scholarly journals From Raw Biodiversity Data to Indicators, Boosting Products Creation, Integration and Dissemination: French BON FAIR initiatives and related informatics solutions

2019 ◽  
Vol 3 ◽  
Author(s):  
Yvan Le Bras ◽  
Aurélie Delavaud ◽  
Dominique Pelletier ◽  
Jean-Baptiste Mihoub
Keyword(s):  
Environmental Data ◽  
Observation System ◽  
Biodiversity Data ◽  
Digital Products ◽  
Raw Data ◽  
Biodiversity Research ◽  
Ecological Information ◽  
Data Products ◽  
Analytical Tools ◽  
Biodiversity Information

Most biodiversity research aims at understanding the states and dynamics of biodiversity and ecosystems. To do so, biodiversity research increasingly relies on the use of digital products and services such as raw data archiving systems (e.g. structured databases or data repositories), ready-to-use datasets (e.g. cleaned and harmonized files with normalized measurements or computed trends) as well as associated analytical tools (e.g. model scripts in Github). Several world-wide initiatives facilitate the open access to biodiversity data, such as the Global Biodiversity Information Facility (GBIF) or GenBank, Predicts etc. Although these pave the way towards major advances in biodiversity research, they also typically deliver data products that are sometimes poorly informative as they fail to capture the genuine ecological information they intend to grasp. In other words, access to ready-to-use aggregated data products may sacrifice ecological relevance for data harmonization, resulting in over-simplified, ill-advised standard formats. This is singularly true when the main challenge is to match complementary data (large diversity of measured variables, integration of different levels of life organizations etc.) collected with different requirements and scattered in multiple databases. Improving access to raw data, and meaningful detailed metadata and analytical tools associated with standardized workflows is critical to maintain and maximize the generic relevance of ecological data. Consequently, advancing the design of digital products and services is essential for interoperability while also enhancing reproducibility and transparency in biodiversity research. To go further, a minimal common framework organizing biodiversity observation and data organization is needed. In this regard, the Essential Biodiversity Variable (EBV) concept might be a powerful way to boost progress toward this goal as well as to connect research communities worldwide. As a national Biodiversity Observation Network (BON) node, the French BON is currently embodied by a national research e-infrastructure called "Pôle national de données de biodiversité" (PNDB, formerly ECOSCOPE), aimed at simultaneously empowering the quality of scientific activities and promoting networking within the scientific community at a national level. Through the PNDB, the French BON is working on developing biodiversity data workflows oriented toward end services and products, both from and for a research perspective. More precisely, the two pillars of the PNDB are a metadata portal and a workflow-oriented web platform dedicated to the access of biodiversity data and associated analytical tools (Galaxy-E). After four years of experience, we are now going deeper into metadata specification, dataset descriptions and data structuring through the extensive use of Ecological Metadata Language (EML) as a pivot format. Moreover, we evaluate the relevance of existing tools such as Metacat/Morpho and DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) in order to ensure a link with other initiatives like Environmental Data Initiative, DataOne and Long-Term Ecological Research related observation networks. Regarding data analysis, an open-source Galaxy-E platform was launched in 2017 as part of a project targeting the design of a citizen science observation system in France (“65 Millions d'observateurs”). Here, we propose to showcase ongoing French activities towards global challenges related to biodiversity information and knowledge dissemination. We particularly emphasize our focus on embracing the FAIR (findable, accessible, interoperable and reusable) data principles Wilkinson et al. 2016 across the development of the French BON e-infrastructure and the promising links we anticipate for operationalizing EBVs. Using accessible and transparent analytical tools, we present the first online platform allowing the performance of advanced yet user-friendly analyses of biodiversity data in a reproducible and shareable way using data from various data sources, such as GBIF, Atlas of Living Australia (ALA), eBIRD, iNaturalist and environmental data such as climate data.

scholarly journals Contribution of Citizen Science to Biodiversity Data Mobilization in Russia

2020 ◽  
Vol 4 ◽  
Author(s):  
Natalya Ivanova ◽  
Maxim Shashkov
Keyword(s):  
New Species ◽  
Protected Areas ◽  
Citizen Science ◽  
Biodiversity Data ◽  
Breeding Bird ◽  
Breeding Bird Atlas ◽  
Research Grade ◽  
Taxonomic Groups ◽  
Species Occurrences ◽  
Biodiversity Information

Currently Russia doesn't have a national biodiversity information system, and is still not a GBIF (Global Biodiversity Information Facility) member. Nevertheless, GBIF is the largest source of biodiversity data for Russia. As of August 2020, >5M species occurrences were available through the GBIF portal, of which 54% were published by Russian organisations. There are 107 institutions from Russia that have become GBIF publishers and 357 datasets have been published. The important trend of data mobilization in Russia is driven by the considerable contribution of citizen science. The most popular platform is iNaturalist. This year, the related GBIF dataset (Ueda 2020) became the largest one for Russia (793,049 species occurrences as of 2020-08-11). The first observation for Russia was posted in 2011, but iNaturalist started becoming popular in 2017. That year, 88 observers added >4500 observations that represented 1390 new species for Russia, 7- and 2-fold more respectively, than for the previous 6 years. Now we have nearly 12,000 observers, about 15,000 observed species and >1M research-grade observations. The ratio of observations for Tracheophyta, Chordata, and Arthropoda in Russia is different compared to the global scale. There are almost an equal amount of observations in the global iNaturalist GBIF dataset for these groups. At the same time in Russia, vascular plants make up 2/3rds of the observations. That is due to the "Flora of Russia" project, which attracted many professional botanists both as observers and experts. Thanks to their activity, Russia has a high proportion of research-grade observations in iNaturalist, 78% versus 60% globally. Another consequence of wide participation by professional researchers is the high rate of species accumulation. For some taxonomic groups conspicuous species were already revealed. There are about 850 bird species in Russia of which 398 species were observed in 2018, and only 83 new species in 2019. Currently, the number of new species recorded over time is decreasing despite the increase in observers and overall user activity. Russian iNaturalist observers have shared a lot of archive photos (taken during past years). In 2018, it was nearly 1/4 of the total number of observations and about 3/4 of new species for the year, with similar trends observed during 2019. Usually archive photos are posted from December until April, but the 2020 pandemic lockdown spurred a new wave of archive photo mobilisation in April and May. There are many iNaturalist projects for protected areas in Russia: 27 for strict nature reserves and national parks, and about 300 for others. About 100,000 observations (7.5% of all Russian observations) from the umbrella project "Protected areas of Russia" represent >34% of the species diversity observed in Russia. For some regions, e.g., Novosibirsk, Nizhniy Novgorod and Vladimir Oblasts, almost all protected areas are covered by iNaturalist projects, and are often their only source of available biodiversity data. There are also other popular citizen science platforms developed by Russian researchers. The first one is the Russian birdwatching network RU-BIRDS.RU. The related GBIF dataset (Ukolov et al. 2019) is the third largest dataset for Russia (>370,000 species occurrences). Another Russian citizen science system is wildlifemonitoring.ru, which includes thematic resources for different taxonomic groups of vertebrates. This is the crowd-sourced web-GIS maintained by the Siberian Environmental Center NGO in Novosibirsk. It is noteworthy that iNaturalist activities in Russia are developed more as a social network than as a way to attract volunteers to participate in scientific research. Of 746 citations in the iNaturalist dataset, only 18 articles include co-authors from Russia. iNaturalist data are used for the management of regional red lists (in the Republic of Bashkortostan, Novosibirsk Oblast and others), and as an additional information source for regional inventories. RU-BIRDS data were used in the European Russia Breeding Bird Atlas and the new edition of the European Breeding Bird Atlas. In Russia, citizen science activities significantly contribute to filling gaps in the global biodiversity map. However, Russian iNaturalist observations available through GBIF originate from the USA. It is not ideal, because the iNaturalist GBIF dataset is growing rapidly, and in the future it will represent more than all other datasets for Russia combined. In our opinion, iNaturalist data should be repatriated during the process of publishing through GBIF, as it is implemented for the eBird dataset (Levatich and Ligocki 2020).

scholarly journals Assessment of riparian environments through semi-automated procedures for the computation of eco-morphological indicators: Preliminary results of the WEQUAL project

2019 ◽  
Vol 70 (3) ◽  
pp. 131-145 ◽  
Author(s):  
Raimondo Gallo ◽  
Gianluca Ristorto ◽  
Alex Bojeri ◽  
Nadia Zorzi ◽  
Gabriele Daglio ◽  
...  
Keyword(s):  
Data Collection ◽  
Unmanned Aircraft ◽  
Environmental Data ◽  
Shared Environment ◽  
Surface Model ◽  
Riparian Areas ◽  
Raw Data ◽  
Ecological Criteria ◽  
Web Platform ◽  
The Web

Summary The aim of WEQUAL project (WEb service centre for QUALity multidimensional design and tele-operated monitoring of Green Infrastructures) is the development of a system that is able to support a quick environmental monitoring of riparian areas subjected to the realization of new green infrastructures (GI). The Wequal’s idea is to organize a service center able to manage both the Web Platform and the whole data collection and analysis processes. Through a personal account, the final user (designer, technician, researcher) can get access to the service and requires the evaluation of alternatives GI projects. On the Web Platform, a set of algorithms runs in order to calculate, through automatic procedures, all the ecological criteria required to evaluate a quality environmental index that describes the eco-morphological value of the monitored riparian areas. For this aim, the WEQUI index was developed, which uses 15 indicators that are easy to monitor. In this paper, the approach for environmental data collection and the procedures to perform the automatic assessment of two of the ecological criteria are described. For the computation, the implemented algorithms use data including the vegetation indexes, Digital Terrain Model (DTM), Digital Surface Model (DSM) and a 3D point cloud classification. All the raw data are collected by UAVs (Unmanned Aircraft Vehicle) equipped with a 3D Lidar, multispectral camera and RGB camera. Interpreting all the raw data collected by these sensors, using a multi-attribute approach, the WEQUI index is assessed. The computed ecological index is then used to assess the riparian environmental quality at ex-ante and ex-post river stabilization works. This index, integrated with additional not-technical or not-ecological indicators such as investment required, maintenance costs or social acceptance, can be used in multicriteria analyses in order to evaluate the intervention from a wider point of view. The platform is expected to be attractive for GI designers and policy makers by providing a shared environment, which is able to integrate the method of detection and evaluation of complex indexes and a multidimensional evaluation supported by an expert guide.

scholarly journals The efficient use of small plots in a fynbos phytosociological study in the northern Cederberg: a quick way to collect plant-environmental data

Bothalia ◽  
1993 ◽  
Vol 23 (2) ◽  
pp. 265-269
Author(s):  
P. J. Mustart ◽  
E. J. Moll ◽  
H. C. Taylor
Keyword(s):  
Plant Communities ◽  
Environmental Data ◽  
Vegetation Patterns ◽  
Environmental Relationships ◽  
Ecological Information ◽  
Small Plot ◽  
Phytosociological Study

A phytosociological survey of selected plant communities in the northern Cederberg was made using small (4-16 m') plot sizes. A satisfactory phytosociological table was obtained, and plant-environmental relationships were inferred from it. The use of small plot sizes enabled ecological information about plant communities to be quickly, easily and efficiently obtained. This method could be of considerable use for establishing and monitoring vegetation patterns.

scholarly journals DiSSCo, iDigBio and the Future of Global Collaboration

2019 ◽  
Vol 3 ◽  
Author(s):  
Gil Nelson ◽  
Deborah L Paul
Keyword(s):  
Working Group ◽  
Application Programming Interface ◽  
The United States ◽  
Common Source ◽  
Data Generation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Data Accessibility ◽  
The Us ◽  
Biodiversity Information

Integrated Digitized Biocollections (iDigBio) is the United States’ (US) national resource and coordinating center for biodiversity specimen digitization and mobilization. It was established in 2011 through the US National Science Foundation’s (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program, an initiative that grew from a working group of museum-based and other biocollections professionals working in concert with NSF to make collections' specimen data accessible for science, education, and public consumption. The working group, Network Integrated Biocollections Alliance (NIBA), released two reports (Beach et al. 2010, American Institute of Biological Sciences 2013) that provided the foundation for iDigBio and ADBC. iDigBio is restricted in focus to the ingestion of data generated by public, non-federal museum and academic collections. Its focus is on specimen-based (as opposed to observational) occurrence records. iDigBio currently serves about 118 million transcribed specimen-based records and 29 million specimen-based media records from approximately 1600 datasets. These digital objects have been contributed by about 700 collections representing nearly 400 institutions and is the most comprehensive biodiversity data aggregator in the US. Currently, iDigBio, DiSSCo (Distributed System of Scientific Collections), GBIF (Global Biodiversity Information Facility), and the Atlas of Living Australia (ALA) are collaborating on a global framework to harmonize technologies towards standardizing and synchronizing ingestion strategies, data models and standards, cyberinfrastructure, APIs (application programming interface), specimen record identifiers, etc. in service to a developing consolidated global data product that can provide a common source for the world’s digital biodiversity data. The collaboration strives to harness and combine the unique strengths of its partners in ways that ensure the individual needs of each partner’s constituencies are met, design pathways for accommodating existing and emerging aggregators, simultaneously strengthen and enhance access to the world’s biodiversity data, and underscore the scope and importance of worldwide biodiversity informatics activities. Collaborators will share technology strategies and outputs, align conceptual understandings, and establish and draw from an international knowledge base. These collaborators, along with Biodiversity Information Standards (TDWG), will join iDigBio and the Smithsonian National Museum of Natural History as they host Biodiversity 2020 in Washington, DC. Biodiversity 2020 will combine an international celebration of the worldwide progress made in biodiversity data accessibility in the 21st century with a biodiversity data conference that extends the life of Biodiversity Next. It will provide a venue for the GBIF governing board meeting, TDWG annual meeting, and the annual iDigBio Summit as well as three days of plenary and concurrent sessions focused on the present and future of biodiversity data generation, mobilization, and use.

Three Frontiers for the Future of Biodiversity Research Using Citizen Science Data

BioScience ◽  
2020 ◽  
Author(s):  
Corey T Callaghan ◽  
Alistair G B Poore ◽  
Thomas Mesaglio ◽  
Angela T Moles ◽  
Shinichi Nakagawa ◽  
...  
Keyword(s):  
Citizen Science ◽  
Secondary Data ◽  
Science Research ◽  
Single Species ◽  
Data Sets ◽  
Biodiversity Data ◽  
Science Data ◽  
Biodiversity Research ◽  
Research Areas ◽  
The Future

Abstract Citizen science is fundamentally shifting the future of biodiversity research. But although citizen science observations are contributing an increasingly large proportion of biodiversity data, they only feature in a relatively small percentage of research papers on biodiversity. We provide our perspective on three frontiers of citizen science research, areas that we feel to date have had minimal scientific exploration but that we believe deserve greater attention as they present substantial opportunities for the future of biodiversity research: sampling the undersampled, capitalizing on citizen science's unique ability to sample poorly sampled taxa and regions of the world, reducing taxonomic and spatial biases in global biodiversity data sets; estimating abundance and density in space and time, develop techniques to derive taxon-specific densities from presence or absence and presence-only data; and capitalizing on secondary data collection, moving beyond data on the occurrence of single species and gain further understanding of ecological interactions among species or habitats. The contribution of citizen science to understanding the important biodiversity questions of our time should be more fully realized.

scholarly journals Sharing Environmental Data through GEOSS

2012 ◽  
pp. 266-281 ◽  
Author(s):  
Gregory Giuliani ◽  
Nicolas Ray ◽  
Stefan Schwarzer ◽  
Andrea De Bono ◽  
Pascal Peduzzi ◽  
...  
Keyword(s):  
System Of Systems ◽  
Earth Observation ◽  
Environmental Data ◽  
Decision Makers ◽  
Observation System ◽  
Earth System ◽  
Seamless Integration ◽  
Agreed Framework ◽  
Earth Observation System ◽  
Different Sources

Understanding the complexity of earth-system processes is crucial to convey improved information on the environment to decision-makers and the general public. Addressing this need by sharing environmental data is challenging because it requires a common agreed framework that allows easy and seamless integration of data from different sources. In this regard, the Global Earth Observation System of Systems (GEOSS) portends major benefits through various sharing mechanisms and by giving access to services that could be linked together to process and generate new understandable knowledge and information. Various United Nations projects could greatly benefit from the GEOSS approach.

scholarly journals African Biodiversity Challenge: Integrating Freshwater Biodiversity Information to Guide Informed Decision-Making in Rwanda

2018 ◽  
Vol 2 ◽  
pp. e26367
Author(s):  
Yvette Umurungi ◽  
Samuel Kanyamibwa ◽  
Faustin Gashakamba ◽  
Beth Kaplin
Keyword(s):  
Decision Making ◽  
Natural Resources ◽  
Economic Transformation ◽  
Freshwater Ecosystems ◽  
Data Availability ◽  
Biodiversity Informatics ◽  
Freshwater Biodiversity ◽  
Biodiversity Data ◽  
Albertine Rift ◽  
Biodiversity Information

Freshwater biodiversity is critically understudied in Rwanda, and to date there has not been an efficient mechanism to integrate freshwater biodiversity information or make it accessible to decision-makers, researchers, private sector or communities, where it is needed for planning, management and the implementation of the National Biodiversity Strategy and Action Plan (NBSAP). A framework to capture and distribute freshwater biodiversity data is crucial to understanding how economic transformation and environmental change is affecting freshwater biodiversity and resulting ecosystem services. To optimize conservation efforts for freshwater ecosystems, detailed information is needed regarding current and historical species distributions and abundances across the landscape. From these data, specific conservation concerns can be identified, analyzed and prioritized. The purpose of this project is to establish and implement a long-term strategy for freshwater biodiversity data mobilization, sharing, processing and reporting in Rwanda. The expected outcome of the project is to support the mandates of the Rwanda Environment Management Authority (REMA), the national agency in charge of environmental monitoring and the implementation of Rwanda’s NBSAP, and the Center of Excellence in Biodiversity and Natural Resources Management (CoEB). The project also aligns with the mission of the Albertine Rift Conservation Society (ARCOS) to enhance sustainable management of natural resources in the Albertine rift region. Specifically, organizational structure, technology platforms, and workflows for the biodiversity data capture and mobilization are enhanced to promote data availability and accessibility to improve Rwanda’s NBSAP and support other decision-making processes. The project is enhancing the capacity of technical staff from relevant government and non-government institutions in biodiversity informatics, strengthening the capacity of CoEB to achieve its mission as the Rwandan national biodiversity knowledge management center. Twelve institutions have been identified as data holders and the digitization of these data using Darwin Core standards is in progress, as well as data cleaning for the data publication through the ARCOS Biodiversity Information System (http://arbmis.arcosnetwork.org/). The release of the first national State of Freshwater Biodiversity Report is the next step. CoEB is a registered publisher to the Global Biodiversity Information Facility (GBIF) and holds an Integrated Publishing Toolkit (IPT) account on the ARCOS portal. This project was developed for the African Biodiversity Challenge, a competition coordinated by the South African National Biodiversity Institute (SANBI) and funded by the JRS Biodiversity Foundation which supports on-going efforts to enhance the biodiversity information management activities of the GBIF Africa network. This project also aligns with SANBI’s Regional Engagement Strategy, and endeavors to strengthen both emerging biodiversity informatics networks and data management capacity on the continent in support of sustainable development.

scholarly journals Making Biodiversity Data Social, Shareable, and Scalable: Reflections on iNaturalist & citizen science

2019 ◽  
Vol 3 ◽  
Author(s):  
Carrie Seltzer
Keyword(s):  
Social Interaction ◽  
Citizen Science ◽  
Biodiversity Informatics ◽  
Strategic Decisions ◽  
Biodiversity Data ◽  
Helping Others ◽  
Advance Research ◽  
Biodiversity Information

Since 2008, iNaturalist has been crowdsourcing identifications for biodiversity observations collected by citizen scientists. Today iNaturalist has over 25 million records of wild biodiversity with photo or audio evidence, from every country, representing more than 230,000 species, collected by over 700,000 people, and with 90,000 people helping others with identifications. Hundreds of publications have used iNaturalist data to advance research, conservation, and policy. There are three key themes that iNaturalist has embraced: social interaction; shareability of data, tools, and code; and scalability of the platform and community. The keynote will share reflections on what has (and has not) worked for iNaturalist while drawing on other examples from biodiversity informatics and citizen science. Insights about user motivations, synergistic collaborations, and strategic decisions about scaling offer some transferable approaches to address the broadly applicable questions: Which species is represented? How do we make the best use of the available biodiversity information? And how do we build something viable and enduring in the process?

scholarly journals Sharing Environmental Data through GEOSS

2011 ◽  
Vol 2 (1) ◽  
pp. 1-17 ◽  
Author(s):  
Gregory Giuliani ◽  
Nicolas Ray ◽  
Stefan Schwarzer ◽  
Andrea De Bono ◽  
Pascal Peduzzi ◽  
...  
Keyword(s):  
System Of Systems ◽  
Environmental Data ◽  
Decision Makers ◽  
Observation System ◽  
Earth System ◽  
Access To Services ◽  
Seamless Integration ◽  
Agreed Framework ◽  
Earth Observation System ◽  
Different Sources

Understanding the complexity of earth-system processes is crucial to convey improved information on the environment to decision-makers and the general public. Addressing this need by sharing environmental data is challenging because it requires a common agreed framework that allows easy and seamless integration of data from different sources. In this regard, the Global Earth Observation System of Systems (GEOSS) portends major benefits through various sharing mechanisms and by giving access to services that could be linked together to process and generate new understandable knowledge and information. Various United Nations projects could greatly benefit from the GEOSS approach.

scholarly journals Environmental DNA reveals that rivers are conveyer belts of biodiversity information

2015 ◽  
Author(s):  
Kristy Deiner ◽  
Emanuel A. Fronhofer ◽  
Elvira Meächler ◽  
Jean-Claude Walser ◽  
Florian Altermatt
Keyword(s):  
Spatial Autocorrelation ◽  
Empirical Data ◽  
Spatial Scales ◽  
Environmental Dna ◽  
River Networks ◽  
Water Interface ◽  
Biodiversity Data ◽  
Land Water ◽  
Biodiversity Information ◽  
Game Changer

AbstractDNA sampled from the environment (eDNA) is becoming a game changer for uncovering biodiversity patterns. By combining a conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative way to assess eukaryotic biodiversity for broad spatial scales and across the land-water interface. Using an eDNA metabarcode approach we detected 296 families of eukaryotes, spanning 19 phyla across the catchment of a river. We show for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with classical community assessments by integrating biodiversity information over space. Additionally, we demonstrate that many terrestrial species can be detected; thus revealing that eDNA in river-water also incorporates biodiversity information across terrestrial and aquatic biomes. Environmental DNA transported in river networks offers a novel and spatially integrated way to assess total biodiversity for whole landscapes and will transform biodiversity data acquisition in ecology.“Eventually, all things merge into one, 32 and a river runs through it.” — Norman Maclean

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