Data mobilization skills: training on mobilizing biodiversity data using GBIF and BOLD tools
The course is organised by the Siberian Institute of Plant Physiology and Biochemistry Russian Academy of Sciences (SIPPB SB RAS), University of Bergen, ForBio, Norwegian Centre for International Cooperation in Education (SIU), and Global Biodiversity Information Facility (GBIF) Secretariat. It will take place in association with the International Conference Information Technologies in the Research of Biodiversity (Irkutsk, Sept 11-14 2018).
Biodiversity data mobilization
This part of the course aims to contribute to enhancing the capacity to plan and implement biodiversity data digitization efforts effectively and according to GBIF standards. It will have a strong focus on the technical aspects of data mobilization — in particular, everything related to the data lifecycle: planning, digitization, management and online publishing in order to increase the amount, richness and quality of the data published through the GBIF network. The social aspects of the process will also be considered. The event will have online and onsite components and both will have a strong practical approach including a significant component of group work.
- Learn key concepts of biodiversity informatics, particular to biodiversity digital data management
- Introduction to the Darwin Core Standard and its components
- Learn to understand the different stages for planning a digitization project and how to adapt them to a specific project
- Learn to identify the type of data and how to best digitize relevant information using best practices and existing tools and techniques
- Learn the basic tools and concepts used for data validation and cleaning
- Learn the process of making biodiversity data freely available online, also known as data publishing, utilizing GBIF’s Integrated Publishing Toolkit (IPT)
This part of the course will focus on principles and routine in DNA barcoding. Correct species identification is fundamental for all biological research, for conservation and management of biodiversity, and for a number of practical, commercial and forensic purposes. This block will provide participants with a practical and theoretical introduction to DNA barcoding through Barcode of Life Data Systems (BOLD). Examples of problems will also be demonstrated to show some of the pitfalls and limitations with the DNA barcoding approach.
- How DNA barcodes are produced – workflow from specimen collection to digital data
- Analytical tools with the BOLD database and other useful software
- Barcode Index Numbers (BINs) and taxonomic units – species, populations or what?
- Species concepts - species discovery versus species identification
- Taxonomic feed-back loop and role of voucher specimen
- Interacting with other biodiversity databases (WORMS, GBIF, OBIS etc.)
Biodiversity data mobilization
- Develop a data mobilization strategy customized to a given institutional framework
- Apply a model to build a data mobilization strategy and the associated digitization protocols
- Evaluate a data mobilization strategy to identify potential gaps, inefficiencies and pitfalls
- Apply a digitization protocol to produce digital biodiversity data from analogue sources
- Use software tools designed to facilitate biodiversity data digitization
- Apply data cleaning protocols to evaluate and increase the fitness for use of a biodiversity dataset
- Use software tools to evaluate the fitness-for-use of a biodiversity dataset
- Use software tools designed for (biodiversity) data cleaning
- Apply a biodiversity data publishing mechanism
- Define the publishable data types and subtypes (if any) for a biodiversity dataset
- Use the GBIF IPT to publish biodiversity datasets using the appropriate extensions
- Capacitate others in the digitization, management and publishing of biodiversity data
- Learn how to operate BOLD systems either as a data provider or as a user of the database and DNA identification engine
- Obtain basic understanding of the great potentials in DNA barcoding when applied in biodiversity surveying and monitoring
- Learn how good quality DNA barcode libraries can enhance better understanding of biodiversity to the benefit of nature management, forensics, and many fields of science
Laura Russell - GBIF Secretariat
Dag Endresen - University of Oslo
Endre Willassen - University of Bergen
Torbjørn Ekrem - Norwegian University of Science and Technology
Katrine Kongshavn - University of Bergen
To make best use of the activities around this workshop, the participants should possess the following skills and knowledge:
- Basic skills in computer and Internet use, and in particular in the use of spreadsheets, databases, and tools for geographical data representation (e.g. Google maps, GIS software)
- Basic knowledge about geography and biodiversity informatics: geography and mapping concepts, basic taxonomy and nomenclature rules, and basic knowledge about GBIF and other relevant initiatives working in biodiversity informatics
- A good command of English. Course activities will be conducted in English. Russian-speaking trainers and mentors will be available and translated materials will be available
- Willingness to disseminate the knowledge learned in the workshop with partners and collaborators in your projects by adapting the biodiversity data mobilization training materials to specific contexts and languages maintaining their instructional value
Min 12, max 20 students, including 8 places reserved for participants from Russia and 8 from Norway, as required by the funding rules. Participants will be selected based on the registration forms, which includes a paragraph for motivation and importance for your work.
Local transport from and to Irkutsk, accommodation and meals at the field station are covered for all course participants. ForBio members from Norway and Russian participants enrolled in a MSc or a PhD program are supported in full, including travel. Travel support available for other participants from Russia upon request.
Arrival in the evening of 14 September from Irkutsk to the field station (local transportation provided), settling in. 15–19 September course days. Departures 20 September to Irkutsk. Travel to and from Irkutsk will be arranged for Norwegian ForBio members and Russian participants enrolled in a MSc or a PhD program. Other participants should arrange travel to and from Irkutsk themselves, but in some cases costs can be compensated, see Costs.
Participants are requested to arrange own travel insurance.
English, with limited support in Russian.
Assignment and credits
The course is equivalent to 2 ECTS. ForBio will provide certificates for those successfully completed the course assignment.
May 1st, 2018
Nataliya Budaeva (firstname.lastname@example.org) - ForBio coordinator
Dmitry Schigel - GBIF Secretariat
Alla Verkhozina - SIPPB SB RAS