Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery

Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability

The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration.In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications.To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities.Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement

The Change Imperative: Accelerating the pace of biodiversity discovery and documentation

Taxonomic work is slow and time consuming. Alarm bells have rung for years about the need to go faster, the need to attract and train new taxonomic workers, and the need to convince other branches of science that taxonomic work is vital. Morphological taxonomy is either being overrun or augmented – depending on your perspective – by genomics, artificial intelligence, new imaging methods and species-related data from other branches of science. Ecology is one such branch of science, where defining, documenting and managing information about species traits has emerged as one of the most significant problems in the discipline. Traits have been recorded for aeons, but the resulting data has largely been insulated within cliques. How do we integrate these data and make them available in a form that will help to address significant issues about our environment? The ‘speed bumps’ on the route to a useful solution may be more social than technical. Cross-disciplinary collaboration is required to address the big questions in biodiversity research today, and it will need to extend beyond taxonomy and ecology to other disciplines, such as pharmacology and material science. As Harry Truman said, and John LaSalle often quoted, “It is amazing what you can accomplish if you do not care who gets the credit”. We are challenged to understand and answer the key questions about the world on which we all depend.  What are the challenges and the opportunities to accelerate biodiversity discovery and documentation

The Change Imperative: Accelerating the pace of biodiversity discovery and documentation

Taxonomic work is slow and time consuming. Alarm bells have rung for years about the need to go faster, the need to attract and train new taxonomic workers, and the need to convince other branches of science that taxonomic work is vital. Morphological taxonomy is either being overrun or augmented – depending on your perspective – by genomics, artificial intelligence, new imaging methods and species-related data from other branches of science. Ecology is one such branch of science, where defining, documenting and managing information about species traits has emerged as one of the most significant problems in the discipline. Traits have been recorded for aeons, but the resulting data has largely been insulated within cliques. How do we integrate these data and make them available in a form that will help to address significant issues about our environment? The ‘speed bumps’ on the route to a useful solution may be more social than technical. Cross-disciplinary collaboration is required to address the big questions in biodiversity research today, and it will need to extend beyond taxonomy and ecology to other disciplines, such as pharmacology and material science. As Harry Truman said, and John LaSalle often quoted, “It is amazing what you can accomplish if you do not care who gets the credit”. We are challenged to understand and answer the key questions about the world on which we all depend.  What are the challenges and the opportunities to accelerate biodiversity discovery and documentation

Growth and Collaboration in the Atlas of Living Australia

Over the past three years, the Atlas of Living Australia (ALA), a data infrastructure in its own right and the Australian node of the Global Biodiversity Information Facility (GBIF), has been both enjoying both rapid growth (now with over 50 employees covering a broad project portfolio), and maturing as an organisation with formal processes in place for strategy and workplan development, project management and planning.Having recently upgraded our core infrastructure to align with GBIF and now sharing a code base for our data ingestion pipelines, we have been working on extending the occurrence data model with a focus on ecological survey sites and events and will continue to participate in the development of GBIF's diversified data model. We have been developing a framework with our jurisdictional agencies for managing restricted data, which will see us develop our Sensitive Data Service to handle a broader range of data sensitivity scenarios than the current system, which obfuscates by species rules only, whereas there are requirements to manage sensitivity at the levels of dataset, provider or location. We have begun a cross-agency project for aggregating genomic data for Australian species from multiple platforms, and a new technical roadmap will guide us as we redevelop and modernise our suite of web services and applications. This presentation will give a very brief overview of our current major project work, relating it to our stated strategies to deliver trusted data and robust services, partner for impact, and support decision making

The Atlas of Living Australia: History, current state and future directions

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

Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure.

Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audiences of data users, and have developed a variety of platforms and infrastructures to meet the needs of these audiences. The independent progress of biodiversity data providers has led to innovations as well as challenges for the community at large as we move towards connecting and linking a diversity of information from disparate sources as Digital Extended Specimens (DES). Recognizing a need for deeper and more frequent opportunities for communication and collaboration across the globe, an ad-hoc group of representatives of various international, national, and regional organizations have been meeting virtually since 2020 to provide a forum for updates, announcements, and shared progress. This group is provisionally named International Partners for the Digital Extended Specimen (IPDES), and is guided by these four concepts: Biodiversity, Connection, Knowledge and Agency. Participants in IPDES include representatives of the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), American Institute of Biological Sciences (AIBS), Biodiversity Collections Network (BCoN), Natural Science Collections Alliance (NSCA), Distributed System of Scientific Collections (DiSSCo), Atlas of Living Australia (ALA), Biodiversity Information Standards (TDWG), Society for the Preservation of Natural History Collections (SPNHC), National Specimen Information Infrastructure of China (NSII), and South African National Biodiversity Institute (SANBI), as well as individuals involved with biodiversity informatics initiatives, natural science collections, museums, herbaria, and universities. Our global partners group strives to increase representation from around the globe as we aim to enable research that contributes to novel discoveries and addresses the societal challenges leading to the biodiversity crisis. Our overarching mission is to expand on the community-driven successes to connect biodiversity data and knowledge through coordination of a globally integrated network of stakeholders to enable an extensible technical and social infrastructure of data, tools, and working practices in support of our vision. The main work of our group thus far includes publishing a paper on the Digital Extended Specimen (Hardisty et al. 2022), organizing and hosting an array of activities at conferences, and asynchronous online work and forum-based exchanges. We aim to advance discussion on topics of broad interest to our community such as social and technical capacity building, broadening participation, expanding social and data networks, improving data models and building a backbone for the DES, and identifying international funding solutions. This presentation will highlight some of these activities and detail progress towards a roadmap for the development of the human network and technical infrastructure necessary to support the DES. It provides an opportunity for feedback from and engagement by stakeholder communities such as TDWG and other initiatives with a focus on data standards and biodiversity informatics, as we solidify our plans for the future in support of integrated and interconnected biodiversity data and credit for those doing the work

Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure

Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audiences of data users, and have developed a variety of platforms and infrastructures to meet the needs of these audiences. The independent progress of biodiversity data providers has led to innovations as well as challenges for the community at large as we move towards connecting and linking a diversity of information from disparate sources as Digital Extended Specimens (DES).Recognizing a need for deeper and more frequent opportunities for communication and collaboration across the globe, an ad-hoc group of representatives of various international, national, and regional organizations have been meeting virtually since 2020 to provide a forum for updates, announcements, and shared progress. This group is provisionally named International Partners for the Digital Extended Specimen (IPDES), and is guided by these four concepts: Biodiversity, Connection, Knowledge and Agency. Participants in IPDES include representatives of the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), American Institute of Biological Sciences (AIBS), Biodiversity Collections Network (BCoN), Natural Science Collections Alliance (NSCA), Distributed System of Scientific Collections (DiSSCo), Atlas of Living Australia (ALA), Biodiversity Information Standards (TDWG), Society for the Preservation of Natural History Collections (SPNHC), National Specimen Information Infrastructure of China (NSII), and South African National Biodiversity Institute (SANBI), as well as individuals involved with biodiversity informatics initiatives, natural science collections, museums, herbaria, and universities. Our global partners group strives to increase representation from around the globe as we aim to enable research that contributes to novel discoveries and addresses the societal challenges leading to the biodiversity crisis. Our overarching mission is to expand on the community-driven successes to connect biodiversity data and knowledge through coordination of a globally integrated network of stakeholders to enable an extensible technical and social infrastructure of data, tools, and working practices in support of our vision.The main work of our group thus far includes publishing a paper on the Digital Extended Specimen (Hardisty et al. 2022), organizing and hosting an array of activities at conferences, and asynchronous online work and forum-based exchanges. We aim to advance discussion on topics of broad interest to our community such as social and technical capacity building, broadening participation, expanding social and data networks, improving data models and building a backbone for the DES, and identifying international funding solutions.This presentation will highlight some of these activities and detail progress towards a roadmap for the development of the human network and technical infrastructure necessary to support the DES. It provides an opportunity for feedback from and engagement by stakeholder communities such as TDWG and other initiatives with a focus on data standards and biodiversity informatics, as we solidify our plans for the future in support of integrated and interconnected biodiversity data and credit for those doing the work

The founding charter of the Omic Biodiversity Observation Network (Omic BON)

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities