scholarly journals Biodiversity Portal of the Northern Part of West Siberia, Russia

2019 ◽  
Vol 3 ◽  
Author(s):  
Nina Filippova ◽  
Ilya Filippov ◽  
Natalya Ivanova
Keyword(s):  
Natural Resources ◽  
West Siberia ◽  
Database Management System ◽  
Nature Reserves ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Biological Collections ◽  
Using Data ◽  
Different Sources ◽  
Biodiversity Information

Biodiversity-related studies in the northern part of West Siberia are relatively recent in line with intensive industrial development of the region in recent decades. The region posesses few biological collections within the universities and nature reserves. Still, the Department of Natural Resources pays considerable attention to the sustainable use of natural resources. On the global scale, the success of biodiversity informatics goals largely depends on the local initiatives and progress in data mobilization and sharing. Therefore, organization of regional biodiversity portals is important to promote data mobilization, education and citizen science on local scale. Previous experience of biodiversity information systems in the region was low. The program on digitization of observations of Red Listed species was launched in 2010 under the support of the Department of Natural Resources of Yugra. The information system for Red Listed species registrations was developed through this project and currently includes about three thousand observations. Another example of digitization in Western Siberia was developed by the biological collection of Yugra State University. Its database is based on the database management system Specify and available online through its web portal (http://bioportal.ugrasu.ru). Some collections of nature reserves have their catalogues in digital form. The need of biodiversity data mobilization is well understood and is discussed at regular workshops on biological collections management held in Khanty-Mansiysk. Recently, the biologists curating several biological collections in the region started a project on a regional biodiversity portal development (https://nwsbios.org). The portal has three major components: the database of collections based on Specify software (http://bioportal.ugrasu.ru), the metadata of different sources of biodiversity information in the region, an educational platform for learning biodiversity informatics, using data published via GBIF and DwC standards. the database of collections based on Specify software (http://bioportal.ugrasu.ru), the metadata of different sources of biodiversity information in the region, an educational platform for learning biodiversity informatics, using data published via GBIF and DwC standards. This initiative of biodiversity data mobilization in the region includes the organization of workshops, discussions and newsletters helping to reach potential data holders and coordinate work. Through this work four different organizations from Khanty-Mansi region have registered accounts in GBIF since 2019 and started uploading data to the GBIF portal. At present there are about 25,000 observations mobilized in GBIF from the Khanty-Mansi and Yamalo-Nenets regions. The integrated massive publishing of data in the portal will provide new opportunities for biodiversity research and sustainable management of nature resources in the northern part of West Siberia.

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 Developing Digital Botanical Resources for Pakistan

2019 ◽  
Vol 3 ◽  
Author(s):  
Mary Barkworth ◽  
Mushtaq Ahmad ◽  
Mudassir Asrar ◽  
Raza Bhatti ◽  
Neil Cobb ◽  
...  
Keyword(s):  
Community Of Practice ◽  
Data Use ◽  
Easy Access ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
High Quality ◽  
Research Activities ◽  
The World ◽  
Biodiversity Education ◽  
Using Data

In 2017, funding from the Biodiversity Information Fund for Asia accelerated data mobilization and georeferencing by Pakistani herbaria. The funding directly benefited only two herbaria but, by the end of the project 9 herbaria were involved in sharing data, 2 through GBIF (ISL 2019, SINDH 2019; codes according to Index herbariorum) and 6 others (BANNU 2019, BGH 2019, PUP 2019, QUETTA 2019, RAW 2019, SWAT 2019) through OpenHerbarium, a Symbiota based network. Eventually, all collections in OpenHerbarium are expected to become GBIF data providers. Additional Pakistani herbaria are being introduced to data mobilization and several individuals have expressed interest in learning to use OpenHerbarium to generated documented checklists for teaching and research and others for learning to link information in OpenHerbarium to other resources. These are the first steps to developing a “a large group of individuals … to train, mentor, and champion [biodiversity] data use” in Pakistan, but it is important to remember that good bioidiversity data starts in the field. We need to provide today’s collectors and educators with easy access to a) information about what constitutes a high-quality herbarium specimen; b) tools for making it easier to record and provide high quality specimen data; c) simple mechanisms for sharing data in ways that provide immediately useful resources; and d) learning to make use of the data becoming available. OpenHerbarium addresses the third and fourth needs and also makes it simple for collections to become GBIF data providers. This year, the focus will be on first two of the three steps identified. Introduction of the new resources will be used to introduce collectors and educators to the ideas underlying provision of biodiversity data that is fit for use and reuse. When Symbiota2 is functional, OpenHerbarium will be moved to that system. This will encourage development of additional tools for using biodiversity data. All these activities are essential to helping spread understanding of the concepts integral to biodiversity informatics. It is, of course, possible “to train, build, and champion data use” using data for other parts of the world, or provided by institutions from other parts of the world, but embedding good biodiversity data practices into the fabric of a country’s biodiversity education and research activities better benefits the country if a substantial portion of the data is generated from within the country. It also helps to spread knowledge of the country’s biodiversity among its students. Consequently, our focus in developing Pakistan’s capacity in biodiversity informatics is on engaging collections and collectors in sharing biodiversity data, then helping them discover, use, and create methods for developing the insights needed to encourage wise use of the country’s biological resources, and encouraging interaction. This will lead to a “community of practice” within Pakistan that can both benefit from and contribute to an international “community of practice”.

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 Completeness of Digital Accessible Knowledge of the Plants of Ghana

2016 ◽  
Vol 11 ◽  
Author(s):  
Alex Asase ◽  
A. Townsend Peterson
Keyword(s):  
Geographic Distance ◽  
Northern Ghana ◽  
Biodiversity Informatics ◽  
Primary Research ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Herbarium Data ◽  
Research Grade ◽  
Biodiversity Information

Providing comprehensive, informative, primary, research-grade biodiversity information represents an important focus of biodiversity informatics initiatives. Recent efforts within Ghana have digitized >90% of primary biodiversity data records associated with specimen sheets in Ghanaian herbaria; additional herbarium data are available from other institutions via biodiversity informatics initiatives such as the Global Biodiversity Information Facility. However, data on the plants of Ghana have not as yet been integrated and assessed to establish how complete site inventories are, so that appropriate levels of confidence can be applied. In this study, we assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories. We evaluated the completeness of inventories at ½° spatial resolution using statistics that summarize inventory completeness, and characterized gaps in coverage in terms of geographic distance and climatic difference from well-documented sites across the country. The southwestern and southeastern parts of the country held many well-known grid cells; the largest spatial gaps were found in central and northern parts of the country. Climatic difference showed contrasting patterns, with a dramatic gap in coverage in central-northern Ghana. This study provides a detailed case study of how to prioritize for new botanical surveys and inventories based on existing DAK.

scholarly journals A Google Sheet Add-on for Biodiversity Data Standardization and Sharing

2020 ◽  
Vol 4 ◽  
Author(s):  
José Augusto Salim ◽  
Antonio Saraiva
Keyword(s):  
Information Retrieval ◽  
Data Sharing ◽  
Information Science ◽  
Data Sets ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Data Standardization ◽  
Darwin Core ◽  
Rest Api ◽  
Biodiversity Information

For those biologists and biodiversity data managers who are unfamiliar with information science data practices of data standardization, the use of complex software to assist in the creation of standardized datasets can be a barrier to sharing data. Since the ratification of the Darwin Core Standard (DwC) (Darwin Core Task Group 2009) by the Biodiversity Information Standards (TDWG) in 2009, many datasets have been published and shared through a variety of data portals. In the early stages of biodiversity data sharing, the protocol Distributed Generic Information Retrieval (DiGIR), progenitor of DwC, and later the protocols BioCASe and TDWG Access Protocol for Information Retrieval (TAPIR) (De Giovanni et al. 2010) were introduced for discovery, search and retrieval of distributed data, simplifying data exchange between information systems. Although these protocols are still in use, they are known to be inefficient for transferring large amounts of data (GBIF 2017). Because of that, in 2011 the Global Biodiversity Information Facility (GBIF) introduced the Darwin Core Archive (DwC-A), which allows more efficient data transfer, and has become the preferred format for publishing data in the GBIF network. DwC-A is a structured collection of text files, which makes use of the DwC terms to produce a single, self-contained dataset. Many tools for assisting data sharing using DwC-A have been introduced, such as the Integrated Publishing Toolkit (IPT) (Robertson et al. 2014), the Darwin Core Archive Assistant (GBIF 2010) and the Darwin Core Archive Validator. Despite promoting and facilitating data sharing, many users have difficulties using such tools, mainly because of the lack of training in information science in the biodiversity curriculum (Convention on Biological Diversiity 2012, Enke et al. 2012). However, most users are very familiar with spreadsheets to store and organize their data, but the adoption of the available solutions requires data transformation and training in information science and more specifically, biodiversity informatics. For an example of how spreadsheets can simplify data sharing see Stoev et al. (2016). In order to provide a more "familiar" approach to data sharing using DwC-A, we introduce a new tool as a Google Sheet Add-on. The Add-on, called Darwin Core Archive Assistant Add-on can be installed in the user's Google Account from the G Suite MarketPlace and used in conjunction with the Google Sheets application. The Add-on assists the mapping of spreadsheet columns/fields to DwC terms (Fig. 1), similar to IPT, but with the advantage that it does not require the user to export the spreadsheet and import it into another software. Additionally, the Add-on facilitates the creation of a star schema in accordance with DwC-A, by the definition of a "CORE_ID" (e.g. occurrenceID, eventID, taxonID) field between sheets of a document (Fig. 2). The Add-on also provides an Ecological Metadata Language (EML) (Jones et al. 2019) editor (Fig. 3) with minimal fields to be filled in (i.e., mandatory fields required by IPT), and helps users to generate and share DwC-Archives stored in the user's Google Drive, which can be downloaded as a DwC-A or automatically uploaded to another public storage resource like a user's Zenodo Account (Fig. 4). We expect that the Google Sheet Add-on introduced here, in conjunction with IPT, will promote biodiversity data sharing in a standardized format, as it requires minimal training and simplifies the process of data sharing from the user's perspective, mainly for those users not familiar with IPT, but that historically have worked with spreadsheets. Although the DwC-A generated by the add-on still needs to be published using IPT, it does provide a simpler interface (i.e., spreadsheet) for mapping data sets to DwC than IPT. Even though the IPT includes many more features than the Darwin Core Assistant Add-on, we expect that the Add-on can be a "starting point" for users unfamiliar with biodiversity informatics before they move on to more advanced data publishing tools. On the other hand, Zenodo integration allows users to share and cite their standardized data sets without publishing them via IPT, which can be useful for users without access to an IPT installation. Additionally, we are working on new features and future releases will include the automatic generation of Global Unique Identifiers for shared records, the possibility of adding additional data standards and DwC extensions, integration with GBIF REST API and with IPT REST API.

scholarly journals Outlook of Biodiversity Informatics in Benin: Main achievements

2019 ◽  
Vol 3 ◽  
Author(s):  
Jean Ganglo
Keyword(s):  
Climate Change ◽  
Biodiversity Conservation ◽  
Ecological Niche ◽  
Regional Level ◽  
Global Changes ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Master Program ◽  
Occurrence Data ◽  
Biodiversity Information

Benin became member of the Global Biodiversity Information Facility (GBIF) in 2004 and acceded to the status of voting member in 2011. GBIF Benin through the constant efforts of its node is now very active in GBIF community with respect to capacity building, data mobilization and data uses. GBIF Benin published more than 400 000 occurrence data from about 125 datasets on GBIF portal . As for capacity building, GBIF Benin yearly organizes at least 2 (two) workshops to enhance the capacities of national and regional partners in data mobilization and data uses. At regional level, GBIF Benin is leading a consortium of many countries (Senegal, Côte-d’Ivoire, Niger, Democratic Republic of Congo, Guinea, and Madagascar etc.) to help overcome the challenges of data mobilization and data uses at regional level. From the academic year 2017-2018, GBIF Benin, through its node manager, successfully cooperated with the University of Kansas to create a master program in biodiversity informatics. Biodiversity informatics is a field of investigation relatively new in science and is concerned with massive occurrence data collection on biodiversity as well as on environment; data treatments, analysis, and representations so as to derive sound research products to inform decisions on biodiversity conservation and sustainable uses in the context of climate and global changes. In Benin, the master program in biodiversity informatics is a permanent two-year program structured in teaching units with the following contents: 1) Basics concepts of biodiversity; 2) Biodiversity data capture; 3) Biodiversity inventories; 4) Biodiversity data analysis; 5) Climate change and biodiversity; 6) Ecological niche modeling and strategies for biodiversity conservation; 7) Data-science-policy interface; 8) Public Health and Applications of biodiversity data etc. At completion of their studies, students graduated in the program will be capacitated so as to achieve the following innovative objectives: 1) Use Geographic Information System to map spatial distribution of species; 2) Model the current and the future ecological niche of species in the context of climate and global changes; 3) Characterize biodiversity on scales ranging from local to global; 4) Assess geographic patterns among suites of species (i.e., communities); 5) Refine the knowledge on particular taxonomic groups; 6) Define priority zones of biodiversity conservation; 7) Develop strategies of species conservation; 8) Implement biodiversity conservation strategies; 9) Predict the risks of propagation of infectious diseases (Lassa fever, Ebola fever etc.) which vectors are living organisms, so as to support preventive actions, etc. With such capacities, the graduated students of the master program are obviously the new generation of biodiversity information scientists who are able to address the needs of information so as to contribute to biodiversity conservation and its sustainable uses. Furthermore, in their respective countries and the rest of Africa, they will successfully contribute to the achievements of the Sustainable Development Goals as defined by the United Nations in 2015. With respect to data uses, more and more research products are piling up in Benin and are being integrated into decision makers’ arena. In 2018, the results of our data uses were integrated in the elaboration of the second communication on climate change of Benin.

scholarly journals Game of Tops: Trends in GBIF’s Community of Users

2019 ◽  
Vol 3 ◽  
Author(s):  
Nora Escribano ◽  
David Galicia ◽  
Arturo H. Ariño
Keyword(s):  
Information Exchange ◽  
Full Range ◽  
Open Data ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Research Areas ◽  
Scientific Papers ◽  
Opening Up ◽  
Biodiversity Information

Building on the development of Biodiversity Informatics, the Global Biodiversity Information Facility (GBIF) undertook the task of enabling access to the world’s wealth of biodiversity data via the Internet. To date, GBIF has become, in many respects, the most extensive biodiversity information exchange infrastructure in the world, opening up a full range of possibilities for science. Science has benefited from such access to biodiversity data in research areas ranging from the effects of environmental change on biodiversity to the spread of invasive species, among many others. As of this writing, more than 7,000 published items (scientific papers, reviews, conference proceedings) have been indexed in the GBIF Secretariat’s literature tracking programme. On the basis on this database, we will represent trends in GBIF in the users’ behaviour over time regarding openness, social structure, and other features associated to such scientific production: what is the measurable impact of research using GBIF data? How is the GBIF community of users growing? Is the science made with, and enabled by, open data, actually open? Mapping GBIF users’ choices will show how biodiversity research is evolving through time, synthesising past and current priorities of this community in an attempt to forecast whether summer—or winter—is coming.

scholarly journals Data Leakage and Loss in Biodiversity Informatics

2018 ◽  
Vol 6 ◽  
Author(s):  
A. Townsend Peterson ◽  
Alex Asase ◽  
Dora Canhos ◽  
Sidnei de Souza ◽  
John Wieczorek
Keyword(s):  
Large Scale ◽  
Information Resources ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Science And Policy ◽  
Data Record ◽  
Crucial Information ◽  
Biodiversity Information ◽  
Digital Record ◽  
Data Usability

The field of biodiversity informatics is in a massive, “grow-out” phase of creating and enabling large-scale biodiversity data resources. Because perhaps 90% of existing biodiversity data nonetheless remains unavailable for science and policy applications, the question arises as to how these existing and available data records can be mobilized most efficiently and effectively. This situation led to our analysis of several large-scale biodiversity datasets regarding birds and plants, detecting information gaps and documenting data “leakage” or attrition, in terms of data on taxon, time, and place, in each data record. We documented significant data leakage in each data dimension in each dataset. That is, significant numbers of data records are lacking crucial information in terms of taxon, time, and/or place; information on place was consistently the least complete, such that geographic referencing presently represents the most significant factor in degradation of usability of information from biodiversity information resources. Although the full process of digital capture, quality control, and enrichment is important to developing a complete digital record of existing biodiversity information, payoffs in terms of immediate data usability will be greatest with attention paid to the georeferencing challenge.

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 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.

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