Abstract:
This dataset contains quality-controlled georeferenced occurrence records of three Arctic Calanus species (Calanus finmarchicus, C. glacialis and C. hyperboreus), downloaded from the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) databases. Records span about 150 years of sampling (1870-2017), are located between 30 and 90 degrees north, and are distributed between the surface and 5000m deep. Physical (bathymetry) and environmental (temperature and sea-ice concentration) parameters are matched to each occurrence record. An html file provides the annotated source code for the data processing, analyses and figures produced for the publication: Freer JJ and Tarling GA (2023) Assessing key influences on the distribution and life-history of Arctic and boreal Calanus: Are online databases up to the challenge? Front. Mar. Sci. 10:908112.
This work was funded by DIAPOD (NE/P006213/1) and CHASE (NE/R012687/1) projects as part of the Changing Arctic Ocean Programme, with the former funded by the UKRI Natural Environment Research Council (NERC) and the latter, jointly by NERC and the German Federal Ministry of Education and Research (BMBF). Further support was provided by BIOPOLE National Capability Multicentre Round 2 funding from the Natural Environment Research Council (NE/W004933/1).
Keywords:
Arctic, GBIF, OBIS, sampling bias, winter, zooplankton
Freer, J., & Tarling, G. (2023). Processing and analysis of Arctic Calanus occurrence records from OBIS and GBIF databases (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/a5cbfbe1-6fa6-44cf-96fe-db92c32b69d0
| Access Constraints: | None. |
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| Use Constraints: | Data are released under the Open Government Licence V3.0: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/. |
| Creation Date: | 2023-03-27 |
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| Dataset Progress: | Complete |
| Dataset Language: | English |
| ISO Topic Categories: |
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| Parameters: |
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| Personnel: | |
| Name | UK PDC |
| Role(s) | Metadata Author |
| Organisation | British Antarctic Survey |
| Name | Dr Jennifer J Freer |
| Role(s) | Investigator |
| Organisation | British Antarctic Survey |
| Name | Prof Geraint A Tarling |
| Role(s) | Investigator |
| Organisation | British Antarctic Survey |
| Parent Dataset: | N/A |
| Reference: | Freer JJ and Tarling GA (2023) Assessing key influences on the distribution and lifehistory of Arctic and boreal Calanus: Are online databases up to the challenge? Front. Mar. Sci. 10:908112, https://doi.org/10.3389/fmars.2023.908112. Becker JJ, Sandwell DT, Smith WHF, Braud J, Binder B, Depner J, Fabre D, Factor J, Ingalls S, Kim SH, Ladner R, Marks K, Nelson S, Pharaoh A, Trimmer R, Von Rosenberg J, Wallace G, Weatherall P (2009) Global bathymetry and elevation data at 30 arc seconds resolution: SRTM30_PLUS. Marine Geodesy 32:355-371, https://doi.org/10.1080/01490410903297766. Locarnini RA, Mishonov AV, Baranova OK, Boyer TP, Zweng MM, Garcia H, Reagan JR, Seidov D, Weathers K, Paver CR, Smolyar I (2018) World Ocean Atlas 2018, Volume 1: Temperature. In: Mishonov A (ed) NOAA Atlas NESDIS 81, https://www.ncei.noaa.gov/sites/default/files/2020-04/woa18_vol1.pdf. Walsh JE, Chapman WL, Fetterer F, Stewart JS (2019) Gridded Monthly Sea Ice Extent and Concentration, 1850 Onward, Version 2. NSIDC: National Snow and Ice Data Center, Boulder, Colorado USA, https://dx.doi.org/10.7265/jj4s-tq79. Flanders Marine Institute (2018). IHO Sea Areas, version 3. Available online at https://www.marineregions.org/. https://doi.org/10.14284/323. |
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| Quality: | Data processing steps carried out on the raw downloaded files are outlined in detail in the html file of annotated source code. In brief, records were excluded if they were erroneously located on land, in the Pacific sector or in the southern hemisphere; were not identified to species level; had missing identifiers for month or year of collection. Metadata fields for "sampling protocol" ad "lifestage" were cleaned by re-categorising entries into a condensed set of inputs. Duplicate records were removed as defined by records that had the following identical identifiers: species, longitude, latitude, year, month, day, minimum and maximum collection depth (OBIS), average collection depth (GBIF), life-stage. Lastly, cleaned OBIS and GBIF data were combined into a single dataset and duplicate occurrences between databases were removed using the same identical identifiers listed above. Records where average sample collection depth was greater than bathymetric depth were flagged and removed when creating appropriate figures. | |
| Lineage: | Data from OBIS were accessed on 12-01-2023 and data from GBIF were accessed on 13-01-2023. To maintain consistency, all encounters were treated as presence only, i.e. no weighting was given to records with information on abundance, biomass or number of individuals and no absence records were included. Raw downloaded data and the contributing dataset citations are provided for both databases (see Section "Related datasets"). Subsequent data processing and cleaning steps are outlined in section "Quality". All cleaned records, regardless of dataset origin, were matched to seafloor bathymetry using a 0.25 x 0.25 decimal degree resolution raster grid (Becker et al., 2009). Cleaned records from OBIS had fields for maximum and minimum collection depth. These data were matched to vertically resolved temperature data from the 2018 World Ocean Atlas (Locarnini et al., 2018) and seasonal sea-ice concentration data from the National Snow and Ice Data Centre (Walsh et al., 2019). Both temperature and sea ice grids had a resolution of 0.25 x 0.25 decimal degrees. Code_frontiers_2023.html (22 MB) - HTML output from Quarto (implemented in R) that provides the annotated source code to reproduce the data cleaning, analysis and figures from this dataset has been included in the publication. |
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| Temporal Coverage: | |
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| Start Date | 1870-01-01 |
| End Date | 2017-12-31 |
| Spatial Coverage: | |
| Latitude | |
| Southernmost | 30 |
| Northernmost | 90 |
| Longitude | |
| Westernmost | -180 |
| Easternmost | 180 |
| Altitude | |
| Min Altitude | N/A |
| Max Altitude | N/A |
| Depth | |
| Min Depth | 0 m |
| Max Depth | 5000 m |
| Location: | |
| Location | Arctic |
| Detailed Location | N/A |
| Location | North Atlantic Ocean |
| Detailed Location | N/A |
| Data Collection: | All analyses were carried out in R version 4.2.1. |
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| Data Storage: | calanus_clean_nodups_gbif.csv (24.4 MB) - This file contains the cleaned and quality controlled occurrence records of Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus from the GBIF database. Only relevant fields are included calanus_clean_nodups_obis.csv (51.5 MB) - This file contains the cleaned and quality controlled occurrence records of Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus from the OBIS database calanus_clean_nodups_obis_envdat.csv (59.7 MB) - This file contains the cleaned and quality controlled occurrence records from OBIS that are present in the file calanus_clean_nodups_obis.csv. In addition, bathymetry, temperature and sea ice data have been extracted for each occurrence based on the depth, season and year of the occurrence collection calanus_clean_nodups_gbifobis.csv (56.7 MB) - This file contains the cleaned, quality controlled, and merged occurrence records of Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus from GBIF and OBIS IHO_seas_modified (46 MB), regions (.dbf, .shp, .shx, .cpg, .sbn, .sbx) - shapefile of IHO seas and regions used when plotting counts of Calanus records per region. It is a modified version of original shapefile (Flanders Marine Institute (2018). IHO Sea Areas, version 3. Available online at https://www.marineregions.org/. https://doi.org/10.14284/323), limited to areas of interest and smaller regions combined for ease of plotting 4 x txt with the description of data columns and units for each csv file together with a xcsv header. 3 x zip files of OBIS raw data downloads. |
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