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There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. The first Global Biodiversity Informatics Conference (GBIC) in 2012 delivered the Global Biodiversity Informatics Outlook (GBIO, Hobern et al. 2012), an architectural vision for the major components of a distributed global infrastructure for biodiiversity information, but realigning the work of existing organisations and projects to achieve this vision remains challenging. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. GBIF was asked to coordinate next steps following GBIC2, including publication of a paper, Connecting data and expertise: a new alliance for biodiversity knowledge (Hobern et al. 2019). The supplementary materials for the paper include PDF brochures explaining the concept in eleven languages. During 2019, GBIF is coordinating further consultations to establish an optimal model for the governance and operations of the alliance and to advance collaboration around some of the major building blocks of the GBIO. Collaboration at this scale, and across all aspects of biodiversity information, is essential for effective delivery of important information products such as the Essential Biodiversity Variables and the planned pan-European natural history collections infrastructure, DiSSCo. This presentation explains the goals for this alliance and updates on progress during 2019 in operationalising the concept.

Essential Biodiversity Variables (EBVs) are the latest push toward supporting state of the environment indicators (Pereira et al. 2013). The European Union Funded Creative-B Project (see https://cordis.europa.eu/project/rcn/100345/brief/en) outlined the status and strategy for interoperability between what they termed Biodiversity Research Infrastructures (BRIs: such as the Global Biodiversity Information Infrastructure (GBIF), the Atlas of Living Australia (ALA) and the Integrated Digitized Biocollections (iDigBio)). Toward the end of that project, the group decided that a logical follow-on project should position BRIs to support the production of Essential Biodiversity Variables (EBVs). This idea became the GLOBal Infrastructures for Supporting Biodiversity research (GLOBIS-B) project (http://www.globis-b.eu) and this presentation provides a summary of a case study on generating EBVs (Hardisty et al. 2019). As a part of GLOBIS-B, I suggested that a small team of GLOBIS members should document in detail, each step in the production of an EBV from GBIF and the ALA data for a few invasive species. We wanted address the rarity of detailed recording and justification for each step in the production of a dataset for environmental evaluation. I anticipated that the team would encounter many practical issues, but this case study raised far more significant issues that any of us had anticipated. The EBV chosen for this study was Area of Occupancy (IUCN Standards and Petitions Subcommittee 2017) and the species selected represented various invasion scenarios: Acacia longifolia; Vespula germanica and Bubulcus ibis. The workflow included 20 steps between locating data and publishing an EBV, and these steps were radically different between GBIF and the ALA. The workflow required manual steps such as resolving invasive status of Acacia longifolia subspecies; only one of which was 'invasive'. Datasets of occurrence records had to be exported from the ALA and GBIF to enable filtering for purpose, for example, not all Darwin Core terms are exposed in the current public interface of the ALA. After the record filtering, the ALA and GBIF datasets then required merging and deduplication, for which one-off code had to be written. A few of the 15 significant messages from this study included: a lack of consistency of data between BRIs (e.g., GBIF records should be a superset of ALA records); consistency and adequacy of filtering tools between BRIs; exported data structures massively differed between BRIs; that automation of the workflows may be possible but many manual intervention steps were required. By my figuring, the case study took approximately 10 times longer than anticipated, but the messages to BRIs was clear – consistency and adequacy of data and tools require urgent work.

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. The first Global Biodiversity Informatics Conference (GBIC) in 2012 delivered the Global Biodiversity Informatics Outlook (GBIO, Hobern et al. 2012), an architectural vision for the major components of a distributed global infrastructure for biodiiversity information, but realigning the work of existing organisations and projects to achieve this vision remains challenging. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for ...

Essential Biodiversity Variables (EBVs) are the latest push toward supporting state of the environment indicators (Pereira et al. 2013). The European Union Funded Creative-B Project (see https://cordis.europa.eu/project/rcn/100345/brief/en) outlined the status and strategy for interoperability between what they termed Biodiversity Research Infrastructures (BRIs: such as the Global Biodiversity Information Infrastructure (GBIF), the Atlas of Living Australia (ALA) and the Integrated Digitized Biocollections (iDigBio)). Toward the end of that project, the group decided that a logical follow-on project should position BRIs to support the production of Essential Biodiversity Variables (EBVs). This idea became the GLOBal Infrastructures for Supporting Biodiversity research (GLOBIS-B) project (http://www.globis-b.eu) and this presentation provides a summary of a case study on generating EBVs (Hardisty et al. 2019). As a part of GLOBIS-B, I suggested that a small team of GLOBIS members should document in detail, each step in the production of an EBV from GBIF and the ALA data for a few invasive species. We wanted address the rarity of detailed recording and justification for each step in the production of a dataset for environmental evaluation. I anticipated that the team would encounter many practical issues, but this case study raised far more significant issues that any of us had anticipated. The EBV chosen for this study was Area of Occupancy (IUCN Standards and Petitions Subcommittee 2017) and the species selected represented various invasion scenarios: Acacia longifolia; Vespula germanica and Bubulcus ibis. The workflow included 20 steps between locating data and publishing an EBV, and these steps were radically different between GBIF and the ALA. The workflow required manual steps such as resolving invasive status of Acacia longifolia subspecies; only one of which was 'invasive'. Datasets of occurrence records had to be exported from the ALA and GBIF to enable filtering for purpose, for example, not all Darwin ...

The Atlas of Living Australia (ALA) is Australia's national biodiversity database, delivering data and related services to more than 80,000 Australian and international users annually. Established under the Australian Government's National Collaborative Research Infrastructure Strategy to provide trusted biodiversity data to support the research sector, its utility now extends to government, higher education, non-government organisations and community groups. These partners provide data to the ALA and leverage its data and related services. The ALA has also played an important leadership role internationally in the biodiversity informatics and infrastructure space, both through its partnership with the Global Biodiversity Information Facility and through support for the international Living Atlases programmes which has now delivered 24 instances of ALA software to deliver sovereign biodiversity data capability around the world. This paper begins with a historical overview of the genesis of the ALA from the collections, museums and herbaria community in Australia. It details the biodiversity and related data and services delivered to users with a primary focus on species occurrence records which represent the ALA's primary data type. Finally, the paper explores the ALA's future directions by referencing results from a recently completed national consultation process.

The Global Biodiversity Information Facility (GBIF) was established by governments in 2001, largely through the initiative and leadership of the natural history collections community, following the 1999 recommendation by a working group under the Megascience Forum (predecessor of the Global Science Forum) of the Organization for Economic Cooperation and Development (OECD). Over 20 years, GBIF has helped develop standards and convened a global community of data-publishing institutions, aggregrating over one billion specimen occurrence records freely and openly available for use in research and policy making. These GBIF mediated data range from vouchered museum specimens to observation records generated by humans and machines. New data are being generated from integrated remote sensing, ecological sampling, and molecular sequencing that have strong geospatial components but lack traditional vouchers. GBIF is working with partners to develop best practices of bringing this data into the GBIF architecture. Following discussions during the second Global Biodiversity Information Conference in 2018, GBIF and the European Bioinformatics Institute (EMBL-EBI), supported by ELIXIR, have extended collaboration to share species occurrence records known only from their genetic material. When these data providers contribute data coordinates along with the sequences to the European Nucleotide Archive (ENA), the records will appear on GBIF maps and in spatial searches. This collaboration enables significant new molecular data streams to become discoverable through GBIF.org: by mid-March 2019, over 7.8m individual occurrence records via the ENA, and over 13.2m records as standardized Darwin Core sampling-event datasets via MGnify, a resource that provides taxonomic and functional annotations on sequences derived from environmental sequencing projects. Sequence-based occurrence records published by ENA and MGnify boost representation of microbial diversity which was underrepresented at GBIF. The ELIXIR-ENA-MGnify-GBIF partnership is working on further refinement of the dynamic data linkages, frequency of updates and other improvements. The API-based tool that connects GBIF data infrastructures is open to new data contributors and for indexes of molecular occurrences. Indexing of these data streams is dependent on the presence of a name (any rank) with the sequence. Under the current Codes of nomenclature, animals, fungi, plants, and algae cannot be described based on exclusively sequence data. Yet, a significant volume of biodiversity data has only been represented by DNA sequences. Barcoding and sequence clustering procedures vary among taxa and research communities, but clusters can be related to a taxon with a Latin name. Many DNA similarity clusters do not contain a sequence from a formally described taxon; however these sequence clusters provide provisional molecular names for nomenclatural communication. In the best cases, curated libraries of reference sequences, their metadata, clusters, alignments, and links to individuals and physical material become de facto naming conventions for certain taxonomic groups, and co-exist with Latin names. Integration of molecular names into the taxonomic backbone of GBIF started with Fungi and UNITE, a data management and identification environment for fungal ITS barcodes with 87,000+ fungal species hypotheses demarcating 800,000+ sequence specimens as of March 2019. Checklist publication of all names in UNITE through GBIF.org including Linnaean names and stable, DOI-trackable molecular sequence based 'species hypotheses', enables indexing of fungal metabarcoding data worldwide, such as BIOWIDE. As names are currently essential to indexing the world's occurrence data, GBIF will develop similar linkages with names in the Barcode of Life data system (BOLD) and in SILVA - a resource for high-quality ribosomal RNA sequence data and taxonomy, and welcomes other reference systems to this development. Expanding the molecular data streams (Fig. 1) allows GBIF to address spatial, temporal and taxonomic gaps and biases, and to support large-scale data-intensive research openly and worldwide.

The Global Biodiversity Information Facility (GBIF) was established by governments in 2001, largely through the initiative and leadership of the natural history collections community, following the 1999 recommendation by a working group under the Megascience Forum (predecessor of the Global Science Forum) of the Organization for Economic Cooperation and Development (OECD). Over 20 years, GBIF has helped develop standards and convened a global community of data-publishing institutions, aggregrating over one billion specimen occurrence records freely and openly available for use in research and policy making. These GBIF mediated data range from vouchered museum specimens to observation records generated by humans and machines. New data are being generated from integrated remote sensing, ecological sampling, and molecular sequencing that have strong geospatial components but lack traditional vouchers. GBIF is working with partners to develop best practices of bringing this data into the GBIF architecture. Following discussions during the second Global Biodiversity Information Conference in 2018, GBIF and the European Bioinformatics Institute (EMBL-EBI), supported by ELIXIR, have extended collaboration to share species occurrence records known only from their genetic material. When these data providers contribute data coordinates along with the sequences to the European Nucleotide Archive (ENA), the records will appear on GBIF maps and in spatial searches. This collaboration enables significant new molecular data streams to become discoverable through GBIF.org: by mid-March 2019, over 7.8m individual occurrence records via the ENA, and over 13.2m records as standardized Darwin Core sampling-event datasets via MGnify, a resource that provides taxonomic and functional annotations on sequences derived from environmental sequencing projects. Sequence-based occurrence records published by ENA and MGnify boost representation of microbial diversity which was underrepresented at GBIF. The ELIXIR-ENA-MGnify-GBIF partnership ...

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and nongovernmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data.

Abstract. There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. This paper summarises the GBIC2 discussions and presents a set of 23 complementary ambitions to be addressed by the global community in the context of the proposed alliance. The authors call on all who are ...

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and nongovernmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. This paper summarises the GBIC2 discussions and presents a set of 23 complementary ambitions to be addressed by the global community in the context of the proposed alliance. The authors call on all who are responsible for ...

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. This paper summarises the GBIC2 discussions and presents a set of 23 complementary ambitions to be addressed by the global community in the context of the proposed alliance. The authors call on all who are responsible for ...

BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use.

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals. ; This paper emerged from the first two workshops of the Horizon 2020 project GLOBIS‐B (GLOBal Infrastructures for Supporting Biodiversity research; http://www.globis‐b.eu/). Financial support came from the European Commission (grant 654003). C. A. additionally received funding from the LifeWatchGreece infrastructure (MIS 384676), funded by the Greek Government under the General Secretariat of Research and Technology (GSRT), ESFRI Projects and National Strategic Reference Framework (NSRF). M. O. was supported by the Swedish LifeWatch project funded by the Swedish Research Council (Grant no. 829‐2009‐6278), and J.E. by the Australian Research Council (grant FT0991640).