Setting up data infrastructure to simplify management of (ecological) data, to facilitate publishing using open community standards (foremost as a Darwin Core Archive) was centre stage for the discussion at our miniworkshop this week.

One of the activities we are engaged with currently is to develop R-functionality that help researchers in ecology and related fields to manage their data (see e.g. this blog post for more about the topic). To this end, we have started to collect functions in an add-on library for statistical software R, called LivingNorwayR. The work is just initiated, so the package is very much in development. However, the idea is that we will develop a set of functionality that will facilitate:

• Metadata creation, by reading from the core data files
• Quality control of data
• Matching taxonomy to selected databases
• Mapping to and reading from Darwin Core
• Reading and writing Darwin Core Archives
• Visualizing the geographic extent of data
• …. and many other features

Wednesday this week, we met to discuss the state of the project, including a brain storming session to voice ideas about additional functionality to include as we move forward with the development. There are still some major decisions to be taken regarding the general programming approach, and the functions have not yet found their final form. Please keep watching out for updates on the project!

Want to learn more or contribute – visit our GitHub site for this project:

• GitHub

Good data management routines underpins the FAIR principles for scientific data management and stewardship. For many projects, a starting point will be to set up a logical folder structure in which to store all files associated with the data collected.

Within such a folder structure, different versions of the data (field notes, raw data, mapped data, and scripts used for data transformation and mapping) deserves designated folders. In addition, data documentation (i.e. data management plans and metadata) must be included in the “data package”. Not all projects will rely on the same underlying data flow model, but in our experience most field based ecology projects still have sufficient overlap in terms of data flow to make it worthwhile suggesting a common folder structure for field data projects.

Beyond making it easier for the individual researchers or data management units to keep their data well organized, an important endpoint is to facilitate publication of the “data package” at the appropriate stage in the project life cycle. Thus, the folder structure should facilitate e.g. publishing of the mapped data as a Darwin Core Archive (and preferentially register the data set with GBIF). Also the raw data could be easily extracted and archived in a generalist repository.

As part of our work in Living Norway, we have made a draft function for software R (https://www.r-project.org/) to facilitate setting up such a folder structure. You can read more about the proposed functionality here.

If you have input to the workflow and folder structure and workflow model we are proposing, you are welcomed to contribute by posting an issue on our GitHub repo for this project.

Towards openness and transparency in Applied Ecology

Ecology is a discipline that tries to understand nature and how changes affect it. How is the diversity of organisms dispersed around the world? How do extreme climate changes influence populations of animals and vegetations? These are all questions regularly asked, and topics that are necessary to address for providing evidence for policymaking and management. 

Unfortunately, much ecological data needed to answer these challenges are currently not available to the research community. Even though there is a rapidly increasing awareness of the importance of ecological data, it is equally vital not only to collect the data but also making data Findable, Accessible, Interoperable and Reusable (FAIR). While an open data culture is clearly emerging in ecology, there are many steps that needs to be taken to improve to make most data FAIR.   

These are the challenges Erlend Birkeland Nilsen, project manager for the Living Norway Ecological Data Network and senior scientist at NINA, invites you to explore at a two days colloquium held in Trondheim this fall. You will get the opportunity to discuss solutions to these thrilling challenges in collaboration with Nordic and international partners within the field of biodiversity informatics, says Nilsen.  

Many scientific journals now demand scientists to share their data openly. Nature, for example, recently endorsed the FAIR Data initiative, which entails authors to put their data on public repositories, where available. However, the real benefit of FAIR, Nilsen argues, is that it helps you demonstrate the impact of your research when people re-use and cite your dataset, it leads to new collaborations and hence benefits the researchers to come. 

–I look forward to two days filled with fruitful discussions with some of the best researchers in the field, with policymakers, research publishers and young scientists, he says.    

No parallel sessions – only plenaries!

On day 1, the program will include a range of plenary presentation covering topics related to open science and FAIR data management in applied and basic ecology. Each session will be completed with a panel discussion.

On day 2, we will arrange two workshops that will extend the discussions from day 1. Before lunch, we will arrange a workshop on education and training in open science and FAIR data management. This workshop will be organized in collaboration with SFU bioCEED (https://bioceed.w.uib.no/). After lunch, we will arrange a workshop on statistical modelling of new open data sources. We will, in particular, discuss models that integrate information from a range of different data sources simultaneously. This workshop will be arranged in collaboration with SFF Centre for Biodiversity Dynamics (CBD; https://www.ntnu.edu/cbd).

The conference has an unusual arrangement, all plenaries. All of them are worth attending and makes your schedule all filled up. These means that you do not have to choose; just sit down and enjoy!  

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Join the colloquium either in-person or virtually! During these challenging times of Covid-19, we understand the apprehension about making plans to attend a conference. This is why we are developing plans to ensure that everyone will have an opportunity to participate in the Living Norway Colloquium, be it in person or virtually. Whatever you choose, remember to register for the event.

TENTATIVE PROGRAM

Venue: The colloquium and workshops will be located at NINA-huset in Trondheim, or you can participate virtually.

Date: October 12^th – 13^th 2020.

Registration: You can register to the colloquium, the lunches and dinner here.

The colloquium is supported by funding from the Research Council of Norway.

The plan on day 1 is to have a series of lectures covering three main topics. A panel discussion will follow each session. The lecturers will be from various sectors, both from Norway and abroad. The tentative program for day 1 is as follows: 

Written by Benjamin Cretois, Lasse F Eriksen and Wouter Koch – PhD students at The Norwegian University of Science and Technology.

There is a rapidly increasing awareness of the importance of ecological data. With the climate crisis and global biodiversity loss as a background for much of today’s ecological research, we cannot afford wasting any resources in the search for more knowledge. Thus, as scientists we have to be aware of not only the need for collecting data, but also how we make the most of the data we collect. A part of this is making data Findable, Accessible, Interoperable and Reusable (FAIR). This was highlighted during the 2 days Living Norway seminar at the Norwegian Institute for Nature Research (NINA) last week, where a group of ca. 70 participants met to discuss the challenges, opportunities and infrastructure needed to improve the ways data is shared within the scientific community.  

What is FAIR and how to develop this paradigm within the scientific community, a recurrent theme of this seminar

First day was dedicated to introducing the participants to the Open Science philosophy, emphasizing that a FAIR management of data is a step forward to this scientific ideal. Finding and formatting data is a difficult and time consuming step in research as it can take up 79% of the researcher’s time (Data Science report 2016, CrowdFlower). It is critical that scientists agree on standards for data and metadata as it would facilitate its traceability and use.

Finding data can be difficult and time consuming for a scientist

This way of managing data is also intended to render data more relevant and readable for environmental policy and management structures as Ingunn Limstrand from the Norwegian Environment Agency highlighted this in particular. This would facilitate policy decisions and trust between policy makers and scientists. Even though implementing the Open Science ideal is challenging, big data platforms such as the Global Biodiversity Information Facility (GBIF) are facilitating the process as they pay attention to make their data FAIR.

The second day was rich in ideas and discussion but also disagreements as two workshops took place. The first workshop stressed the importance of data that are not digitized but bear a great value as they carry valuable temporal information. These are called legacy data and can take the form of museum collection samples, paper notes or old undocumented spread sheets. The afternoon workshop aimed to settle an important question: How could and should Open Science be implemented in biodiversity education? Participants agreed that the way to do Open Science and more generally good data management, should be taught as soon as possible in the University curriculum.

Availability of data will enable scientists to dedicate more resources to seek results and less time to perform data collection, thus increase the efficiency in all fields, not the least climate and biodiversity research. In that sense, as Einar Hjorthol from the Norwegian Biodiversity Information Centre reminded us in the introductory talk, this seminar is a part of the work of saving the planet.