This respository contains the slides and Q&A of the SCAR 2022 Structuring and Managing Biological Data Workshop on 8 August 2022.
The Antarctic and Sub Antarctic region are hosts to unique biodiversity. Due to the remoteness and harsh environment, this biodiversity often remains poorly described despite similar threats to the rest of the globe. As such The biodiversity data collected in this region is of high scientific value. This workshop aims to train scientists to structure and manage their biological data more effectively and conform to internationally used biodiversity data standard formats, saving precious time in preparing data for analysis or online archiving. This workshop is organised by the SCAR Antarctic Biodiversity Portal in the framework of the topical collection “Antarctic and Southern Ocean biodiversity” of the Pensoft “Biodiversity Data Journal”. The SCAR Antarctic Biodiversity Portal is a community effort that supports the publication of Biodiversity data in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable) and the provisions of the Antarctic Treaty System (scientific observations and results from Antarctica shall be exchanged and made freely available).
We are still open for submissions. If you would like to submit your dataset for this special issue, please send an email to data-biodiversity-aq(a)naturalsciences.be
Two publications are expected:
- We expect the dataset to be published to GBIF and OBIS (if it is a marine dataset). You can do it through us or other GBIF/OBIS nodes. To publish the dataset to GBIF and OBIS, the dataset has to be compliant to Darwin Core standard. We uses Integrated Publishing Toolkit (IPT) to publish the dataset into Darwin Core Archive which is then harvested by GBIF and OBIS.
- The data paper will be submitted through ARPHA platform. See more in the slides
We recommend to publish microbial data using DNA-derived data extension according to GBIF's guidelines - Publishing DNA-derived data through biodiversity data platforms. Perhaps section 2.1 onwards is most relevant for your reading.
When you login to https://arpha.pensoft.net/, click on the "View dashboard" button. Your manuscripts should be listed in the dashboard.
The publishing organizations in IPT is not a free text field. There are only a number of organizations that are associated with an IPT instance. If you are publishing the dataset with another IPT instance other than ours, please select the organization responsible for publishing (producing, releasing, holding) the dataset. It will be used as the resource's publishing organization when registering this resource with GBIF and when submitting metadata during DOI registrations. It will also be used to auto-generate the citation for the resource (if auto-generation is turned on), so consider the prominence of the role. Please be aware your selection cannot be changed after the resource has been either registered with GBIF or assigned a DOI.
You may want to consider adding the antarctic dataset to the SCAR Network upon publishing it via the IPT.
If the SCAR Antarctic Biodiversity Portal funds you to publish the data paper, please include the following line in acknowledging the funders in the metadata (EML):
The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the Framework of EU-Lifewatch as a contribution to the SCAR Antarctic biodiversity portal (biodiversity.aq)
We would appreciate it if locations in decimal degrees are recorded to at least and ideally 4 decimal places.
We currently set the deadline to be 31 March 2023 for the data paper publication
- ARPHA Writing Tool: https://arpha.pensoft.net/
- Example data paper: https://bit.ly/3JyNfI4
- Pensoft Guidelines: https://zookeys.pensoft.net/about#AuthorGuidelines
- Tidy data: https://r4ds.had.co.nz/tidy-data.html#tidy-data
- Cookiecutter project structure: https://github.com/cookiecutter/cookiecutter
- Naming things by Jenny Bryan: https://speakerdeck.com/jennybc/how-to-name-files
- ANDS FAIR self-assessment tool: https://ardc.edu.au/resources/working-with-data/fair-data/fair-self-assessment-tool/
- FAIRDAT assessment tool (prototype): https://www.surveymonkey.com/r/fairdat
- How FAIR is your data?: https://forms.gle/eBagszpWKVz5NKpp7
- A cartoon that explain coordinate precision: https://xkcd.com/2170/
- OpenRefine: https://openrefine.org/
- Darwin Core validator: https://www.gbif.org/tools/data-validator/about
- WoRMS Taxon Match: https://marinespecies.org/aphia.php?p=match
- PGC Coordinate Converter: https://www.pgc.umn.edu/apps/convert/
- Biodiversity Information Standards (TDWG): https://www.tdwg.org/
- Global Biodiversity Information Facility (GBIF): https://www.gbif.org/
- Ocean Biodiversity Information System (OBIS): https://obis.org/
- SCAR Antarctic Biodiversity Portal: https://www.biodiversity.aq/
- World Register of Marine Species: https://marinespecies.org/index.php
- Bionomia: https://bionomia.net/
- Darwin Core Quick Reference Guide: https://dwc.tdwg.org/terms/
- Darwin Core extension: https://rs.gbif.org/extension/
- OBIS manual: https://manual.obis.org/
- Biodiversity.aq data publication wiki: https://github.com/biodiversity-aq/data-publication/wiki
- Publishing DNA-derived data through biodiversity data platforms: https://docs.gbif.org/publishing-dna-derived-data/1.0/en/
- Pensoft guidelines: https://zookeys.pensoft.net/about#AuthorGuidelines
Thank you Anton Van de Putte for giving the presentation and our student intern Aaron Roex for assisting the workshop organization. We appreciate everyone who attended the workshop. I thank myself for being awesome.