Basics of taxonomy

28 October - 8 November 2019

Course description
Biological taxonomy is the fundamental discipline that deals with the description, naming, classification and identification of organisms. It is the essential unifying backbone for organising and interrelating all biodiversity information. Especially with the current biodiversity crisis, there is an increasing need of sound taxonomic information and expertise for the successful implementation of biodiversity policies and management programs. However, the last decades are witnessing a continuous loss of taxonomic expertise, because of redirected research priorities, budgetary cuts, and the fact that taxonomy is disappearing from academic curricula. The transfer of taxonomic knowledge and skills to new generations is however crucial to counter this trend of declining taxonomic expertise, which hampers the study and conservation of biodiversity. Therefore, there is a pressing need for high quality training that prepares students for future taxonomic careers. Furthermore, as the volume of available biological information is ever-increasing so is the need for digital skills and competencies across scientists. Discovering, evaluating, understanding and analysing data at an unprecedented scale and rate is needed to enable taxonomy to contribute towards urgent societal challenges. To meet this need and to increase the interest, knowledge and skills in taxonomy, a two and a half-weeks theoretical and practical course are be organised to offer students and early career researchers from the WIO-region the opportunity of acquiring fundamental expert knowledge in taxonomy. A wide variety of topics are covered to learn how to describe, illustrate and write about biodiversity using different methods and techniques.

• DELTA (DEscription Language for TAxonomy)
Participants will learn the basics of DELTA as well as the great potential of the program. DELTA is an advanced computer program developed by CSIRO (Commonwealth Scientific & Industrial Research Organisation, Australia) to handle all kinds of taxonomic data in the most optimal way. It is currently regarded as the state of the art tool in modern taxonomy and used by taxonomists to (re)describe taxa in a standardised format, which makes the information readily available for comparative (phylogenetic) studies, cataloguing of fauna lists and construction of interactive illustrated keys. Processing time and quality control of the data is being optimized by DELTA, as all data have to be treated in an identical manner.
The introduction of the course will provide an overview of current international biodiversity aggregators, such as the Global Biodiversity Information Facility, the Ocean Biogeographic Information System, Tree of Life and GenBank. Attention will be given to the Biodiversity Information Standards (developed by the Taxonomic Databases Working Group) which aim to improve efficient exchange of biodiversity data. Subsequently, the main part of the course will focus on learning to use the DELTA program. Participants are encouraged to bring species (or higher level) data of their taxon of interest, which will be used to correctly build a database, construct interactive illustrated keys and generate natural language species descriptions.

• Digital drawing
Participants will learn to make scientific illustrations with the digital drawing method using the software program Adobe Illustrator. In many labs, this has become a standard method for making taxonomic descriptions, as there are great advantages in working speed, editing the illustrations and the ease of creating very smooth lines. The resulting vector graphics have very small file sizes, high resolution and they can be directly processed by most online journals. Photos and micrographs can be used as a master for making the line drawings. A solution for the illustration of complex details (like setae) will be offered by making libraries for these structures. Also, one evening will be dedicated to giving an overview of different techniques for macrophotography, including photography stacking, how to edit in Zerene stacker, and photoshop.

• Scientific illustration
Participants will learn to understand the human perception of illustrations. They will be informed about a variety of illustration methods and will practise a limited number of these. Besides the illustration of biological specimens, specific technical aspects of diagrams, tables, typography and posters will be included as well.
Following topics will be covered:
- Theories behind the use of illustrations for various scientific purposes
- Human perception of illustrations
- Composition, colour theory, choice of illustration method
- Short history of scientific illustrations
- Aids like camera lucida
- Black and white methods like copper graphics, charcoal, pencil and black ink
- Colour methods like watercolour, crayons, coloured pencils, pastel, computer graphics and airbrush

• Scientific writing and communication
Participants will learn the particularities of writing and presenting scientific studies. Main emphasis will be placed on writing the most common form of publication, i.e. the primary scientific paper. The course will explain the current structure of scientific literature, the main features of the scientific information 'industry', and the particular rules and customs followed by the international scientific community when publishing. Particular attention will be given to little taught aspects of the publication process, such as choosing a suitable forum for a scientific paper, practicalities of preparing and submitting a manuscript, dealing with editors and the printing process. Less emphasis will be placed on grammar and use of English, except for certain details of language use and style. The correct preparation of figures and tables for publication will be extensively discussed, as well as the different aspects of participating in international conferences (posters, talks, personal interactions).
Following main topics will be covered:
- The scientific literature: structure, purpose, prestige, types of publications
- How to write scientific papers: before you begin
- Basic decisions: what, how, when. Gathering intelligence about the unknown
- Parts of an article: IMRAD
- How to write the main parts of a scientific paper
- Supporting parts and their importance
- Figures and tables
- Submitting a manuscript
- Stages to publication: what happens when and where?
- How to handle the stages of the publication process
- Other types of papers: posters
- Talks and scientific conferences: how to perform and participate?

e-Taxonomy and biodiversity informatics tools and workflows
This module will provide an overview of the vision, history and future of biodiversity and e-taxonomy informatics. It will develop your understudying of the landscape, key concepts and terminology in the field, the networks, services, tools and standards that make up the informatics assembly and the challenges associated with the design and management of this science infrastructure. Additionally you become familiar with the key actors and platforms in the domain along with samples of how biodiversity informatics is enticing and empowering scientist to use data in new and innovation. Students will utilise a suite of freely accessible biodiversity resources and open tools to tackle biogeographical and taxonomic questions. The module also aims at demonstrating, through hand-on-experience, how students can structure, annotate and publish their datasets online in forms that enable scientific re-use of data.

Course language

Target audience
Late MSc students, PhD students, and early career researchers.
Criteria for selection will be motivation and usefulness of the training for your career.

Storgaten 43
1440 Drøbak


Dr. Matz Berggren, Department of Marine Sciences, University of Gothenburg
Dr. Charles Oliver Coleman, Museum für Naturkunde, Berlin
Dr. Tomas Cedhagen, Department of Biosciences - Aquatic Biology, Aarhus University
Dr. Gábor Lövei, Department of Agroecology - Crop Health, Aarhus University
Dr. Dimitrios Koureas, Naturalis Biodiversity Center

Participant quota
18 people
**Course will be cancelled if the number of 18 participants is not reached.

This includes course fee, teaching material, accommodation, and meals. Travel is not included.

Please fill in the online application here.

Application deadline
1 August 2019

Payment deadline and details will be provided upon acceptance to the course.

ForBio is a co-organiser of this course and provides financial support. It will cover the registration fee and travel costs for members (not associates) registered at Norwegian universities and research institutes.

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith