some 'water body' ENVO:water body

'has participant' some 'algal bloom' ENVO:algal bloom

dbxref

A community bloom process during which at least two of the populations in a community of scyphozoa, in a body of water, undergo rapid growth, resulting in high concentrations of scyphozoa that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.

is a 'community bloom'

'occurs in' some 'water body' ENVO:water body

'has participant' some 'Scyphozoa' NCBITaxon:Scyphozoa

'has related synonym' 'jellyfish bloom process'

dbxref1, dbxref2

A community bloom process during which at least two of the populations in a community of plankton, in a body of water, undergo rapid growth, resulting in high concentrations of plankton that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.

is a 'community bloom'

'has participant' some 'plankton community'

'occurs in' some 'water body' ENVO:water body

dbxref

A plankton bloom process during which at least two of the populations in a community of phytoplankton, in a body of water, undergo rapid growth, resulting in high concentrations of phytoplankton that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.

is a 'plankton bloom process'

'has participant' some 'phytoplankton community'

'part of' some 'surface photoautotrophic biomass formation'

dbxref

A phytoplankton bloom process during which at least two of the populations in a community of diatoms, in a body of water, undergo rapid growth, resulting in high concentrations of diatoms that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.

is a 'phytoplankton bloom process'

'has participant' some 'diatom-dominated community'

A plankton bloom process during which at least two of the populations in a community of zooplankton, in a body of water, undergo rapid growth, resulting in high concentrations of zooplankton that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.

is a 'plankton bloom process'

'has participant' some 'zooplankton community'

dbxref

bloom initiation

A process during which the growth and reproduction rate of at least two of the populations in a community exceeds the rate of death, predation, and or transport, initiating a community bloom.

is a 'population establishment to multiplicative growth transition'

'has part' some 'population bloom initiation'

starts some 'population bloom'

'causally upstream of or within' some 'population bloom'

A process during which the growth and reproduction rate of at least two of the populations in an algal community exceeds the rate of death, predation, and or transport, initiating an algal bloom.

is a 'community bloom initiation'

starts some 'algal bloom process'

'causally upstream of or within' some 'algal bloom process'

A process during which the growth and reproduction rate of at least two of the populations in a plankton community exceeds the rate of death, predation, and or transport, initiating a plankton bloom.

is a 'community bloom initiation'

starts some 'plankton bloom process'

'causally upstream of or within' some 'plankton bloom process'

A process during which the growth and reproduction rate of at least two of the populations in a phytoplankton community exceeds the rate of death, predation, and or transport, initiating a phytoplankton bloom.

is a 'plankton bloom initiation'

starts some 'phytoplankton bloom process'

'causally upstream of or within' some 'phytoplankton bloom process'

A process during which the growth and reproduction rate of at least two of the populations in a zooplankton community exceeds the rate of death, predation, and or transport, initiating a zooplankton bloom.

is a 'plankton bloom initiation'

starts some 'zooplankton bloom process'

'causally upstream of or within' some 'zooplankton bloom process'

A physical quality which inheres in a bearer by virtue of that bearer having a two dimensional surface layer which is partially or completely surrounded by ice. 

is a 'physical quality'

‘inheres in’ some (independent continuant (has part 'surface layer' and ((adjacent to some atmosphere) or (adjacent to some 'outer space'))))

'has exact synonym' 'ice coverage'

An ice cover quality which inheres in a bearer by virtue of that bearer being completely surrounded by ice. 

is a 'ice cover'

'has exact synonym' 'completely ice covered'

An ice cover quality which inheres in a bearer by virtue of that bearer being partially surrounded by ice. 

is a 'ice cover'

'has exact synonym' 'partially ice covered'

'inheres in' some 'organism or virus or viroid'

An organismal quality inhering in a bearer by virtue of the bearer's inability to sustain directed movement to overcome displacement by physical forces such as currents.

is a 'organismal quality'

dbxref

An osmolarity quality inhering in a bearer by virtue of the bearer's amount of solute, composed primarily of dissolved ionic compounds, per liter of solution.

is a osmolarity

dbxref1, dbxref2,

//see PCO issue #62 perhaps it would be better not to cede the following two classes to ECOCORE until ECOCORE has resolvable purls.

A quality that inheres in an ecosystem.

is a quality

'inheres in' some ecosystem

current PCO definition:

The maximum number of individuals that can be supported in a population that is growing according to logistic growth. new definition:

A quality inherent in an an ecosystem, in which a population residing within and depending upon such ecosystem, is restricted to a maximum sustainable population size.

is a 'quality of an ecosystem'

dbxref

A heterotrophic process during which living cells acquires food and energy by engulfing solid organic particles.

is a heterotrophy

'has exact synonym' phagotrophy

'occurs in' some ('unicellular organism' or 'part of' some 'multicellular organism') CARO:unicellular organism, CARO:multicellular organism

dbxref1, dbxref2

A disposition which is realized by an ecosystem or system parts thereof.

is a disposition

'inheres in' some ecosystem

A disposition of an ecosystem in which the absence of a material or non-material entity from an ecosystem, essential for the growth of a population or community of organisms within an ecosystem, is realized by the limitation of growth of a population or community within an ecosystem.

is a 'deposition of an ecosystem'

'realized in' some ('population growth' or 'community growth') PCO:population growth, PCO:[population growth](no purl yet)

'has related synonym' 'growth limiting factor'

dbxref

A chemical entity which serves as a nutrient and is essential for the growth of organisms in an ecosystem, which when lacking in an ecosystem, will limit the growth of a population or community of organisms.

is a 'chemical entity' CHEBI:chemical entity

'has role' nutrient CHEBI:nutrient

'has disposition' 'disposition to limit the growth of an ecological assemblage'

'has related synonym' 'euphotic zone'

'causally downstream of or within' some 'algal bloom process'

autotrophic biomass formation classes //I could potentially see these going to ECOCORE instead of ENVO

A process during which an organism produces biomass from abiotic components using an autotrophic growth process.

is a 'environmental system process'

'formed as result of' some ECOCORE:'autotrophy'

'has related synonym' 'primary productivity'

A process during which an organism produces biomass from abiotic components using photosynthesis.

is a 'autotrophic biomass formation'

'formed as result of' some ECOCORE:'photoautotrophy'

'occurs in' some 'planetary photic zone'

'has part' some photosynthesis

'has synonym' 'photosynthetic biomass formation'

is a 'photoautotrophic biomass formation' 'has participant' some 'algae' PCO:[algae](to get new purl)

A process during which organisms, at the surface of a planetary photic zone, produce biomass from abiotic components during photosynthesis.

is a 'photoautotrophic biomass formation'

'formed as result of' some ECOCORE:'photoautotrophy'

'occurs in' some ('planetary photic zone' and 'adjacent to' some 'planetary surface') //may have to change to located in if zone is a site.

'has exact synonym' 'surface primary productivity'

currents and water masses:

//previously marine current

A water flow process during which a continuous, directed movement of marine water is generated by forces such as breaking waves, wind, the Coriolis force, temperature and salinity differences and tides caused by the gravitational pull of the Moon and the Sun. Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength.

is a 'water flow process'

'has quality' 'flow rate' PATO:flow rate

A hydroform which is primarily composed of a marine water mass held in shape by the directed movement of a marine current flow.

Alternative definition:

A hydroform which is part of a marine water body and which overlaps the continuous, directed movement of marine water generated by the forces acting upon that water body.

is a hydroform

'formed as result of' some 'marine current flow'

'has part' some 'water mass'

'has part' some 'marine water mass'

A mass of marine water.

new def:

A mass of marine water which bears distinctive physical properties such as temperature, salinity, and chemical isotopic ratios inhered during its formation process. 

is a 'water mass'

'has quality' some temperature PATO:temperature

'has quality' some 'mass density' PATO:mass density

'has quality' some salinity PATO:[salinity](no purl yet)

An environmental system process during which a water body is separated into at least two portions of water differentiated by physicochemical properties, typically temperature and salinity, which results in the formation of marine water masses. 

is a 'environmental system process'

'results in formation of' min 2 'marine water mass'

xref

A process during which water inherent within separate water masses within a water body, are mixed and exchanged due to physical forces such as wind mixing or water movement along a temperature gradient. 

is a 'environmental system process'

'occurs in' some 'water body'

'has participant' min 2 'water mass'

dbxref

A water mass mixing process during which water inherent within separate water masses within a water body, are mixed and exchanged along an axis perpendicular to the surface of the water body. 

is a 'water mass mixing in a water body'

'has related synonym' 'vertical mixing'

'has quality' vertical PATO:vertical

A water body which is characterized by distinct layers of water masses of different densities which result from chemical properties of the water such as salinity, temperature and oxygenation. 

is a 'water body'

'has part' some 'cline'

'has quality' stratified PATO:stratified

'causally upstream of, negative effect' some 'vertical water mass mixing in a water body'

comment

A stratified water mass can serve as a barrier to vertical water mixing processes, potentially hindering the mixing of nutrients and oxygen between water layers, leading to anoxia and or oligotrophic surface waters.

A marine water body which is characterized by distinct layers of marine water masses of different densities which result from chemical properties of the water such as salinity, temperature and oxygenation. 

is a 'stratified water body'

A process during which parts of a mass differentiated by density, separate into layers which overlay one another due to their densities.

is a 'material transport process'

'results in formation of' min 2 layer //can we add that these layers have quality density into this axiom?

A stratification process during which water within a water body is separated by density into layers which sit atop one another.

is a 'stratification process'

'occurs in' some 'water body'

'results in formation of' some 'stratified water body'

'results in formation of' min 2 'aquatic layer'

'has synonym'` 'water stratification'

'causally upstream of, negative effect' some 'vertical water mass mixing in a water body'

A water body stratification process during which water within a marine water body is separated by density into layers which sit atop one another.

is a 'water body stratification'

'occurs in' some 'marine water body'

'results in formation of' some 'stratified marine water body'

'results in formation of' min 2 'marine layer'

clines

A layer within a fluid where the salinity composition changes rapidly with depth.

is a 'chemocline'

'has quality' some salinity PATO:[salinity](no purl yet)

xref

A halocline caused by a strong, vertical salinity gradient within a body of marine water. 

is a 'halocline'

'part of' some 'marine water body'

'causally upstream of, positive effect' some 'marine water body stratification'

comment:

Because salinity affects the density of seawater, a halocline can increase vertical stratification in a water body.

xref

'part of' some 'marine water body'

sea ice related classes:

An icemelt process during which meltwater is produced by the melting of sea ice, increasing stratification in the underlying water column, and increasing the amount of electromagnetic radiation absorbed within the site previously occupied by sea ice, which acted as a medium by which to attenuate and reflect incoming electromagnetic radiation. 

is a 'ice melt'

'has input' some ('sea ice' and ('adjacent to' some troposphere) and ('adjacent to' some 'marine water body')) and 'decreased degree of illumination' PATO:decreased degree of illumination

'has output' some (meltwater and ('adjacent to' some troposphere) and ('adjacent to' some 'marine water body')) and 'increased degree of illumination' PATO:increased degree of illumination

'causally upstream of' some 'marine water body stratification'

dbxref, dbxref2, dbxref3

An environmental zone in which is the site of the transition between the open ocean and sea ice. 

is a 'environmental zone'

'has quality' 'partial ice cover'

'location of' some 'sea ice' and 'marine water body' //not sure if we need this with when we have the overlaps axiom

overlaps some ('sea ice' and 'marine water body')

'causally upstream of, positive effect' some 'phytoplankton bloom process'

'causally upstream of, positive effect' some 'photoautotrophic biomass formation'

'has related synonym' 'sea ice edge' //could maybe make a separate class for this.

dbxref1, dbxref

A material transport process during which an ice mass is displaced and moved.

is a 'material transport process'

'has input' some 'ice mass'

Biogenic particle flux & carbon pump classes

Detritus which is sourced from the the growth of surface organisms in the photic zone of a water body, which slowly descends from the upper layers of the water column in a body of water.

is a detritus

'located in' some 'water body'

previous definition:

Marine snow is a continuous shower of mostly organic detritus falling from the upper layers of the water column. Its origin lies in activities within the productive photic zone.

new definition:

Detritus which is sourced from the the growth of surface organisms in the photic zone of a marine water body, which slowly descends from the upper layers of the water column in a body of marine water.

is a 'aquatic detritus in a water body'

'located in' some 'water body'

'has part' some 'carbohydrate' CHEBI:carbohydrate

'has part' some 'lipid' CHEBI:lipid

'has part' some 'protein' CHEBI:protein

A material accumulation process during which particulate matter consisting primarily of organic detritus sourced from the the growth of surface organisms in the photic zone of a water body, collide and stick together forming particulate aggregates.

is a 'material accumulation process'

'has input' some detritus

'has output' some 'aquatic detritus in a water body'

'occurs in' some ('planetary photic zone' and 'adjacent to' some 'water body')

'causally downstream of or within' some ('surface photoautotrophic biomass formation' and 'located in' some 'water body')

A material accumulation process during which particulate matter consisting primarily of organic detritus sourced from the the growth of surface organisms in the photic zone of a marine water body, collide and stick together forming particulate aggregates known as marine snow.

is a 'aggregation of suspended particles in a water body'

'has input' some detritus

'has output' some 'marine snow'

'occurs in' some ('marine photic zone' and 'adjacent to' some 'marine water body')

'has related synonym 'marine particle aggregation process'

A material transport process during which suspended particle aggregates consisting of organic detritus sourced from the the growth of surface organisms in the photic zone, descend vertically in a water body. 

is a 'material transport process'

'has input' some 'aquatic detritus in a water body'

'has output' some ('part of' some ('sea floor' and 'biogenous sediment'))

'occurs in' some 'water body'

'has related synonym' 'vertical particle flux'

A sinking process during which suspended particle aggregates consisting of organic detritus sourced from the the growth of surface organisms in the photic zone, descend vertically in a marine water body. 

is a 'sinking of suspended particle aggregates in a water body'

'has input' some 'marine snow'

'has output' some (('organic material' or ('part of' some 'biogenous sediment')) and 'part of' some 'ocean floor')

'occurs in' some 'marine water body'

'has exact synonym' 'marine snow sinking'

//I'm not sure if this class is necessary being that it is a union of the marine snow formation marine particle sinking classes.

A material transport process during which particulate matter consisting primarily of organic detritus sourced from the the growth of surface organisms in the photic zone of a marine water body, collide and stick together forming particulate aggregates, which descends vertically in a marine water body reaching the underlying

is a 'material transport process'

'causally downstream of or within' some ('surface photoautotrophic biomass formation' and 'located in' some 'water body')

'has part' some ('marine snow formation process' and 'marine particle sinking process')

'has related synonym' 'biological carbon pump'

Environment determined by, pre and post composition class examples // we could change these to Ecosystem determined by ...

An environmental system which has an ecological community as part, such that the community exerts a strong causal influence on the function of the environmental system, and the removal of the community would cause the environmental system to collapse. 

is a 'environmental system'

'determined by' some 'ecological community' PATO:ecological community

A marine environmental system which has an ecological community as part, such that the community exerts a strong causal influence on the function of the marine environmental system, and the removal of the community would cause the marine environmental system to collapse. 

is a 'environment determined by an ecological community'

'determined by' some 'marine water body'

A marine environmental system which has an phytoplankton community as part, such that the phytoplankton community exerts a strong causal influence on the function of the marine environmental system, and the removal of the phytoplankton community would cause the marine environmental system to collapse. 

is a 'marine environment determined by an ecological community'

'determined by' some 'phytoplankton community' PATO:[phytoplankton community](no purl yet)

A marine environmental system which has an diatom-dominated community as part, such that the diatom-dominated community exerts a strong causal influence on the function of the marine environmental system, and the removal of the diatom-dominated community would cause the marine environmental system to collapse. 

is a 'marine environment determined by a phytoplankton community'

'determined by' some 'diatom-dominated community' PATO:[diatom-dominated community](no purl yet)

using post composition we could recreate the same class

A marine environmental system which has an diatom-dominated community as part, such that the diatom-dominated community exerts a strong causal influence on the function of the marine environmental system, and the removal of the diatom-dominated community would cause the marine environmental system to collapse. 

is a 'environmental system'

'determined by' some (('ecological community' and 'composed primarily of' some Bacillariophyta) and 'marine water body')

NCBITaxon:Bacillariophyta

community bloom

An environmental system which has a community bloom as part, such that the rapid growth of at least two of the populations in a blooming community, exert a strong causal influence on the function of the environmental system, and the removal of the blooming community would cause the environmental system to collapse. 

is a 'environmental system'

'determined by' some 'community bloom' PATO:[community bloom](no purl yet)

A marine environmental system which has a community bloom as part, such that the rapid growth of at least two of the populations in a blooming community, exert a strong causal influence on the function of the marine environmental system, and the removal of the blooming community would cause the marine environmental system to collapse. 

is a 'environment determined by a community bloom'

'determined by' some 'marine water body'

A marine environmental system which has a phytoplankton community bloom as part, such that the rapid growth of at least two of the populations in a blooming community of phytoplankton, exert a strong causal influence on the function of the marine environmental system, and the removal of the blooming phytoplankton community would cause the marine environmental system to collapse. 

is a 'marine environment determined by a community bloom'

'determined by' some 'phytoplankton bloom process' PATO:[phytoplankton bloom process](no purl yet)

'causally downstream of, negative effect' some 'marine water body stratification' //for the competency question about processes causally downstream of sea ice melting

A marine environmental system which has a diatom community bloom as part, such that the rapid growth of at least two of the populations in a blooming community of diatoms, exert a strong causal influence on the function of the marine environmental system, and the removal of the blooming diatom community would cause the marine environmental system to collapse. 

is a 'marine environment determined by a community bloom'

'determined by' some 'diatom bloom process'

using post composition we could recreate the same class

A marine environmental system which has a diatom community bloom as part, such that the rapid growth of at least two of the populations in a blooming community of diatoms, exert a strong causal influence on the function of the marine environmental system, and the removal of the blooming diatom community would cause the marine environmental system to collapse. 

is a 'environmental system'

'determined by' some (('community bloom' and 'has participant' some ('ecological community' and 'composed primarily of' some Bacillariophyta)) and 'marine water body')

// is a 'community bloom' and 'has participant' some 'diatom-dominated community' //'diatom-dominated community' = 'ecological community' and 'composed primarily of' some Bacillariophyta