the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
PANABIO: A point-referenced pan-Arctic data collection of benthic biotas
Dieter Piepenburg
Thomas Brey
Katharina Teschke
Jennifer Dannheim
Paul Kloss
Miriam L. S. Hansen
Casper Kraan
Abstract. Profound environmental changes, such as drastic sea-ice decline, leave large-scale ecological footprints on the distribution and composition of marine biotas in the Arctic. Currently, the impact of such stressors is not sufficiently understood due to the lack of pan-Arctic data that allow for estimating ecological baselines, as well as modelling current and forecast potential changes in benthic biodiversity and ecosystem functioning. Here, we introduce a PAN-Arctic data collection of benthic BIOtas (PANABIO), and discuss its timeliness, potential, and details of its further development. The data collection contains records of benthic fauna at genus-level or species-level identified in field samples obtained by means of grabs, towed gear, or seabed imaging. Currently, it includes records of 2,968 species or genera, ranging from presence to counts, densities or biomass, grouped per sample. The data represent the pan-Arctic realm, covering all major marine areas, i.e., the central Arctic Ocean, Chukchi Sea, East Siberian Sea, Laptev Sea, Kara Sea, Barents Sea (incl. White Sea), Svalbard waters, Greenland Sea, Norwegian Sea, Canadian Archipelago, Beaufort Sea, and Bering Sea. All data are point-referenced sampling locations. Currently, 124,040 records from 10,645 samples taken at 10,631 stations between 1800 and 2014 are included, but these numbers will increase with more data becoming available. The data collection is available in a PostgreSQL-based data warehouse that can be accessed and queried through an open-access frontend web service at https://critterbase.awi.de/panabio. A snap shot of the current data collection (of 26 June 2023) is also available from the data publisher PANGAEA.
- Preprint
(5612 KB) - Metadata XML
- BibTeX
- EndNote
Dieter Piepenburg et al.
Status: final response (author comments only)
-
RC1: 'Comment on essd-2023-263', Paul E. Renaud, 22 Aug 2023
Review of Piepenburg et al: PANABIO
With the recognition by researchers and funding agencies of the importance of archiving of research data we have seen a large increase in the availability of data for future comparative studies, use in other research activities (e.g. broad-scale modelling), and potentially a knowledge base for management. This will certainly increase the longevity and usefulness of the data, but this has also led to many (relatively) small data sets published in a wide variety of data outlets, many of which are not fully accessible and/or require registration, passwords, etc. This is counterproductive for the goals of requiring data publication. This ms describes a compilation of data from fragmented and previously unpublished data sources such that it useful. Benthic biota are important integrators of ecological conditions, and thus have the potential to track regional changes due to climate variability and other human impacts. Therefore, PANABIO, is an extremely valuable extension of the (not publicly available) ArcOD database.
This descriptive manuscript justifies and describes the database quite well. It gives a range of potential uses and ideas for upgrades that may be made in the future. The text is well written and the manuscript is complete. There are several inaccuracies/inconsistencies I would like to see remedied before final publication. But please see the last comment below regarding access to the database itself (not the ms).
- In several locations the data are summarized at 'genus or species' level. A quick look at the data suggests that, contrary to the text on l 77, there are also data from fauna identified only to higher taxonomic levels (listed under 'Ranks' in Critterbase). Please clarify.
- On l 60 it is indicated that the domain of the database is the AMAP definition of the Arctic, but Fig. 2 and Table 1 indicate data from around 1500 stations from the Sea of Japan and Gulf of Ohkotsk. This area is not included in the AMAP definition so the text should be modified to both include these regions and explain why it is important to include them in a treatment of Arctic benthos.
- On l 69-70 the authors indicate that more data will be added with a wider temporal range and spatial sampling density. This implies that some data sets/repositories have been identified. Perhaps a list of these would be useful. I am also curious how this will be accomplished. Is this an automated or semi-automated process or are we dependent on future funding (making this perhaps less likely to occur)?
- Is it important that data sets on seafloor topography, chl a etc. (l 128) be included in a database on benthic fauna? Sure this could be helpful for someone who is looking for just these parameters to evaluate these data, but there is an entirely different set of files, data sources, and challenges involved. I suggest this database focus on faunal data.
- I am a little surprised that the numbers of stations and samples in the database are nearly identical. Benthic (grab) sampling is often conducted with triplicate (or higher) levels of replication. Were replicates pooled or omitted in some way?
- Note: I have gone into the database and it seems the front-end needs a bit of work to be user friendly. I was also not able to download any data, and it seems to hang up. Perhaps it is not quite ready for public use yet (there is a news item on the Critterbase site indicating major upgrades are being done). Shouldn't this all be in place when/before this ms is published/ officially accepted?
Citation: https://doi.org/10.5194/essd-2023-263-RC1 -
RC2: 'Comment on essd-2023-263', Anonymous Referee #2, 07 Sep 2023
The ms presents a PANABIO data collection that gathers records of benthos at species and/or genus level collected by various sampling gears. At the moment it holds over 124,000 records from samples taken at over 10,000 stations in years from 1800 to 2014. It is a very valuable initiative and such open databases are very needed for the Arctic scientific (and not only) community. I fully agree with Authors that open access databases, especially with quantitative ecological data, are essential for pan-Arctic comprehensive analyses and crucial in our work on understanding ecological processes in the Arctic Ocean, and I think Authors well justify the need for such data collection. They also provide good overview of what PANABIO offers in comparison to other available databases and good arguments why PANABIO is needed. In my opinion presented data set is significant and very useful, and of high quality, and should be published.
I have however some minor questions that are listed below.
- Material and Methods, 2.1. Authors refer to Fig. 1 and Table 1 which shows the pan-Arctic study area. It does however look very broad with Table 1 listing also e.g. Sea of Japan in the Pacific and the Fig. 1 is probably bit misleading as it shows quite far south locations in both Pacific and Atlantic e.g. North Sea (which are however not listed in Table 1). Adding a line showing the most southern border of the data (stations) included would be helpful, and maybe a short justification for including non-Arctic locations can also be added.
- Material and Methods 2.3 – are only species and genus included or also higher taxonomic levels? If in original data set only higher taxonomic levels were present were these excluded from PANABIO?
- Data availability – a detailed information on the number of records and samples is provided. Later Authors say that the data set is expanding and new records are being added continuously. If this is the case it would be useful to add the exact date (instead of saying just “currently”).
- Outlook – Authors declare that there are plans to collect and include more information on the environmental settings that will supplement the existing data on benthos. That would be a very valuable add-on. Since plans to expand the benthic data are mentioned earlier a short information on that process here would be useful.
- A general comment: I visited PANABIO and tried to download some data. It does however work very slow and I was not successful with neither downloading nor showing data on the map. Is that because the work is still in progress?
Citation: https://doi.org/10.5194/essd-2023-263-RC2 -
RC3: 'Comment on essd-2023-263', Anonymous Referee #3, 19 Sep 2023
The overall goal of the manuscript is to describe the open access availability of benthic data (genus and species level, presence, abundance and/or biomass) obtained from various archives over the pan-Arctic scale. The ability to link data sets from various archives into one open access portal will provide a valuable and timely location for accessing data within a changing Arctic system. The plan for PANABIO is to connect both benthic faunal data sets as well as include associated environmental data. The strength of this effort is to have one open access portal for benthic faunal data that would be QA/QC'd for accuracy. It is important that there be doi numbers to the original data sets so that the user could go back to the original archived files for evaluating data quality, lead investigator interactions, and find associated detailed metadata that may not be translated directly to the PANABIO file. I do see some missing benthic files that would be appropriately linked to PABABIO, so there should be a clear mechanism for interested scientists to direct PANABIO managers to connect to those published data files. Overall, I rank the manuscript as well-written and publishable, with minor revisions as listed above and more specifics below.
Specific comments:
Line16-17: species or genus samples, but only the means of replicates will be provided. Files that have actual individual replicate data vs. means should also be identified in a table on the site.
Line 18-19: You mention the pan-Arctic collections, but your data files go further than the defined area. Since this is an Arctic-centric paper (central arctic basins and shelf systems), shouldn’t you only list those species occurring in the pan-arctic region and not other areas, such as off Japan?
Line 24: I was able to look at the snapshot of data, but not download the file. Is this something that would be live by the time the paper is published?
Line 35 and line 43: You cite the footprint paper for Wassmann et al 2011, but not the updated footprint paper by Brandt et al 2023. Should you not include the results from this updated footprint paper in your manuscript?
Line 38: please correct the portion of sentence “…not only represents an own, specifically…” What is “an own” referring to?
Line 69-71: The data citation location is an example of an initial evaluation and the authors state that more data will be added as the project progresses. There should be an easy and explicit procedure for the community to send doi numbers of already nationally archived species/genera benthic data to this open source project. How will you engage with the wider science community to solicit further benthic data that has already been submitted to individual country data archives to connect to the PANABIO project? Also, there needs to be a detailed record of where the raw data is located, the doi number in the national archive, and associated metafiles.
Line 127-129: The authors suggest adding raster information on bottom depth, sea-ice and ocean dynamics, or Chlorophyll a distribution patterns. However, this should be secondary activities or even just listing the doi for those type data available in archives to start. I suggest the ice cover parameter is not at a low enough scale, but some metric of the percent ice cover over a certain amount of days over the sampling site is more appropriate. Also, sediment parameters (TOC, grain size, sediment chlorophyll) would be valuable data for future modeling activities. Again, the authors should provide clear mechanisms for scientists interested in collaborating on PANABIO to connect known benthic data and ancillary environmental data doi numbers to the open access plans for this program.
Table 1 and Figure 1 show data zones outside the pan-Arctic direction of PANABIO. The authors should explicitly explain why regions outside the pan-Arctic focus are being included in PANABIO.
Citation: https://doi.org/10.5194/essd-2023-263-RC3
Dieter Piepenburg et al.
Dieter Piepenburg et al.
Viewed
| HTML | XML | Total | BibTeX | EndNote | |
|---|---|---|---|---|---|
| 215 | 44 | 14 | 273 | 7 | 8 |
- HTML: 215
- PDF: 44
- XML: 14
- Total: 273
- BibTeX: 7
- EndNote: 8
Viewed (geographical distribution)
| Country | # | Views | % |
|---|
| Total: | 0 |
| HTML: | 0 |
| PDF: | 0 |
| XML: | 0 |
- 1