Shelley James, Lauren Gardiner, Amber Horning

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Mobilizing international Australian collections locally for global benefit.

From the earliest days of Australian colonization and exploration, botanical collections have been sent to herbaria overseas for western scientific study. Where there is a duplicate set, collections have been repatriated back to Australia with time, but many specimens remain solely housed overseas. These specimens document the floral diversity of Australian ecoregions that have now been altered, and of species that have not yet been described and may now have been lost to our ecosystems. Many such collections are type specimens, and others have historical exploration and botanical significance, all of which are not readily available for Australian taxonomic and cultural research. The Cambridge University Herbarium (CGE) is the fourth largest herbarium in the UK, and contains an estimated 12,000 specimens of Australian origin. A collaborative project between the Western Australian Herbarium (PERTH) and CGE, supported by the The Winston Churchill Memorial Trust, Australia, is enabling Australian collections to be located, updated, digitized, mobilized, and shared - decolonization and repatriation in digital form. Data and high resolution images will be made available to the scientific community, historians, and the public via a citizen science platform for curation and annotation by taxonomists and the public alike. Access will be invaluable for botanical research in this age of accelerated biodiversity loss, and as travel to, or shipping of, physical specimens is increasingly fraught and costly.

Karma Wangchuk, Tsheten Tsheten

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Bhutan’s biodiversity dilemma: abundance unseen – navigating the challenges of rich biodiversity and limited awareness

Bhutan’s strong commitment to environmental preservation is evident by its maintenance of over 60% of total land under forest cover. This has enabled Bhutan to maintain a rich reserve of biodiversity, with a staggering 11,248 species of flora and fauna, including a diverse array of vascular plants, insects, mammals, birds, fishes, amphibians, and reptiles.



The Bhutan Biodiversity Portal (BBP) is an initiative aimed at enhancing access to biodiversity information by the National Biodiversity Centre (NBC), as part of Bhutan’s conservation efforts. The BBP is a web-based platform that shares information on Bhutan’s rich biodiversity. Since its inception in 2013, the BBP has been instrumental in shaping conservation planning, policy development, and decision-making processes by providing invaluable insights into the country's rich biodiversity. With close to 8,100 species documented, over 108,000 observations recorded, and 45 informative maps available, the BBP represents a rich reservoir of knowledge crucial for informed environmental management.



However, the BBP faces challenges due to limited utilization resulting from sparse awareness among the general public and citizen scientists. To bridge this gap, NBC has initiated targeted awareness programs aimed at diverse stakeholders. The program extends beyond traditional conservation areas to include towns, municipalities, schools, and local governments involved in development planning.

Diego Tavares Vasques, Atsuko Takano, Atsushi Ebihara, Hiroshi Ikeda, Atsushi Kawakita

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

History and importance of the fern herbarium collections in Japan, with focus on the University of Tokyo herbarium

Japan's fern flora is renowned for its biodiversity, which includes 676 native species, and hundreds of hybrid taxa. Historically, ferns in Japan have been widely studied, both by academic researchers, and by groups of enthusiasts, like the Nippon Fernist Club. As a result, a vast number of publications are available for the study of non-seed vascular plants in Japan. Combined with that, Japanese herbaria hold a prominent collection of voucher specimens. In Japan, 74 herbaria are registered with Index Herbariorum, accounting for more than 13 million fungi and plant specimens. Within those, the University of Tokyo’s TI Herbarium is the oldest in Japan, being founded in 1877. Its collection holds more than 1,900,000 specimens, from which ca. 20,000 are type specimens of several vascular plant groups. The collection at the TI Herbarium includes plants from Japan, as well as important collections from the Korean Peninsula, Manchuria, Taiwan, the Himalayan region, and many other Asian countries. The TI collection is an important testament to the history of taxonomy in Japan, particularly regarding fern diversity. We have been working on databasing and cataloging all fern type specimens in the collection. So far, we have databased more than 1,000 potential type specimens of ferns and lycophytes, from Japan and surrounding countries, across 28 families, and accounting for more than 300 species namesdescribed by T. Makino, T. Nakai, B. Hayata, H.Ito et al.In this presentation, we will revisit the history of fern taxonomy in Japan, and discuss how databasing and curating the TI herbarium collection is key for future taxonomic and conservation studies.

Liselot Breyne, Wim Allegaert, Yann Collignon, Johan Van Huylenbroeck, Marc Heyndrickx, Kris Hostens, Maarten Trekels

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

DiSSCo Flanders and ILVO-CMS: unlocking and enhancing the management of natural science collections in Belgian research institutes

Effective management of natural science collections is crucial to maximizing their scientific value. Research institutes often harbor several smaller collections, which are seldom managed properly, as collection management is not their core business, and they lack direct connections to the Natural Science collection community.

Within the DiSSCo Flanders consortium of fourteen Belgian institutes, we inventoried the collections utilizing the SYNTHESYS+ survey and evaluated their state and management practices using the Collections Self-Assessment Tool. At the Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), we cataloged 15 collections comprising over 556,000 items. Approximately 95% are marine fish otoliths, used for age determination and stock assessments of commercial species. Additionally, we have ca. 21,000 food- and plant-related items in culture collections, encompassing fungi, viruses, and bacteria. Smaller collections include insects, macrobenthos reference species, seeds, azalea cultivars, marine and agricultural soil samples, and DNA from several of the aforementioned.

Adhering to the FAIR principles (Findable, Accessible, Interoperable, Reusable) and to connect with the DiSSCo Europe Research Infrastructure, ILVO developed an in-house Collection Management System (CMS). This ASP.Net web application, built in C# and utilizing a normalized MS SQL relational database structure, enhances organization, accessibility, and exchangeability of our collections. All collections and vocabularies (largely Darwin Core-based) are managed in the back end, and the multilingual user interface and collection-specific vocabularies are dynamically generated. The platform is custom-developed for our institute, but its adaptability enables easy customization for other institutes and (smaller) collections globally. Future goals for ILVO-CMS include the incorporation of 3D images and the further development of a user-friendly interface to facilitate the (re-)use of ILVO collections, internally and externally.

Our experience demonstrates that through opportunities like DiSSCo Flanders, bringing in temporary means and fostering a culture of collaboration, also non-museal research institutions may contribute to global Natural Science collections.

Renata Borosova, Ana Rita Giraldes Simoes, Cheung Tang, Gabriel Ameka

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Enhancing taxonomic skills in West Africa and supporting the growth of GC Herbarium (Ghana)

Two years ago, the Royal Botanic Gardens Kew, in collaboration with University of Ghana and the Ghana Herbarium (GC) delivered the first of a series of Plant Taxonomy Skills for Conservation and Ecology training courses funded by Schroder & Mallinckrodt Foundations in Africa. 15 participants from 8 African countries joined this hybrid course. This course then quickly developed into a larger partnership and was the first step towards a long-term collaboration where the ultimate objective has been to create the necessary conditions, both in infra-structure and human capacity to deliver the Flora of Ghana and to curate and protect the herbarium collection in the long term. Further grants were then submitted, regular meetings set-up, materials ordered, training delivered, and skills shared. In the presentation I would like to discuss expected learning outcomes of the training, opportunities that the partnership between Kew and GC herbarium has brought to enhancing local capacity, subsequent success stories, as well as challenges that had to be overcome so that similar partnerships could follow in other places.

Ashleigh Whittaker, Sarah Phillips, Marie-Hélène Weech, Laura Green

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Digitising Kew’s Science Collections: upscaling and delivering at pace

The Royal Botanic Gardens, Kew (Kew) houses the largest and most diverse botanical and mycological collections in the world with over 8.25million objects. The collections facilitate Kew’s scientific research and are used to understand the evolution of plants and fungi, identify gaps in taxonomy, and support extinction risk assessments (Canteiro et al., 2019). To ensure that the collection endures the test of time and continues its role in supporting research, not just at Kew but around the world, an ambitious four-year Digitisation Project started and will be completed in 2026.

Knowledge from past projects that were limited in scope provided a basis on which to upscale to an institution-wide effort that has, and continues to, utilise curatorial and research knowledge. Established workflows have evolved with the project, and new workflows have been created to enable progress at an increased volume and with time limitations. The typical herbarium sheets are digitised by an external supplier, which allows the in-house team to digitise the families and specimens that require more time and expertise. Those include Arecaceae(Palms),Orchidaceae(Orchids) and exceptional specimens, such as those with more than one specimen per sheet. Incorporating a dual approach to such a large digitisation project has its challenges, including the standardisation of image and data quality as well as continually addressing the conservation needs of the collection.

From the intensive training of new staff to the development of workflows and quality assurance of data, the complete digitisation of Kew’s collection will ultimately fill knowledge gaps, facilitate global research, and hopefully inspire the next generation of collection users.

Marla Spencer, Sarah Vincent, David Smith, Jutta Buschbom, Ben Collier, Lucy Ellis, Itan Grinberg, Tzy-Ting Hsu, Brad Hunn, Josh Humphries, Mike Sadka, Elaine Tsai, Kirstie Toth, Matt Woodburn, Steen Dupont

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Pioneering Museum Data Transformation: Unifying Legacy Systems and Enhancing Data Integrity

In the digital era, museums confront the challenge of modernising legacy data systems to align with current standards. Part of the RECODE (Rethinking Collections Data Ecosystems) programme examines the complex transition from disparate departmental object models to a unified system, reflecting the broader museum community's struggle with data standardisation. The case study centres on consolidating five distinct data models accumulated over two decades, each tailored to different departmental needs under various constraints. The data mapping process identifies and aligns similar fields across models, facilitating the integration of analogous data points and exposing redundancies and unique practices embedded over years. Major challenges include data complexity, diversity, and quality issues (cleaning, standardizing, and deduplicating), compounded by the massive scale of the data: currently, 262,831,590 records across 8,175 fields, and total volume of 12 TB that define both the ongoing data modelling work and our future data migration.

A key innovation in our process is the immediate visibility of data issues upon migrating to Amazon Web Services (AWS), which is used as the staging environment for the transition to the new NHM CMS and provides an unprecedented platform for directly addressing these challenges.

The core of this presentation is sharing "lessons learned" from navigating the intricacies of an ongoing CMS transition within a museum. The endeavor to untangle and unify diverse data models is a common challenge, highlighting the importance of community engagement and knowledge exchange. Our findings underscore the necessity of cross-departmental collaboration and the benefits of a data driven data modelling approach.

By sharing our journey and the developed comprehensive object model, we aim to contribute valuable insights to museums undergoing similar transformations. The RECODE Programme sheds light on the practical aspects of CMS modernisation through the analytics and knowledge derived from over 2 decades of collections data and data use.

Clara Baringo Fonseca, Karlo Gregório Guidoni Martins, Yohana Pereira Ditzel, Keila Elizabeth Macfadem Juarez

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

DarwinCoreBrazil: translations, examples and open discussions

The use of the DarwinCore standard for sharing biodiversity data and information has been increasing in Brazil. There is a growth in data publications on national and international platforms by institutions, foundations, programs, and research projects in biodiversity. However, due to the heterogeneity of data types, collections, and taxonomic groups, doubts persist about the adequate completion of each field in the datasheet. Although the DarwinCore standard has resolved much of the issue, the open content for some terms complicates the search and comparison of data and information across different data sets. In order to facilitate understanding of the DarwinCore term content, the Sistema da Informação sobre a Biodiversiade Brasileira (SiBBr) has created the page DarwinCoreBrasil with translations, best practices in using each term, as well as examples for the entire community through the interactive GitHub platform. Interested parties can participate in discussions by providing examples of controlled vocabulary by term or data type. These can be discussed through issues by experts. As demand and necessity arise, new extensions and other standards may be suggested, such as Plinian or the new Humboldt Core extension, with translations and examples and good metadata practices. The goal of DwC Brazil is to engage the Brazilian scientific community in discussions and bring publishers and institutions closer together. We hope this will improve searches and data analysis on visualization portals like the Living Atlas - SiBBr. Finally, we recognize that the current Darwin Core standard may not meet all Brazil's biodiversity data demands. In some cases, environmental agencies and other institutions must include information such as license code, funding agency, or project name. Thus, DarwinCoreBrasil is also a space for discussion about new terms to be used for later submission to TDWG as a suggestion for inclusion in the DwC standard.

Bradley Bishop, Jaxx Fox, Sidney Gavel, Emily Chapin, Sarah Kansa

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Biocollections Managers: Perspectives and Processes on Curating Physical Collections and their Digital Objects

Natural history collections retain a plethora of samples and objects for research purposes across domains. The data derived from these physical collections informs scientific discovery, but often aggregating data within even a single domain relies on navigating institutional and discipline-specific catalogs and repositories. Differing curation practices, shifts in methods for measurement, and changing theoretical and funding priorities, make the US biocollections infrastructure a patchwork quilt of objects and their associated metadata that has greatly improved through the efforts of many but still needs additional investments. Any exact science builds knowledge from these invaluable collections, collected once in real-time without substitute. In today’s context of AI readiness and public access, building a cyberinfrastructure atop this foundation should include revisiting the existing practices in preserving, conserving, and managing the physical collections and the subsequent research data curation processes of the digital objects. Scientific domains that rely on physical collections to create knowledge work within today’s machine-actionable context need more FAIR-aligned data, that also accounts for ethical reuse (i.e., CARE Principles for Indigenous Data Governance), as well as funding agencies expectations for data that are as open as possible. The purpose of this study is to understand the curation perceptions and behaviors of physical collections managers across biocollections to inform cross-disciplinary research data management services and resources. Six focus groups were conducted with eighteen participants across six physical biocollections-- entomology, two herbaria, herpetology, ichthyology, and palaeontology. Participants responded to open-ended questions about the collection overview, storage, data collection, metadata, organization, findability, and reuse. Results indicate that these natural history collection managers use global metadata and storage standards to increase discoverability but reuse of these physical collections and associated digital objects require more investment in personnel and cyberinfrastructure to enhance reusability of these invaluable natural history collections.

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Bringing invisible genetic samples into focus – a new tissue archive with cultural permissions and international data standards in mind

In 2022, the Threatened Species Tissue Archive (Fishes and Turtles), held at Tāmaki Paenga Hira Auckland War Memorial Museum, was created in collaboration with the Department of Conservation, New Zealand. This project aimed to develop the Museum’s tissue holdings alongside the Threatened Species Tissue Archive to include nationally important collections and samples that are tenuously held within universities, and to support the growing interest in biodiversity genomics. The curation of these samples within a Tissue Archive maximizes their scientific value and allows the samples and any research outputs to be tracked. The Archive’s creation also provided an opportunity to bring the museum’s existing tissue collection and its associated data up to global standards by making modifications to the database and to the way samples are registered, tracked and stored. Our vision included supporting the research community in transitioning toward ethical research practice that is respectful and inclusive of Indigenous communities by establishing cultural controls for the storage, use and disposal of tissue samples. Two years on, the Land Vertebrate Department tissue collection has increased by 70% and the Marine Department by 22%. Scientifically significant samples of threatened marine species have been added to the archive from offices and labs around the country, now visible on online data repositories and already being utilised. The Tissue Archive has a solid foundation of procedures to allow it to expand, while maintaining global standards.

Jhu-Jyun Jhang, Melissa Jean-Yi Liu, Daphne Z Hoh, Chun-I Chang, Mao-Ning Tuanmu

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Supporting biodiversity dataset preparation: An introduction to the TaiBIF Open Data Toolkit

The Darwin Core standard (DwC) and the GBIF data framework provide a flexible set of biodiversity data fields to accommodate various thematic datasets. However, this flexibility can make it challenging for data providers to get started, often leading to frustration when trying to map their original data fields to DwC terms. Additionally, while data cleaning is crucial for enhancing data quality, it requires significant expertise and effort, which may hinder the mobilization of high-quality data. To address these common pain points in data mobilization, the Taiwan Biodiversity Information Facility (TaiBIF) developed the TaiBIF Open Data Toolkit by integrating various thematic dataset templates, DwC terms, the Nansen Legacy Excel Template Generator, Excel data editing interfaces, GBIF Data Validator, and the OpenRefine. We combined the strengths of each tool to create a straightforward workflow from data sheet generation, data validation, data cleaning to dataset packaging. We hope the toolkit aligns with the needs of data publishers and facilitates a smoother and more user-friendly process of data management and publishing.

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Bioacoustic and ecoacoustic data in AudiovisualCore

AudiovisualCore is the TDWG standard for metadata related to biodiversity multimedia. Recently the Maintenance Group has been working to expand the standard to provide the terms necessary for handling sound recordings. AudiovisualCore can now handle acoustic metadata related to biodiversity from single species (bioacoustics) to the ecosystem scale (ecoacoustics). Additionally, the recently added concept of a "region of interest" allows for annotation of sound files, identifying multiple species within a single recording with both time and frequency bounds.

The use of well-defined annotations has the potential to generate large amounts of training data for machine learning models, as well as providing a standard for generating observation records from these models that can be verified by linking them to segments of audio within a much larger recording.

This talk demonstrates the use of these new tools to manage and annotate audio files, including through the Natural History Museum's new acoustic pipeline and Data Ecosystem. It also demonstrates prototype aggregators for recording and annotation metadata.

These additions have been created to be as versatile as possible, so finally, their relation to other media types, such as images and videos, will be discussed.

Michelle Luane Hamer, Adriaan Jordaan, Shanelle Ribeiro, Jacobus Christiaan Steenkamp, Ian Andrew Engelbrecht, Bronwynne Petersen, Mahlatse Kgatla, Fulufhelo Tambani, Shaun Pieterse

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Between a wet and dry place: the value of community in assessing the state of South Africa’s natural science collections

Natural science collections are invaluable spatio-temporal repositories of biological data and play a vital role in humanity’s overall understanding of the natural world. These collections not only function as centres of foundational biodiversity research but also provide a point of departure to understand and address the impacts stemming from the current biodiversity crisis on society and overall human well-being. Despite the critical link natural science collections form between people and nature, they suffer globally from fiscal and human capital constraints. This inadvertently poses considerable risks to their longevity to function and be managed as research infrastructure by hampering access to data, and providing adequate care and maintenance.Considering this, in order to effectively safeguard collections it is imperative to understand the factors and underlying mechanisms affecting the state of these collections. This understanding is vital for implementing preventive measures and allocating funding appropriately.

In 2023, the Natural Science Collections Facility (NSCF) network embarked on a comprehensive assessment of the participating institutions' collections, building on previous assessments dating back to 1999. The assessment, known as the Iqoqwana Initiative, employed a unique approach in that it was to be utilised for a dual purpose: determining the state of the collections; and the process to be a consultative, action learning and capacity-building journey that brought the community together. Feedback was constructive, focusing on improvement rather than criticism. A structured approach using questionnaires and data visualisation tools aided in identifying areas needing attention and prioritising actions. Methodologies included assessing risks and mitigation measures through standardised risk scoring, evaluating the implementation status of collection management practices, and comparative assessments with previous data.

The NSCF's collaborative and community-based efforts aim to improve the state of natural science collections in South Africa, ensuring the long-term viability and accessibility of the collections.

Komlan Edjèdu SODJINOU, Kodjo Djidjolé ETSE, Benziwa N. Johnson, Aboudou R. RADJI, Akossiwa Marie-luce Quashie, kouami KOKOU

Komlan Edjèdu SODJINOU

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Contribution to the Update of the Orchids Flora in the Southern Zone of the Togo Mountains.

The southern region of the Togo Mountains harbors a remarkable diversity of orchids that requires better understanding for the valorization of biodiversity and to support conservation efforts of this precious plant family in Togo. This present work updates the knowledge on the orchid flora of this zone in Togo and provides a list of 70 taxa, among which 7 are cited for the first time in the Togolese flora. A brief description and illustrations of these 7 taxa are provided to facilitate their identification. This study also contributes to assessing the conservation status and distribution of these taxa, essential for better understanding the dynamics of local orchid flora, in order to formulate recommendations for its sustainable preservation.

Keywords: Orchids, conservation status, taxonomy, biodiversity, Togo.

Carlos Garcia-Robledo, Erin K. Kuprewicz

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

From data points to data swarms: preserving specimens and their interactions in tropical food webs

Biological collections are a unique resource to understand organismal ecology and evolution. One challenge is to integrate the information associated with an individual specimen (a data point) to biotic associations, geographic records, and molecular data (data swarms). A second challenge is to make such records accessible to researchers and the public. Here we describe an approach to integrate morphological, ecological, and molecular data in a complex interaction network. Over the past two decades, we have worked on the ecology, evolution, and effects of global warming on interactions between plants in the order Zingiberales, the banana-like plants, their insect herbivores (Cephaloleiarolled-leaf beetles, Chrysomelidae), their pollinators (hummingbirds), and their associated phoretic mites. Specimens deposited in biological collections (NMNH, Smithsonian, Biodiversity Research Colletions, U of Connecticut) include labels cross-referencing interacting species. Our collection includes 2464 beetles identified to species, 4300 beetle mites, 1631 flower mites, and 2169 arthropods, including flie, and predators such as ants, spiders and other carabid beetles. We have also amplified the DNA barcode CO1 for all arthropod specimens. With the support of the Encyclopedia of Life (EOL), allCephaloleiaspecies records, and DNA barcodes are publicly available online. Specimen records are associated with Barcode of Life (BOLD) records. Plant-insect herbivore associations were used to develop tags in Darwin Core to connect specimens and interactions across databases. We will discuss our strategy to include specimen records in ecological publications to ensure that physiological records can be also associated with museum specimens as part of the extended specimen concept.

Erin Bilyeu, Emily Conforto, Cailin Meyer, Jessica Nakano

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Mitigating Risk in an ABS World: Navigating Third-Party MTAs

Since the signing of the Nagoya Protocol in 2010 and its implementation in 2014, researchers and museum professionals around the world have been grappling with what it means to provide fair and equitable access to genetic resources. Legislative restrictions impact how biological material is transferred and tracked around the world. Natural History collections in non-signatory countries are just as impacted by new regulations and risk running afoul of complex agreements.

As museums develop agreements to implement new laws created by national legislatures, it is necessary to determine a standard community practice and pathway for reviewing, understanding, and accepting mutually agreed terms for access and benefit sharing. Specifically, the concept of transferring or loaning material under a primary MTA to a third party by creating a new agreement (“third-party MTA”) is one that needs further consideration. The Registration team at the Smithsonian National Museum of Natural History (NMNH) will present the long-term impacts of third-party MTA restrictions and obstacles for specimen tracking and use. We wish to engage the natural history collections and data communities to collaborate and identify a common approach to creating, accepting, and passing on restrictions to third-party recipients. This presentation will discuss the NMNH’s interpretation of a variety of MTAs that NMNH has received, and the challenges created by those restrictions for collections management resources, data standards and museum-wide policy priorities. We will present our ideas for the community to consider, and welcome feedback and discussion for meeting this global need.

Dmitry Mozzherin, Geoffrey Ower

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

SQLite: a 'frictionless' solution for biodiversity data exchange?

Biodiversity data exchange heavily depends on established standards, such as Darwin Core, Audiovisual Core, Taxon Concept Schema (TCS), etc. Standards provide terms with defined semantic meaning and structures (e.g., TCS v1, Darwin Core Archive) for data exchange. A notable challenge is the complexity involved in the ingestion and exportation of data across various formats. Data in formats such as Darwin Core Archive or TCS is 'inert' and requires effort to parse, query, and reformat.

Most data exchange is based on CSV, XML, or JSON, and needs to be parsed and imported into a database before it can be queried. We propose a paradigm shift toward using 'active,' queryable SQLite-based files for data exchange.

SQLite is a lightweight database that is installed on almost all computers by default. It integrates a database into a single file, facilitating straightforward data exchange and compression. Its robust engine is able to manage terabytes of data. SQLite developers are committed to maintaining backward compatibility of both binary and text file versions until 2050. Connectivity to the database is supported by all popular programming languages. The United States Library of Congress endorses SQLite alongside XML and JSON for data archival, attesting to its reliability and long-term utility.

Implementing an SQLite-based approach for biodiversity data exchange would enable direct data queries without the need for specialized parsers. We at Species File Group experiment with using SQLite to create a universal converter, where an SQLite database serves as an intermediate data storage format. In conclusion, we believe that adopting SQLite for biodiversity data exchange can reduce operational friction, enhance data accessibility, and promise a streamlined and universally compatible data management framework.

Fritz Pichardo Marcano, Alyson Cain, Sofia Lara, Mackenzy Primrose, Sorgalim Rivera, Austin Mast

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Future-Proofing Biodiversity Collections via Improved Alignment with the Success Metrics of Parent Organizations

We are studying the success metrics used at US biodiversity collections and their parent organizations (e.g., a museum or university), as described in their strategic plans, annual reports, and webpages. Our analysis of 146 strategic plans and annual reports from 127 parent organizations of biodiversity collections coded as of April 2024 showed key collection topics appear in less than half of them. 43% of documents from 42% of parent organizations mentioned the topics of biodiversity and conservation (38%), collections (21%), or digitization (10%). However, these topics appeared much more frequently in documents from museums and botanical gardens (80% of documents) than universities and other academic institutions (30% of documents). This lower frequency of the topics at academic institutions might reasonably be explained by the broader scope of topics addressed by those organizations, but it might also suggest an urgent need to mainstream biodiversity in more of our academic organizations. A review of 105 webpages and strategic plans from 87 herbaria identified success metrics primarily related to digitization, funding, inclusivity and diversity, collaboration and exchange, conservation, collection scope, accessibility, community engagement, education, and research. Some of the success metrics related to these topics were also found in documents from parent organizations, with a higher prevalence of metrics related to inclusivity and diversity (55.7%), education (51%), funding (52%), and community engagement (38%), but with a lower emphasis on conservation (8%) and digitization (2%). We will discuss why the importance of some of these less prominent success metrics merit attention both at our parent organizations and in our international collections community, the latter being where many of the baselines for them have yet to be developed. We will also discuss how some of the topics more commonly embraced in our parent organizations (e.g., inclusivity and diversity) merit attention in more of our collections.

Kristen Lewers, Peter Adler, Alanna Rebello, Elisa Van Cleemput, Katie Suding, Ben Poulter, Aiya Lindquist, Meghan Hayden, Cibele Hummel do Amaral, Laura Dee

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

NASA BioSCape: Modeling Biodiversity and Invasion in the Greater Cape Floristic Region Using Advanced Remote Sensing and MultiScale Imagery Techniques

In the face of increasing ecological threats posed by invasive species, accurate detection and modeling are essential for effective management and mitigation. This presentation details a groundbreaking study focused on the invasion of non-native tree species in the Greater Cape Floristic Region(GCFR) of South Africa, a biodiversity hotspot, where these species threaten the native fynbos vegetation. Thisnot only explores the question of how we can model invasion using hyperspectral data and multiscale imagery at a large scale, but also how effective it is at predicting low density invasion when using validated data? Utilizing an integrated remote sensing approach, this research leverages data from the Sentinel Satellite, alongside advanced airborne imaging sensors mounted on NASA’S G3 and G5 research aircraft. Notably, this project marks NASA's inaugural Biodiversity field campaign that integrates airborne imaging spectroscopy, lidar, and field observations, setting a new standard for ecological monitoring and biodiversity conservation using remote sensing technologies.




The study employs innovative analytical techniques, including band dimensionality reduction and principal component analysis to enhance the understanding of spectral signatures that differentiate invasive from native plant species. The data is used to calculate three diversity metrics: alpha, beta, and gamma to understand diversity in and between communities. By analyzing these diversity metrics, the research identifies specific areas most at risk and provides crucial data to inform conservation strategies.




The ecological impacts of invasive species in this region are profound, contributing to larger available fire fuels and increased groundwater consumption. These factors exacerbate the risk of severe wildfires, posing significant challenges to ecosystem stability and resource management. This presentation will discuss the implications of these findings and suggest pathways for incorporating remote sensing into broader conservation practices. In particular, the presentation explores cross-disciplinary collaboration and emphasizes the importance of FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Debora Drucker, José Augusto Salim, Jorrit Poelen, Filipi Soares

CTRB01 General Presentations: Enhancing local capacity, elevating global standards

Collectively working towards plant-pollinator interactions data interoperability and reuse: lessons learned from the WorldFAIR project

The WorldFAIR Case Study on Agricultural Biodiversity addressed the challenges of advancing interoperability and mobilizing plant-pollinator interaction data for reuse. In the first phase of the project, the discovery phase, we performed a landscape analysis and found that a significant amount of data on plant-pollinator interactions available as supplementary files of research articles, in a range of formats such as PDFs, Excel spreadsheets, and text files. The diversity of approaches and the lack of appropriate data vocabularies lead to confusion, information loss, and the need for complex data interpretation and transformation.

In the second phase of the project, the pilot phase, we performed six pilot studies to adopt standards recommended in the discovery phase.Our approach for plant-pollinator data standardization was based on Darwin Core, in conjunction with a data model and vocabulary proposed by the Brazilian Network of Plant-Pollinator Interactions (REBIPP) and with the Ecological Data Language (EML). The pilot studies also underwent a process of “FAIRification” (i.e., transforming data into a format that adheres to the FAIR data principles - findable, accessible, interoperable, reusable) using the Global Biotic Interactions (GloBI) platform. Two pilot studies also explored the publishing model for Biotic Interactions, as part of the GBIF New Data Model.

We successfully promoted the adoption of standards and increased the interoperability of plant-pollinator interactions data. This process allows for tracing data provenance and facilitates the reuse of datasets. This effort led to the development of ‘FAIR best practices’ guidelines for sharing plant-pollinator interaction data, as well as an FAIR assessment tool designed to help researchers and institutions evaluate adherence to the FAIR principles.

Moving from diverse approaches and siloed initiatives to widely available FAIR plant-pollination interactions data for scientists and decision-makers will enable the development of integrative studies that enhance our understanding of species biology, behaviour, ecology, phenology, and evolution.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Uncovering a history of our natural history collections: an early-career experience digitizing Californian museum specimens

Collections serve as storehouses of information, and their associated data tells not only the story of the specimen, but the habitat, reproductive condition, or professors’ backyard in which it was collected. For the past year, and across three Californian institutions, I have worked to digitize and publish specimen trait data through the NSF-funded Ranges grant. Each collection has not only contributed raw data associated with tens of thousands of specimens, but data that reflects the unique history of each museum and its local community. At the Cal Poly Humboldt Vertebrate Museum, I georeferenced specimens to, among others, a lumber mill that used to be located on campus and a student housing trailer park. Meanwhile, the California Academy of Sciences lost the majority of their collections following the 1906 earthquake, and as a result, many of their local historic specimens were donated from private collectors or college museums. Lastly, UC Berkeley’s Museum of Vertebrate Zoology contains one of the oldest mammal collections on the West coast, including original data from founding ecologists such as Joseph Grinnell. Viewing specimens holistically can provide unintentional windows into the past. Just as a collection tracks evolutionary changes, they also reflect the ways in which we interact with and view the value of wildlife for research.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Migrating two Collection Management Systems (CMS) during a global pandemic, lessons learnt from the Royal Botanic Garden Edinburgh.

In 2019 the Royal Botanic Garden Edinburgh started a process to migrate from the long-standing (25 years) Collections Management System (CMS) – BG-BASETM to two separate systems, one for the living collection - Iris BG and one for herbarium specimens - Specify v7.

This resulted in all members of the collections teams having to develop from scratch or embrace new workflows, new work patterns, and software.

To add complexity to the issue, we undertook the main body of the work during the COVID pandemic when staff were working from home / furloughed or under extreme external pressure.

The resulting positives and negatives of migrating the two systems simultaneously provide interesting insights into the highpoints and pitfalls of a CMS migration.

Giuditta Parolini, Mareike Petersen

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

What is sustainability? A reflection from the perspective of biodiversity informatics

In recent years, the word sustainability has been used in connection to multiple domains ranging from finance to packaging and the list of products and activities which claim to be sustainable grows day after day. As a general and unambiguous definition of the term sustainability is not available and might not even be advisable (Ramsey, 2015), it remains a task for all the fields that strive to be sustainable to carve out a working definition that suits their needs.




The talk will reflect on the meaning of sustainability in biodiversity informatics with special reference to data practices and infrastructures. Starting from the financial dimension of sustainability that has been mainly discussed in biodiversity informatics so far (Cook and Cochrane, 2023; Kalfatovic et al., 2023), it will argue that environmental and social sustainability are equally important and interconnected to the financial aspects. It will also contend that only a community effort can lead to an agreed upon and effective definition of sustainability in biodiversity informatics and pave the way to set indicators to measure sustainability progress.




The aim of the talk is to open up a discussion on sustainability within the biodiversity community and to promote an exchange on the topic among different stakeholders interested in biodiversity data and working with them.






References

Cook C, Cochrane G (2023) The Global Biodata Coalition: Towards a sustainable biodata infrastructure. BISS 7: e112303.https://doi.org/10.3897/biss.7.112303 [https://doi.org/10.3897/biss.7.112303]



Kalfatovic, MR et al. (2023) Safeguarding Access to 500 Years of Biodiversity Data: Sustainability planning for the Biodiversity Heritage Library. BISS 7: e112430.https://doi.org/10.3897/biss.7.112430 [https://doi.org/10.3897/biss.7.112430]



Ramsey, JL (2015) On Not Defining Sustainability. J. Agric. Environ. Ethics 28, 1075–1087. https://doi.org/10.1007/s10806-015-9578-3 [https://doi.org/10.1007/s10806-015-9578-3]

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Planning for the Future: Is it Time to Subsample Types?

DNA degrades slowly over time at room temperature. Most museum vertebrate specimens are more than 80 years old and lack an associated frozen tissue sample. The prospect of extracting high-quality DNA from these historical museum specimens is already unfavorable and will become progressively less favorable over time. Alternatively, many researchers expect advances in DNA extraction techniques to outpace the current rate of DNA degradation and have already begun using ancient DNA extraction techniques to obtain partial genomes from historical specimens. After thoughtful consideration, the National Museum of Natural History, Division of Birds made the decision to subsample toepads or skin fragments from our oldest and most valuable specimens for cryopreservation in the National Museum of Natural History Biorepository. This ‘cryobanking’ method aims to preserve what is left of the DNA for future use. The initial targets for this phase of the project are Primary Types (~4000 specimens) and rare/endangered/extinct taxa (~2000 specimens). To date, we have sampled over 1000 of these specimens. I will present an overview on the decision-making process to sample types as well as the methodology used to collect the samples and then track them in our database.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Introduction of the freshwater organism specimen storage at Nakdonggang National Institute of Biological Resources, Republic of Korea

With growing interest in establishing national biological resources sovereignty and biodiversity, an organization called the Nakdonggang National Institute of Biological Resources (NNIBR) under the Ministry of Environment was established in 2015. The purpose of establishing NNIBR as Asia’s best freshwater bioresources research institute is to contribute to the acquisition of sovereignty over freshwater organisms, biodiversity conservation, and sustainable use of biological resources. Currently, over 540,000 biological specimens are deposited in NNIBR, and the specimens are divided by taxonomic group and type and managed in seven storage facilities of 2,000 m2, which can store a total of 6 million specimens. By securing and storing 70,000 specimens annually, biological resources are made into national assets and permanently preserved. Among the seven storages, three storages – dried animal and plant, and liquid-preserved animal – are operating digitizing studios to produce high-definition multi-focus digital images and 3D images. In particular, NNIBR is leading the production of 3D images and videos using X-ray CT for the first time in Korea. As of now, about 3,400 digital images have been generated, and in addition, since last year, digital images have been uploaded through the NNIBR’s website, making them easily accessible and usable for anyone. NNIBR is devoting itself to research with the ultimate goal of constructing digital collection storage through the continuous collection and management of biological specimens and the production and sharing of digital images.

Catherine Hazel M. Aguilar, Markus Oppermann, Stephan Weise

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Opportunities and limitations of the FAIR principles for collections of plant genetic resources

Global research is becoming increasingly data-intensive. Wherever possible, scientific data should be available to everyone and at all times. This can lead to a reduction in duplication of work and thus increase the efficiency of research. Research results become more comprehensible and new questions can be developed from existing findings. The possibility of automated processing plays an increasingly important role here. The FAIR principles (Findable, Accessible, Interoperable, Reusable) were developed to achieve these and other goals (Wilkinson et al. 2016). They are intended to make research and research results more transparent and efficient and increase sustainability.

The application of FAIR principles is also becoming increasingly important in the management and stewardship of data on plant genetic resources (PGR). The better material is described, the better it can be exploited and utilised (Weise et al. 2020). In addition to the classic passport data for ex situ and in situ collections, this is also relevant for the integration of data from other domains, such as phenotypic data, image data and genetic data. In Europe, the European Search Catalogue for Plant Genetic Resources (EURISCO) is working towards this goal (Kotni et al. 2023). Through consistent application, the creation of a FAIR-compliant European PGR information system is possible in principle in the medium term.

However, the application of the FAIR principles to each of the relevant data domains in this area is associated with a number of challenges. The presentation will shed light on the applicability of the FAIR principles to PGR data and highlight their limitations and challenges. It will then propose solutions to progressively improve the FAIR compliance of PGR data. This also includes the question of how FAIR the data of the respective domains really needs to be.

David Yuan, Nicole Fisher, Federica Turco

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Making every type count: the type digitisation pipeline at the Australian National Insect Collection (ANIC)

Primary type specimens are among the most valuable specimens in a natural history collection providing a stable foundation to taxonomy and biological science more generally. The Australian National Insect Collection (ANIC) currently holds over 12 million specimens and an estimated 19,000 primary type specimens, making it the largest insect collection in the southern hemisphere and the largest repository of Australian type specimens (accounting for nearly one-third of the Australian insect fauna). With such a vast and valuable entomological collection, ANIC has provided over many decades, valuable support and resources to entomological studies, attracting countless researchers from all over the world. Recently, ANIC has made it a mission to improve the management and accessibility of these virtually irreplaceable specimens for their importance to science. The ANIC curatorial, digitisation and molecular teams have come together and initiated the Type Digitisation Project, aiming to document the morphological condition, label data, and DNA data of the 19,000 types.

In the 2024 SPNHC-TDWG Conference, we aim to showcase a ‘behind the scenes’ story of this important type collection through the eyes of a type curator, providing a sneak peek of how the wheels are turning within the Type Digitisation Project, sharing our strategy, workflow, imaging equipment, challenges we encountered, the development of the project, team delegation and the results we are delivering.

Cynthia Wang-Claypool, Emily Blank, Breda Zimkus

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Review of practices for preserving animal genetic resources

Genetic samples require specialized storage to maintain their viability, but the manner by which they are initially preserved also greatly affects their utility in future research. Methods of preservation are often chosen based on planned study goals and practical considerations associated with the collecting event, such as the availability of cold-storage equipment in the field or regulations associated with transporting preservatives or samples. Limitations of the institution housing these samples also play a role in their long-term viability. We review the most commonly used methods of initial preservation for animal tissue samples and provide insights into our experience with cryovials and labeling techniques. We discuss practical considerations and workflows for collecting events that span multiple taxa (e.g., endo- and ectoparasites, microbiome, stomach contents), both in the field and upon return to the home institution. This information will aid researchers in maximizing extended data collection from voucher specimens given the ever-increasing challenges of collecting in the field.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

eHerbarium - a Global Platform for Exploring and Sharing Herbarium and Live Plant Images to Enhance Biodiversity Preservation

Historically, herbarium has been instrumental in preserving and studying of plant biodiversity. The widespread use of smartphones has led to a surge in the digital documentation of plants. Over the last decade, herbarium digitizing projects are also underway. Combining the latest mobile, cloud and AI technologies as well as plant taxonomy and herbarium artifacts, the mission of eHerbarium is to provide an accessible digital platform for plant enthusiasts around the world to collect, identify and share the plant and herbarium images. It promotes data collection and data sharing around the globe for biodiversity preservation. It further provides educational benefits for plants and plant biodiversity around us and the world.



What does eHerbarium offer?



* Explore a vast collection of herbarium images from Kew’s Herbarium, the Royal Botanical Garden, grouped by level 2 regions as defined by Biodiversity Information Standards (TDWG). Dive into the world of botany with high-quality visuals at your fingertips
* Effortlessly snap and share plant photos or herbarium images, or load images from your existing plant or herbarium collections. Customize with licenses for community use or download, enhancing the collaborative botanical exploration experience
* Unlock plant identification with AI-powered tool
* Get autocomplete suggestions for taxonomy details like scientific names, common names, and families. Use our proprietary technology to automatically populate scientific name with common name or automatically populate the common names with scientific name. Making botanical data entry seamless and accurate
* Automatically pin image locations to level 2 regions as defined by TDWG, enriching botanical records with precise geographical data



eHerbarium has received 5,000 installations since its debut one month ago on March 18, 2024. We encourage further collaborations to expand our repositories for herbarium and live plant images. We also welcome partnerships to tailor the application to specific needs.

The link to eHerbarium app: https://play.google.com/store/apps/details?id=com.ptr.herbaria [https://play.google.com/store/apps/details?id=com.ptr.herbaria]

One-minute Youtube video:

https://youtu.be/UAuT2sSHviA [https://youtu.be/UAuT2sSHviA]

Rachel Haderlé, Visotheary Ung, Jean-Luc Jung

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

VeTAPRH: A taxonomic assignment protocol for vertebrates applied to eDNA metabarcoding data, including molecular, taxonomic and ecological criteria

Exploring biodiversity requires a meticulous and exhaustive identification of species present in certain environments. Environmental DNA (eDNA) refers to DNA extracted from an environmental sample (Taberletet al. 2018). By combining metabarcoding approaches (Taberletet al. 2012) with eDNA, it is possible to carry out in-depth naturalist inventories (Valentini et al. 2009). Once the samples have been collected, DNA is extracted, targeted barcode is amplified, and related amplicons are sequenced (Deiner et al. 2017). The resulting datacontainsmillions of reads (Mathon et al. 2021). Bioinformatics processing is then a particularlyimportant stepin the analysis and pipelines associating multiplesoftwareswhich implement carefully designed algorithms are used to complete taxonomic assignments (Hakimzadehet al. 2023).

The main limitations of computerised protocols are that various cases of taxonomic misidentification may occur (for instance, intraspecific variations may be greater thaninterspecifics, like in theDelphininaesubfamily). These limitations may also relate to shortcomings in reference databases (Hleapet al. 2021, Meglécz et al. 2023), in which case it is recommended to rely onspecificallyconstructed databases (e.g. Blackman et al. 2023, Meglécz et al. 2023), butthismight not enable to detectunexpectedchanges in the range of taxa (Gold et al. 2021, Jung et al. 2016). Considering ecological features (Coissacet al. 2012, Deiner et al. 2017, Blackman et al. 2023) or compiling information from different databases (Bourret et al. 2023) may improveassignments. The most powerful approachremainsto involve taxonomic experts (Clarke et al. 2017, Porter andHajibabaei, 2018).

The aim of this study is to develop a taxonomic assignment protocol (in the form of a flow chart) applicable to vertebrates MOTUs/ASVsemergingfrom a metabarcoding analysis bioinformatic pipeline to check their automated assignment and consistency. One challenge is to associate molecular,taxonomicand ecological similarity criteria.

Emily Veltjen, Pieter Asselman, Wim Baert, Steve Baeyen, Lise Beirinckx, Liselot Breyne, Dimitri Brosens, Tim Claerhout, Sari Cogneau, Laura Cuypers, Karen Cox, Lynn Delgat, Philippe Desmeth, Jordi de Raad, Lore Esselens, Maria-Rose Eves Down, Frederik Leliaert, Kenny Meganck, Zjef Pereboom, Nathalie Smitz, Gontran Sonet, Maarten Trekels, An Vanden Broeck, Charlotte Van Driessche, Aaike De Wever

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The “key” to bringing DNA collections to the next level: a DiSSCo Flanders working group product

The DiSSCo Flanders consortium, with the goal of maturing and unlocking their DNA collections, identified 1) the need for actively sharing best practices regarding the management of DNA collections; and 2) a need for guidance on how to bring theory into practice.

During the DiSSCo Flanders project, a DNA collection working group was created. The working group is open to all biodiversity related DNA collections associates in Belgium in diverse roles such as researchers, lab technicians, collection managers and data managers. Around 50 people from 13 organizations participate. The community is intended to be small and local, supported with an atmosphere of empowerment. Members are allowed to be passively (reading only) or actively engaged (joining events) with the group.

The strength, as well as the challenge, of the DiSSCo Flanders community lies in its variety of contexts: universities, governmental and non-governmental research institutions, and museum institutes. This translates to a variety of DNA (or biobank) collection organizations such as decentralized or centralized; cold or room temperature storage; managed by an appointed curator or a lab technician.

The working group organizes meetings and workshops, tours to each other's collections, and shares a mailing list and a document space. As its principal output the group has co-created a tool: “The key to bringing DNA collections to the next level”. The tool is available in its first version, with the ambition to test the tool and to provide online user consultancy sessions for its use as a next step.

The working group and the co-created tool are positive examples of how a local community, sometimes managing smaller, or less conspicuous, types of Natural Science collections, can work together and use their unique perspectives, experiences and needs to contribute to the international Natural Science collection and biobanking communities.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Adapting Conservation: Tales from NHMD's specimen restoration

The Natural History Museum of Denmark (NHMD) in Copenhagen is currently preparing specimens for eventual display in a newly constructed facility, built to house approximately 3,000 scientific specimens. In a project of this scale, conservators often face the challenge of limited time, a finite budget, and evolving display methods. This paper looks at two conservation treatments – a tiger shark skull and an okapi taxidermy mount – and explores how adaptability, innovation, and flexibility were crucial to meet the demands of the project.



First this paper will discuss the treatment of a historic okapi taxidermy mount, which was removed from a habitat diorama at the now closed Zoological Museum. Removal from its dimly lit diorama revealed unexpected condition issues, including a large separation in the original stitching running from the neck all the way down to the torso and legs. Despite the increased treatment demands, I remained steadfast in meeting deadlines, relying on creative ways to incorporate standard conservation adhesives (Lascaux 498 HV and BEVA 371) and materials (Japanese tissue paper, QoR paints, orasol dyes, acrylic inks) to restore the specimen.



The treatment of a tiger shark skull also proved to be challenging, albeit in a different way. The skull, previously used for research, had undergone extensive destructive sampling, resulting in numerous drill holes throughout and damage to the cartilage. However, as one of the only specimens with a complete chondrocranium and jaw, it was selected by the exhibition team for display and needed to be repaired. Despite the challenges of this specimen and the restraints of the new museum project, I again adapted conservation techniques and materials to the specimen.



As we continue to prepare for the new building, these tales of adaptation underscore the importance of remaining flexible and creative in conserving natural science specimens for display.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

A Three-Year Digitization Project for Devonian Invertebrate Fossil: The Roles of Staff, Interns and Volunteers to Insure Error-Free Data Entry

The Institute of Museum and Library Services awarded a three-year Museums for America grant to the Field Museum and Milwaukee Public Museum. A partnership whose goal is to convert 37,000 paper-based records from handwritten labels, locality data cards, and catalog entries into EMu database records. The work is carried out with paid interns and volunteers. At the Field Museum four interns each summer will enter label data into EMu and photograph labels and fossils. Volunteers will also photograph labels and fossils allowing the interns more time to enter data into EMu.

Converting a diverse array of handwritten records can require cross-references (catalog books, locality cards, field notes) and consultation with curatorial and collections staff. Based on experience from similar projects interns will average six to ten specimen records per hour.

Interns enter specimen data directly into EMu using our custom designed entry screens with drop down menus and standardized vocabularies that reduce data entry mistakes. The standardized vocabularies insure mistake free data entry, but comes at a cost. Localities, formation names, and taxonomy not already entered into EMu cannot be added by the interns. Instead a Google Sheets document is created for the interns to enter any data that are not already in EMu. Staff must then go through these entries and verify their authenticity before adding to EMu. Taxonomy is further researched to find current synonyms. During the first year of the grant 1,470 records nearly 25% of all records entered into EMu that summer had at least one field that had to be verified and added to EMu by staff.

Finally, errors in catalog numbers are detected when multimedia records are linked to catalog records and ongoing error-trapping will involve our database users providing feedback to us.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Exploring Ethics in Museum Pest Management

Integrated Pest Management (IPM) has been a widely used and effective method to control or eliminate pest populations within museums. IPM emphasizes the use of targeted treatments and pesticide alternatives including low temperature, oxygen reduction or replacement with gasses such as nitrogen, and species-specific lures on sticky traps. These treatments, combined with routine inspections, monitoring, good housekeeping, and exclusion, create a more holistic and less toxic environment for the museum’s collections and people. And what about the pests themselves? The definition of a “pest” varies within each industry and it is paramount to consider ethical standards when implementing a pest management program not just for the environment and people, but for the insects, arachnids, and other animals targeted. Efforts have been made to minimize harm to rodents and other mammals deemed “pests,” such as banning certain poisons and using catch-and-release methods. This talk endeavors to further explore ethics in museum IPM practices and foster a better understanding of our relationship with these living beings.

Alyson Wilkins, Cody Bedke

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

A Little Buggy: Creative Thinking and Insect Digitization

Creativity and failure are essential to any museum. Insects are one the largest groups of life represented in museums, theyare one of the less digitized groups. Whether it be due to the scale of collections or lack of resourcesavailablethere is still a lot of dark data in insect collections. Using creative thinking and a willingness to accept failuretheNatural History Museum of Utah is increasing the rate at which we can digitize insect collections on a budget. From single specimen imaging to flatbed scanning andturntableswe will outline the metamorphosis of insect digitization at the museum and how it can applied in any museum.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Determining the age of four unknown taxidermized specimens at the Natural History Museum of Denmark

This thesis evaluates the possibility of determining the age of taxidermized specimens without associated data. Four herpetological specimens are investigated, a Calumma parsonii, Ceratophrys aurita, a young crocodile and an iguana, species not identified. For this is used SEM-EDX (Scanning Electron Microscope-Energy Dispersive X-ray) to determine the presence or absence of characteristic insecticidal chemicals, As and Hg. Microscopy is utilized to identify the stuffing materials in each specimen. FTIR (Fourier-transform infrared spectroscopy) is used to determine the presence of potential organic compounds in the testing material. Further methods incluce seeking out potential extant but dissociated data in archival material. Methods used show some ability to approximate the age of old taxidermy, in the case of the Ca. parsonii specimen determined to be from the 1700s, through investigation of inventory texts from previous collections, x-ray photography, microscopy identification of the stuffing material and other extant data. The Ce. aurita is concluded to originate in 1837 through investigating the old journals, disproving what was known from newer labels attached to the specimen. Other specimens show inconclusive results, which can be attributed to the taxidermy techniques used being too unique, or too common over longer periods; they are determined to be younger than 200 years old through presence of arsenic as preservative. Results show that determining of the specimen age is possible through these methods, and likely that all avenues for the investigation are not yet exhausted. Large-scale, museum-wide investigations may not be viable, but determining the age of single unknown specimens is possible when the need arises. Finally, to help future similar research, a simple timeline of taxidermy techniques is proposed.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

It’s Complicated: The Benefits and Drawbacks of Multi-Departmental Curatorial Assistants

Making the most out of grant funding, in particular smaller grants, can be a difficult task for natural history collections. Finding someone with applicable skills and expertise in the areas needed who is available to work, and is willing to accept a temporary, part-time position can be asking too much for many people, leaving funding underutilized. Who would take a three-month position for eight hours a week? Volunteers and interns can fill some of these roles, but they usually do not possess the expertise and reliability of an employed staff member. Enter the “floater”, the Frankenstein-esque Curatorial Assistant, who pieces together all the little projects, maximizing multiple departments’ funding usage, moves projects forward, is onsite five days a week, and has the potential for introducing interdepartmental collaboration. At the California Academy of Sciences, we have several employees filling these roles - regularly employed by multiple departments on multiple projects, whose scope of work and focus areas change as projects come and go, while retaining full-time status. This talk will cover some of the benefits and challenges of these positions, and the path to implementing a similar role at your institution.

Pei-Yu Tsai, Mao-Ning Tuanmu

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Spatiotemporal and environmental completeness of eBird data in Taiwan

Recent development of citizen sciences has significantly enhanced the availability of biodiversity data. Associated open data platforms, such as eBird, have become the major data source supporting scientific research and biodiversity conservation, and the primary challenge for utilizing biodiversity data is transitioning from data scarcity to data biases. Over 10.7 million bird observation records, including historical data spanning 40 years, from Taiwan are currently available on the eBird platform. However, the data's completeness remains unclear, limiting its applications. To address this gap, we evaluated the data’s completeness in representing species richness across spatial and temporal scales and examined the representativeness of the data along several environmental gradients. Using the iNEXT package in R, we found an increase in data completeness with increasing spatial scales, with the mean proportion of bird species represented being increased from 14.0% at the 1 km scale to 68.0 and 82.9% at the 5 and 10 km scales, respectively, across Taiwan. We also found an exponential improvement of data completeness over time. At the 5 km scale, the represented species proportion increased from 6.78 and 32.14% in the 1980s and 1990s to 36.86 and 63.56% in the 2000s and 2010s, with the data in the last decade alone achieving similar completeness with the entire four-decade data. Along environmental gradients, the areas with good data completeness (i.e., over 80%) were well-represented in terms of annual precipitation, but showed a bias toward areas at lower elevations and with lower forest coverage. These results indicate overall good data completeness of the eBird dataset for representing bird species richness in Taiwan. However, this study also highlights some data gaps, especially at finer scales, that need attention when using the dataset. This information is crucial for shaping future research designs and survey plans, aiming to enhance the applications of biodiversity data.

Brenda Daly, Fhatani Ranwashe

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Curating in context with biodiversity images

Currently, the absence of readily accessible biodiversity information poses risks of ill-informed decisions in managing natural resources, potentially leading to biodiversity loss. While some biodiversity data exists, mainly in the form of occurrence records, it remains largely inadequate, presenting a significant threat to South Africa's biodiversity. Achieving conservation goals and meeting obligations under agreements like the Convention on Biological Diversity requires addressing the shortcomings associated with occurrence data, such as limited coverage, temporal changes and inconsistencies, and issues with data quality like misidentification, sampling errors, and incomplete locality data. Herbarium collections offer a resource to address these shortcomings, however, these collections are not digital, and access to the data is limited.

Initiatives involving imaging and transcription not only expedite the digitisation process but also improve access to herbarium collections and enable contributions from citizen scientists. However, curating a comprehensive collection of biodiversity images is both time-consuming and expensive. Furthermore, it's crucial to understand the broader context in which these images are to be utilised, ensuring their relevance and alignment with specific objectives or contexts.

This article outlines the processes and challenges inherent in managing a collection of biodiversity images, covering topics such as imaging techniques, transcription procedures, infrastructure requirements, quality assurance measures, workflow management, and planning for human resources.

Alan Paton, John Adcock, Evgeniy Meyke, Udayangani Liu, Chris Soh, Richard Dodd, Rob Turner

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Lessons Learnt from Implementing a New Collection Management System – A Case Study from RBG Kew, UK

Development of RBG Kew’s Integrated collection management system (ICMS) is a fundamental part of a larger programme of work to ensure open access to 8.25M digitised plant and fungi specimens, by 2026. The ICMS, built in collaboration with Earthcape Oy, is vital to provide a modern, secure, and compliant system to manage and disseminate Kew’s data, locally and globally.



This presentation will focus on the planning, choosing, and implementing our new ICMS. The ICMS project is time critical to replace the historic collection management systems and datasets which had become outdated and non-compliant with relevant legislation such as that on access and benefit sharing obligations. This carried an unacceptablerisk of data loss and limited accessibility for science and research. We will cover understanding and collating the business requirements for each collection and procuring a supplier who could collaborate with Kew, providing a system which could be developed to support Kew’s collection data requirements across all collections.



We will provide an insight of the End User’s and Development Teams experience of the implementation work to move RBG Kew’s collection data from existing well known internal systems to a modern integrated system (ICMS). Although positive, there are number of areas where End Users and the Development Team found the experience sometimes frustrating, daunting, and challenging while at the same time working and managing their daily activities. The presentation will cover the lessons learnt through the implementation process of developing and testing the system for each collection data.We hope that this presentation will be of interest to all those considering changes to their collection management systems and supporting staff through the process.

Alice Gimat, Victor Naud, Vincent Cuisset, Marc Herbin, Sophie Cersoy

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

How do fishing lines behave in wet collections jars ?

Fishing lines are sometimes used to mount specimen of wet collections and preferred tocotton threads for their transparency. Despite their attested resistance for water,they may behave differently in preserving fluid and although they seem less sensitive to the fluids than metal or silk wires, elongation of the lines may happen within a few weeks, leading to the necessity to renew or change the mounting.To ensure a stable mounting, it appears determinant to choose a line that resists the fluid exposure, has a good tensile strength, does not get slack and remains as transparent as possible.

This project aimed at assessing the performance of different kind of fishing line in various types of fluids, so as to figure out the best choice for a preparation. Several kinds of lines (including polyamide and fluorocarbon polymer), with different diameters and strengths, were immerged in four fluids:

* ethanol 75%,
* formaldehyde 37%(w/w):a saturated solution of formaldehyde in water
* formalin 10%: one part offormaldehyde 37% solutiondiluted with nine parts of water,buffered at pH 6.8,
* modified Kaiserling III solution with the addition of thymol).

After various exposure time, we have compared their visual appearance and their mechanical properties (tensile strength, elongation). These analyses were completed with FTIR measurements to assess possible chemical changes. To reproduce more realistically their use in collection, a second experiment was carried out, by immersing the line with a weight to apply a mechanical constraint on it and their elongation was monitored versus time. These two experiments give an insight into their durability in collections.

Francisco Pando, María A. Mora, Manuel Vargas, Camila Andrea Plata, Gloria Martínez-Sagarra

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Plinian Core, a data specification for species pages, in the real world

Plinian Core is a set of vocabulary terms that can be used to describe different aspects ofbiological species information [https://en.wikipedia.org/wiki/Biodiversity_informatics]. Under "biological species Information" all kinds of properties or traits related to taxa —biological and non-biological— are included. Thus, for instance, terms pertaining to descriptions, legal aspects, conservation, management, uses, demographics, nomenclature, or related resources are incorporated (https://github.com/tdwg/PlinianCore [https://github.com/tdwg/PlinianCore]).

Having a data specification is the beginning, but it is just a small piece of what it takes to prepare and publish species information. Different aspects of Plinian Core and its development have been presented in the past (Pando 2018,https://doi.org/10.3897/biss.2.25869 [https://doi.org/10.3897/biss.2.25869]; Pando & al. 2022,https://doi.org/10.3897/biss.6.91584 [https://doi.org/10.3897/biss.6.91584]). In this contribution we shift the focus somewhat out of the specification itself, to other key aspects of species information dissemination. As Plinian core has been already put in use in various real-world scenarios for diverse objectives we aim to preset the most significant lessons learned in its implementations (e.g.https://datos.iepnb.es/visor/ [https://datos.iepnb.es/visor/],https://catalogo.biodiversidad.co/ [https://catalogo.biodiversidad.co/],https://enciclovida.mx/ [https://enciclovida.mx/]). We also aim to show some current and future developments, especially in the context of the Living Atlases community (https://living-atlases.gbif.org/ [https://living-atlases.gbif.org/]).Thus, we will explore other elements involved in sharing species information such as GBIF's IPT extensions, SPARQL Endpoints, Frictionless Data Packages, RO-Crates, and integration with Atlas of Living Australia modules (https://github.com/AtlasOfLivingAustralia/ [https://github.com/AtlasOfLivingAustralia/]).

Urmas Kõljalg, Kadri Põldmaa, Henrik Nilsson, Kessy Abarenkov

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Taxon Hypotheses and Communication of Taxa

The taxon hypothesis (TH) paradigm covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. Generic comparison between Taxon Concept Schema and TH will be presented.

Victoria Pickering, Mark Carine, Jawad Sadek, Andreas Vlachidis, Julianne Nyhan

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The Sloane Lab: mobilising historical botanical data at the Natural History Museum in London

As part of the Sloane Lab project, digital humanities work has enabled digital access to the Natural History Museum’s founding botanical collection for the first time. This collection, also known as the Sloane Herbarium, comprises 265 bound volumes containing over 121,000 dried and pressed plant specimens, collected before 1753. It is a global collection containing material gathered by over 300 named individuals from over 70 countries and dependencies worldwide. It is a unique source of information on the natural world, how it has changed and how we have interacted with it over the last 300 years. Hans Sloane (1660-1753) brought these volumes together during his life and left them to the British nation when he died. During this process of collecting, Sloane and his assistants catalogued and classified these specimens using a paper-copy of John Ray’s Historia Plantarum (published in three volumes in 1686, 1688 and 1704). This was a pre-Linnaean work that sought to list all of the then known plants, at a time when thousands of new plants were being introduced to British and European taxonomists every year. This paper copy of Historia Plantarum contains thousands of hand-written references to the locations of specimens in the Sloane Herbarium, thereby making it the physical entry point into the museum’s historical botanical collection. This paper will reflect on the process of mobilising these historical botanical data about plants and provenance, employing AI and humanly validated techniques of page segmentation and transcription. It will highlight the challenges of making this collection digitally searchable, and the references to the herbarium locations digitally accessible, for the first time, while also considering the wider significance and impact of this interdisciplinary work and research.

Gary P. Aronsen, Catherine Mas, Katherine Walls, Gregory Watkins-Colwell

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Abreu's Apes: Historical, cultural and scientific structures surrounding an orangutan (Pongo ssp.) collection at the Yale Peabody Museum.

Global natural history museum vertebrate zoology collections exhibit diversity in provenance and documentation. Primate collections are of great interest due to their close association with the human species, and they reflect complex wild, captive and medical histories. Here, we present a case study as a nexus where all three origins are present.

The Yale Peabody Museum holds four orangutan (Pongo ssp.) individuals whose story begins at the menagerie of the Cuban philanthropist Rosalía Abreu, an early 20th century pioneer of primate captive management and breeding. We describe Abreu’s work and her connection to Robert Yerkes and Yale University’s Institute of Human Relations, which endeavored to unite multiple fields of anthropology, biology and medicine. We then follow the life histories of these four individuals to their eventual accession by the Yale Peabody Museum.

These animals and their available documentation reflect the sometimes difficult historical realities behind medical research and museum collections. On one hand, the data from these orangutans provide invaluable baseline metrics as individuals of known body size, age, sex, and medical conditions. On the other, aspects of unethical collection practices, historical racism and sexism are also evident.In toto, this study shows how multidisciplinary inquiries of natural history collections provide insights into the past, present and future of collection procurement, management and curation.

Juan Saez Hidalgo, Ricardo Segovia, Francisco Squeo, Pablo Guerrero

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

PyDwCA: A tool for integrating biodiversity data

The Darwin Core Archive (DwC-A) format, based on the Darwin Core standard, facilitates the exchange, management, and integration of biodiversity data from multiple sources. This ability to collate biodiversity data allows datasets to be aggregated at community 'staging posts', merged in different combinations, meta-analyzed and submitted to public repositories. Thus, the DwC-A's serve as unifying archives in concatenated collective efforts, such as biodiversity inventories at different spatial and taxonomic scales.

Here we describe PyDwCA, a Python library implemented to handle the "star scheme" of DwC-A. This new library reads compressed zip files containing the expected meta.xml and uses it to assign the core component and its extensions. It also provides Python classes to define the core, the extensions, and the metadata file for creating an archive and writing it into a compressed zip file. PyDwCA also implements functionality to select, filter and merge DwC-A files.

We present this new tool in the context of the construction of the Chilean National Biodiversity Inventory, but PyDwCA serves as a versatile technical solution applicable to different contexts in the field of biodiversity informatics (e.g.integration of datasets from biological collection and sampling events). To exemplify how PyDwCA works, we present the step-by-step integration of the Chilean Catalogue of Vascular Plants on a matrix provided by the Catalogue of Life, filtered with the species with occurrences recorded for Chile in GBIF.

Armando Mendez, Arianna Bernucci, Phaedra Kokkini, Gavin Broad, Robert McLeod, Noelia Galan

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Who’s sleeping in your goldilocks cabinet? An IPM case study and alert.

For the past few years, the London Natural History Museum has been preparing for one of the largest collections moves in its long history.



As part of the preparation for the move, a dedicated team of specialists has been conducting an extensive survey of collections.



Since 2022 and to date, we have been experiencing a surge in infestations of Tineola bisselliella and Anthrenusspp. discovered in random, closed cabinets, in some cases with no evidence of external activity or point of entry; located in store areas with stable environmental conditions and strict IPM protocols in place.



After investigation, we have several hypotheses about the origin of these infestations, the strongest one being that they pre-date our current quarantine protocols, and that the living organisms have remained dormant at an early stage of development in their life cycle.



A dormant stage facilitated by the stable conditions inside the cabinets, a kind of ‘evil goldilocks’ condition, that when altered by the opening of the cabinets for the recent survey, sprang back to reinitiate their life cycles.



We know that both Anthrenus and T. bisselliella undergo diapause/dormancy, and that infestations in collections kept under conditions which induce dormancy may be restarted if the environmental conditions change.



Could insects remain dormant at early life cycle for over 10 or 20 years or longer, in stable, ideal conditions? Will low oxygen also be a contributing factor to dormancy on top of the RH and temperature?



The aim of this presentation and case study is to alert curators, researchers, and collection managers worldwide of this potential IPM risk when conducting surveys and how the introduction of several spot checks after the initial survey could help avoid damage to collections.

Dmitry Dmitriev, Thomas Pape, Neal Evenhuis, Geoffrey Ower, Matthew Yoder, Edward DeWalt

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

History extended: Migration of Systema Dipterorum into TaxonWorks

Now 40 years old, SD was originally digitized in the FileMaker database by F.C. Thompson and currently by N.L. Evenhuis and T. Pape. Recent conversations as to its future led to an effort to transition SD into TaxonWorks (https://taxonworks.org [https://taxonworks.org]). A web-based platform tailored to the requirements of biodiversity-informatics scientists, TaxonWorks meets SDs evolving needs. TaxonWorks provides tools designed to facilitate data migration, management, validation, and packaging for exports, such as Darwin Core-Archives (DwC-A) and Catalogue of Life's (CoL) COL-DP formats.

While TaxonWorks offers batch upload functionality, the intricate nature of SD necessitated specialized handling, i.e. a custom migration script. A version of SD is now accessible for preview and validation. This preview is particularly valuable for nomenclature validation, as TaxonWorks includes many tools ensuring compliance with the rules of Zoological Nomenclature. Additionally, this preview version now feeds the pipeline serving SD to the CoL.

By migrating SD into TW a wide range of utilities expanding the decades of effort behind the data are unlocked. TaxonWorks enables the creation of paper-style catalogs and the sharing of data via its public interface, TaxonPages. For an example of TaxonPages representation of Systema Dipterorum in TaxonWorks, visithttps://sfg-taxonpages.github.io/sysdipterorum/#/ [https://sfg-taxonpages.github.io/sysdipterorum/#/]. The data are also accessible via a JSON API, enabling computing (e.g. scripted synonymy queries) against the dataset.

While many technical hurdles are resolved, major challenges remain in building a new community around SD, one that will collectively take over the efforts of the few curators who have worked for so long on this broadly used resource.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Aspects of NCBI GenBank as a Biodiversity Information Resource

INSDC (International Nucleotide Sequence Database Collaboration) now requires that all submissions include the sampling location and date. In addition to the "lat_lon" (latitude and longitude) and "collection_date" tags, GenBank, a sequencing database, has designed tags such as "specimen_voucher", "collected_by", and "identified_by". This indicates that GenBank has the potential to be an information resource for DNA biodiversity occurrence. I surveyed the biodiversity information assigned to GenBank records to determine the potential of GenBank as a biodiversity resource.

I downloaded all GenBank data as of August 2023 from the FTP site. Specimen IDs were introduced into GenBank in 1997 as described in the "specimen_voucher" section. And 527,215 records (37.8%) for fish, 3,096,112 records (40.3%) for insects, 1,505,556 records (39.0%) for flowering plants had this data. The qualifier of specimen_voucher is currently written in the style of "[<institution-code>: [<collection-code>:]] <specimen_id>". Here, institution-code and collection-code are optional, and previously specimen_voucher could be written in free text. In fact, less than 10% of records have specimen IDs listed using this structured description. These ambiguous specimen IDs in GenBank may need to be cleansed using databases such as NCBI BioCollections, GRSciColl (Global Registry of Scientific Collections) or AI to map them to IDs in the specimen database to utilize them effectively. GenBank provides the type_material qualifier for describing the type of voucher (e.g., holotype of Asphondylia bursicola). In GenBank insect data, there were over 2,000 records for type material, and approximately 450 species were mentioned, including 269 for holotype. We found approximately 3,000 records with type information by including “notes” and “specimens_voucher” qualifiers in addition to “type_material”. Thus, GenBank has potential as a biodiversity information resource, but for more effective use, data mining and linkage with other biodiversity databases such as specimen databases are essential.

Laura A. Rincón Rodriguez, Jessica Goodheart

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The Malacology collection at the American Museum of Natural History (AMNH): Challenges and Successes

TheAMNHMalacologycollection wasestablishedin1874 withthe first donation of 50,000 specimens.Nowadays,theMalacology collectioncontainsapproximately 500,000 lots and an estimated 1.25 to3millionmarine,freshwater,and terrestrialspecimensworldwide, with emphasis on North America and the Eastern Pacific. The collection has the strongest representationofmarine gastropods and bivalves, scaphopods, and chitons.This collectionhas not had full-time Malacology staff since2007. However,in 2022 Dr. JessicaGoodheartwas hired as the Curator for Malacology, andLaura Rincón has been the Museum Specialist since 2023.Sincetheirarrival,theyhaveencounteredseveral challenges, including the lack of writtendocumentation,specimens at risk due to environmental conditions, and old collection material (e.g.,Bakelitelids).20%of the collection is databased, and even fewerare fully digitized, meaningmany of the records for our collection are not accessible to the public. However, through our collaborative work as biologists and museum studies professionals,we are developing tools and procedures to put into practice collections management theories for the benefit of our collection and its broader use. As a result, we have welcomed museum studies students into our collection, drafted a collections plan, begun addressing wet specimen preservation issues,purchasenew cabinets for at-risk specimen in thedry collection, host tours from biology and museum studies perspectives, and we are building resources to connect people with the specimens inside our cabinets. With this collaboration, we are moving closer toward our collective goal: to make the AMNH Malacology collection more accessibleand preserve it for future generations.

Guy Cochrane, Charles Cook

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The global biodata infrastructure and the drive for sustainability

Progress in life and biomedical sciences fundamentally depends on biodata resources—databases comprising biological data and services around those databases. These resources together comprise a critical global infrastructure that supports researchers by providing access to open public data and through enabling deposition and analysis of research data. Unlike other scientific infrastructures, biodata resources are globally distributed and lack central coordination. This decentralisation supports innovation, but reduces the long-term sustainability of individual resources and the infrastructure as a whole. The Global Biodata Coalition (GBC) brings together life science research funding organisations that recognise these challenges and acknowledge the threat that the lack of sustainability poses.




In 2022 and 2023 a working group of the GBC and its member organisations explored ways in which funders of biodata resources might better cooperate to enhance their sustainability. The working group produced a consultation setting out the challenges to providing long-term support for biodata resources and presenting a series of options for enhancing cross-funder cooperation. This consultation was then opened for comment by the wider body of GBC’s stakeholders. Based on the feedback received, GBC is now developing a white paper that will set out how GBC will work with its member funders, biodata resources, and other stakeholders to enhance sustainability of the global biodata infrastructure.




In this presentation, we will summarise the results of the consultation and look ahead to the white paper, including a set of nine principles that are proposed as a framework for developing cooperative approaches to fund and sustain biodata resources into the future. Additionally, the white paper will set out a series of models by which cooperative funding might be implemented. This work will be of interest to SPNHC and TDWG members who both manage biodiversity-related data resources and depend on other types of biodata resources for their work.

Pamela J. Horsley, Christiana R. Mojica, Kesler A. Randall, Thomas A. Deméré, Christina N. Piotrowski, Charlotte A. Seid, Lindsey T. Groves

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

A dry collection talk: Revitalizing the San Diego Natural History Museum Marine Invertebrate Collection

In 2021, the San Diego Natural History Museum (SDNHM) received funding from the US Institute of Museum and Library Services to improve the condition, management, and accessibility of our dry Marine Invertebrate Collection. Fornearly 25years, the collection has been unstaffed andnearly inaccessible, but withnew staffand funding, this underutilized scientific resource is being revived. The collection is believed to house millions of regionally, temporally, and taxonomically important specimens, but suffers from data inaccessibility and inadequate physical and taxonomic curation. This project is mitigating these weaknesses through specimen digitization, collection analysis, and rehousing.

Historically, each specimenlotin the collection was recorded on a paper catalog card. After scanning all 93,000+ cards, we employed Optical Character Recognition (OCR) technology and large-scale data cleaning to producean initialdigital dataset, now available online viaInvertEBase. Review by trained volunteers maximized our dataset's quality, culminating in the collection’s first comprehensive and publicly accessible digital specimen catalog.

Collection analyses yielded interesting findings, including an incredible geographic spread, extreme data quality disparities, and many unlabeled specimens and outdated scientific names. Alongside digital advancements, this project is improving physical storage and expediting specimen retrieval through drawer reorganization, labeling with updated scientific names, modernization of drawers and cabinets, and creation of an efficient specimen inventory locator.

This project lays the groundwork for future curatorial and scholarly work in this collection, through enhanced collection accessibility and ease-of-use. A refined triage strategy informed by the digitized collection and aided by organizational improvements of this project will guide upcoming efforts for potential deaccession of irrelevant materials. We are exploring collaborations with other institutions and research initiatives to maximize the scientific impact of the collection. The SDNHM is now positioned to revitalize this collection as a leading, efficient, and lasting resource for the North Pacific region.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Datahub, A Comprehensive Data Integration Service for Natural History Museum Berlin

MfN Datahub (Museum fuer Naturkunde Berlin Data Hub) as a central data integration service has been developed to perform multiple automated data integration and migration scenarios in a continuous and parallel workflow for the Natural History Museum in Berlin to support the scientific data management systems of the museum.

The produced or consumed data has to follow a particular structure required per project and use case. Therefore, harmonizing several data flows simultaneously could be complex, depending on the data structure and the target systems. To address this issue, DataHub is designed as an open-source web service to be scalable and comprehensive by following a general and simple design that could process different data types from multiple sources. This service as a workflow engine would iterate over the datasets and migrate them to a target system, to handle several data pipelines automatically.

DataHub has access to the storages and resources that are produced in the digitization pipeline and integrates them via APIs to the known internal target systems of the museum, e.g. Media Repository and Collection Management Systems, and also the external target systems e.g. DiSSCO; following the requirements of the collection, digitization, data integration and the target systems.

Upon the establishment and initiation of a new project within DataHub, the subsequent automated data pipeline initiates, using predefined automation scripts, which follow “ETL” as an industrial methodology for such procedures, to “Extract” data from the source, “Transform” it, according to the requirements and standards of the target, and finally “Load” the data into the target system. The software and hardware of DataHub are optimized to perform as many tasks as possible in parallel, to maximize the speed and efficiency. The source code is accessible publicly on GitHub and it could be applicable in the other institutes.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Using empathy best practices to interpret natural history collections

Incorporating empathy and social-emotional learning into interpretation has become an important interpretive tool for zoos and aquariums. Through empathetic interpretation, we can engender a sense of protection, correct misconceptions, and foster community through educational storytelling. If our end goal is the conservation of a collection, institution, or even a whole species, starting with empathy is an important strategy to build a feeling of ownership and protection within our guests.




In this talk, we will discuss what empathy best practices are and how they can be applied to both living and non-living collections. We will discuss strategies for incorporating these practices into interpretations ranging from docent talks to signage to public programming. We will also discuss methods of measuring participants' empathy output through the use of various evaluative tools.

Grant Fitzsimmons, Theresa Miller

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Digitization Planning for Large Collections and Agencies with Specify 7

The Specify Collections Consortium supports research collections around the world with an intuitive, robust, and highly-customizable software platform to digitize their holdings and manage their collections. For over 25 years, Specify has provided and sustained biological research museums and biorepositories with software for managing, integrating, and publishing collections information.




The Specify Consortium has been increasingly engaged with very large collections managed by institutions ranging from universities to individual government departments to entire federal agencies, to envision a framework to support standard computerization workflows and best practices.




We will discuss the process we have followed with these very large collections institutions, especially the requirements analysis, training, and the types of issues that have arisen on how to implement Specify on a large scale over multiple collections with central coordination while allowing the individual collections to support their unique data needs.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The Traditional Model

Traditionally, each specimen in a collection is assigned a single identifying name, or “determination.” For biological specimens, the identity is usually a genus and species. From a modeling perspective, this practice represents a one-to-one relationship between collection object and determination. Here, we refer to this relation as theSimple Specimen Model. This flat “simple” model works well for most biological collections, and nearly all existing collections management systems and data publishing standards are based on this model.

Challenges with the Simple Model

However, theSimple Specimen Modelcannot accurately represent the nature of many geological specimens. These frequently contain a variety of distinct earth materials that are bound together by physical attachment. A real-life example of this kind ofcompoundspecimen would be a reddish limestone rock that contains ammonites (a type of fossil), and two of the ammonites have calcite and celestine mineralization (a type of mineral). We refer to these specimens as compound specimens.

A New Conceptual Data Model

In this presentation, we present theCompound Specimen Model, a conceptual data model that supports the complete representation of compound specimens. We will summarize the model's structure relative to its Simple Specimen Model counterpart, discuss its overarching impact on the geological collections community, and explain how it fits within larger ongoing projects such as GeoKOS and the TDWG Mineralogy Extension.

Sofie Gelardi Munksgaard, Kristian Murphy Gregersen, Michela Gambino

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Which bacteria are actively responsible for the maceration of bones?

Bacterial maceration is anold, commonly used and well known technique for cleaning bones.Askinned and de-fleshedcadaver is placed in a closed containertopped upwith waterand leftforthe fleshtonaturallyrot awayfrom the bones,probably via an anaerobicbacterial process. The process can often vary, both in the procedure and in the results,andthe microorganisms responsible for it remainunknowndespite the method’s long history.Here, weset up an experimenttooptimizeDNA extraction methodsandidentify thebacteria present during maceration.Tenskinned andde-fleshedrat cadaverswereplacedin glass vesselsfilledwith waterandstopperedtokeep the environment anaerobic.Since maceration canproceed at different temperatures, fiveplacedat room temperature(approx.22°C)andfivewere incubatedat39 °C.Samples from themaceration liquid were extracted from the vessels at regular intervalsandusedbothfor culture-independent and-dependent methods.Different DNA extraction methodsbased oncommercial kits,wereoptimizedfor microbiomesequencingto improve DNA yield and quality. At the same time, samplesfromthe maceration liquidwereextracted andplatedin ordertoisolate,cultivateand further identifytheanaerobic bacteria.Resultscollected so farwill be presented.

Natalie Mastick, Rachel Welicky, Whitney Preisser, Katie Leslie, Katherine Maslenikov, John Kinsella, Timothy Essington, Chelsea Wood

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Marine mammal recovery is associated with the resurgence of a nematode parasite

As the oceans change, the abundance of parasites and risk of infection to marine mammals may also be changing. Nematodes in the family Anisakidae can harm marine mammals and recent studies have revealed a global increase in these parasites, but the cause is unknown. We sought to determine how anisakid risk in Puget Sound had changed over 98 years by conducting parasitological analysis of museum specimens of the prey species of marine mammals. We dissected Pacific herring, walleye pollock, surf smelt, Pacific hake, and copper rockfish collected between 1920 and 2018. We found that the larval anisakid Contracaecum spp. was the most abundant marine mammal parasite in these prey fish. We ran a state-space model to assess the relationship between Contracaecum spp. abundance and time, with harbor seal abundance and sea surface temperature as potential drivers. We detected an overall decline in Contracaecum spp. abundance, with a recent uptick starting in 1989 and correlated with increasing harbor seal abundance. While these data reveal a regional trend, increases in marine mammal parasites in response to marine mammal protection have occurred elsewhere, and could be occurring in additional systems. Marine mammals in Puget Sound are probably less burdened by anisakids than they were historically, but the recent recovery of anisakids could impact the health of these hosts, which today face very different stressors than they did historically.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Standard or Scrappy?: Considerations When Implementing Direct and Indirect Label Data Transcription Workflows.

The California Academy of Sciences Invertebrate Zoology (CASIZ) collection is one of 19 collaborators of the Documenting Marine Biodiversity Through Digitization of Invertebrate Collections (DigIn) TCN. This initiative targets underrepresented non-molluscan marine invertebrate specimens within US natural history collections to broaden access to diverse historical marine biodiversity collection data. To accomplish our target of digitizing 60,000 previously uncataloged lots across numerous phyla, the CASIZ curatorial staff developed comprehensive digitization workflows incorporating label scanning and direct data entry, leveraging the assistance of volunteers to efficiently capture specimen information from fluid and dry collections.




Given the understaffed nature of natural history collections, which often heavily rely on volunteer labor to support curatorial duties, determining the effectiveness and efficiency of various digitization workflows provides valuable insights for optimizing resource allocation and more rapidly enhancing access to collections data.




In this presentation, we'll highlight CASIZ's efficiency gains from DigIn digitization workflows, showcasing how focused strategies and volunteer engagement accelerated progress toward our goals. By sharing our experiences, we aim to contribute practical insights to a broader discourse on natural history collection digitization, offering guidance for similar initiatives.

Regina Wetzer, N. Dean Pentcheff

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Digitizing marine wet specimens: High-speed approaches for a slow job

Marine invertebrate specimens, preserved in museum collections, provide an indispensible window on our planet’s biodiversity. Centuries of collecting have resulted in millions of specimen lots, each documented internally with label information. Exposing that information digitally is essential both for providing access to specimens and for direct use of the occurence data. But capturing data from labels in small jars and tiny vials is so time consuming that it has taken a major NSF-funded initiative, the DigIn digitization program, to make data capture possible across multiple institutions in the U.S. The digitization effort at the Natural History Museum of Los Angeles County has developed a range of accelerated approaches to maximize the speed of primary data capture from these specimens, including dedicated workstations, custom-designed labelling, and dedicated software. The goal is rapid and accurate collection of skeletal specimen data records (taxon, collection date, collecting location, etc.). A key challenge stems from the heterogeneity of label data. Label content may be anything from fully written collecting data to just a pencilled expedition station number. Capturing data across all these label types to maximize throughput and minimize error has driven the design of an adaptable approach using direct data entry with real-time custom error checking and selective label photography. This framework has permitted us to capture primary data on marine specimens for hundreds of thousands of specimen lots at a rate of about 40 seconds per lot for data-only capture, and 2 minutes per lot for label-photo capture. Achieving this rate of digitization is essential to capture and share this essential biodiversity information.

N. Dean Pentcheff, Regina Wetzer

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Digitizing marine wet specimens: Transforming primary data capture into specimen information

The DigIn digitization program is successfully capturing primary taxonomic and collection data from hundreds of thousands of lots of wet preserved marine invertebrate specimens at the Natural History Museum of Los Angeles County. In most cases, the data captured include expeditionary station identifiers, and in some cases are label photographs. The digitization effort has been designed to be as rapid and accurate as possible. But capturing a collecting station identifier or a label photograph is only the first part of the digitization process. In some cases, collection information must simply be transcribed from photographs of written or typed labels. In many cases, the collecting expedition must be identified and the station data must be acquired so that specimens can be linked to their collecting data, based on the expedition and station identifier. Station data are not digitally available for the majority of the relevant marine expeditions, and have been located, scanned, and processed into standard collecting event and locality formats. We use a balancing set of criteria to determine whether it is worthwhile to digitize entire expeditionary datasets (depending on the number of relevant specimens and the difficulty of digitizing the dataset) or just hand-enter the few stations needed. For fully digitized expeditions, numerical and visualization tools are helping us identify and correct the inevitable instances of erroneous station data (whether those errors are in the initial data or were introduced in the scanning, OCR, and formatting procedures). In the end, the process of minimal primary data collection from specimen labels, followed either by transcription or linkage with expeditionary collection records, is yielding hundreds of thousands of digital specimen records published to the world at aggregators such as iDigBio, GBIF, OBIS, and Invert-E-Base.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The art of minerals: the impact of mineral aesthetics on collection biases

Many factors govern the decision to acquire specimens for natural history collections, some of which can introduce biases into those collections. Collection biases introduced by individuals are classed as anthropogenic biases, and these can potentially affect studies using existing collection data. For example, when collecting in the field and depositing their specimens at an institution, individual scientists and/or collectors may focus on their particular areas of expertise, leading to relative differences in sampling favouring a particular species or geographic area. Similarly, conscious or unconscious biases related to sexism, racism, homophobia, and/or colonialism may also impact potential acquisition decisions in terms of sampling location, sources of collaboration, collection contacts, or other factors. Biases in biological collections, extant and fossil, related to anthropogenic factors have been explored, but the sources of similar biases in geological collections remain understudied.



Another consideration of particular relevance to minerals specimens, in addition to their scientific value, concerns their consideration as natural works of art. Mineral galleries show off many specimens selected for their beauty/aesthetics when engaging the public on mineral science. For mineral collections, the acquisition of aesthetic mineral specimens in addition to other acquisition methods common to other natural history collections could contribute to these biases. This may lead to the over-representation of some mineral species, forms, or particular localities that are known for being particularly beautiful or pristinely preserved. People responsible for acquisitions may also have preferences towards certain minerals, colours, or forms. Additionally, the acquisition method of purchasing minerals may also introduce some biases, such as localities with well-known aesthetic specimens being mined more frequently due to their value on the commercial market, and their associated data sometimes being less precise than specimens collected directly by scientists.

Lindsay Nottingham, Emma Rosko, Amisha Anand, Michael Donovan, Laura Wilson

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Creating a Curatorial Framework for the Sternberg Museum of Natural History’s Coal Ball Collection

Coal balls are concretions of primarily plant material found in some coal seams that yield significant insights into the biology and ecology of Carboniferous Era swamps. Due to their geochemical makeup, any pyrite in them will destabilize via oxidation in the presence of water and oxygen, destroying the internal structures of the specimens in a process called pyrite decay.

The Sternberg Museum Paleobotany Collection houses seven lots of coal balls that are in various states of disarray and in dire need of curatorial attention to preserve this important part of the fossil record. Looking at two of these lots, we applied a simple pyrite decay classification system developed in 2023 at the Field Museum to rapidly assess the severity of pyrite oxidation in vulnerable coal ball collections. Additional stages were added to the scale to account for gradational differences observed in the Sternberg collection. From this modified method, a framework for approaching the curation of the Sternberg’s coal balls was developed, with the different stages of pyrite decay serving as the core. In order to prioritize specimen conservation, approaches for accession, specimen housing, making cellulose acetate peels, and data collection were developed for each stage of the scale.

The application of pyrite oxidation scales will help institutions assess their coal ball collections, and through the application of a curatorial framework derived from those scales, institutions can prioritize specimens in most need of care.

Destiny Gonzalez, Joseph Cook, Jonathan Dunnum

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Historic Collections Can Save Lives: Integrating Natural History Specimens into Pandemic Forecasting

As novel zoonotic diseases emerge, specimens can be utilized for research aimed at identifying, mitigating, and monitoring pathogens. The Museum of Southwestern Biology (MSB) Mammal Collection (>350,000 specimens, >650,000 cryopreserved tissues) is leveraging a long history of engagement with public health initiatives to build One Health infrastructure. Many specimens arise through collaborative efforts with both emergent pathogen sampling and long-term disease monitoring efforts globally. Examples include >30,000 mammals specimens and associated pathogen serology data from the initial outbreak and identification of Sin Nombre Orthohantavirus in the early 1990s, long-term Hantavirus studies in the SW US, and Panamanian specimens and serology data for Choclo and Calabazo Orthohantavirus over a 20 year span. As a result of these efforts, 18 novel orthohantaviruses have been described from MSB symbiotypes, and others are currently under investigation. In addition to forming primary infrastructure for traditional studies in mammalogy, specimens are providing crucial data for a diverse array of symbiotic studies, including viral, fungal, microbiome, and ecto- and endoparasitic based questions under the One Health umbrella. More than 5000 holistic specimens (e.g. voucher, multiple tissues, ecological field notes, microbial taxa, ecto- and endoparasites) are cataloged annually from a broad suite of globally distributed taxa. MSB emphasizes engagement through diverse collaborations with natural history museums, public health officials, wildlife managers, virologists, parasitologists, and other interested collaborators.

Niels Klazenga, Johan Liljeblad

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

The thing that makes taxa so hard to deal with is that taxa are hard to define, so one can not speak directly about taxa, but always needs to speak about them in the context of a particular taxonomy or taxonomic position. Therefore, there is a complicated many-to-many relation between the labels and the definition of taxonomic groups and one cannot see from a taxon name to exactly what taxonomic group it applies or even whether it is always applied to the same taxonomic group or can be applied to groups of different composition.

The new version of the Taxon Concept Schema (TCS) currently has properties that can be used to identify individual Taxon Concepts and properties that can be used to align different Taxon Concepts. The challenge now is to add information to the Taxon Concepts from which people, and preferably also machines, can understand what taxonomic group the Taxon Concept is about and how different Taxon Concepts can be aligned, i.e., whether they are congruent, or one is more or less inclusive than the other, or they partially overlap, or are disjoint.

The one thing in the taxonomic data we currently exchange that can serve as circumscription are the accepted name and synonyms, which works because names have types, which are specimens, but is crude, because the coverage is very small. The contributions to this symposium will present different techniques that provide better descriptions that can be reasoned with by at least humans, if not machines, and will start us on a path to include terms in TCS that allow us to exchange richer taxonomic data and will promote better name resolution.

CTRB02 Contributed oral presentations related to any aspect of SPNHC or TDWG interest

Environmental and Biological Sample Banking in MENA Nations

Sample banking in the Middle East and North Africa (MENA) region involves collecting, storing, and managing environmental (soil, water, air) and biological (tissues, blood, DNA) samples for research, monitoring, and conservation. Establishing sample banks in MENA countries can advance science, protect the environment, and enhance understanding of regional biodiversity. Proper sample collection protocols, secure storage facilities, data management systems, and ethical considerations are key. Collaborations between researchers, government agencies, and local communities are vital for success. MENA countries can contribute to global scientific knowledge, promote sustainable development, and preserve their unique ecosystems for future generations by investing in sample banking. Sample banks can aid biodiversity research by storing genetic material from various species, contributing to conservation efforts, and supporting crop improvement programs by preserving plant genetic material. They can also play a crucial role in medical research by storing biological samples for studying diseases, developing new treatments, and understanding genetic factors in health and disease. By investing in sample banking, MENA countries can position themselves as leaders in scientific research and innovation, paving the way for advancements in various fields.

Evgeniy Meyke, Natalia Sinjushina

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

EarthCape CMS - platform customization for multiple collection types and specific institutional needs

EarthCape is a database and application platform designed to facilitate the management of biodiversity data, encompassing everything from collections in museums and research institutions to environmental monitoring and laboratory results. It provides a centralized database for managing a vast array of data types, offering tools for data entry, analysis, and visualization. With its advanced features, EarthCape supports the entire lifecycle of biodiversity data management, including data collection, curation, research, and sharing. The platform's key integrations and support for data interoperability, alongside import/export functionalities and connections with platforms like GBIF, Zenodo, and Checklist Bank, empower institutions to efficiently manage data sharing and maintain alignment with external data sources.

Our upcoming demonstration will highlight EarthCape CMS's exceptional customization capabilities, showing how the system can be precisely adjusted to meet various institutional needs. We will also cover the platform's capacity for managing GIS and molecular laboratory data, showcasing EarthCape's adaptability across diverse research requirements. For this demonstration, we are privileged to utilize real-life databases from leading institutions in the field, providing an authentic glimpse into how EarthCape operates in real-world scenarios.

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

Advancing the FAIRness of scientific working collections: U.S. Geological Survey ReSciColl (Registry of Scientific Collections) Demonstration

The U.S. Geological Survey (USGS) has recently released a new catalog for working scientific collections owned by USGS and U.S. State Geological Surveys. ReSciColl relies on the mdEditor metadata creation tool to populate the catalog with rich, standards-based metadata describing the collections, to advance the FAIRness of these collections. This presentation will demonstrate the functions of mdEditor and ReSciColl, walking through the workflow of creating a collection-level entry in mdEditor, uploading it to ReSciColl, and exploring ReSciColl to discover collections.

Katie Pearson, Edward Gilbert, K. Samanta Orellana, Gregory Post, Lindsay Walker, Jenn Yost, Nico Franz

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

Building the extended specimen: Linking records to extended data in Symbiota portals

The Digital Extended Specimen has become a theoretical ideal for biodiversity specimen records, but what does an extended specimen look like in practice, and how can it be created? Symbiota (https://symbiota.org/ [https://symbiota.org/]),an open source biodiversity data management and sharing software used to create themed data portals (https://symbiota.org/symbiota-portals/ [https://symbiota.org/symbiota-portals/]),has tackled this challenge by developing tools for linking records to extended data, batch uploading linked data, and dynamically linking and updating records between Symbiota portals. Here we demonstrate how collection and data managers can extend their specimens using these tools and provide examples of how these tools are being used in Symbiota portal communities. Over 60 Symbiota portals currently share data for over 91 million records from 1,900 collections, more than 1000 of which use the portal as their primary collection management system. This growing network of collections provides a rich landscape of potential linked data, between portals, other collection management systems, other aggregators, and beyond.

Theresa Miller, Grant Fitzsimmons

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

Advancing Biological Collections Computing: A Year of Transformational Updates to Specify 7

The Specify Collections Consortium (SCC) is excited to announce that its web-based, open-source collection management platform, Specify 7, now contains novel, exciting capabilities to support the natural history collection computerization, including the cataloging and collection management of geoscience collections.




The SCC has augmented the Specify data model, data processing logic, and its customizable web forms interface to streamline and optimize workflows for digitizing, integrating and publishing data on collection holdings. These improvements include new capabilities to repatriate data, cataloging heterogeneous collection object types within a single Specify collection, intuitively describing compound collection objects, and more robust support for paleontological and geological specimens.




We will present several Specify 7 enhancements and their significance and answer questions about existing and planned capabilities.

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

echinopscis (an extensible notebook for open science on specimens): demonstrating contextually relevant information retrieval from Wikidata

echinopscis (https://echinopscis.github.io [https://echinopscis.github.io]) is an experiment in creating an extensible notebook for open science on specimens. It is built on a generic note-taking framework (Obsidian) which emphasises local data storage (using simple text format files on the local file system) and has a wealth of community resources available online - including plugins, user guides, demonstration videos, user forums etc. The demonstration will show how echinopscis can be used for e-taxonomic research, accessing specimen and literature data from remote authorities, and displaying contextually relevant information from Wikidata.

Matthew Yoder, Deborah Paul, Dmitry Dmitriev

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

TaxonWorks (https://taxonworks.org), an open-source web-based workbench, has a very broad range of functionality aimed at facilitating work in biodiversity informatics. We take a whirlwind tour through it stopping for gasping-breaths to highlight modalities of data input, output, and quality. Buckle-up, turbulence may be expected, but the destination is filled with wonder*.

*Type of wonder unspecified.

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

StaDocGen: A Human-readable Process Model

The Standards Documentation Generator or ‘StaDocGen’ is a web application and set of utilities for generating human-readable normative and non-normative web-based documentation for TDWG standards. Instead of ‘reinventing the wheel’, the application builds upon the existing TDWG process model (https://github.com/tdwg/rs.tdwg.org [https://github.com/tdwg/rs.tdwg.org]) in adherence with the TDWG Standards Documentation Specification (https://github.com/tdwg/vocab/blob/master/sds/documentation-specification.md [https://github.com/tdwg/vocab/blob/master/sds/documentation-specification.md]) without any additional requirements or processes.

Built using Python Flask, the application transforms the current set of CSV files described in the TDWG Process Model for generating RDF into human-readable normative and non-normative documentation. Current practices require that documentation be managed manually, which can lead to inconsistencies between standards and misalignments between the machine and human-readable components of a standard. This procedural disconnect between the machine and human-readable documentation processes was the original motivation for creating StaDocGen.

StaDocGen was developed alongside the review and subsequent ratification of Latimer Core from 2023 – 2024. Latimer Core was an excellent test case due to its size and complexity. The latest human-readable documentation for Latimer Core generated using StaDocGen is available here:https://ltc.tdwg.org/ [https://ltc.tdwg.org/]. Building on the success of the Latimer Core, the Minimum Information about a Digital Specimen or ‘MIDS’ (https://www.tdwg.org/community/cd/mids/) and Mineralogy Extension (https://www.tdwg.org/community/esp/mineralogy/) are slated to integrate StaDocGen in the latter half of 2024. This presentation will include a demonstration of the application, an overview of its generalized usage across TDWG, a short summary of the short-term and long-term plans for the application, and an update on its use with MIDS and Mineralogy Extension.

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

Bringing biodiversity data to LUX: enabling collections information discovery in linked, open, useful data

The Yale Peabody Museum has partnered with the other galleries, libraries, archives, and museums of Yale University to develop LUX (https://lux.collections.yale.edu/ [https://lux.collections.yale.edu/]), a platform that exposes collections information in linked, open, useful data (LOUD). The Peabody Museum serves data to the Global Biodiversity Information Facility’s Integrated Publishing Toolkit (GBIF IPT, https://www.gbif.org/ipt [https://www.gbif.org/ipt]) and other data aggregators but also to this new platform which coalesces collections information, digital assets, and metadata from each partner collection in one location. This harmonization of collections data enables discovery of relationships between scientists and artists, objects, concepts, places, events, paintings, field notes, digitized specimens, and more in a unified data discovery environment.

Platforms like LUX not only leverage standards, controlled vocabularies, schemas, and ontologies but also promote interoperability with external information sources, especially Wikidata, one of the world’s largest open knowledge graphs. This demo of the LUX platform aims to introduce the SPNHC and TDWG communities to a vision of interconnected communities and data sources by extending semantic relationships between and among institutions and their data. The source code for the LUX project is publicly available at https://github.com/project-lux [https://github.com/project-lux] and we encourage interested parties to explore this platform and how it might help promote extensible relationships between data, institutions, and people for the advancement of an interconnected ecosystem of cultural heritage and natural history.

William Weaver, James Mickley, Jason Best, Brad Ruhfel, Kyle Lough, J Ryan Allen, Alexander Henrie, Brendan Norman, Stephen Smith

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

More than one way to transcribe a label: Using VoucherVision to explore four LLM-powered transcription schemas

An outstanding bottleneck in global efforts to make natural history specimen vouchers findable, accessible, interoperable, reusable (FAIR) is the label transcription process; manual transcription is slow and laborious. However, large language models (LLMs) have proven capable of significantly automating this step in the digitization workflow, transforming collections staff into editors rather than scribes.




In the DemoCamp session, we will demonstrate the capabilities of our tool, VoucherVision, which employs an ensemble of optical character recognition (OCR), handwriting recognition (HWR), and vision large language models (v-LLM) to extract text and then uses LLMs to produce formatted JSON dictionaries for ingestion by collections databases. In exploring various LLM implementations, we have identified four main schemas that produce high-quality label transcriptions. Initially, we utilized off-the-shelf foundational models including OpenAI’s GPT-4 and GPT-3.5, Google’s PaLM2 and Gemini, Meta’s Llama models, MistralAI’s models, and Anthropic’s Claude models. These models require well-engineered prompts to consistently yield high-quality, properly formatted transcriptions. Secondly, we fine-tuned locally hosted LLMs trained to reformat unstructured OCR text directly into the desired JSON dictionary. Our fine-tuned models run on a variety of consumer-grade hardware and are easily customizable for different institutional needs. Thirdly, we implemented a system of LLM-powered agents, both foundational and fine-tuned, that collaborate to transcribe a label. A supervising agent directs the transcription process and corrects any errors from subordinate agents, significantly enhancing accuracy. Lastly, we evaluated the effectiveness of GliNER, a named entity recognition model that uses a bidirectional transformer encoder for dynamic entity extraction.




Recognizing that LLMs are fallible, we will also present our complementary editing interface, developed in collaboration with partner institutions to reduce human-induced errors. This interface is specifically designed to minimize the chance that the user accepts incorrect transcriptions, such as hallucinations or omissions, into the official records.

Michelle L. Gaynor, Natalie N. Patten, Douglas E. Soltis, Pamela S. Soltis

DEMO01 DemoCamp: Live demonstrations of technology for natural history collections and biodiversity data

An introduction to Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data

How many digitized records exist for the Southern Appalachian endemic,Galax urceolata(Diapensiaceae)? Here we will demonstrate the many ways to download occurrence records for this monotypic genus and introduce our streamlined approach to downloading biodiversity data from two major biodiversity aggregators. With our new R package, gatoRs (Geographic and Taxonomic Occurrence R-Based Scrubbing), we provide users with tools to streamline the downloading and processing of biodiversity data. With gatoRs, you can download records from both GBIF and iDigBio based on a list of user-provided synonyms. Overall, our download increases the number of unique records obtained from iDigBio for your taxa of interest with a pseudo-fuzzy match to circumvent iDigBio's exact match search logic. We also streamline data processing for research applications by providing functions for identifying missing data, taxonomic harmonization, locality filtering, duplicate record correction, correcting for spatial bias, and other filters. We designed gatoRs to be both efficient and accessible to promote the use of biodiversity data in research and education.

Siobhan Leachman, Lucy Schrader

Delving into Te Papa research expedition data

The Te Papa Research Expeditions projecthttps://www.wikidata.org/wiki/Wikidata:WikiProject_Te_Papa_Research_Expeditions [https://www.wikidata.org/wiki/Wikidata:WikiProject_Te_Papa_Research_Expeditions]was a 12 week long pilot project, funded by Wikimedia Aotearoa New Zealand and supported by the Museum of New Zealand Te Papa Tongarewa. It aimed to test the practical implementation of the TDWG Research Expedition working group’s proposed data schema for research expeditions in Wikidata and to provide feedback on improving the same.




During the pilot project information was collated about Te Papa-related research expeditions and added to Wikidata, thus making that information available in a structured form to both the museum and the general public. The project assisted in improving Te Papa’s collection management system by feeding into an internal model for expeditions, helping link expedition data to related participants, specimens and archives. Documentation was drafted at the conclusion of the pilot project reporting back on the successes and challenges and giving guidance to other institutions wanting to reproduce this type of project. Finally the pilot project provided recommendations to the TDWG research expeditions working group helping to improve the proposed Wikidata schema and the draft best practice documentation.




We will present on how the Te Papa research expeditions project was conceived, funded and organised, as well as a summary of the challenges overcome and the results achieved. Guidance will be provided on how the pilot project can be replicated, thus assisting natural history institutions to use Wikidata to improve the interconnectedness of their expedition data to other institutions, expedition participants, specimens, archives and publications generated as a result of research expeditions.

Robyn Drinkwater, Robert Cubey

Effective public engagement with Herbaria: Frankenstein’s Plants, a case study from the Royal Botanic Garden Edinburgh

As part of the Edinburgh Science Festival we have run Frankenstein’s Plants, an activity to engage children and the wider public with the work of Herbaria and highlighting the herbarium at Edinburgh.

Participants create their own herbarium specimens using prepared pressed and dried plant material. The public mount the material on card, add “collection data” and create their own scientific binomial from a selection of genera and species epithets provided. The last step is to digitise their specimen and for it to be added to our virtual herbarium.

Our aims from the events have been to raise awareness of the herbarium at Edinburgh and how it is used by scientists globally, how specimens are made and the idea of a scientific name and how it is constructed. The event also comes under the STEM Ambassadors Scotland project, to promote the prospects and variety of STEM (science, technology, engineering, or maths) careers.

The event has been successful and over the three years we have run the event we have engaged with around 1000 ‘collectors’ ranging in age from 3-95 age. Post-event on-site feedback has been monitored and has been recorded as exceptional.

The herbarium staff traditionally with a more inward-looking role, enjoy getting out into the public and sharing the basics of the work they undertake in the herbarium, the event is also staffed by students from the RBGE MSc in Biodiversity and Taxonomy of Plants.

What can knowledge graphs can tell us about who is doing taxonomy, whereabouts, and who is funding them?

Despite the conceptual elegance of knowledge graphs (“link all the things!”), we have few concrete examples of using knowledge graphs to learn things we don’t already know. Instead, audiences are more likely to have heard talks on either how hard (or joyful) it is to make knowledge graphs, or how wonderful things will be when we have them. But what can we learn from them?

For this talk, I set myself the challenge of trying to gain insights into the current state of taxonomic research by constructing a simple knowledge graph for publications and authors who have recently published new taxonomic names. My BioRSS tool https://biorss.herokuapp.com [https://biorss.herokuapp.com] (inspired by work by the late David Remsen) endeavours to keep track of the recent taxonomic literature by subscribing to journal Really Simple Syndication (RSS) feeds. Data from BioRSS, together with data mining taxonomic databases, gives us a set of recent taxonomic papers together with their Digital Object Identifiers (DOIs). Using those DOIs we can retrieve Open Researcher and Contributor IDs (ORCIDs) for authors, which in turn gives us access to information about where those authors work, and who funds them.

Using these sources we can create a simple knowledge graph connecting people, places, publications, and organisations. I will discuss how this graph can help determine who is publishing taxonomic work, what organisations fund this research, and where those researchers and funders are based. The utility of knowledge graphs for undertaking this research will be discussed, together with what this knowledge graph tells us about the current state of taxonomic research.

The Dream of Mainstream in BIS/TDWG

Standards service the research community while requiring significant research themselves. TDWG, SPNHC and GBIF have been providing nuts and bolts to biodiversity research for decades, but does this translate into visibility for the community of users? While the annual conferences gather a rather persistent group of practitioners who showcase the workings and products of the community, do their target customers gaze through the glass into the luminous shop, or do they merely profit from the shine to walk their footpath more safely?

One way to put our groups in perspective is to look at how our products are recognized by mainstream science. GBIF, for example, has long been keeping track of papers and research using the records it serves, as well as literature about GBIF itself. TDWG, on the other hand, while also keeping a record of its history, does not have a similar mechanism—perhaps because TDWG’s (and SPNHC’s) preferred outlets may not be on a par with the usual scientific outlets: standard, peer-reviewed, indexed papers. Amazingly for such relevant work, much of work seems to be known only through conferences’ abstracts, presentations, and posters, which even though they are actually peer-reviewed do not truly conform to the gold standard (pun intended) of scientific publications and are often contemplated as fringe research by many actors such as evaluation agencies.

In this presentation, I take a representative sample of standards-related production and ask whether they are comparatively known in mainstream science by extracting a number of publication and citation patterns.

Results show that the ratio of indexed vs non-mainstream production is indeed tiny and could certainly be much improved, but on the other hand mainstream biodiversity literature seems to resort to that non-regular production… rather regularly. We may be fringe, but usher the main stream like river banks.

Exploring size bias of natural history museum specimens: Comparing historic taxidermy mammals to contemporary populations

Specimen sex biases in museum vertebrate collections have been well-documented. This known male sex bias equates to body size bias for mammal groups that exhibit high rates of sexual-size dimorphism, such as ungulates and carnivores. Past work on specimen sex bias has focused on research-grade specimens with complete data taken from animals prior to skinning. However little attention has been paid to the more public-facing specimens housed in natural history collections: taxidermy mounts. As educators and stewards of nature, those who care for taxidermy collections aim to exhibit accurate representations of our natural world. However, taxidermy mammals exhibited to the public may bias impressions of what contemporary wild mammals look like, regarding body size and weaponry/ornamentation (antlers, horns). Human hunters preferentially hunt out the largest animals of a population, leaving smaller animals to survive and reproduce. Taxidermy mammal collections acquired by museums via donations from trophy hunters may show off extraordinary specimens with much larger body sizes and impressive ornamentation than animals seen in the wild today. Here, I present a preliminary case study comparing body size measurements of taxidermy ungulates (48 Artiodactyla specimens, 1 Perissodactyla specimen) and Carnivora (14 specimens) from the Connecticut State Museum of Natural History to body size measurements of current populations of each respective species. We found that sizes (head-body length, shoulder height, muzzle width) of taxidermy mammals were larger than mean sizes of current mammal populations (MammalBase, Amniote Database). At museums, we strive to inspire awe and wonder, and big mammals do a great job of affecting the public positively. Despite that, we need to be cognizant of the bias we may be promoting via display of larger-than-extant-living mammals. Acknowledging the fact that exceptionally large individuals no longer appear in current populations allows us to highlight how anthropogenic activities affect wild animal populations.

Ben Scott, Arianna Salili-James, Sanson Poon, Vincent Smith

Cobots at the Museum: The Role of Robotics in Digitisation

In the last decade, the Natural History Museum, UK (NHM), has been at the forefront of the digitisation of natural history collections; with almost 6 million of its 80 million specimens digitised. This momentous undertaking has led to numerous innovations on how to optimise digitisation workflows. One avenue that is currently being explored is the use of collaborative robots – cobots.

Since acquiring a Techman TM5 900 robotic arm in 2023, we have been experimenting with its capabilities. Experiments begun with simple pick-and-place tasks, using artificial specimens. Next, we focused on two use-cases, based on the digitisation of shark teeth, and pinned-insects. Both shark teeth and pinned insects are in abundance at the NHM, making their manual digitisation a tedious task. Currently, we have trained the cobot to pick up a specimen, move it elsewhere to photograph, scan the specimen and move it back to its original position. Thus far, this has all been coordinate-based.

Soon we will be establishing workflows that incorporate computer vision (CV) and machine learning (ML). This will enable us to expand our robotics capabilities, with pipelines that could significantly enhance efficiency. Broadly, these ML-based pipelines can be split into four sections:

1. SpecimenIdentification:CV/ML tolocateindividualspecimensor certain parts of specimens e.g.,pinheads withinpinned insects.
2. Handling: with custom grippers, thecobotwillpickand placespecimensdelicately.
3. Scanning: thecobotwillscan andphotograph specimens. Furthermore, using ML,specimenlabels can beidentified,segmented,andautomatically transcribed withbuilt-inOpticalCharacter Recognitionprocesses.
4. Identifiers: thissteprequires thecobotto attachidentifierlabelstospecimensor drawers, afterlocatingtheoptimalposition using CV/ML.

Here, we will discuss the progress of the NHM’s cobot research and explore the future of robotics for the digitisation of natural history collections.

Building Modern Standards for Resolving Legacy Acquisitions: A Reassessment of the NMNH Entomology Transaction Records

In recent decades, entomologists and entomology collections have experienced significant culture shock as countries have rapidly changed their regulations regarding collecting and export permits for insects. Historically, entomologists were less impacted by regulatory requirements that focused more heavily on vertebrate and botanical samples and ignoring invertebrates unless they were endangered or CITES restricted.

As the regulatory landscape for insect collecting has changed, entomological collections are forced to update their procedures to keep pace with international laws and new legal compliance requirements that had not applied to insects previously. These procedural updates help preserve biodiversity by providing a framework for ethical collecting and access and benefit sharing with countries that host that biodiversity. For the Smithsonian National Museum of Natural History’s (NMNH) Department of Entomology, this has involved a multi-phase change in registration practice involving 1) hiring a dedicated registrar; 2) updating procedures related to documentation and regulatory compliance; and 3) setting standards for new acquisitions that promotes advance planning for collecting expeditions. Each phase brings the department into full legal compliance with global standards. Complicating this issue is a 40+ year history of non-standardized registration practices, resulting in a significant backlog. This created a daunting task of resolving 1,700+ legacy acquisitions using a contemporary framework.

How do we resolve legacy acquisitions with modern standards and with difficult and often contradictory laws regarding wildlife collection by scientists? How do we better inform and educate collectors and scientists about new regulations and registration practices? This presentation will examine the steps the NMNH Department of Entomology is taking to ensure new and legacy acquisitions adequately conform to modern standards. Multiple test cases will be presented to demonstrate the different actions needed to resolve each of them.

Chia-Yun Lee, Jin-Ying Lee, Mao-Ning Tuanmu

Enhancing acoustic data mobilization: A user-friendly data platform for the Asian Soundscape Monitoring Network

Passive acoustic monitoring (PAM) has emerged as a crucial tool in monitoring efforts to track environmental changes and evaluate conservation measures in response to the biodiversity crisis. PAM now offers long-term and continuous insights into biodiversity, with many acoustic indices correlating with biodiversity and deep-learning tools aiding in the detection and identification of animal sounds. However, managing and mobilizing original recordings remains challenging due to their large size and lack of structure, hindering broader applications of the valuable data. Established in 2014 by Academia Sinica and Taiwan Forestry Research Institute, the Asian Soundscape Monitoring Network has amassed over 20 million minutes of audible and ultrasonic recordings from diverse landscapes, including forests, wetlands, urban parks and farmlands across Malaysia, Thailand, Taiwan and Vietnam. To enhance data mobilization and utilization, we developed a user-friendly data platform enabling browsing, searching, visualization, exploration and retrieval of the original recordings, as well as derived data such as acoustic indices and species occurrences, along with associated weather records. Detailed information about the monitoring sites and recorder deployment is provided. Each recording is tagged with a Creative Commons license, and a unique Archival Resource Key is assigned to every data retrieval for persistent identification, facilitating data reuse. Additionally, recordings containing human voices are identified and restricted to protect privacy. Our aim with this data platform is to streamline the mobilization of acoustic data, foster diverse applications, and enhance the overall value of the data.

Challenges and Opportunities at the Intersection of AI and Biodiversity

We are currently witnessing an unprecedented loss of biodiversity, yet biodiversity is vital to sustainable development, public health, and mitigating climate change. To better understand and hopefully mitigate this loss, natural-world data is being collected at unprecedented scales from networks of ground-level sensors, satellites, drones, DNA collections, and community science platforms. There is valuable scientific information stored in these raw data, the vast majority of which are as-yet inaccessible due to the time and resources needed to process the data by small groups of relevant human experts. AI will prove crucial to facilitate efficient extraction of scientific insight from quickly-growing repositories of natural world data, but in order to realize the goal of global-scale, near-real-time biodiversity monitoring we must shift the AI research paradigm beyond highly curated datasets to capture the complexities of the real world, including strong spatiotemporal correlations, imperfect data quality, fine-grained categories, and long-tailed distributions. Beyond the inherent challenges of the data itself, the target is also moving - taxonomies are constantly debated and in flux, data infrastructure and protocols aren't standardized, and there are ongoing and important discussions about data ownership, sovereignty, and the risks of sharing data, particularly for at-risk species. I will discuss the implications of these challenges and the impactful new avenues of research they outline at the intersection of AI and Biodiversity, and highlight exciting recent efforts towards AI-enabled biodiversity monitoring that operate within and overcome these constraints.

一期一会(Ichi go ichi e) One lifetime, one chance meeting

What started as a single conversation with Dr. Rika Kigawa at the 2001 Pest Odyssey conference in London, England about the transition away from methyl bromide fumigation and the applicability of alternatives to the protection of cultural property became a 23-year collaboration with Japanese colleagues.

Over the following year we conversed about the changes in Canada that I had participated in from the mid-1980’s to 2000’s and the positive examples for Japan. In 1999, Dr. Kigawa had started a five-year federal research program to respond to the loss of MeBr for cultural property protection. In 2003 we visited five Canadian institutions with long running IPM programs to interview staff on the success and challenges with adopting IPM. By 2004 we had organized a three-dayworkshop with practicum on IPM that introduced many professionals from Japan and Korea to the insects and alternative methods required to carry out IPM programs in their university collections and museums.

By 2005 MeBr use was limited and ceased to be available in Japan. Subsequently many institutions no longer had access to MeBr fumigation for eradicating insect pests unless they switched to carbon dioxide or anoxic methods. Ethylene oxide has remained available as a major fumigant for treating mould and as a quarantine treatment for importing foreign sourced objects, however it will no longer be available for cultural sectors by March 2025. A few mid-sized pest control firms had interest in providing alternative methods to museums, were engaged in the education process, and now have a long running association as service providers.

While low temperature thermal control predominated, interest remained in elevated temperature approaches. When the UNESCO World Heritage site at Nikko was determined to have a pernicious threat from novel anobiid species threatening 103 buildings, Dr. Kigawa’s research applied moisture-content controlled heating for timber structure disinfestation.

Birgit Gemeinholzer, Hugo de Boer, Quentin Mauvisseau, Dag Endresen, Niels Raes, Barbara Gravendeel, Sydney Wizenberg, Panagiotis Madesis, Ioanna Karamichali, Fotis Psomopoulos, Nikolaos Pechlivanis, Rui Figueira, Pedro Beja, Paulo Celio Alves, Vanessa Mata, João Queirós, Eugeni Belda, Eric Chenin, Youcef Sklab, Edi Prifti, Jean-Daniel Zucker, Auguste Gardette, Mihael Ichim, Ancuta Cristina Raclariu-Manolica, Patrick Ruch, Donat Agosti, Daniel Lundin, Olaf Banki, Steven Janssens

LTNG02 Diversity and Commonalities of AI Applications to Biodiversity Issues and Data

METAPLANTCODE – Harmonizing plant metabarcoding pipelines in Europe

Currently, ~2 out of 5 plant species are threatened with extinction. Plant loss will also affect other groups of organisms and the environment in ways that are not yet understood, as plants have important functional dependencies in complex organism networks. METAPLANTCODE presents a unique collaborative and transnational approach to test, optimize, harmonize and recommend best practices for plant metabarcoding for samples with varying degrees of species complexity, contamination and DNA degradation using case studies across Europe. The METAPLANTCODE project aims to test and optimize pan-European case studies on metabarcoding, provide best practice recommendations, optimize analysis pipelines for species identification, and create easy-to-use reference databases. The project will identify and specify gaps, publish best practice documents on FAIR data publishing of plant metabarcode data to GBIF and the INSDC databases, and implement ELIXIR-compatible multimodal DL models in novel tools for stand-alone metabarcoding analyses using different data sources. The project will enhance species identification accuracy through GBIF records and metadata and map regional, national, and international botanical taxonomic checklists, red lists, and floras to the Catalogue of Life (COL) through COL ChecklistBank. Furthermore, taxonomic and floristic literature will be semantically enriched with new entity recognition and relationship extraction modules to support the enhanced identification of species via domain-specific descriptive/phenotypic features. An interface will be provided to link taxonomic names to treatments, identify homonyms and synonyms, and facilitate the conversion and annotation of flora, red lists, and ecological treatments. All METAPLANTCODE products will be FAIR+. Stakeholder engagement, training, and outreach efforts are planned to ensure that plant metabarcoding becomes a routine standard for biodiversity monitoring in Europe and beyond in the future.

Elie Mario Saliba, Éric Chenin, Régine Vignes-Lebbe

LTNG02 Diversity and Commonalities of AI Applications to Biodiversity Issues and Data

Traits for efficient navigation and search in natural history collections

Digitized collections are currently constituted by massive image bodies, such as the ~ 10 million 2D and 3D images in botany and zoology available from French natural history collections. The metadata available so far to search through these bodies is fairly limited. Artificial intelligence techniques in the field of computer vision and text mining can be used to extract characteristics linked to specimens and taxa, which will enrich searches in digitized collections in the future. This is one of the aims of the French national E-Col+ project.

To select the traits to be searched for by AI, scientists and curators working on taxa and specimens of very different natures (fossils, microscope slides, botanical plates, specimens in alcohol or naturalized) were consulted. This presentation outlines the findings of these interviews. Some of these traits are at the specimen level (e.g. visible morpho-anatomical traits, or traits related to the specimen’s specific characteristics -state of conservation, presence of envelopes, presence/absence of organs like roots, flowers, fruits, etc.-) and can be extracted using computer vision AI techniques. Other traits are at the taxon level (e.g. morpho-anatomy, ecology, phenology, spatial distribution, or related to the taxon’s uses by man) and can be acquired by NLP AI techniques. Interestingly, taxon-level traits extracted from texts, when visible on the specimens themselves, can be used in computer vision training.

A key asset of this study is that it deals with one of the most complete collections of specimen images worldwide (all taxonomic groups, all types of images). This leads to a very concrete and thorough survey of the various use cases, covering all types of issues including taxonomic concerns, anthropic use, collection curation, and biomimetism.

LTNG02 Diversity and Commonalities of AI Applications to Biodiversity Issues and Data

The new EU Artificial Intelligence Act : Impact on the Biodiversity Information Community

In February, the EU endorsed the AI Act and launched the new European Artificial Intelligence Office. This legislation governs how AI is developed, deployed and used in Europe. The obligations will incrementally become mandatory until 2030. While the Act was primarily designed to protect humans from risks of manipulation and illicit use of AI, it will not be without impact on the Biodiversity Community. AI in our domain will mostly be ranked as no to low risk. However we will have to adhere to the transparency requirements and be particularly attentive when combining AI with Citizen Sciences initiatives affecting potentially the general public. A further point of attention with our worldwide scope, is that non-European AI initiatives or tools to be allowed deployment or usage in Europe will have to commit to follow both the AI Act and the the GDPR (General Data Protection Regulation) and have a reference person or institution with legal address in Europe.

Future EU projects can be audited any time during their execution period on how they comply with both legal and ethical requirements of AI with risks to be put on hold or even stopped.

Current discussions at the EU level are on how they can remain competitive in AI compared to other countries where less legal or ethical barriers exist, while judged essential there are no doubts that they slow down the development and implementation processes. The balance between open collaboration and free sharing of data and knowledge are challenged by concerns about so called strategic autonomy and competitiveness.

As an introduction to this session, this talk will go to the best of our knowledge over this new EU AI Act requirements and how it may affect future AI linked activities in our Natural Sciences domain.

Jonas Grieb, Claus Weiland, Alexander Wolodkin, Leyla Jael Castro, Stian Soiland-Reyes, Maya Beukes, Martin Jansen

LTNG02 Diversity and Commonalities of AI Applications to Biodiversity Issues and Data

Using webby FDOs to integrate AI Taxon Identification and Citizen Science

Camera traps and passive acoustic devices are particularly useful in providing non-invasive methods to document wildlife diversity, ecology, behavior, and conservation. The application of autonomous devices such as IoT sensors is constantly developing and opens up new application possibilities for research and nature conservation. Furthermore, the amount of associated recorded digital photos, videos, and audio files is growing at a rapid pace producing too much data to make human annotation feasible.

Machine-learning in contrast can generate (baseline) annotations at scale on high-throughput data but may not capture all details compared with the complex contextual understanding of human annotators.

We developed the WildLIVE platform (https://wildlive.senckenberg.de [https://wildlive.senckenberg.de]) to effectively combine machine-learning (taxon identification and individual identification of animals) and “Human-in-the-Loop” citizen science. Our primary objective is to enable the curation of digital image, audio, and video content from biodiversity monitoring based on crowd-sourcing with (semi-)autonomous data processing by machines, and their subsequent mobilization as machine-actionable knowledge units.

To this effect, the data model of WildLIVE features a “webby FAIR Digital Object approach” leveraging on RO-Crate and FAIR Signposting to enable packaging of an observing process’ contextual information (e.g. metadata of sensors, geolocation, and links to content stream) together with operational semantics giving machines the information needed to autonomously process the actual data (e.g. calculate the inference on an image). To represent the semantics of data capture events, we designed an ontology, the WildLife Monitoring Ontology (WLMO), which provides a formal description of fundamental concepts and relations.




The talk will provide an overview of the platform’s development status and the technology stack employed (combining RO-Crate and FAIR Signposting with AI plus “Humans-in-the-Loop”) for data exchange with emerging Biodiversity-related integrated dataspace projects such as the Green Deal Data Space.

Youcef SKLAB, Hanane Ariouat, Eric Chenin, Edi Prifti, Jean-Daniel Zucker

LTNG02 Diversity and Commonalities of AI Applications to Biodiversity Issues and Data

Towards a Deep Learning-Powered Herbarium Image Analysis Platform

Global digitization efforts archived millions of scans worldwide in herbarium collections, which are essential for studying plant evolution and biodiversity. Recolnat hosts at present over 10 million images. However, analyzing these datasets poses crucial challenges for botanical research. The use of deep learning in biodiversity analysis, especially in examining herbarium scans, has shown promising results in numerous tasks.

Within the e-Col+ project, we are developing multiple deep learning models aimed at identifying plant morphological traits. The dataset is composed of 4000 images annotated for 23 morphological traits. We have developed pipelines and models for cleaning, analyzing, and transforming herbarium images, including models for: i) detecting non-vegetal elements, such as barcodes, envelopes, labels, etc.; ii) detecting plant organs, including leaves, flowers, fruits, etc.; iii) segmenting to recognize plant parts. We are also developing models for classification tasks related to various morphological traits, including i) binary and multi-label classification; ii) multimodal learning, integrating contrastive models, such as image-text.

Deploying these models in a generic platform is crucial for validation, generalization, usability and allow users to add additional annotations to train and enhance the existing models catalog. Therefore, we are developing a platform, called PlantAI, which allows users to upload images, create custom datasets, and access various AI models for image analysis. It facilitates result comparison and tracks model performance over time. It integrates APIs tailored to herbarium image analysis. It includes: i) a database housing a collection of 6 million herbarium images; ii) a search engine to facilitate navigation through the image collection; iii) APIs for interacting with deep learning models; iv) a pipeline for automated dataset creation and management; and v) a system for testing deep learning models on prepared datasets. This platform, could be highly beneficial for botanists, enhancing the efficiency and effectiveness of biodiversity analysis from herbarium scans.

Eren Karabey, Kate Gill, Eve Lucas, Nicky Nicolson

LTNG02 Diversity and Commonalities of AI Applications to Biodiversity Issues and Data

Deconstructing the monograph: building multi-modal datasets for machine learning

Monographs are gold-standard taxonomic outputs, which collate many different kinds of richly interlinked data, evidenced through citation to persistent specimen resources. Advances in collections digitisation and data mobilisation mean that many of these specimen metadata records and images are now available online for linking and reuse. Now that we have this rich - but distributed - set of data, we are interested in the applying machine learning and computer vision techniques to help with species identification. Accurate, accessible, expert-curated data is crucial for the development of machine learning models. Traditionally monographs have been aimed at the botanical researcher, but the information contained within these publications represents a valuable resource for machine learning researchers. By gathering openly accessible data, it is possible to deconstruct the monograph to a set of multi-modal datasets which interlink (i) species descriptions (enumerating traits) with (ii) specimen images used as reference for the species (as listed in the material examined section) and (iii) scientific illustrations which depict diagnostic features (which are linked to the specimen used as the reference for the illustration). We will describe work on a pipeline process to automate this deconstruction and to populate a machine learning platform with citable datasets to enable different kinds of reuse. We will discuss the potential for the wider application of this technique to a range of different monographic sources.

Life after death, the value of zoo animals in museum collections.

In July 2020, “Floyd”, one of the oldest reticulated giraffes at the San Francisco Zoo (SF Zoo) died at age 18. He was an ambassador for his species at the zoo and was beloved by visitors of all ages. My personal experience with Floyd began in 2013 when I first saw him at the zoo while visiting with my 1 year child. He was a stunningly calm and elegant animal that inspired everyone to care about giraffes. When his skull was transferred to the Ornithology and Mammalogy Department at the California Academy of Sciences (CAS), as a Curatorial Assistant, it was an honor to prepare it for the scientific collection. Now he can be part of any future study onGiraffa camelopardalis reticulata,aspecies considered “vulnerable” by the International Union for Conservation of Nature (IUCN) because their population has been decreasing. With this presentation, I want to express the importance of partnerships between museums and other institutions like zoos, aquariums, wildlife hospitals and government agencies, that can help to build scientific collections.In our collection we have created 50 accessions and received about 70 specimens from the SF Zoo in just the last 14 years, mostly mammals. Before 2012, Ray Bandar, a researcher associated with CAS, received and processed approximately 35 animals from the SF Zoo during the 1970’s and 1980’s building an amazing collaboration between CAS and the SF Zoo. This partnership added more than 100 specimens to the collection providing valuable information for the scientific research community.

David Yuan, Julie Beckman, Jaime Florez Fernandez, Juanita Rodriguez

Urban Insect Housing Market: Mud Dauber Wasp Sceliphron formosum and its Nest Ecology

Mud dauber wasps, Sceliphron formosum(Hymenoptera: Sphecidae), are native to Australia and commonly found in urban areas where they build mud nests on human constructions. Mud nests are served as brooding rooms for their larvae, in which paralysed spiders are provided as food. Amongst all recorded Sceliphronspecies in Australia, S. formosumis the only species that built mud nests containing single cells and was observed frequently in urban areas in ACT. Our research dived into its nest ecology and revealed that not only are those mud nests used for their offspring but also used by other native insect as shelters in the urban area. With such high demand for these “mud nest real estate”, a complicated hosts, parasitoids and opportunistic insect web is formed, with a total of 16 families including 23 species of insects being recorded utilising the mud nests. A small collection of the Sceliphron formosumspecimens, its mud nests and all the insects that are associated with the use of mud nests was deposited in the Australian National Insect Collection, CSIRO.

In this presentation I will introduce you S. formosumand its nesting behaviour, as well as briefly talking about three intriguing discoveries in this study:

1. Small headed flies that utilise the spiders prepared for mud dauber wasp larvae died from trapping inside the mud nests.
2. An undescribed bee fly host on Crabronid wasps that utilise empty mud nests.
3. New species of spider wasp reported co-habiting with a larva of mud dauber wasp.

Lizard with a Double-Ended Tail - is that all?

Specimen GLAHM:120240 has been on display in The Hunterian Anatomy Museum at the University of Glasgow for more than 50 years labelled as “Lizard with Double-ended Tail”, an interesting enough reason for display and being under a spotlight perhaps? But a recent, serendipitous, investigation of the specimen revealed that it is not just any lizard, but an endemic species once only found on Jamaica. The Jamaican Giant Galliwasp (Celestus occiduus) is presumed to have gone extinct in the 1850s, there are only a few specimens in collections around the world so to find one sitting openly on a shelf was a fantastic moment. Further investigation of an old register even provided collector names and dates and a description of the species in life. Its discovery was very timely as it was made when another C. occiduus specimen in The Hunterian was in the process of being repatriated back to Jamaica. Zoological specimens can be hidden in plain site in many other collections so keep your eyes open.

One of one, now one of many: How a chance encounter saved Prunus 'Tai-haku’ from extinction

In the summer of 2019, the Royal Horticultural Society (RHS) opened a new welcome building which draws our visitors into the garden. Greeting the visitors is a long avenue of trees, which are a spectacular sight from spring into late autumn. As I write this specimen spotlight it is early April and the trees are at their most flamboyant.

As a Herbarium Collections Curator for the RHS, the sight of these trees inspired my quest to discover which cherry tree specimens were contained within the collection. Little did I know at the time, that this simple question would lead me to the fascinating story of Collingwood ‘Cherry’ Ingram and the Prunus ‘Tai-haku’. Who was the intriguing sounding Cherry Ingram and why was he invited to Japan in the 1920s?

This specimen spotlight will explore the value of a dried plant specimen beyond its use in science and scientific research, and the story of how one man’s lifelong passion brought the glorious Great white flowering cherry back from the brink of extinction.

150 years in front of our eyes, yet undiscovered: Another story of long lasting shelf life of museum specimens

The Aquazoo Löbbecke Museum in Düsseldorf (Germany) is engaged in a fruitful cooperation with the Club Conchylia e.V., a German club of malacological ethusiasts, collectors and scientists. In 2021 one such private collector, Roland Günther, was visiting the institute’s historical collection, discovering a new species of sea snail right away. In honour of Theodor Löbbecke (1821-1901), the founder of the museum (which today is a zoo and aquarium, too) the newly discovered species was named „Löbbecke‘s Dolphinsnail, Angaria loebbeckei“, a species description of which was published in 2022. This talk will highlight (again) the enormous shelf life of specimens that often comes prior to their actual discovery and species description. Moreover it will shine a light on the value of volunteers at natural history collections, especially in small museums with only few employed experts.

Suzanne Ryder, Roberto Portela Miguez

What does a quarantine facility plan, an art installation and a white rhino taxidermy specimen have in common?

In 2022 the Natural History Museum (NHM) London, opened a temporary art installation featuring a digitally reproduced, northern white rhino. Alexandra Daisy Ginsberg, artist and exhibition curator of The Lost Rhino – ‘The Substitute’ featured a life size projection of a rhinoceros that slowly comes to life, transforming from a series of pixilated forms into a high-resolution reproduction of an adult northern white rhino, before disappearing completely. The thought-provoking artwork questions our fascination with creating or recreating new life forms rather than conserving existing species. Accompanying the digital centre piece were a few artifacts that presented different representations of a rhinoceros.

One of the specimens exhibited alongside the artwork was a 100 year old white rhino taxidermy specimen from the collections at the NHM. Displaying a specimen such as this precipitates practical, ethical and security challenges that had to be overcome by the curatorial, conservation and exhibition teams at the NHM before installation.

This specimen is significant to me because one of my roles at the NHM has been, Integrated Pest Management (IPM) coordinator. The NHM has had a comprehensive IPM programme in place for many years and one of biggest achievements for the IPM group was securing funding and support for a state-of-the-art quarantine facility. This space opened in 2012. The IPM group worked with designers to make this bespoke space work for multitude of users and objects. When deciding on the size of the large walk-in freezer we specified that it should be able to accommodate a taxidermy specimen of an adult rhino. As result of the exhibition for the first time the freezer was actually used to freeze an adult rhino!

Triple Threat: A unique herbarium specimen crosses three categories of natural history collections

The Harvard University Herbaria (HUH) houses over 5.5 million specimens, the majority of which consist of one organism with a single preparation (e.g., one pressed plant on one sheet; one dried moss in one packet). These “simple” specimens are stored based on taxonomic identification. However, a growing number of specimens are being recognized as “mixed collections” with more than one organism per preparation, such as two lichens attached to a shared twig, or a fungal infection on a pressed vascular plant. These require decisions to be made about attribution, curation and storage.



One mixed collection in HUH’s collection is particularly diverse: a fungus (Columnomyces electri) growing on an insect (Proptomaphaginus alleni) preserved in Dominican amber. This object is a type specimen for both the fungus and the insect and represents three categories of natural history collections: botanical, entomological, and mineralogical. It is stored in Harvard University’s Botany Libraries alongside HUH’s other amber collections and is a unique example of the interdisciplinary nature of natural history collections.