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working datasets
Here are a working list of 6 datasets types for which I will attempt to create an knowledge graph to interlink different AWI data types. My rationalization/ working down to such a list is documented here
For Data sets added to datastore see here
Potential Datasets to use
Chlorophyll a measured on water bottle samples
Physical oceanography and currents
Diatom Phenology in the Southern Ocean: Mean Patterns, Trends and the Role of Climate Oscillations
Bacterial sequence information
Unused Data sets
Diversity of benthic megafaunal communities
Diatom Phenology in the Southern Ocean: Mean Patterns, Trends and the Role of Climate Oscillations paper. Data to get from Pier.
Associated publication: Biogeography of Deep-Sea Benthic Bacteria at Regional Scale (LTER HAUSGARTEN, Fram Strait, Arctic)
1 Event label 2 Latitude of event 3 Longitude of event 4 Elevation of event 5 DEPTH, sediment/rock 6 Depth, top/min 7 Depth, bottom/max 8 File name 9 Sample code/label 10 Sample comment 11 Domain, biology 12 Region, genetic 13 Instrument 14 Laboratory 15 Comment 16 Method comment 17 Primers 18 Barcode, genetic 19 Run 20 Date 21 Comment 22 Accession number, genetics
Also associate is Pier's paper Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait).
Her paper Biogeography and Photosynthetic Biomass of Arctic Marine Pico-Eukaroytes during Summer of the Record Sea Ice Minimum 2012 Paper from Dr. Katja Metfies has data about physical oceanography data and nutrient data measurements of ARKXXVII1-3 (in PANGAEA), Sea ice concentration (website Meereisportal) and genetic sequences European Nucleotide Archive (ENA) under Accession PRJEB1449. could serve as the data set I'll work with for the thesis. If I can't assembly anything useful from this I could also ask her for metadata about microbial observatory. Christian wolf one of her scientists may have the data published under his name.
From this I will use her 18S rRNA data figure 6 to make use of the phytoplankton dominated classes. The paper has Dinophycaea syndiniales, phaeocystacea, Bacillariophyceae (diatoms)
Figure 5 has them as the class level: Syndiniales, Dinoflagellates
Biogenic particle flux 10 parameters seems quite relevant
Associated publication: Particle sedimentation patterns in the eastern Fram Strait during 2000–2005
This paper may also help later to make the connection between surface plankton and particle flux Lateral supply and downward export of particulate matter from upper waters to the seafloor in the deep eastern Fram Strait
1 DEPTH, water 2 DATE/TIME 3 Date/time end 4 Duration, number of days 5 Sample code/label 6 Seston flux 7 Calcium carbonate flux 8 Carbon, organic, particulate flux per day 9 Nitrogen, organic, particulate flux per day 10 Silicon, particulate flux
Inorganic nutrients 12 parameters relevant for ocean biogeochemistry
Example in datastore as inorganic_nutrients.csv
No obvious accompanying publication. This paper Physical and ecological processes at a moving ice edge in the Fram Strait as observed with an AUV cites the data and could possibly serve as some interesting links.
1 Event label
2 Optional event label
3 Date/Time of event
4 Latitude of event
5 Longitude of event
6 Elevation of event
7 DEPTH, water
8 Nitrate //nitrate CHEBI:17632
9 Nitrite //nitrite CHEBI:16301
10 Silicate //the chemical formula is Si(OH)4 which links to the chebi silicic acid
11 Phosphate //the proper link for CHEBI phosphate seems to be phosphate(3−) with ID = CHEBI:18367 for the phosphate 3- anion PO4 3-
12 Ammonium //CHEBI:28938 ammonium
Physical oceanography and current meter data 11 parameters seems quite relevant
Example in datastore as physical_oceanography.csv
GROUP PI Wilken-Jon von Appen.
Looking through similar data publications we have the useful abstract and data publication which has the link to this paper Exchange of warming deep waters across Fram Strait which seems to be a relevant use of the plethora of physical oceanography and current meter data
1 DATE/TIME 2 Gear identification number 3 DEPTH, water 4 Pressure, water 5 Temperature, water 6 Salinity 7 Current velocity, horizontal 8 Current direction 9 Current velocity, east-west 10 Current velocity, north-south 11 Oxygen
Snow height on sea ice and sea ice drift from autonomous measurements 11 parameters height repeated from multiple sensors but also some other data which could be interesting to link up air temp and pressure.
1 DATE/TIME 2 LATITUDE 3 LONGITUDE 4 Snow height 5 Snow height 6 Snow height 7 Snow height 8 Snow height 9 Pressure, atmospheric 10 Temperature, air 11 Temperature, technical
EOS news article about the data AWI webpage about sea ice physics energy budgets which could be a good source of terms to ontologize
Influence of snow depth and surface flooding on light transmission through Antarctic pack ice, supplementary data
//Additional data set on snow height and surface light affecting blooms.
example dataset here is linked to this publication by Nicolaus Marcel's group Influence of snow depth and surface flooding on light transmission through Antarctic pack ice with parameters:
1 DATE/TIME 2 LATITUDE 3 LONGITUDE 4 Distance, relative, X 5 Distance, relative, Y 6 Sea ice thickness 7 Signal strength
These data sets would be cool and interesting to do but I have chosen to omit them for now (at least for the first round of my masters thesis time trajectory) to focus on data more relevant to plankton blooms. Perhaps during the refinement stages I could come back to these and try to integrate them back into the project. But for now I don't have time to attempt to incorporate them.
Diversity of benthic megafaunal communities 10 parameters relevant for ocean biogeochemistry
Associated publication Dynamic benthic megafaunal communities: Assessing temporal variations in structure, composition and diversity at the Arctic deep-sea observatory HAUSGARTEN between 2004 and 2015
1 Event label 2 Date/Time of event 3 Latitude of event 4 Longitude of event 5 Elevation of event 6 DEPTH, sediment/rock 7 File name 8 Shannon index of diversity 9 Pielou evenness index 10 Alpha diversity 11 Gamma diversity 12 Beta diversity 13 Area 14 Number of species 15 Number of species
Marine Litter quantities on six Beaches of northern Svalbard in 2016 determined by citizen scientists 15 parameters plus links to various sediment types. Work can be done to harvest these terms into ENVO plus an expansion of sediment classes.
Associated publication Citizen scientists reveal: Marine litter pollutes Arctic beaches and affects wild life
1 Event label 2 Latitude of event 3 Longitude of event 4 DATE/TIME 5 Method comment 6 Sediment type 7 Method comment 8 Area 9 Marine litter, plastic 10 Marine litter, plastic 11 Marine litter, fabric 12 Marine litter, metal 13 Marine litter, glass 14 Marine litter, biotic 15 Marine litter, total