AndreaBozzo/ceres-open-data-index huggingface dataset:
The Australian Chlorophyll a Database (1965 - 2017)

Chlorophyll a is the most commonly used indicator of phytoplankton biomass and is a proxy for primary productivity in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173,333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys to long ocean voyages. This dataset concentrates on samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). Here we collate all available chlorophyll a data from Australian waters, gathered from researchers, students, government bodies, state agencies, councils and databases, along with the associated metadata. The Australian Chlorophyll a Database is available through the Australian Ocean Data Network portal (AODN: https://portal.aodn.org.au/), the main repository for marine data in Australia. The Australian Chlorophyll a Database will be maintained and updated through the CSIRO data centre, with periodic updates sent to the AODN. A snapshot of the Australian Chlorophyll a Database at the time of this publication has been assigned a DOI and will be maintained in perpetuity by the AODN. These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and / or the relationships with other trophic levels such as zooplankton or fish.

This metadata record was based on the following CSIRO metadata record:  https://marlin.csiro.au/geonetwork/srv/eng/search?uuid=4c72fe3b-bddf-44da-a809-1791033a6ac5.

Tags: Continents | Antarctica, Countries | Australia, Countries | Indonesia, Countries | New Caledonia, Countries | New Zealand, Countries | Papua New Guinea, Countries | Solomon Islands, Countries | Timor-Leste, Countries | Vanuatu, Earth Science | Oceans | Ocean Chemistry | Chlorophyll, Fluorometers, Global / Oceans | Indian Ocean, Global / Oceans | Pacific Ocean, Global / Oceans | Southern Ocean, HPLC (High Performance Liquid Chromatography), Marine Features (Australia) | Bass Strait, TAS/VIC, Marine Features (Australia) | Great Australian Bight, SA/WA, Marine Features (Australia) | Great Barrier Reef, QLD, Offshore Islands (Australia) | Macquarie Island, Regional Seas | Arafura Sea, Regional Seas | Coral Sea, Regional Seas | Solomon Sea, Regional Seas | Tasman Sea, Regional Seas | Timor Sea, Spectrophotometers, States, Territories (Australia) | New South Wales, States, Territories (Australia) | Northern Territory, States, Territories (Australia) | Queensland, States, Territories (Australia) | South Australia, States, Territories (Australia) | Tasmania, States, Territories (Australia) | Victoria, States, Territories (Australia) | Western Australia
Organization: Australian Ocean Data Network
EcoRRAP Coral Demographic Data

This dataset provides information on coral survival and growth for eleven taxa at EcoRRAP sites across the Great Barrier Reef and Torres Strait (see SOP #14: Reef monitoring sampling methods | AIMS).

This dataset was generated through the segmentation of coral colonies on EcoRRAP orthomosaics (EcoRRAP Benthic Orthomosaics - AIMS) using the software TagLab. Colonies of specific taxa were identified and digitised on orthomosaics generated from the first year of monitoring. Digitisation was either conducted manually or through the use of an AI classifier followed by manual review and verification. Colony segments were then transferred to the corresponding orthomosaic for the next time point and segments were refined to align with coral colony edges. Growth is recorded here as change in planar area of a colony between time points. This dataset also contains colonies whose species identification has been verified in the field by a coral taxonomist as well as colonies that have been sampled for genetic purposes.

A subset of taxa have been uniformly digitised across all EcoRRAP sites, including: table Acropora (where possible, A. hyacinthus and A. cytherea were identified to species level), corymbose Acropora (where possible, A. millepora and A. tenuis were identified to species level), digitiate Acropora (where possible, A. humilis and A. gemmifera were identified to species level), Pocillopora verrucosa, Pocillopora damicornis, Stylophora pistillata, massive Porites (species complex of 7 Porites species), Goniastrea (where possible, G. edwardsi and G. retiformis were identified to species level), and Platygyra. Five additional taxa have been unformly digitised in the Central EcoRRAP cluster to investigate the 2022 bleaching event, however, these taxa have not been consistently digitised in other EcoRRAP sites. These additional taxa include staghorn Acropora, Seriatopora hystrix, Lobophyllia sp., encrusting Montipora, and Isopora sp. 

Data is currently available for four time points (three transitions) from 2021-2024. Data is available for each year of monitoring in the form of .csv and .shp files as well as in a joined form that links individual coral colonies across all time points. 

See summary stats document associated with this record for preliminary summary stats on the dataset.

Organization: Australian Ocean Data Network
Vessel Pacific Sun : a platform of the IMOS Ships of Opportunity – Sea Surface Temperature Sensors for Australian Vessels Sub-Facility

The PV Pacific Sun is a platform of the Ships of Opportunity facility.
The vessel is a holiday class cruise ship (callsign 9HA2479), 223 m length (beam 28 m, draught - 7.5 m). It performs year-round cruises from Sydney to the South Pacific and tropical North Queensland.

Bulk SST is measured by SBE48 hull contact sensor. The sensor is installed in the engine compartment at the depth of 3 meters. SST data (along with meteorological data from ship AWS) are instantaneous, collected every 1 hours.

The data are quality controlled by the Bureau of Meteorology. The daily data files are available from the AODN shortly after 0000 UTC.

Tags: Atmosphere | Atmospheric Pressure | Atmospheric Pressure, Atmosphere | Atmospheric Temperature | Air Temperature, Atmosphere | Atmospheric Water Vapor | Dew Point, IMOS Platform | 9HA2479 | Pacific Sun, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Winds | Surface Winds
Organization: Australian Ocean Data Network
IMOS - Ships of Opportunity - Sea Surface Temperature data collected on the Merchant Vessel Wana Bhum

This dataset contains Sea Surface Temperature (SST) underway observations collected on trips of a merchant vessel Wana Bhum (callsign HSB3403). This data stream has now been discontinued (April 2013). 

Bulk SST is measured by SBE48 hull contact sensor. The sensor is installed in the bow thruster room at 8.5m depth. 

Observed data are 1-minute median SST values and are retrieved from the vessel once an hour and quality controlled at the Bureau of Meteorology. A daily file is available after 0100 UTC. High-resolution 1-minute median data are available in the delayed mode approximately every 3 months.

Tags: Oceans | Ocean Temperature | Sea Surface Temperature, latitude, longitude, platform_course, platform_speed_wrt_ground, sea_surface_temperature
Organization: Australian Ocean Data Network
IMOS - Ships of Opportunity - Sea Surface Temperature data collected on the Research Vessel L'Astrolabe

Sea Surface Temperature Sensors for Australian Vessels Sub-Facility aims to supply near real-time  SST data (within 24 hours) from vessels of opportunity and research vessels in the Australian region.  

The data files contain SST underway observations from an SBE 38 sensor installed in a seawater intake collected on trips of a French research and Antarctic resupply vessel participating in the Australian Volunteer Observing Fleet (RV L'Astrolabe - FHZI) between Hobart (Tasmania) and Dumont D'Urville (Antarctica). The voyages take place during the Austral summer. The data are instantaneous hourly measurements. The data have been quality controlled by the Bureau of Meteorology.

Tags: Atmosphere | Atmospheric Pressure | Atmospheric Pressure, Atmosphere | Atmospheric Temperature | Air Temperature, Atmosphere | Atmospheric Water Vapor | Dew Point, Continents | Antarctica, Global / Oceans | Southern Ocean, IMOS Platform | FHZI | L'Astrolabe, Named Locations (Antarctica) | Dumont D'Urville Sea (France), Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Winds | Surface Winds, Offshore Islands (Australia) | Macquarie Island, air_pressure, air_temperature, dew_point_temperature, sea_surface_temperature, wind_from_direction, wind_speed
Organization: Australian Ocean Data Network
IMOS - Ships of Opportunity - Sea Surface Temperature data collected on the PV Pacific Sun

This dataset contains Sea Surface Temperature (SST) underway observations collected on trips of the PV Pacific Sun (callsign 9HA2479).

Bulk SST is measured by SBE48 hull contact sensor. The sensor is installed in the engine compartment at the depth of 3 metres. SST data (along with meteorological data from ship AWS) are instantaneous, collected every 1 hour.

The data are quality controlled by the Bureau of Meteorology. The daily data files are available from the AODN shortly after 0000 UTC.

Tags: Atmosphere | Atmospheric Pressure | Atmospheric Pressure, Atmosphere | Atmospheric Temperature | Air Temperature, Atmosphere | Atmospheric Water Vapor | Dew Point, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Winds | Surface Winds, air_pressure, air_temperature, dew_point_temperature, latitude, longitude, platform_course, platform_speed_wrt_ground, sea_surface_temperature, wet_bulb_temperature, wind_from_direction, wind_speed
Organization: Australian Ocean Data Network
NERP TE Project 4.3 - Ecological risk assessment of pesticides, nutrients and sediments on water quality and ecosystem health – Phase 1, 2011-2012 (CSIRO, JCU)

This project undertook a scoping study to develop a robust approach that will allow us in Phase 2 to carry out an ecological risk assessment (ERA) of nutrients, fine suspended sediments, and pesticides used in agriculture in the GBR region including ranking the relative risk of individual contaminants originating from priority catchments to the GBR ecosystems using a systematic, objective and transparent approach.

The researchers will specifically look at a method able to evaluate relative risk to different ecosystems and their keynote species from the different contaminants, e.g. suspended sediments versus nitrogen (and different forms of nitrogen) versus phosphorus (different forms) versus pesticides (different types).

The results of the Phase 1 study were used to secure support to carry out a full risk assessment.

Tags: National Environmental Research Program Tropical Ecosystems Hub, marine
Organization: Australian Ocean Data Network
Ecology and genetics of the palm Carpoxylon macrospermum from Vanuatu

An extensive survey in 1994 which visited 12 islands (Aneityum, Futuna, Tanna, Erromango, Efate, Tongoa, Epi, Malakula, Ambrym, Pentecost, Ambae and Espiritu Santo), an earlier survey on Espiritu Santo in 1993, and subsequent investigations, documented a total population of the endangered palm, Carpoxylon macrospermum, comprising 154 reproductively mature individuals, ± 145 juveniles and ± 640 seedlings. Of the mature individuals, 122 (80% of total) are known to have been planted in village/garden situations. Naturally occurring mature individuals total 32 and occur on Aneityum, Tanna and Futuna. Two populations on Aneityum and Tanna were studied in detail: the Anetchininbeke site on Aneityum was visited on 9 November 1994 and the Lown'ock site on Tanna was visited on 14 November 1995 - refer to the paper for further details. A total of 114 seeds were collected from 26 sites on the islands Aneityum, Tanna, Malakula, Espiritu Santo and Epi. Of the 114 seeds collected, 86 (from 19 of the 26 collection sites) provided embryos that were in a fit condition for DNA extraction. Seeds from 1994 were mature, fallen seeds that had to hydrated prior to DNA extraction. Those collected in 1995 were mostly taken directly from the palms and the endosperms were still hydrated and the embryos extracted immediately upon arrival at AIMS.Genetic variation within the population was determined by random amplified polymorphic DNA (RAPD) analysis. At only 2 (Lawn'oek and Yeruareng on Tanna) of the 19 sites sampled was any significant variation detected. Seed locations, whether from a naturally occurring population, the number of embryos from which DNA could be extracted and the numbers of seeds providing reliable RAPD patterns with each primer (AP3 to AP13) were recorded: the number of RAPD patterns produced from all seeds, with all primers, was 757.Cluster analysis of RAPD patterns of Carpoxylon macrospermum was carried out.
 To determine any genetic variation within the population of the endangered palm, Carpoxylon macrospermum.

Organization: Australian Ocean Data Network
DOT Bathymetry Composite Surfaces Index - Raw data

This dataset is the underpinning raw data that makes up the publicly available raster format hydrographic surveys owned by DoT. Raster surveys include multibeam, laser and lidar surveys. The dataset does not include surveys held by DOT but owned by a third party e.g. Port Authorities.  Data is stored at Pawsey Supercomputing Centre.

Tags: Albany, Alkimos, Augusta, Bremer Bay, Broome, Bunbury, Burns Beach, Busselton, Cambridge Gulf, Carnarvon, Cockburn - Fremantle, Coral Bay, Cottesloe, DOT, Dampier, Denham, Denmark, Dension, Downloadable Data, Esperance, Exmouth, Geraldton, Greenhead, Hillarys, Jurien Bay, Kalbarri, Lancelin, Mandurah - Dawesville - Peel-Harvey, Margaret River, Ocean Reef, Onslow, Peaceful Bay, Quinns, Rottnest Island, Scarborough, Seabird, Swan - Canning Rivers, Two Rocks, WA, Warnbro Sound, australia, bathymetry, coast, depth, hydrography, levels, marine, ocean, sea, singlebeam, survey
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Expert Assessment – Pressure – Shipping (marine vessel activity)

The Marine chapter of the 2021 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "Pressures on the marine environment - shipping (marine vessel activity)". 
<strong><em>A PDF of the full Expert Assessment, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "EXPERT ASSESSMENT 2021 - Shipping (marine vessel activity)"</em></strong>



DESCRIPTION OF PRESSURE
Australia as an island relies heavily on shipping for transportation of its domestic freight and international imports and exports. Australia relies on sea transport for 99 per cent of its international trade (by volume) [1]. In the 2017/18 financial year approximately 1554 million tonnes of cargo were loaded (+21.9% increase since 2013/14), and 155 million tonnes discharged (+2.6%) at Australian wharves by 5859 vessels (+6.5%) that made 34,117 port calls (+18.8%) [2]. As well as commercial vessels, many smaller vessels use Australian waters and provide an important recreational pastime for many Australians. 

DATA STREAM(S) USED IN EXPERT ASSESSMENT
not supplied



2021 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details]

• 2021 •
Assessment grade: Low impact
Assessment trend: Deteriorating
Confidence grade: Adequate
Confidence trend: Limited
Comparability: Grade and trend are comparable to the 2016 assessment 
• 2016 •
Assessment grade: Low
Assessment trend: Deteriorating
Confidence grade: High level of consensus
Confidence trend: High level of consensus
Comparability: Comparable
• 2011 •




CHANGES SINCE 2016 SOE ASSESSMENT
No change.

Tags: anthropogenic pressures, expert assessment, shipping
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Expert Assessment – State and Trend – Inner shelf (0-30 m) – invertebrate species

The Marine chapter of the 2021 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "State and Trend of inner shelf (0-30 m) – invertebrate species". 
<strong><em>A PDF of the full Expert Assessment, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "EXPERT ASSESSMENT 2021 - Inner shelf (0-30 m) – invertebrate species"</em></strong>



DESCRIPTION OF SPECIES/HABITAT/COMMUNITY/PROCESS FOR EXPERT ASSESSMENT
A wide range of both sessile and mobile invertebrate species inhabit the continental shelf. Large areas of soft sediments are dominated by infauna and mobile epifauna, but there are also areas that have abundant sessile epifauna — which are covered in other sections. 

DATA STREAM(S) USED IN EXPERT ASSESSMENT
Peer reviewed publications, fishery stock assessment reports and data from the IMOS autonomous underwater vehicle facility. 



2021 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details]

• 2021 •
Assessment grade: Good
Assessment trend: Unclear
Confidence grade: Limited evidence
Confidence trend: Low evidence or consensus 
Comparability: Comparable
• 2016 •
Assessment grade: Good
Assessment trend: Unclear
Confidence grade: Limited evidence
Confidence trend: Low evidence or consensus 
Comparability: Somewhat comparable
• 2011 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Limited evidence
Confidence trend: Limited evidence



CHANGES SINCE 2016 SOE ASSESSMENT
not supplied

Tags: community structure, expert assessment, inner shelf, invertebrates
Organization: Australian Ocean Data Network
Merchant Vessel OOCL Houston: a platform of the IMOS Ships of Opportunity – Sea Surface Temperature Sensors for Australian Vessels Sub-Facility

The Merchant Vessel OOCL Houston is a platform of the Ships of Opportunity facility. The vessel is a container ship (callsign VRDE7, IMO Number 9355757) of 260 m length (beam 32 m, draught – 12.6 m). It performs regular transects around Australian East and West coasts up to Singapore via Indonesian waters.

SST data are processed from the hull-contact sensor SBE48 which is located in the bow thruster room at approximately 8 m depth.

Observed data are 1-minute median SST values and are retrieved from the vessel once an hour and quality controlled at the Bureau of Meteorology. A daily file is available after 0100 UTC.

Tags: IMOS Platform | VRDE7 | OOCL Houston, Oceans | Ocean Temperature | Sea Surface Temperature
Organization: Australian Ocean Data Network
IMOS - Ships of Opportunity -Temperate Merchant Vessels Sub-Facility - Data collected on the Spirit of Tasmania I during transect between Melbourne and Devonport (Delayed mode).

The IMOS Ships of Opportunity - Sensors on Temperate Merchant Vessels Sub-Facility collects data from an autonomous marine monitoring system on the Spirit of Tasmania I to monitor long-term climate change indicators and measures of ecosystem health in Bass Strait surface waters and coastal waters of Victoria and Tasmania. The Sub-Facility maintains an underway sampling Seabird SBE45 thermo-salinograph (TSG), a Wetlabs combination fluorometer and turbidity sensor (ECO-FLNTU), a GPS were deployed in June 2008 on the Spirit of Tasmania I (VLST) for initial trials. Routine data collection commenced on 28 August 2008. Transects are dependent upon Spirit of Tasmania 1 operating schedule. These are typically undertaken 7:30pm to 7am with subsequent in-port monitoring 7am-7:30pm at Port Melbourne/Geelong and Devonport docks. During summer and holiday periods the vessel undertakes continuous transects with 2-3 hour turnaround at the ports. Transect data files are available through the IMOS OPeNDAP server. Graphic representation of the temperature, salinity, turbidity, chlorophyll-a by distance are also available.

Provision of data from 2014 onwards will resume early in 2024.

Tags: Coastal Cities / Towns (Australia) | Devonport, TAS, Coastal Cities / Towns (Australia) | Melbourne, VIC, Countries | Australia, Marine Features (Australia) | Bass Strait, TAS/VIC, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Optics | Fluorescence, Oceans | Ocean Optics | Turbidity, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Salinity/density | Conductivity, Oceans | Salinity/density | Salinity, States, Territories (Australia) | Tasmania, States, Territories (Australia) | Victoria
Organization: Australian Ocean Data Network
Secchi Disk Depth (a measure of water clarity), 1992 - 2006 (MTSRF 1.1.5, AIMS, QDPI-F)

This study characterises spatial patterns in water clarity. Water clarity is a key indicator for water quality and is an essential environmental factor for phototrophic organisms that dominate coral reefs, seagrass meadows and the seafloor microphytobenthos. Secchi disk depthis a commonly used standardised way to quantify water clarity.

This data set combines Secchi disk depth data collected as a one-off survey systematically covering the whole Great Barrier Reef by the seagrass monitoring project of the Queensland Department of Primary industry and Fisheries (QDPI-F), and data collected on an opportunistic basis by the Australian Institute of Marine Science (AIMS).

As part of the Reef Atlas project (now the eAtlas) the Secchi disk depth observations were interpolated over the whole GBR by Glenn De'ath using Generalized Additive Models with a Quasipoisson fit. This produced a gridded version of the dataset and is available as a KML and an ASCII gridd file.

Data Units: Depth in meter

References:
- De'ath G (2007) The Spatial, Temporal and Structural Composition of Water Quality of the Great Barrier Reef, and Indicators of Water Quality and Mapping Risk. Report to the Australian Government’s Marine and Tropical Sciences Research Facility. 59 pp.
- De'ath G, Fabricius K.E (2008) Water quality of the Great Barrier Reef: distributions, effects on reef biota and trigger values for the protection of ecosystem health. Final Report to the Great Barrier Reef Marine Park Authority. Australian Institute of Marine Science, Townsville: 104 pp
- Coles R et al (submitted)

Tags: marine
Organization: Australian Ocean Data Network