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ideas and concepts
Ideas source material relevant to the work to be sources of material to ontologize.
Global warming associated information
Diatom Phenology in the Southern Ocean: Mean Patterns, Trends and the Role of Climate Oscillations
Particle sedimentation patterns in the eastern Fram Strait during 2000–2005
Physical and ecological processes at a moving ice edge in the Fram Strait as observed with an AUV
Influence of snow depth and surface flooding on light transmission through Antarctic pack ice
from the eskp linked litter database page there is a nice info graphic showing the global composition of marine litter. thus to add to envo to support the marine plastics dataset I am working with here
additionally this work has various sediment types as data, so expanding ENVO sediment types to fit this and cleaning that up is in order.
to help locate the data lat long depth
for depth import pato depth make water depth: a water body which bears quality depth ...
ideas from DOOS talking about the oceans absorbing the heat accumulated in the climate, terms like:
thermal expansion (in water)
Carbon sequestration
Essential Ocean Variables. terms from PHYSICS, BIOGEOCHEMISTRY, BIOLOGY AND ECOSYSTEMS which GOOS is wanting to make more connectable. Thus it could be cool to add this. links to GOOS version of physical ones here Also expressed on the International Ocean Carbon Coordination Project page
Perhaps in addition to ontologizing information around the awi dataset: Snow height on sea ice, I could address some of the sea ice related issues in this eskp article
Biogeography and Photosynthetic Biomass of Arctic Marine Pico-Eukaroytes during Summer of the Record Sea Ice Minimum 2012 Paper from Dr. Katja Metfies
ideas to ontologize from her paper:
Light penetration through first-year ice is significantly higher than through multi-year ice
I've already created these sea ice classes in my rotation so I could reuse those classes to help ontologize light penetration in sea ice.
if the sea ice volume decline continues, a point may be reached in the future when not enough sea ice is advected into the Nansen Basin for halocline formation to occur and a regime shift to deep convection would occur (B. Rudels, personal communication 2015).
Compared to the Central Arctic, the stratification was relatively low in eastern Fram Strait with a density difference between 10 and 50 m This is conducive to mixing of the water in the euphotic zone with the waters below and therefore nutrients can be resupplied to the euphotic zone during the growth period.
Distribution of Chl a biomass and biogeographic patterns of pico-eukaryote communities were best understood in relation to ambient water mass characteristics and sea ice coverage.
Ideas for classes:
sea ice advection
halocline*
halocline formation process*
halocline formation region* (perhaps spatiotemporal location?)
primary productivity
marine water masses* (of different salinity, temperature, stratification and nutrient concentration.)
marine water masses mixing process* (can lead to nutrient resupply of deep nutrient rich waters to nutrient replete photic zone waters).
passive lateral advection (in the water column)
vertical mixing (in the water column)
cyclonic boundary current
salinity stratification (density difference with depth)
freezing line of sea water ("Arctic halocline")
isopycnals
nutrient replete waters (nutrient poor waters, perhaps a quality of water mass?)
continental runoff
riverine discharge
Chl a maximum
phytoplankton biomass
nutrient supply in marine water mass
sea ice coverage (spatiotemporal location where sea ice covers water) * this could be super useful for the Tilman satelite data we are going to work with.
light availability
marginal ice zone (MIZ)
Transpolar Drift
euphotic zone
sea ice retreat
nutrient limited ice covered regions
Postponed ENVO terms:
Changes in the phytoplankton phenology are therefore sensitive indicators of environmental change ref
ideas to ontologize:
diatom bloom (subclass of phytoplankton bloom)
Southern Antarctic Circumpolar Current Front
maximum sea ice extent (maximum sea ice cover)
ENSO El Niño-Southern Oscillation
Southern Annular Mode (SAM)
spring bloom a plankton bloom event which occurs in spring
surface mixed layer depth
sea ice cover
sea ice temperature
plankton blooms having biomass, timing, magnitude and duration
carbon pump
iron-limited water (subclass of nutrient limited waters)
Circumpolar Deep Water (not at this level of detail).
light penetration depth
subsurface plankton blooms (deeper than light penetration depth)
high solar zenith angle
Maximum Sea Ice Extent
some potential qualities: cloudiness, sea surface temperature, sea-level pressure, surface air temperature and the zonal and meridional components of the surface wind
ocean colour (to investigate phytoplankton phenology)
diatom associated chlorophyll a
seasonal ice zone
melting of ice increases the stratification of the water column which favors to maintain the phytoplankton in the euphotic zone
mixed layer depth
The end of the bloom occurs when the mixed layer deepens due to wind forcing, which dilutes the phytoplankton in the water column [12] and can bring them to lower light levels.
sea ice advection
sea ice temperature increase
sea ice melting
solar radiation
water column stability
water column mixed layer
water column mixed layer deepening process
diapycnal diffusion
surface waters
pelagic nutrient recycling
grazing pressure
algal viruses
upwelling
Ekman transport
polar aerosols
sea ice cover*
sea surface temperature
plankton biomass
integrate algal material (which Pier is adding to ENVO)
mixed layer depth
wind speed and direction
diatom biomass
environmental anomalies
// leads to a marine water mass formation process.
quotes from paper:
The location of the ice edge in the eastern Fram Strait is strongly controlled by wind and the advection of the warm Atlantic water. The latter provides heat, which is necessary to melt ice, from the south.
//so we need to represent the ideas that the spatiotemporal location of the ice edge, which Pier says to represent as an edge.
elevated fluxes during winter were attributed to sedimentation of ice-rafted detritus from the Svalbard region, released by melting of ice caused by the warm Atlantic surface waters in the area
// so warm surface water causually upstream of ice melting. // ice-rafted detritus gets sedimented.
The presence or absence of ice also fosters pelagic production, through influencing light penetration and stabilizing of the near surface water layer by melt water formation.
// stratification, vertical mixing govern nutrient supply and biomass formation in the euphotic zone (make sure we have these)
The presence or absence of ice also fosters pelagic production, through influencing light penetration and stabilizing of the near surface water layer by melt water formation.
//todo get terms and relations from this
// They discuss a bit about how sea ice melt (affected by winds currents and the mixing of water masses) seems to affect plankton communities and sedimentation of matter, there is a bloom following sea ice as it melts
// regions of ice cover, sea ice is transported by marine currents
// ice releases lithogenic matter
// the ice edge increases sedimentation
species assemblages that indicate the influence of the warm Atlantic water masses: pteropod Limacina retroversa, the coccolithophore Emiliania huxleyi and diatoms of the Rhizosolenia/Proboscia group.
species that indicate the influence of cold water masses pennate diatoms, Fragilariopsis spp. (mainly Fragilariopsis cylindrus) accompanied by species of the genus Navicula and Nitzschia. These species are regarded as cold-water and ice-associated organisms (von Quillfeldt, 2000, 2004)
// This is neat how people have identified plankton (seems like mainly diatom) species associated with cold and warm water masses. Could this serve as an ocean indicator? How would this be represented, would it have to be on an instance level because these species serve as indicators for specific water masses however if we know that physiologically certain species are cold or hot water adapted it should serve as universal.
Variations in the surface currents and ice regime seemingly trigger changes in patterns and composition of sedimenting matter and plankton communities in the eastern Fram Strait.
ideas for classes unmoved to envo page:
// primary production is casually upstream of sedimentation of biogenic components
// these three being dealt with by autotrophic biomass formation
//marine particles //already exists in ENVO.
// has an associated bloom I think I have this idea already
phytoplankton biomass // possible envo term?
(chlorophyll a) and nutrients // have this.
Atmospheric forcing and the presence of the melt water front are assumed to be mainly responsible for the complexity of the water column.
// figure out what they mean by atmospheric forcing and
// make a link between sea ice melting creating meltwater meltwater mixing the water column, encouraging mixing
wind driven frontogenesis likely contributed to vertical water movements
// figure out what is wind driven frontogenesis
proposed classes:
An environmental zone in which ...
is a 'environmental zone'
'causally upstream of, positive effect' some 'phytoplankton bloom process'
'causally upstream of, positive effect' some 'photoautotrophic biomass formation'
//promotes promotes phytoplankton blooms and enhanced biological productivity
//existing PCO term with definition:
A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat.
new definition:
A population growth process during which the size of a population increases, following a logistic (S-shaped) curve controlled by both the population's growth rate and carrying capacity in a particular habitat. Models of such growth process generally assume that the population growth rate declines with increasing population as fewer resources are available to each individual within the population as the population size increases.
is a PCO:population growth
has quality PCO:carrying capacity
has quality PCO:population growth rate
occurs in NCBITaxon:cellular organisms
//should the quality of a population hierarchy be ported to PATO?
dbxref1 dbxref2 [dbxref3](ISBN-13: 978-0691123448)
//for organisms in a state such as sporalation or other 'persistor' bacteria
A process during which a population of organisms within an unfavorable environment, divert the majority of their energy and resources to survive the stresses inherent within their environment.
Editors note:
To be used for bacterial persisters, or bacteria engaged in a sporulation process.
PATO: //I think I need to get rid of these population growth rate classes, replacing them with simpler PATO qualities, like exponential rate linear rate.
A quality of a single process inhering in a population of organisms by virtue of the populations's non changing rate of growth. Generally due to the population undergoing adaptation to environmental conditions such that they may begin to grow.
is a PATO:growth quality of occurrent
A quality of a single process inhering in a population of organisms by virtue of the populations's exponential rate of growth.
is a PATO:growth quality of occurrent
A quality of a single process inhering in a population of organisms by virtue of the populations's non changing rate of growth. Generally due to the population having reached the carrying capacity of a given environment.
is a PATO:growth quality of occurrent
A quality of a single process inhering in a population of organisms by virtue of the populations's decreasing rate of growth. Generally due to the population's growth rate being lower than the population's death rate.
is a PATO:growth quality of occurrent
ENVO:
//process for deepening of marine wind mixed layer
//causally downstream of a process shrinking the ENVO:marine photic zone
synonym water column mixed layer deepening``
//process
'material transport process'
marine vertical particle flux
is a material flux
'has synonym' 'vertical particle flux'
//particle aggregation process
// marine particle sinking process
from particle flux paper:
// this has to do with plankton remains very relevant could keep only this and organic carbon flux if necessary
A population process during which a population's growth rate is beneath the carrying capacity supported by their environment.
is a 'population process'
'occurs in' some CARO:'organism or virus or viroid'
//should it be subcritical population growth process //or would this be assuming that they have to be increasing to be growing.
A population process during which a population's growth rate is above the carrying capacity supported by their environment.
is a 'population process'
'occurs in' some CARO:'organism or virus or viroid'
//removed: This generally occurs as a population previously undergoing lagged growth has sufficiently adapted to their environmental conditions and begins to undergo exponential growth, increasing the rate of population increase above zero.
//removed: This generally occurs when a population is nearing over consumption of an essential growth substrate or is being subject to increasingly unfavorable growth conditions, decreasing the rate of population increase to below zero.
comment:
This generally occurs when a population size is nearing the maximum size dictated by the carrying capacity of its environment, subsequently slowing the rate of population increase to zero.
A plankton bloom which arises from a rapid increase or accumulation in the population of phytoplankton followed by a population crash.
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
overlaps a marine current flow
//has a bloom associate with the edge as it retreats. // how is this related to the Marginal Ice Zone?
'has quality' some 'opacity' PATO:opacity //sea-ice reduces light penetration into the water column
// perhaps make this //all particulate matter organic and inorganic which is suspended in a water body. //http://www.wordnik.com/words/seston
Generally, sea-ice cover can influence phytoplankton blooms in a variety of ways: Firstly, sea-ice reduces light penetration into the water column, which negatively affects the growth of algae in and under the sea ice (Rysgaard et al., 1999; Smetacek and Nicol, 2005).
Secondly, during the ice melt, sea-ice plankton, nutrients and trace elements are released into the upper ocean layer. This process can accelerate the spring bloom (Schandelmeier and Alexander, 1981; Smetacek and Nicol, 2005).
Furthermore, melting of sea-ice increases the upper ocean stability since freshwater is released into the upper ocean layer. This can either promote blooms by keeping plankton closer to the surface where light levels are favorable (Doney, 2006; Gradinger and Baumann, 1991; Lancelot et al., 1993; Smith et al., 1987), or suppress them by increasing grazing pressure from zooplankton (Banse, 1992; Behrenfeld, 2010). Stratification can also limit nutrient supply from deeper layers and thus constrain phytoplankton growth.