The International Science Council’s Committee on Data (CODATA) and World Data System (WDS), and the Research Data Alliance (RDA) are delighted to announce that the 2021 edition of International Data Week (IDW 2021) will be held on 8–11 November 2021 in Seoul, South Korea. IDW 2021 will be hosted by the Korea Institute of Science and Technology Information (KISTI), committed by the ...
The World Data System of the International Science Council (ISC) together with ISC's Committee on Data , GO FAIR , and the Research Data Alliance (RDA)—the four major international data organizations—are pleased to outline their joint commitment to work together to optimize the global research data ecosystem and to identify the opportunities and needs that will trigger federated ...
Owing to the exceptional circumstances the world is currently facing concerning the COVID-19 pandemic, the International Science Council has decided to extend the deadline for EoIs to Sunday, 31 May 2020. The WDS International Programme Office (WDS-IPO) was created in March 2011. Since then, it has been hosted by the National Institute of Information and Communications Technology (NICT) ...
We are very sorry that, in light of the current circumstances, WDS, ABC, FAPESP, and RDA have agreed to POSTPONE the Second LAC Workshop to a future date, not yet defined. This was a very difficult decision to take, and we hope the community understands. The event has attracted considerable attention, with over 200 people pre-registered, and we want to ensure that it will ...
WDS–ECR Data Curation and Management Workshop
A Blog post by Agneta Ghose (2019 WDS–ECR Training Workshop Participant)
If ‘Data is the new gold’ then it certainly must be managed. Science has always valued data. Scientific data are not only an output of research but also an input to new hypotheses, enabling scientific insights and driving innovation. Therefore, accountability, transparency, and verifiability of science make data preservation and sharing part of scientific integrity.
The World Data System (WDS) recently organized a training workshop for early career researchers (ECRs) on data curation and management. The workshop was held at the Institute de Physique du Globe, Paris on 6–8 November 2019. The objective of this workshop was to familiarize ECRs with the methods and jargon used in research data management in addition to introducing future challenges and technological solutions to data management. In this blog, I would like to share the key messages from the informative presentations at this workshop.
Members of the WDS Scientific Committee (WDS-SC), Programme and Technology Offices, and ECR Network presented and discussed methods to ensure how research data remains findable, accessible, interoperable and reuseable (i.e., FAIR). This was reinforced by an interactive exercise, in which the attendees spoke about their personal challenges in accessing, storing, and managing data. This discussion showed us how the challenges are similar across scientific disciplines.
The workshop began with an introduction into understanding what are ‘data’ and their attributes. Aude Chambodut and Alice Frémand explained the characteristics of research data such as their origin, type, size, and format. These characteristics influence data management; specifically, how to access, process, store, and reuse data. We were introduced to the data lifecycle, which refers to the sequence of stages that data go through from their initial generation to their eventual archival and/or deletion at the end of their useful life. The longevity of research data can be increased by implementing a Data Management Plan (DMP), which provides guidelines on how data are to be handled throughout their lifecycle, (i.e., during and after a research project). In principle, a DMP is a pre-requisite when applying for major EU funding, but Isabelle Gärtner Roer and Alice Frémand explained to us the practicality of developing and implementing these plans in relation to our research. Ensuring a robust DMP increases research efficiency, re-enforces scientific integrity, and most importantly promotes innovation by improving the accessibility of data. Most universities and research institutions have platforms that provide advice and support on research data services. For an ECR, it is worth reaching out to these services to understand the recommended DMP in their research domain.
Research Data Life Cycle. Sourced from Massey University: https://www.massey.ac.nz/massey/research/library/library-services/research-services/manage-data/manage-data_home.cfm
We were introduced to the resources available for rigorous data management that will ensure our research data remain FAIR. Sandy Harrison explained the value of Open Data in scientific research. She elaborated on how datasets produced from scientific work are increasingly deposited into data repositories. This is a better alternative to including these only as supplementary materials to a journal paper. Repositories provide long-term data archiving; ensure high technical standards with the possibility of updates. Moreover, publishing research data on Open Access platforms adds to their discoverability. It is important to note that not all research data needs to be openly available. Data can be kept private, but information that the data exists and what are the pre-conditions of accessing it must be shared. Ensuring data accessibility must not take away credit from those who produce data. To prevent or discourage unauthorized use or commercial exploitation, it is important to disclose knowledge (data) safely. Ioana Popescu discussed the importance of copyright and licensing. Different conditions and types of Creative Common Licenses are available to ensure data providers receive due credit, or to determine whether the data is available for commercial use, and so on.
On data interoperability, Elaine Faustman introduced ontologies and knowledge graphs, which define the concepts and relationships between data. Ontologies are useful to turn data into machine-readable formats, and thus connect them to the semantic web: an extension of the World Wide Web that contains machine-readable data. Embedding semantics is advantageous, especially when working with heterogeneous data sources. Karen Payne discussed how data have increased in volume, velocity, and variety over the years (i.e., Big Data). In 2018, the International Data Corporation estimated the global data sphere had reached 33 zettabytes (1 zettabyte = 1 x 1012 gigabytes). The volume and variety in data influences their management. To address issues with Big Data and complex computing, cloud computing resources have been developed that are delivered over the Internet. Cloud computing refers to virtual resources—such as infrastructure resources, services, and applications—orchestrated by management and automation software so they can be accessed by users on-demand through self-service portals. Automatic scaling and resource allocation support these portals.
Technical barriers to data sharing include incomplete datasets or unguaranteed services such as datasets that do not contain what they claim to! Moreover, certification standards play an important role in establishing trust, and hence sustaining the opportunities for long-term data sharing. Rorie Edmunds presented the certification procedures and framework available for data repositories. Certification standards such as the CoreTrustSeal look at technical, organizational, and financial infrastructure, as well as legal aspects, workflows, and risk management. Depositing data into certified repositories ensures longevity, discoverability of one’s data, in addition to access to recognized expertise to address technicalities. On the other hand, those using data from certified databases have the ability to verify results, know the provenance, and even give feedback to the data producer.
With an overview of the various resources available for data management, participants were asked to revisit both the DMPs they had started to create on their respective research projects, as well as the challenges identified at the beginning of the workshop. The workshop definitely helped clarify most of the concerns the attendees had expressed. Personally, it was a great learning experience, and I am grateful to have been selected for this workshop. During the past few months since the workshop took place, I have become much more aware about data management within the realm of my project, as well as having discussions on this with my colleagues. I know that this workshop was the first WDS training event for ECRs, I am glad to have been a part for it, and would definitely recommend it to my peers. Finally, I acknowledge the work of everyone involved in the organization of the workshop. I hope that there are many more such workshops in the future, and especially aimed at ECRs.
Isabelle Gärtner Roer and Aude Chambodut ask whether the Workshop addressed the participants’ RDM Challenges
Metadata Stewardship in Genetic Research: Enabling a Research Community Toward Best-practice
A Blog post by Libby Liggins (2019 WDS Data Stewardship Award Winner)
For over four decades, scientists have been collecting genetic DNA sequence data for thousands of the world’s species. In the biodiversity and eco-evolutionary sciences, these data are generated to describe new species, define their evolutionary relationships, determine the levels of dispersal among populations, and assess levels of genetic diversity across a species range. The rate at which we accrue these DNA sequences has increased over time as the use of genetic data has diversified, and the sequencing technologies used to decode the DNA sequences of organisms have become faster, cheaper, and much higher through-put. As this trend continues into the future, it is anticipated that we may soon have more DNA sequences in a digital form than we have existing in the natural world.
This massive and growing data resource could now be consolidated for multiple species and populations and reused to better understand the world’s biodiversity at the genetic level. Genes are recognized as a fundamental component of the biodiversity hierarchy, but have received less attention than species- and ecosystem-level measures of biodiversity. In part, this may be due to synthetic analyses of genetic data being challenging and sometimes impossible, as there has been no concerted effort towards the curation and stewardship of this valuable data resource. While funding agencies and publishers advocate deposition of DNA sequence data in open-access repositories (such as the National Center for Biotechnology Information; and the European Bioinformatics Institute), they do not require the deposition of standardized metadata such as the sampling location, date, and habitat of the sampling event (Pope et al. 2015). This ‘metadata gap’ means that information essential for multispecies analyses to better understand biodiversity and evolutionary patterns across our globe, has not been readily available.
The Genomic Observatories MetaDatabase (GEOME; Deck et al. 2017) has recently provided a solution to this metadata gap. GEOME links ecologically and evolutionarily relevant metadata with DNA sequences uploaded to open-access repositories. The metadatabase incorporates the latest international standards for biodiversity and genomic data, and helps researchers store and access genetic data relevant to studies concerning large scale biodiversity and conservation problems. In conjunction with the open-access DNA sequence repositories, GEOME ensures that researchers and projects generating genetic data can adhere to the FAIR Principles (Findable, Accessible, Interoperable, Reusable; Wilkinson et al. 2016), promoting research community best-practice.
The Ira Moana Project logo. The Māori phrase Ira Moana could be interpreted as meaning ‘ocean genes’ or ‘dot in the ocean’. Both seem appropriate when thinking about the scale of DNA in the vastness of the ocean. The use of te reo Māori (Māori language) resonates with the project objectives that are uniquely New Zealand, as is the Māori language. Yet, moana is used to describe the ocean by many Pacific nations, reminding us of the connections that New Zealand’s biodiversity has with the wider Pacific region.
The Ira Moana Project has partnered with GEOME both to enable a collaborative network of researchers to adhere to these standards in community best-practice, and deliver a searchable metadatabase for the genetic data of Aotearoa New Zealand’s marine organisms. The Project aims to build and maintain the most comprehensive national database of marine genetic data in the world, ensuring kaitiakitanga (guardianship and stewardship) and creating opportunities for data synthesis to inform New Zealand’s future research directions and conservation decisions. The Ira Moana Project builds on the success of the Diversity of the Indo-Pacific Network (DIPnet) that through the use of GEOME and multi-national collaboration, has created the largest population genetic database in the world. DIPnet consolidated over 200 genetic datasets for Indo-Pacific marine organisms, and is now delivering novel biodiversity insights for the Indo-Pacific Ocean (e.g., Crandall et al. 2018), which is the largest and one of the most threatened biogeographic regions on our globe.
The Ira Moana Project is similarly founded in concern for the marine environment. New Zealand is a marine nation—we have one of the largest exclusive maritime economic zones in the world, which sustains our marine and tourism industries, and provides significant recreational and social benefits for New Zealanders. Nationally, and as global citizens, we are under pressure to make informed decisions regarding commercial and recreational activities, and how they can be balanced with the protection of our marine ecosystems. Such decisions of environmental, economic, and societal impact need to be transparent and based on robust information, as well as including knowledge about biodiversity that stretches from ecosystems to genes. The Ira Moana Project has established that there are over 430 genetic datasets for New Zealand marine organisms, and is now working to consolidate these data for the benefit of future researchers and generations of New Zealanders.
The data lifecycle in genetic research. DNA sequence data is routinely deposited into open-access genetic data repositories (under OUTPUTS). Despite metadata being accrued at every step of research (*), starting with COLLECTION, the practice of depositing metadata into repositories such as the Genomics Observatory Metadatabase (GEOME) is very recent. The Ira Moana Project is one of the project’s using the infrastructure provided by GEOME. Stewardship of metadata alongside DNA sequence data ensures that genetic research in the biodiversity, ecological, and evolutionary sciences can be reproducible, the genetic data can be re-used, and that the provenance of the genetic data and the rights of the local communities involved in the research are maintained.
As the first national project to make use of the GEOME infrastructure, the Ira Moana Project has worked with GEOME to extend the capability of the metadatabase to additionally acknowledge indigenous rights. It has become apparent that what is considered fair and equitable research practice within the research community, may not be fair and equitable within broader society. Through collaboration with Local Contexts and Te Mana Rauranga (the Māori Data Sovereignty Network), the Ira Moana Project and GEOME are now beta-testing the capacity for researchers to add Notices (such as the Traditional Knowledge Notice; TK Notice) and new Biocultural Labels as metadata for DNA sequence data. Notices signal that there are accompanying Indigenous rights needing further attention for any responsible and equitable future use of the data. Biocultural Labels further allow the addition of provenance information and community expectations for future use based on Indigenous Data Sovereignty principles—including the CARE Principles (Collective Benefit, Authority to Control, Responsibility, Ethics) launched by the Global Indigenous Data Alliance—thereby enabling Indigenous stewardship and persistent recognition of Indigenous rights within an international framework (complying with the Nagoya Protocol to the Convention on Biological Diversity). The implementation of Notices and Biocultural Labels using GEOME infrastructure is a first for a biological resource and for genetic data, establishing new ethical standards in this research community.
Workshops and datathons for New Zealand researchers have encouraged uptake and use of the metadata infrastructure provided through the Ira Moana Project and GEOME. There are now greater than 85 researchers who have joined the Ira Moana Project Network; being part of the network means being ‘on-board’ both with the things that the Ira Moana Project is trying to achieve for New Zealand, and the metadata standards that GEOME is accommodating for researchers worldwide. As there is a global community of researchers who generate genetic data, it will be some time before there is universal uptake of these newly recognized standards of best-practice. Nonetheless, we should be encouraged by the fact that as a community, we have made similar transformations in our practice in the past; since the introduction of the Joint Data Archiving Policy, it has been considered standard practice to deposit genetic data into open-access repositories. As such, we anticipate that the Ira Moana Project metadatabase will continue to grow and serve New Zealander’s, and there will be increasing uptake of the services that GEOME provides to the research and wider community.
– Crandall ED, Riginos C, Bird CE, Liggins L, Treml E, Beger M, Barber PH, Connolly SR, Cowman PF, DiBattista JD, et al. 2019. The molecular biogeography of the Indo-Pacific: Testing hypotheses with multispecies genetic patterns. Global Ecology and Biogeography. 58(5):403–418.
– Deck J, Gaither MR, Ewing R, Bird CE, Davies N, Meyer C, Riginos C, Toonen RJ, Crandall ED. 2017. The Genomic Observatories Metadatabase (GEOME): A new repository for field and sampling event metadata associated with genetic samples. PLoS Biology. 15(8):e2002925.
– Pope LC, Liggins L, Keyse J, Carvalho SB, Riginos C. 2015. Not the time or the place: the missing spatio‐temporal link in publicly available genetic data. Molecular Ecology. 24(15):3802-9.
– Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 3
Use of Data from Citizen Observatories to Complement GEOSS Repositories – Experiences from EU Funded Projects
A Blog post by Ioana Popescu (WDS Scientific Committee Member)
Citizen science is getting more and more attention worldwide; in particular, there is a growing interest in involving citizens in data collection due to its capability to complement the acquisition of data classically accomplished through existing complex instrumentation networks. Scientists have experimented with multiple forms of citizen science projects, which have been successfully implemented in many fields. The value of using citizen contributions has been proven—or at least explored—in almost all scientific domains, and its potential is currently also being investigated in the processes of decision- and policy-making.
There are many definitions of citizen science. The definition most often used is that of Buytaert et al. (2014): The participation of the general public (i.e. non-scientists) in the generation of new knowledge. In this blog post, I focus on citizen science from the perspective of data collected by citizens and the use of these data, but there is also much research looking into how to involve citizens, and consequently, how they are participating in the collection of data. Taking the latter viewpoint, there is now lots of terminology that can be found in the literature; for example, citizen observatory (CO), citizen sensing, trained volunteers, crowdsourcing, community-based monitoring, volunteered geographic information, eyewitnesses, and so on.
As mentioned in the title, I would like to spend the remainder of this blog post briefly introducing four Horizon 2020 funded projects that have used innovative technologies for collecting data with the help of citizen scientists. The projects ran from the second half of 2016 until mid-2019, and were clustered under WeObserve, which examines the challenges faced by COs in terms of awareness, acceptability, and sustainability. They shared the specific goal that their final (analyzed and processed) data products would not only complement existing data elements within the Global Earth Observation System of Systems (GEOSS), but also become new GEOSS contributions.
SCENT (Smart Toolbox for Engaging Citizens into a People-Centric Observation Web)
Citizens were engaged in environmental monitoring of land-cover/use changes using their smartphones and tablets, enabling them to become the ‘eyes’ of the policymakers. In particular, the project looked at two pilots—the urban case of the Kifisos river in Attica, Greece and the rural case of the Danube Delta in Romania—where the citizen-collected data were used to assess flood models and flooding patterns. You can read more about this project here.
LANDSENSE (Connecting citizens with satellite imagery to transform environmental decision making)
The focus of this project was on the potential of Earth observations taken by citizen scientists to augment and improve the way we see, map, and understand the world. Three main areas of application were selected as demonstrators: urban landscape dynamics, agricultural land use, and forest and habitat modelling. Read more about LANDSENSE here.
Data collection cycle for citizen science campaigns in water management. The study focus is highlighted in yellow. (Taken from IEEE article: Citizens’ Campaigns for Environmental Water Monitoring: Lessons From Field Experiments.)
Groundtruth2.0 (How to impact decision making with citizen observatories)
The interaction was investigated between people and technology when it comes to setting up a successful system for land and natural resources management. The project combined the social dimensions of COs and enabling technologies so that the implementation of each observatory was tailored to its envisaged societal and economic impacts with a specific emphasis on flora and fauna, as well as water availability and quality. Find out more about the project here.
GROW (Grow Observatory)
In this project, citizen scientists collected information on land, soil, and water resources to answer a long-standing challenge for space science; namely, the validation of soil moisture detection from satellites. Read more here.
Buytaert, W., et al: Citizen science in hydrology and water resources: opportunities for knowledge generation, ecosystem service management, and sustainable development, Front. Earth Sci., 2, 26, doi: 10.3389/feart.2014.00026, 2014.
Health Data Challenges Regarding ‘Scientific Medical Processing Challenges’
A Blog post by Marc Nyssen (WDS Scientific Committee Member)
Recently, the biomedical and clinical engineers who are associated with the International Federation for Medical and Biological Engineering (IFMBE) and also belonging to the International Union for Physical and Engineering Sciences in Medicine (IUPESM)—the umbrella organization linking the engineers at IFMBE and the medical physics experts at the International Organization for Medical Physics—took the initiative to include competitions called ‘scientific challenges’ as a part of their conferences. The purpose of these challenges is to encourage young researchers to develop their skills by showing how they can extract information from biomedical datasets and report on their results.
A ‘challenge call’ is made public a few months before the conference alongside a deadline for the result papers, which are then evaluated by a jury. Introduced by Prof Paulo Carvalho from Coimbra University in Portugal and Prof Ratko Magjarevic from Zagreb University in Croatia, the challenges have proved quite successful, with the participation of 20–30 groups of young researchers responding to the first call.
A major problem for the organizers, however, has been to find adequate datasets containing well-documented biomedical data, such as respiratory measurements, electroencephalography recordings, electro-cardiac recordings, and the like. While many state that Big Data is widely accessible and available, well-documented and consistent biomedical datasets are difficult to find. This has resulted in the IFMBE having to actually sponsor teams to collect appropriate datasets of biomedical measurements specifically for the ‘scientific challenge’ competitions!
To address such issues, programmes are now being started that encourage universities and research groups in the Biomedical Sciences to make their datasets public while taking adequate precautions to protect the privacy of patients when such datasets are linked to physical persons. IFMBE is currently exploring practical ways to constitute collections of well-documented biomedical datasets that comply with the FAIR principles and that are made publicly available to researchers via a repository. Moreover, it is encouraging member societies at large to take up similar schemes either themselves or via universities.
To be continued...