AndreaBozzo/ceres-open-data-index huggingface dataset:
NERP TE Project 11.2 - Improved approaches for detection of disease and prevention of spread in Torres Strait, 2011-2014 (JCU)

This project focuses on improving methods to detect the introduction of exotic animal diseases into the Torres Strait. The researchers will examine the environmental factors that influence the establishment and persistence of wildlife diseases in the region. They will study insect disease vectors and the incidence of disease in birds in a range of habitats in order to identify where disease risk is greatest. Field studies will be conducted using replicated mosquito trapping and mist netting of birds in Torres Strait, at sites identified from previous projects.
Outcomes include:
<ol>
<li>

Developing a model of disease dynamics across the Torres Strait based on past and ongoing epidemiology and ecological studies on vectors, reservoir hosts and known disease prevalence including the influence of inter-island and PNG traffic on insect vectors.
</li>
<li>

Undertake a fieldwork program that tests and improves upon our understanding (the model) of how diseases are maintained and dispersed across the islands.
</li>
<li>

Use the results to identify appropriate responses for minimizing the risks associated with disease incursion.
</li>
<li>

Develop capacity in north Queensland in the identification and sampling of vectors and diseases
</li>
</ol>

Tags: National Environmental Research Program Tropical Ecosystems Hub, marine
Organization: Australian Ocean Data Network
NERP TE Project 10.2 - Socio-economic systems and reef resilience, 2012-2014 (JCU)

This project focuses on relationships between socio-economic systems and the Great Barrier Reef (GBR). It comprises three interrelated activities to investigate:
<ol>
<li>

Resident and tourist views about the relative ‘value’ of key ecosystem services that are provided by the reef. Researchers will design, distribute and analyse the results of a survey instrument to assess the relative value of different goods and services produced by the GBR to stakeholder groups using both traditional money-based valuation techniques and Larson’s non-monetary based technique. 
</li>
<li>

Tourist views about the relative value of key attributes of reef health, and the likely consequence if reef health deteriorates such as fewer visits and less expenditure. 
</li>
<li>

Researchers will develop  proxies for rainfall, water quality, land use and economy at the catchment scale. Analyses of these data will be used to determine the extent to which variations in beef prices, the exchange rate and other socio-economic variables (in conjunction with biophysical variables) influence water quality in the GBR lagoon.
</li>
</ol>

Tags: National Environmental Research Program Tropical Ecosystems Hub, marine
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Case Study – Baselines, monitoring and integrated ecosystems assessements: Supporting status reporting and decsion-making for Australia's marine environment and Blue Economy

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 Case Study "Baselines, monitoring and integrated ecosystems assessements: Supporting status reporting and decsion-making for Australia's marine environment and Blue Economy". 
<strong><em>A PDF of the full Case Study, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "CASE STUDY 2021 – Baselines, monitoring and integrated ecosystems assessements"</em></strong>



DESCRIPTION OF THE CASE STUDY
Recommendations in the National Marine Science Plan 2015-25 (NMSP; Treloar et al 2016) are crucial for Australia to achieve sustainable use of our marine environment and to reap the full benefits from the Blue Economy. Two recommendations are particularly relevant to SoE and other national status and trend reporting (e.g. State of the Climate, Status of Australian Fish Stocks): 
 -- Establish and support a National Marine Baselines and Long-Term Monitoring Program; 
 -- Develop a dedicated and coordinated science program to support decision-making by policy makers and marine industry in the face of challenges such as cumulative impacts, multiple pressures and social and economic considerations. 
Implementing these recommendations will also provide more complete data and information to support assessment of cumulative impacts and management effectiveness. 
Two working groups were established by the National Marine Science Committee (NMSC) to develop advice on establishing and supporting these national programs. Reports from the two working groups (Hedge et al 2021; Smith et al 2021) have recently been endorsed by the NMSC. 



[see attached Case Study for more]

DATA STREAM(S) USED IN CASE STUDY
Synthesis of literature published and expert knowledge of case study authors.

Tags: baselines and monitoring, case study, state of the environment (SoE)
Organization: Australian Ocean Data Network
WAMSI PhD Top-up - 3.9.5 - Ecology of the Indo-pacific humpback dolphin (Sousa chinensis) and bottlenose dolphin (Tursiops truncatus) found in the Ningaloo Marine Park

As part of the WAMSI PhD Top-up scholarship - the population dynamics and habitat usage of the Indo-pacific humpback dolphin (Sousa chinensis) and bottlenose dolphin (Tursiops truncatus) were studied in the Ningaloo Marine Park.

Tags: Oceans | Marine Biology | Marine Habitat, Oceans | Marine Biology | Marine Mammals
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Expert Assessment – State and Trend – Oceanic reefs

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 oceanic reefs". 
<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 - Oceanic reefs"</em></strong>



DESCRIPTION OF HABITAT/COMMUNITY/PROCESS FOR EXPERT ASSESSMENT
Assemblages of plants and animals found on shallow offshore reefs in the 0-30 m depth range. This largely relates to reefs in the Coral Sea, Elizabeth and Middleton Reefs, Lord Howe Island, Norfolk Island, and the offshore reefs in the North and North-west, based on results from the national case study ‘Australia’s changing reefs’.

DATA STREAM(S) USED IN EXPERT ASSESSMENT
Underwater visual census data from Reef Life Survey, as reported in references.  NW and Elizabeth &amp; Middleton reefs surveyed in 2013 and 2018, Lord Howe Island 2006, 2008, 2009, 2010, 2012, 2014, 2016, 2018 and 2020. Coral Sea 2012, 2013, 2016, 2017, 2018, 2019 (2020 data not yet available for assessment), Norfolk Island (2009, 2013). 
While results were based on those regions covered in the national case study ‘Australia’s changing reefs’ in which quantitative comparisons were made with standardised data, other relevant monitoring data have been collected by the Australian Institute of Marine Science, James Cook University, CSIRO and the Sydney Institute of Marine Science. It is uncertain whether trends reported here are consistent with those indicated by those other monitoring programs.



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

• 2021 •
Assessment grade: Good
Assessment trend: Deteriorating
Confidence grade: Adequate
Confidence trend: Adequate/limited
Comparability: High. This is the second assessment in a row based on standardised quantitative data from the same sources (noting that 2016 assessment was titled “Offshore banks, shoals, islands”)
• 2016 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Adequate high-quality evidence or high level of consensus
Confidence trend: Limited evidence or limited consensus
Comparability: Grade and trend are somewhat comparable to the 2011 assessment
• 2011 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Limited evidence or limited consensus
Confidence trend: Limited evidence or limited consensus



CHANGES SINCE 2016 SOE ASSESSMENT
not supplied

Tags: community structure, expert assessment, offshore reefs
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Case Study - Marine biodiversity protection in Australia

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 Case Study "Management of shared marine biodiversity values". 
<strong><em>A PDF of the full Case Study, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "CASE STUDY 2021 – Management of shared marine biodiversity values"</em></strong>



DESCRIPTION OF THE CASE STUDY
This synopsis describes arrangements for protecting marine biodiversity in accordance with Australia’s national responsibilities for the marine estate and as a party to international conventions including those for Biological Diversity, Migratory Species, World Heritage and Wetlands of International Importance.

ISSUES OF IMPORTANCE
Threats to Australia’s marine biodiversity include increasing use of the marine domain, pollution, habitat modification or loss and climate change.  Direct impacts include harvest (e.g., commercial, recreational and Indigenous fishing), bycatch, habitat disturbance and pollution, all of which may indirectly impact all ecosystem components. These pressures may act cumulatively to increase the overall impacts. 

DATA STREAM(S) USED IN CASE STUDY
Synthesis of literature published, and expert knowledge of the case study authors.

Tags: biodiversity values, case study, marine management, state of the environment (SoE)
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Expert Assessment – Management Effectiveness – Anthropogenic noise

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 "Effectiveness of Management – Anthropogenic noise". 
<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 - Effectiveness of Management – Anthropogenic Noise"</em></strong>



DESCRIPTION OF THE APPROACH TO MANAGING THE PRESSURE
The approach for managing and regulating marine activities that produce underwater noise (see marine noise pressures assessment for a full list of activities) and associated impacts on the marine environment varies, with not all sectors having formal policies for managing inputs across all relevant jurisdictions. There is currently no centralised mechanism or framework for assessing or regulating underwater noise generating activities across sectors or jurisdictions in Australia. Consideration of impacts and management measures is largely sectoral, with varying degrees of external consultatory processes. Because of this, consideration of interactions with other pressures (e.g. climate change, other sectors) and cumulative effects is often lacking (see Samuel 2020).  

DATA STREAM(S) USED IN EXPERT ASSESSMENT
Guidelines, policies and legislation produced by sectors, state/territory and Commonwealth government and processes outlined by sector regulators. See minerals, oil and gas management effectiveness for legislation associated with oil and gas extraction and production, mining and dredging activities. 
See "Supplemental information" for full list of sources.



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

• Approach •
Assessment grade: Partially effective
Assessment trend: Improving
Confidence grade: Adequate
Confidence trend: Adequate
Comparability with 2016: Comparable
• Outputs •
Assessment grade: Partially effective
Assessment trend: Improving
Confidence grade: Adequate
Confidence trend: Adequate
Comparability with 2016: Comparable
• Outcomes •
Assessment grade: Partially effective
Assessment trend: Improving
Confidence grade: Adequate
Confidence trend: Adequate
Comparability with 2016: Comparable



CHANGES SINCE 2016 SOE ASSESSMENT
Components of the assessment have changed, otherwise the assessment is consistent with that produced for the 2016 assessment (i.e. no change).

Tags: anthropogenic noise, environmental management, expert assessment, pressures
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Case Study – Australia's Blue Economy

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 Case Study "Australia's Blue Economy". 
<strong><em>A PDF of the full Case Study, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "CASE STUDY 2021 – Australia's Blue Economy"</em></strong>



DESCRIPTION OF THE CASE STUDY
The ‘blue economy’ is an increasingly accepted term for ocean-based industries that maintain environmental and social stewardship and protection (UNEP 2016, Voyer et al 2018).



[see attached Case Study for more]

DATA STREAM(S) USED IN CASE STUDY
tba

Tags: blue economy, case study, state of the environment (SoE)
Organization: Australian Ocean Data Network
Coastal Data and Charts: Department for Planning and Infrastructure, Government of Western Australia

The Department for Planning and Infrastructure has a key coastal management and protection role, which encompasses responsibilities for marine safety, the provision of maritime facilities and the sustainable use of the Western Australian coastline. An essential part of this role is the acquisition, analysis and presentation of coastal data. Here you will find a wealth of information on Western Australia's ocean conditions, including near real time wave data, tide predictions and storm surge data. To view this data click on the relevant links below.

Tags: Atmosphere | Atmospheric Temperature | Air Temperature, Oceans | Coastal Processes | Storm Surge, Oceans | Ocean Temperature | Water Temperature, Oceans | Ocean Waves | Swells, Oceans | Ocean Winds | Wind Shear, Oceans | Tides | Tidal Range, WESTERN AUSTRALIA, sea_level, sea_surface_swell_wave_significant_height, tide_height, wind_speed
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Expert Assessment – Pressure – Climate Change – Frequency and severity of extreme weather events

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 - climate change - frequency and severity of extreme weather events". 
<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 - Frequency and Severity of Extreme Weather Events"</em></strong>



DESCRIPTION OF PRESSURE
Extreme weather events represent pressures to the marine and coastal environments through severe storm-induced winds (including tropical and extratropical cyclones) which can cause wind damage and storm surges, heatwaves or shorter-term heat extremes which can stress infrastructure and natural barriers, extreme rainfall events which can cause flooding and erosion, and extreme dry conditions – in particular drought – which can stress natural coastal systems such as mangroves. Aside from the delimited identification of cyclones as either tropical (north of the Tropic of Capricorn (ToC)) and extratropical (south of the ToC), all other listed pressures can affect all coastal regions of Australia.

DATA STREAM(S) USED IN EXPERT ASSESSMENT
Literature.



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

• 2021 •
Assessment grade: High impact
Assessment trend: Unclear
Confidence grade: Somewhat adequate: Adequate high-quality evidence or high level of consensus at a national scale
Confidence trend: Limited evidence or limited consensus 
Comparability:  N/A – new assessment



CHANGES SINCE 2016 SOE ASSESSMENT
Not previously assessed.

Tags: anthropogenic pressures, climate change, environmental pressures, expert assessment, extreme weather
Organization: Australian Ocean Data Network
2021 State of the Environment Report Marine Chapter – Expert Assessment – State and Trend – Tuna and billfish

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 tuna and billfish". 
<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 - Tuna and billfish"</em></strong>



DESCRIPTION OF TAXONOMIC GROUP FOR EXPERT ASSESSMENT
This assessment focuses on those tuna and billfish species that are caught in commercial and recreational fisheries in Australian waters. Southern bluefin tuna are caught predominantly by commercial fisheries in the south-west and temperate east bioregions with recreational catches occurring in the north-west and south-east bioregions. Yellowfin, bigeye and albacore tunas, swordfish and striped marlin are predominantly caught by commercial and recreational fisheries in the north-west, south-west, temperate east and north east bioregions with recreational catches occurring in the north and in the south-east seasonally. Blue and black marlin are caught recreationally in the north, north-east, temperate east, and north-west bioregions with commercial catches of the species not permitted (Larcombe et al. 2020, NSW DPI 2018; Patterson et al. 2020a; Williams et al. 2020).

DATA STREAM(S) USED IN EXPERT ASSESSMENT
Assessment based on review of most recent stock assessments conducted by Regional Fisheries Management Organisations – see references for spatial and temporal coverage of data incorporated into assessments.



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

• 2021 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Adequate high quality evidence or high level of consensus
Confidence trend: Adequate high quality evidence or high level of consensus
Comparability: Grade and trend are comparable to the 2016 assessment
• 2016 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Adequate high quality evidence and high level of consensus
Confidence trend: Adequate high quality evidence and high level of consensus
Comparability: Grade and trend are not comparable to the 2011 assessment



CHANGES SINCE 2016 SOE ASSESSMENT
Assessment has not changed.

Tags: billfish, expert assessment, fisheries management, population status, tuna
Organization: Australian Ocean Data Network
Australian Natural Resources Atlas (ANRA)

The Australian Natural Resources Atlas (ANRA) was developed by the National Land and Water Resources Audit  to provide online access to information to support natural resource management. The Atlas was managed and maintained within the Department of the Environment, Water, Heritage and the Arts. The Atlas comprises of a number of tools and information on Australia's natural resources:

<code>* Australia's Resources Online: Generate a report containing the latest available data on Australia's natural resources against the Natural Resource Management Monitoring and Evaluation framework . (See below).
* Map Maker: View and query the data from the Atlas or make a map of a region of interest
* Natural Resource Topics: View National, State and regional theme assessments of Australia's natural resources undertaken by the National Land and Water Resources Audit in 2000-2002, and find links to other sources of natural resource data.
</code>

Tags: AUSTRALIA INCLUDING EXTERNAL TERRITORIES, Hydrosphere | Ground Water | Aquifers, Hydrosphere | Surface Water | Lakes, Hydrosphere | Surface Water | Rivers/streams, Hydrosphere | Surface Water | Stream Chemistry, Hydrosphere | Surface Water | Water Depth, Hydrosphere | Surface Water | Water Yield, Hydrosphere | Water Quality | Acid Deposition, Hydrosphere | Water Quality | Ph
Organization: Australian Ocean Data Network
Sampling of planktonic microorganisms for metagenomic, metaproteomic and metatranscriptomic analyses

Large volumes of water (200 - 500 L) were filtered and fractionated by size for various planktonic components: eukaryotic phytoplankton, prokaryotic picoplankton, and marine viruses.  Sample sites were chosen to generate the widest diversity, and included planktonic blooms, oligotrophic zones, small polynyas near sea ice, nearshore areas, and Antarctic bottom water from coastal, canyon and deepwater areas.  Half of each sample will be used for DNA library construction, and the other half will be used for meta-proteomic analysis.  Random shotgun sequencing of the marine genomic libraries should produce a metagenomic snapshot of planktonic life in a variety of marine habitats. 

This work was completed as part of ASAC project 2899 (ASAC_2899).

Tags: AMD, AMD/AU, CASO > Climate of Antarctica and the Southern Ocean, CEOS, EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > AQUATIC ECOSYSTEMS > PLANKTON > PHYTOPLANKTON, GEOGRAPHIC REGION > POLAR, IPY > INTERNATIONAL POLAR YEAR, OCEAN > SOUTHERN OCEAN, R/V AA > R/V Aurora Australis, SHIPS, phytoplankton
Organization: Australian Ocean Data Network
eDNA metabarcoding data for the publication 'Passive environment DNA (eDNA) sampling is effective for monitoring vessel biofouling in the Southern Ocean'

This data accompanies the paper 'Passive environment DNA (eDNA) sampling is effective for monitoring vessel biofouling in the Southern Ocean'. 

Samples were collected from the MPOV Aiviq in the Port of Hobart (-42.87, 147.34) and Macquarie Island (-54.500, 158.950) between September 2022 and October 2022. Passive absorption was used to collect eDNA, with perforated plastic balls with cellulose sponges inserted inside the balls were used as the eDNA absorption material. 

Samples were collected at four time points, prior to in-water cleaning (Hobart), during in-water cleaning (Hobart), post in-water cleaning (Hobart) and at Macquarie Island. All eDNA samples were amplified with two universal metabarcoding markers targeting the 18S rRNA gene V1-V3 region and part of the mitochondrial cytochrome c oxidase subunit I (COI) gene to gain a wide overview of taxa present. For species-level identification of arthropod and mollusc taxa, samples were also amplified with two group-specific metabarcoding primer sets, each targeting a region of the 16S rRNA gene 

For each sampling period, we have included the raw, unmerged FASTQ data for each marker, the zOUT fasta files and the processed zOTU table with taxonomy. The R-files for the processing pipeline of FASTQ files and data analysis pipeline are also included to complete all the analysis detailed in the manuscript.

Tags: ADS > Automated DNA Sequencer, AMD, AMD/AU, BIOFOULING, BIOSECURITY, CEOS, CONTINENT > AUSTRALIA/NEW ZEALAND > AUSTRALIA > HOBART, EARTH SCIENCE > BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > EXOTIC SPECIES, EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > PELAGIC > OCEANIC ZONE, EARTH SCIENCE > ENVIRONMENTAL ADVISORIES > MARINE ADVISORIES > MARINE BIOLOGY, EARTH SCIENCE > HUMAN DIMENSIONS > ENVIRONMENTAL IMPACTS > WATER RESOURCES, EARTH SCIENCE > HUMAN DIMENSIONS > INFRASTRUCTURE > TRANSPORTATION, EARTH SCIENCE > OCEANS > MARINE ENVIRONMENT MONITORING > MARINE SURFACE ELEMENTS > MARINE VESSELS, EDNA, ENVIRONMENTAL DNA, GEOGRAPHIC REGION > POLAR, MPOV AIVIQ, OCEAN > SOUTHERN OCEAN > MACQUARIE ISLAND, PCR, Ships
Organization: Australian Ocean Data Network