The Corvids Literature Database - 500 years of ornithological research from a crow’s perspective

Corvids (Corvidae) play a major role in ornithological research. Because of their worldwide distribution, diversity and adaptiveness, they have been studied extensively. The aim of the Corvids Literature Database (CLD, http://www.corvids.de/cld) is to record all publications (citation format) on all extant and extinct Crows, Ravens, Jays and Magpies worldwide and tag them with specific keywords making them available for researchers worldwide. The self-maintained project started in 2006 and today comprises 8000 articles, spanning almost 500 years. The CLD covers publications from 164 countries, written in 36 languages and published by 8026 authors in 1503 journals (plus books, theses and other publications). Forty-nine percent of all records are available online as full-text documents or deposited in the physical CLD archive. The CLD contains 442 original corvid descriptions. Here, we present a metadata assessment of articles recorded in the CLD including a gap analysis and prospects for future research

Global Genome Biodiversity Network:saving a blueprint of the Tree of Life - a botanical perspective

Background Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. Scope The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on ‘harvesting’ the Tree of Life for vascular plant taxa to enable genome-level studies. Conclusion While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera

Life in Data”—Outcome of a Multi-Disciplinary, Interactive Biobanking Conference Session on Sample Data

©Sara Y. Nussbeck et al. 2016; Published by Mary Ann Liebert, Inc. This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. The article attached is the publisher's pdf

The Global Genome Biodiversity Network (GGBN) Data Portal

The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] The attached file is the published pdf

GGBN Data Portal, GGBN Data Standard and GGBN Document Library

The GGBN Data Standard (https://terms.tdwg.org/wiki/GGBN_Data_Standard) provides a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. It builds upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA samples as well as sequences. The standard has been recently extended to support environmental DNA and High Throughput Sequencing (HTS) library samples. Both, eDNA and HTS library sample use cases have been published in the GGBN Sandbox (http://sandbox.ggbn.org) and will be presented here. The use case collection is documented in the GGBN wiki (http://wiki.ggbn.org/ggbn/Use_Case_Collection). In addition a general overview of the GGBN Data Portal (http://www.ggbn.org) will be given. Based on ABCD, DwC and the GGBN Data Standard the GGBN Data Portal is the gateway to standardized access of DNA, tissue and environmental samples and their associated specimens. The third core piece of GGBN is the GGBN Document Library (https://library.ggbn.org), today containing more than 300 documents about research, management and legal aspects of biodiversity biobanks. We will provide an overview of covered topics and gaps that the community can help to fill. Finally an outlook of goals and priority tasks for the next two years will be given

Big Data Knowledge of Major Lineages of Life and Priorities for Genomic Research

Genomic science is revolutionizing and accelerating biodiversity research. For collections-based institutions to continue to lead and support biodiversity research, they must adapt to this new reality. Simultaneously, “big data” is accumulating so rapidly that we have unprecedented capacity to plan strategically to use genomics to advance basic and applied science on multiple fronts. For example, seven “big data” sources have the following numbers of records (2018 data): Global Biodiversity Information Facility (GBIF), ~1B; Biodiversity Heritage Library (BHL), ~3.6M;  National Center for Biotechnology Information (NCBI), ~220M; Open Tree of Life (OToL), 1.9M;  Barcode of Life Data System (BOLD), ~6.3M; Encyclopedia of Life (EOL), ~99K;  Global Genome Biodiversity Network (GGBN), ~2M. Collectively, they offer more than 1.2B records on biodiversity. At the scale of species (~2M described, multiple millions undescribed), these data are still too sparse to permit comprehensive conclusions. At the scale of families (i.e. deeper clades of life), the situation is far more promising: about 9,911 families are known, and relatively few are discovered each year. This suggests that at the family rank (and above), our knowledge of life on Earth is reasonably complete. Approximately 160,000 valid and accepted genera exist, but certainly many new genera await discovery and description. Genomics is the fastest way to group species into more inclusive lineages such as genera and families, and is certainly faster than traditional alpha taxonomy. Synergistically, these “big data” answer four important questions at deeper clade levels: What is it? Where is it? What do we know about it? What do we know about its genome? Approximately 4,500 eukaryotic genomes have been sequenced. The converse of what we know is what we do not know, another meaning of “dark taxa.” We can use the distribution and density of big data at deeper clade levels (families, genera) to quantitatively analyze “dark taxa” and therefore to strategically optimize knowledge and preservation of biodiversity at a global scale. Technicalities of the quantitative prioritization scheme are debatable, but some initial, simple scoring systems can help to prioritize lineages for collection and genetic research so as to most efficiently illuminate regions in the tree of life that that are neither preserved, imaged, geo-located, studied, nor known genomically. This analysis presents criteria and goals for collaborating to build a global genomic collection to maximize efficient acquisition of biodiversity genomic knowledge, and identifies the most valuable and highest priority taxa for genomic research

An Evolving Business Model for a Biodiversity Biobank Network: GGBN

GGBN, the Global Genome Biodiversity Network, is a consortium of virtually linked biodiversity biobanks that provide unified open access to their sample data through a web portal (www.ggbn.org), together improve best practices and develop standards. Since its inception in 2011, GGBN has largely been supported by external grants and in-kind support from its members. Starting with representatives from thirteen organizations across Africa, Australia, Europe, North, Central, and South America, preliminary plans for an international coordinating mechanism for biodiversity biobanks was developed. In 2013, an interim executive committee was established and an MOU (memorandum of understanding) was distributed to 17 potential collaborators for signature. Subsequently a governance and business model were developed based on input from across the collections and research communities. As the network grew, the interim executive committee solicited letters of intent to transition GGBN into a formal member-driven organization. In 2016 with 12 biodiversity collections online through GGBN’s data portal, the organization was launched and the business model implemented. This included a general and a technical secretariat, an executive committee and general assembly of its, at that time, 41 members. Having grown to encompass 87 general assembly members and 22 collections online in two years, GGBN is assessing its current business model, with focus on increasing revenue, and marketing strategy. Results of this assessment and associated next steps for GGBN are presented and discussed

SYNTHESYS+ Molecular Collections in the Age of Genomics: Standards and processes

The aim of the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org) is to foster collaboration among biodiversity biobanks on a global scale in order to further compliance with standards, best practices, and to secure interoperability and exchange of material in accordance with national and international legislation and conventions. Thus, key aspects of GGBN’s mission are to develop a network of trusted collections, establishing standards, and identifying best practices by reaching out to other communities. This is especially critical in the light of new international legislation such as the recent Nagoya Protocol on Access and Benefit Sharing (ABS). Biological repositories such as but not limited to natural history collections, botanic gardens, culture collections and zoos are facing a series of challenges triggered by the rapid acceleration in sequencing technology that has put added pressure on the use of samples, which just a few years ago were considered inaccessible for sequencing. ABS legislation applies to nearly all collection types, and with biodiversity biobanks increasing in number worldwide, there is an urgent need to streamline procedures and to ensure legislative compliance. Within Europe it is necessary to 1) reach common standards for biodiversity and environmental biobanks; 2) define best practices for the use of molecular collections; and 3) try to ease exchange of samples and related information, while staying compliant with legislation and conventions. Within the EU funded SYNTHESYS+ project (http://www.synthesys.info), GGBN is leading Network Activity 3 (NA3). An overview of planned activities and tasks will be given here with special emphasis on linkages within and beyond SYNTHESYS+

Furthering Genomic Research Infrastructures: The Global Genome Biodiversity Network

Most successful research programs depend on easily accessible and standardized research infrastructures. Until recently, access to tissue or DNA samples with standardized metadata and of a sufficiently high quality, has been a major bottleneck for genomic research. The Global Geonome Biodiversity Network (GGBN) fills this critical gap by offering standardized, legal access to samples. Presently, GGBN’s core activity is enabling access to searchable DNA and tissue collections across natural history museums and botanic gardens. Activities are gradually being expanded to encompass all kinds of biodiversity biobanks such as culture collections, zoological gardens, aquaria, arboreta, and environmental biobanks. Broadly speaking, these collections all provide long-term storage and standardized public access to samples useful for molecular research. GGBN facilitates sample search and discovery for its distributed member collections through a single entry point. It stores standardized information on mostly geo-referenced, vouchered samples, their physical location, availability, quality, and the necessary legal information on over 50,000 species of Earth’s biodiversity, from unicellular to multicellular organisms. The GGBN Data Portal and the GGBN Data Standard are complementary to existing infrastructures such as the Global Biodiversity Information Facility (GBIF) and International Nucleotide Sequence Database (INSDC). Today, many well-known open-source collection management databases such as Arctos, Specify, and Symbiota, are implementing the GGBN data standard. GGBN continues to increase its collections strategically, based on the needs of the research community, adding over 1.3 million online records in 2018 alone, and today two million sample data are available through GGBN. Together with Consortium of European Taxonomic Facilities (CETAF), Society for the Preservation of Natural History Collections (SPNHC), Biodiversity Information Standards (TDWG), and Synthesis of Systematic Resources (SYNTHESYS+), GGBN provides best practices for biorepositories on meeting the requirements of the Nagoya Protocol on Access and Benefit Sharing (ABS). By collaboration with the Biodiversity Heritage Library (BHL), GGBN is exploring options for tagging publications that reference GGBN collections and associated specimens, made searchable through GGBN’s document library. Through its collaborative efforts, standards, and best practices GGBN aims at facilitating trust and transparency in the use of genetic resources