AndreaBozzo/ceres-open-data-index huggingface dataset:
Salmon Coded-Wire-Tag Fishery Sampling -- Location Data

The Coded-Wire Tag (CWT) database contains the Release, Recovery, Catch/Sample, and Location data. CWT is the Pacific Region’s centralized Oracle database that holds adult salmon escapement data.

Location Data 

The geographic locations of release, sample, and specific recovery of fish are also assembled by specific location reporting agencies. Collectively, these are called Location data and are submitted to the RMPC along with all other classes of data.
There are five types of locations. Within each type of location, the location record is uniquely identified coastwide by a 19-character Location Code. That code is associated with a textual description of the location and a geographical reference to the location.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Chemical and Biological Oceanographic Conditions on the Scotian Shelf and in the Eastern Gulf of Maine during 2022

Chemical and biological oceanographic conditions observed in the Maritimes Region in 2022 are presented. Surface and deep inventories of nitrate and silicate were near or above normal in the eastern part of the region while the surface and deep phosphate inventories remained near or below normal across the region. Inventories of in situ chlorophyll-a have indicated important spatial and temporal variability across the region apart from the Bay of Fundy where below normal levels have been observed since 2014. Abnormally high surface chlorophyll-a concentrations measured by remote sensing were observed during winter 2022. Observations in recent years suggest earlier and longer spring phytoplankton blooms with higher-than-normal amplitude and magnitude. Diatom abundance has remained lower than normal in the Bay of Fundy while reaching near-normal levels on the central Scotian Shelf in the last two years. The overall zooplankton biomass and the abundance of Calanus finmarchicus and Arctic Calanus species remained mainly below normal levels in 2022. Observations from the Continuous Plankton Recorder confirm the main regional trends observed in phyto- and zooplankton abundances. Observations in Bedford Basin in recent years have indicated generally warmer-than-normal conditions, near-normal chlorophyll-a concentrations, and mainly near or higher-than-normal bottom nutrient (nitrate, silicate and phosphate) concentrations

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Ecological Risk Assessment Framework (ERAF) feasability and suitability evaluation based on a subset of Significant Ecological Components (SEC) from the Pacific North Coast Integrated Management Area (PNCIMA)

The Pacific Region ERAF provides a comprehensive approach for assessing all threats to marine ecosystems by evaluating cumulative risk from multiple activities to multiple ecosystem components for ecosystem-based management (EBM), improving upon international and national best practices in risk assessment that focus solely on single activities (e.g., ERAFs for assessing fisheries impacts) or single ecosystem-components (e.g., habitat-based risk assessments). This project aims to apply this ERAF in the Pacific Region to the Pacific North Coast Integrated Management Area (PNCIMA) as a pilot project to assess the feasibility and suitability of the ERAF as a tool for determining risk of harm to ecosystem components, and its usefulness for providing transparent and defensible science-based advice on prioritising ecological risk of different activities for ecosystem-based management and MPA management.  Because it is based on a subset of SECs and stressors affecting PNCIMA and the resulting scores have not been vetted by experts, the results of this pilot application should not be used for policy or management decisions at this stage.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Productivity (Recruits-per-Spawner) data for Sockeye, Pink, and Chum Salmon from British Columbia

We assembled productivity (i.e. recruits per spawner) estimates for British Columbian Sockeye, Pink, and Chum Salmon. Annual estimates, by brood year, of spawner numbers, catch, and population and age composition were obtained from regional experts and organized in a simple database. Time series were organized by species and biological or spatial unit (Conservation Unit, Pacific Fisheries Management Area, or aggregates of these). Data quality criteria that delineated three categories of data quality, unique to each data type (spawner, catch, and age structure estimates), were used to rate each data type by return year in each time series, and the overall recruit-per-spawner estimates were rated by brood year. The annual data quality ratings of the component data were then used to rate annual recruit-per-spawner data by species and biological or spatial unit and also to generate global estimates across all years for each time series. These data replace previously published estimates, given our more detailed exploration of temporal changes in both field assessment methods and data quality, where both will serve as a useful starting point to assist analysts with their interpretation of data reliability and results.

Ogden, A.D., Irvine, J.R., English, K.K., Grant, S., Hyatt, K.D., Godbout, L., and Holt, C.A. 2015. Productivity (Recruits-per-Spawner) data for Sockeye, Pink, and Chum Salmon from British Columbia. [Can. Tech. Rep. Fish. Aquat. Sci.](http://waves-vagues.dfo-mpo.gc.ca/Library/359366.pdf) 3130: vi + 57 p.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Important areas for Harp seal pupping and migration in the Gulf of St. Lawrence and Atlantic Ocean

This layer represents important areas for the Harp seal (Pagophilus groenlandicus). It includes the three main pupping areas for this species and migratory pathways used by Harp seals to migrate between its summering (Baffin Bay) and wintering (Gulf of St. Lawrence and Newfoundland and Labrador coasts) areas. Note that this dataset do not represent the Harp seal distribution.

Reference:

DFO. 2020. 2019 Status of Northwest Atlantic Harp Seals, Pagophilus groenlandicus. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2020/020.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Newfoundland Marine Refuge Fish Classification Dataset (N-MARINE)

N-MARINE is a marine-taxa detection and classification dataset collected in 2021 using underwater video cameras mounted on crab pots equipped with lights and bait, deployed at depths of 400–500 m within a small portion of the Northeast Newfoundland Slope Closure. Further details on survey design and acquisition procedures are provided in [1]. The dataset contains 23,936 high-resolution images (1920 × 1080 px; ~1 MB per image; ~30 GB total), each annotated with bounding boxes and species labels. Nine marine species are documented, and images may contain multiple individuals per frame. 


N-MARINE is a curated subset of 185 videos drawn from a larger corpus of 221 videos originally collected to study the impacts of seismic activity. Each video is approximately five minutes long, recorded at 30 fps. From each video, 1,500 frames were annotated, but only a subset of these annotated frames is included in the open-source release, resulting in a total of 23,936 images in the dataset. A single Fisheries and Oceans Canada (DFO) ecologist annotated all images in DIVE [2], labeling all visible organisms, including partially occluded and truncated individuals.


Images are organized by source video, and filenames/metadata encode both the video identifier and frame index, enabling users to determine whether images originate from the same or different videos. For each species, up to 3,000 positive images were randomly sampled, with all available images included when fewer than 3,000 examples existed. Additionally, 3,000 negative (background) images were randomly sampled from across the 185 videos. Annotations are provided only in YOLO-style per-video CSV files, which include both absolute pixel coordinates and normalized coordinates for each bounding box.


Morris, C. J., Ayyagari, K. D., Porter, D., Nguyen, Q. K., Hanlon, J., & Whidden, C. (2025). *Newfoundland Marine Refuge Fish Classification Dataset (N-Marine)*. Government of Canada Open Data Portal. https://open.canada.ca/data/en/dataset/2ae46860-f82a-4127-bb1f-b02e36ef6a70


Funding was provided by Fisheries and Oceans Canada and the Environmental Studies Research Fund.



References
[1] Corey Morris, Joshua Barnes, Dustin Schornagel, Christopher Whidden, and Phillippe Lamontagne. Measuring effects of seismic surveying on groundfish resources off the coast of newfoundland, canada. Journal of Ocean Technology, 16(3):57–63.
[2] VIAME Contributors. VIAME: Video and Image Analytics for Marine Environments, 5 2017.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Bellevue Beach Surface Tows - Capelin

Five fixed sites at Bellevue Beach inshore area have been sampled with surface plankton tows from 2001-2021. Emergent larvae are sampled from the first to last day of emergence in the summer (July-August), which can result in surface tows being conducted every 24-72 hours for 6-8 weeks. This larval index is an important fishery-independent index used in the capelin stock assessment. See Nakashima and Mowbray (2014) DFO Can Sci Advis Sec Res Doc 2013/091 v+27 p. for details.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Herring Biological Database (Commercial) - NL Region

We present a long-term dataset of Atlantic herring (Clupea harengus) biological and catch information collected from 1974 to 2023 in NAFO Divisions 2J3KL, in Newfoundland and Labrador, Canada. Samples were obtained from commercial catches and processed by the Department of Fisheries and Oceans (DFO). Each record corresponds to an individual fish and includes catch details (date, area, locality, gear type) and biological measurements (length, whole and gutted weight, sex, maturity, gonad weight, spawning season, age). Standardized protocols were applied but have evolved through the decades.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Chemical and Biological Oceanographic Conditions on the Scotian Shelf and in the Eastern Gulf of Maine during 2023

Casault, B., Johnson, C.L., Devred, E., and Beazley, L. 2025. Chemical and Biological Oceanographic Conditions on the Scotian Shelf and in the Eastern Gulf of Maine during 2023. Can. Tech. Rep. Fish. Aquat. Sci. 3658: vi + 57 p. https://doi.org/10.60825/4d69-8120

Nutrient and plankton metrics are assessed in the context of physical conditions observed in the Maritimes region in 2023. Sub-surface (50-150 m) nitrate inventories were spatially variable across the region in 2023 but indicated a gradual return toward near-normal levels, except in the Bay of Fundy (i.e., at Prince-5) where a record-low value was observed in 2023. Bottom nitrate concentrations during summer were predominantly below normal across the region in 2023. In situ chlorophyll-a inventories were on average higher than normal in the region in 2023. Surface chlorophyll-a concentrations measured by satellite remote sensing reached record-high values in some sub-regions in 2023. The spring phytoplankton bloom timing was later than normal with a mainly lower-than-normal intensity in 2023. The fall bloom was generally earlier than normal with a higher-than-normal intensity. Diatoms abundance at Halifax-2 indicates increasing levels over the last three years. The abundance of Calanus finmarchicus was on average slightly above normal in the region in 2023, contrasting with the low abundances observed since 2011. Pseudocalanus spp. abundance was on average above normal in the region while zooplankton biomass and the abundance of Arctic Calanus species remained mainly near or below normal levels in 2023.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Pacific Circulation Index (Winter)

This index is the cumulative summation of negative northwesterly atmospheric circulation frequency anomalies: Z (westerly), M1, (northwesterly), and M2 (southwesterly) for December through March. An increasing trend in Pacific Circulation Index (PCI) reflects increased westerly and southwesterly atmospheric circulation off the west coast of Canada.

Correct citation: J. R. King, V. V. Ivanov, V. Kurashov, R. J. Beamish, G. A. McFarlane. General circulation of the atmosphere over the North Pacific and its relationship to the Aleutian Low. (NPAFC Doc. No. 318). 18 p. Dept. of Fisheries and Oceans, Sciences Branch - Pacific Region, Pacific Biological Station, Nanaimo, BC, Canada, V9R 5K6. Arctic and Antarctic Research Institute, 38 Bering Street, St. Petersburg, Russia, 199397.

Full document: https://waves-vagues.dfo-mpo.gc.ca/Library/40961357.pdf

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Beach Core Data - Capelin

Beach core data samples consist of capelin eggs and larvae extracted from beach sites using sediment cores at high, medium and low tide. These sites are identifiable by a location or community code.  The capelin egg totals and pre-emergent larvae totals are computed annually and daily. Data series is from 1990-2012. See Nakashima and Taggart (2002) ICES J Mar Sci 59:897-908.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Aleutian Low Pressure Index

This index measures the relative intensity of the Aleutian Low pressure system of the north Pacific (December through March). It is calculated as the mean area (km²) with sea level pressure <= 100.5 kPa and expressed as an anomaly from the 1950-1997 mean. A positive index value reflects a relatively strong or intense Aleutian Low. The index was completely regenerated using a new method in 2015.  The new method produces Aleutian Low Pressure Index (ALPI) values that are comparable to previously published values (1900-2008), and there is no difference in the periods with positive or negative values. To make use of this index, you are requested to cite the manuscript (below).  

Correct citation: Surry, A.M., and King, J.R. 2015. A new method for calculating ALPI: The Aleutian Low Pressure Index. Can. Tech. Rep. Fish. Aquat. Sci. 3135: v + 31 p.

Full document: http://waves-vagues.dfo-mpo.gc.ca/Library/359380.pdf

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Pacific Region Commercial Salmon Fishery Post-Season Catch Estimates

The Fishery Operations System (FOS) is the Department of Fisheries and Oceans Canada’s (DFO) centralized Oracle database that holds commercial salmon fishery catch, effort and biological data. The FOS database was built in 2001 and continues to be the current repository for all data pertaining to DFO’s Pacific Region Commercial Salmon Logbook program. The Commercial Salmon Logbook program was initiated in 1998 with fleet wide participation made mandatory during the 2001 season. The program requires all commercial salmon fishers to record their daily catch and effort information in a harvest logbook and to subsequently report it to DFO using a service provider within deadlines defined in the conditions of licence. A portion of the information collected from the logbook program contains fisher personal information and is therefore protected and un-releasable. Fishery Managers use the fisher reported catch and effort, in addition to information collected from other sources such as overflights, to calculate post-season catch estimates.

NOTES:
This report contains ONLY commercial catch estimates; it DOES NOT include test fishing, recreational or First Nations data.
Consult the applicable Fishery Manager or Biologist as to the status of particular catch estimates.
All catch estimates are reported in pieces (numbers of fish).
Catch estimates include adults and jacks combined. 

DFO Salmon Catch Statistics and Logbook Reports: http://www.pac.dfo-mpo.gc.ca/stats//smon/index-eng.html

DFO Integrated Fisheries Management Plans (IFMP): http://www.pac.dfo-mpo.gc.ca/fm-gp/ifmp-eng.html

DFO Management areas - Pacific Region: https://www.pac.dfo-mpo.gc.ca/fm-gp/maps-cartes/areas-secteurs/index-eng.html

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01–1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.

Cite this data as: Lisa A. Johnson, Suzanne C. Dufour, Derek D.N. Smith, Anthony J. Manning, Bulbul Ahmed, Sherry Binette, Dounia Hamoutene. Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. Ecotoxicology and Environmental Safety. Volume 268. 2023. 115683. ISSN 0147-6513. https://doi.org/10.1016/j.ecoenv.2023.115683

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Modelling the dispersion of infectious salmon anemia virus from Atlantic salmon farms in the Quoddy Region of New Brunswick, Canada and Maine, USA

Pathogen dispersal from infected aquaculture sites into the surrounding ocean poses risks of infection to wild and farmed species but is difficult to predict. This study aimed to build a framework using an ocean circulation and a particle tracking model in conjunction with a dynamic infection model and a virus inactivation model to simulate the dispersal of the infectious salmon anemia virus (ISAV) from Atlantic salmon farms. Simulated particles were released from hypothetically infected farms and advected by modelled currents. Inactivation of viral cohorts by ambient ultraviolet radiation and natural microbial communities was simulated during advection. Simulations showed that ISAV concentration varied spatiotemporally with the progression of the outbreak, current speed and direction, tidal elevation amplitude, and environmental decay. Connectivity among aquaculture sites varied in relation to seaway distances, though simulations showed that connectivity can also be asymmetrical between farm sites. Sensitivity analyses showed that the dispersal of ISAV was moderately sensitive to uncertainty associated with the viral decay model, highlighting the importance of obtaining accurate estimates of inactivation rates of ISAV. This framework provides an approach to simulate waterborne viral transmission that considers the biology and epidemic features of significance for pathogens and the dynamic conditions of the ocean.

Cite this data as: Fuhong Ding, Nellie Gagné, Delphine Ditlecadet, Brady K. Quinn, and Marc Trudel. 2024. Modelling the dispersion of infectious salmon anemia virus from Atlantic salmon farms in the Quoddy Region of New Brunswick, Canada and Maine, USA. FACETS. 9(): 1-19. https://doi.org/10.1139/facets-2023-0156

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Chemical and Biological Oceanographic Conditions on the Scotian Shelf and in the Eastern Gulf of Maine during 2024

Casault, B., Johnson, C.L., Devred, E., Clay, S., and Beazley, L. 2025. Chemical and Biological 
Oceanographic Conditions on the Scotian Shelf and in the Eastern Gulf of Maine during 2024. 
Can. Tech. Rep. Fish. Aquat. Sci. 3744: vi + 58 p. https://doi.org/10.60825/p6ad-1k52
Nutrient and plankton conditions were assessed in the context of physical conditions observed 
in the Maritimes Region in 2024. Nutrient depletion was widespread across the region, with 
Prince 5 (P5) station recording its tenth consecutive year of below-normal surface and 
subsurface nitrate inventories, while Cabot Strait section recorded record-low inventories for 
surface nitrate, silicate, and phosphate. Lower nutrient conditions likely influenced 
phytoplankton productivity, as chlorophyll-a measured in situ or derived from satellite remote 
sensing was mainly near or below normal across the region. The spring phytoplankton bloom 
was earlier than normal in the eastern area, near normal in the central area, and later than 
normal in the western area of the region. The intensity of the spring bloom was mainly normal to 
slightly below normal regionwide (except for Lurcher Shoal). The onset of the fall phytoplankton 
bloom was delayed across most areas, with the Eastern Scotian Shelf indicating a record-late 
onset. The intensity of the fall bloom was variable but mainly within near-normal ranges.
Calanus finmarchicus abundance was near normal for the core sections, but negative and 
positive anomalies were recorded at the Halifax-2 (HL2) and P5 stations, respectively. 
Pseudocalanus spp. abundance reached record-high levels for the Halifax section, but was 
otherwise near normal. Mesozooplankton biomass was above normal at P5 but mainly below 
normal elsewhere, with record-low biomass observed at HL2. Arctic Calanus species and 
warm-water offshore copepods mainly remained at or below normal abundances, while 
warm-water shelf copepods showed near-normal abundances except for negative anomalies 
observed for the Halifax section and at P5.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada