SYM01 Standards alignment: which and how?

Session Type: Symposium (unsolicited presentations considered)

Organizers: Anton Güntsch, Freie Universität Berlin, Berlin, DE; Stan Blum, Biodiversity Information Standards (TDWG), San Francisco, US; David Fichtmüller Freie Universität Berlin, Berlin, DE

Over the past decades, numerous standards have been developed that are used for the exchange of biodiversity data at various levels. Due to different technical and content-related requirements, these standards were often developed independently, although their scope overlaps considerably in some cases. A prominent example are the TDWG standards ABCD and DarwinCore, which have been developed in parallel and are widely used in the community. The symposium will present examples of standards that could potentially be merged or aligned with other standards in the future. We will also discuss effective methods for standards alignment and merging.

SYM02 Use and re-use of images and their metadata in biodiversity research

Session Type: Symposium (unsolicited presentations considered)

Organizers: Patricia Martin-Cabrera, Flanders Marine Institute, Oostend, BE; Maarten Trekels, Meise Botanic Garden, Meise, BE

Many fields in biodiversity research are generating a vast amount of images. Examples are the mass digitization of natural history collections or automatic sensor-collected images. The amount of images is growing exponentially, and new methodologies such as machine learning are generating derived taxonomic data and metadata. Handling these images imposes new challenges: ranging from visualizing them to storage and sharing of data and metadata. In this symposium we want to give an overview of the use of metadata standards in biological imagery and the various issues that might arise from it, and how to integrate image information. Do existing standards cover well the user needs associated with image handling? What standards exist? Can we learn from other community driven standards (e.g. IIIF)?

SYM03 Enhancing connections with the global neighbourhood through expanding partnerships

Session Type: Symposium (unsolicited presentations considered)

Organizers: Constance Rinaldo, Harvard University, Cambridge, US; Colleen Funkhouser, Biodiversity Heritage Library, Washington, US

The Biodiversity Heritage Library (BHL) is more than a digital library, it is a key resource for data related to biodiversity. Data such as museum specimens, taxonomic names, environmental and geolocation variables is embedded in the published and unpublished literature found in BHL.Over the past year, BHL has developed a five year strategic plan designed to bring more focus on data, technology and partnerships. BHL is already well-established within the global bibliographical knowledge base. The plan for the symposium is to highlight some new directions and identify synergies and connections with current, new and potential partners in the biodiversity knowledge infrastructure.

SYM04 Challenges of the alignment of collection management systems across the globe and different domains

Session Type: Symposium (unsolicited presentations considered)

Organizers: Heimo Rainer, NHM Vienna, Vienna, AT; Falko Glöckler, Museum für Naturkunde Berlin, Berlin, DE

In the domain of natural history a manifold of collection management systems exist. Each system has been developed for serving the different requirements of the community. Consequently, there are systems specialized for botany, zoology, geology etc. and implemented with different frameworks, programming languages and database systems. However, all share the common goal of managing collection holdings. Thus, there is a huge overlap in the basic features of these systems. As there is no system that is capable to cover all needs as a monolithic solution, it seems that lots of redundant work is being done while maintaining and further developing these systems.

In our symposium we would like to invite different vendors and users of collection management systems in order to align the respective systems towards necessary compliance and increased compatibility regarding the following challenges: (1) fitness for use / data quality; (2) accomplishing data exchange via existing and new data standards (eg. ABCD, DarwinCore, CD, MIDS and MICS) in the light of desired mass digitization efforts; (3) supporting state of the art research data management by meeting the criteria of e.g. the FAIR principles and CoreTrustSeal; (4) data provision to global linked data infrastructures like GBIF, DiSSCo, BHL, iDigBio etc.; and (5) rapidly changing technology.

The aim of the symposium is to identify and discuss common grounds for addressing these topics.

SYM05 Using Collections to Mitigate and Prevent Zoonotic Disease: Data Mobilization and Integration

Session Type: Symposium (unsolicited presentations considered)

Organizers: Pamela Soltis, University of Florida/iDigBio, Gainesville, US; Deborah Paul, iDigBio/Florida State University, Tallahassee, US

The COVID-19 pandemic, zoonoses, and pathogens in general provide key opportunities to highlight the predictive value of collections and the information specimens and related materials (e.g. genetic / genomic data, associated species data, trait data) can contribute to ecological understanding, tracking the origin and transmission of disease, policy development, and global infrastructure needs. In addition, the current pandemic highlights (and has encouraged) much-needed cross-disciplinary collaboration and the impetus to advance changes needed in standards of practice. For these reasons, representatives from SPNHC, iDigBio, NSCA, and the US mammalogy, virology, and disease ecology communities formed the ViralMuse task force. Leadership from SPNHC, GBIF, iDigBio, Pensoft, and Plazi, along with relevant domain scientists, joined the COVID-19 Task Force convened by CETAF and DiSSCo to identify both short-term responses and longer-term prediction and mitigation roles for these communities. Ongoing efforts show data and knowledge gaps for pathogens and their hosts as well as possible solutions for data integration. Behind these data integration efforts are needs for standards development and adoption.

SYM06 You’ve got what in your collection?

Session Type: Symposium + discussion (no unsolicited presentations)

Organizers: Deborah L. Paul, iDigBio, Florida State University, Tallahassee, US; Cat Chapman, iDigBio, University of Florida, Gainesville, US

Digitization and publishing of museum specimen data is happening worldwide. While many museums are actively engaged in this process, others have yet to begin. Information about what collections hold is urgently needed by many stakeholders including the collections themselves, funders, researchers, policy-makers, countries, industry, and educators. At higher levels, museums can start by sharing what they know about their holdings, long before each item has its own record. But, if we are going to aggregate this “metadata” information from all natural science collections, the data need to be “standard.” If everyone shared in their own format, we could not compare or add up what we have, for example. To share this data in its most effective format, it needs to be standardized. But where does this standard come from, and how can it be used in practice?

This session will include presentations that introduce the first version of the new TDWG Collection Descriptions data standard, and examples of trying out the standard with real world collection descriptions use cases. It will also, through a short talk and discussion session, consider the bigger picture of a communal approach to describing our collections at a global level, building on the outputs of GBIF’s recent open consultation on “Advancing the Catalogue of the World’s Natural History Collections”.

SYM07 New standards development to support the transformation of collection data into digital specimens

Session Type: Symposium (no unsolicited presentations)

Organizers: Wouter Addink, Naturalis Biodiversity Center, Leiden, NL; Alex Hardisty, Cardiff University, Cardiff, UK

The session will report on development of new standards in support of the Digital Specimen concept as described here: https://dissco.tech/2020/03/31/what-is-a-digital-specimen/. These include Collection Descriptions (CD), Minimum Information for Digital Specimen (MIDS) and the Open Digital Specimen standard (OpenDS). The session aims to disseminate the current state of development.

SYM08 Introduction to the new Living Atlases community

Session Type: Symposium (no unsolicited presentations)

Organizers: Marie-Elise Lecoq, VertNet – Living Atlases Community, San Francisco, US; Anders Telenius, Swedish Museum of Natural History, Stockholm, SE

For a few years, we have presented the Atlas of Living Australia platform and Living Atlases community to the TDWG. We managed to show you how this community has moved forward and how we have grown from a group of developers to a more stable community. We will use this new session to present what we have achieved since the last conference.

We will explain the work done by both coordinators helped by all the participants and the Living Atlases Management Committee to consolidate this new version of the community. It will include the description of the Memorandum of Understanding, the remote session organized by the technical coordinator and the improvement that we made regarding the technical and non-technical documentation. A presentation of Atlas of Living Australia’s pipeline will close this new symposium.

SYM09 Technical and standards implications in data liberation and semantic publishing for biodiversity

Session Type: Symposium (no unsolicited presentations)

Organizers: Donat Agosti, Plazi, Bern, CH; Lyubomir Penev, Pensoft, Sofia, BG

We don’t know what we know about biodiversity, because the big biodiversity data is hidden in the published record of an estimated 500 M printed pages and ongoing PDF based closed access publications. We do not know what new research results are published everyday and thus what exciting new discoveries we miss. We recently found out that our biodiversity research results are hardly accessible to contribute in a timely way in a pandemics like Covid-19.

In this symposium we will report on a workflow, a solution to promote to first class status the data in publications immediately upon release, by making it open FAIR data via the Biodiversity Literature Repository, and ultimately contributing to GBIF. Liberated through the Plazi workflow or directly semantically published by Pensoft, a third of the annually new described species are immediately available in GBIF, tens of thousands of taxa are uniquely accessible in GBIF’s taxonomic backbone and hundreds of thousands of figures and taxonomic treatments of taxa are deposited as open FAIR data on the Biodiversity Literature Repository.

The goal of this symposium is to describe the underlying concepts, the processing and quality control workflows, the FAIR standards used, and to provide an assessment of the fitness for use of the output data for the principle data re-users.

PD01 Avenues into integration: communicating taxonomic intelligence from sender to recipient

Session Type: Panel Discussion (unsolicited presentations considered)

Organizers: Nathan Upham, Arizona State University, Tempe, US; Beckett Sterner, Arizona State University, Tempe, US

“What is crucial for your ability to communicate with me… pivots on the recipient’s capacity to interpret–to make good inferential sense of the meanings that the declarer is able to send.” (Rescher 2000, 148)

Conventional approaches to reconciling taxonomic information in biodiversity databases have been predominantly based on string matching for unique taxonomic name combinations (e.g., ‘Genus species’). However, in their original context these names pertain to specific usages or taxonomic concepts, which can vary in meaning for the same name according to different sources and usages. “Taxonomic intelligence” is the ability and challenge to adequately represent and propagate this complex name/usage interaction within and across trusted biodiversity data networks. New approaches are making progress on key obstacles. An important critique of proposals to use name-to-concept relationships for data aggregation has been the difficulty of scaling them up to reach comprehensive coverage. However, growing efforts by medium-scale data providers and taxonomic authorities suggest an all-or-nothing approach is not required. Nonetheless, with multiple parallel efforts in this domain come potential problems for coordination — how do we ensure that senders and recipients of biodiversity data not only can share messages but do so with “good inferential sense” of their respective meanings? Here we aim to provide a space for brief reviews of diverse, ongoing initiatives in biodiversity AI, logical reasoning, and geospatial analysis to implement taxonomic intelligence. This will set the stage for discussing practical challenges, including reaching broader coverage for name-to-concept alignments, the leveraging of museum specimen metadata, and novel computational tools.

PD02 The Biocultural Labels Initiative: Supporting Indigenous Rights in Data derived from Genetic Resources

Session Type: Panel Discussion (no unsolicited presentations)

Organizers: Jane Anderson, New York University / ENRICH, New York, NY; Maui Hudson, University of Waikato, Hamilton, NZ

The Biocultural (BC) Labels and Biocultural (BC) Notices are two distinct tools within the Local Contexts ecosystem for recognizing Indigenous rights in data derived from genetic resources. Prioritizing provenance and transparency in data collected in collaboration and partnership with Indigenous peoples or on Indigenous lands and waters, the 6 Biocultural Labels provide a mechanism for Indigenous communities to directly integrate associated responsibilities, obligations and relationships as accompanying metadata. The Biocultural Labels allow for cultural protocols to be digitally expressed and connected with data and to travel with data over time – enhancing engagement with, connection to and recognition of Indigenous interests. As a complimentary, yet distinct mechanism the Biocultural Notices are a tool for researchers and institutions to use and apply to data when there are underlying Indigenous rights or interests in collected data. This increases researcher integrity when working with Indigenous communities, and transparency across the Indigenous data lifecycle. The BC Labels and Notices have been developed as a direct Ethical, Legal and Social Implications (ELSI) intervention for the equitable and ethical future use of Indigenous data.

With the development of these digital tools questions about standards and appropriate metadata fields for the Labels and Notices within DwC standards have arisen. This is partly because both the BC Labels and the BC Notices potentially could be used at a record level in multiple ways – for instance as rightsHolder, accessRights and potentially License. It is also possible that given the absence of Indigenous interests in the larger formation of the DwC standards, that something new might need to be created that can adequately represent these interests, and the integrity in research practice that they promote. This panel brings together the founders of the Biocultural Labels initiative with users of the Labels within researcher and institutional contexts to discuss development, implementation, scaling, standards and metadata fields.

PD03 Enabling digital specimen and extended specimen concepts in current tools and services

Session Type: Panel Discussion (no unsolicited presentations)

Organizers: Falko Glöckler, Museum für Naturkunde Berlin, Berlin, DE

Digital specimens represent physical collection objects in cyberspace and consist of references to data and metadata related to the collection object. Through continuous processes of digitizing legacy data, gaining new knowledge from research, annotating and linking to related resources a digital specimen can evolve independently from the original physical object. In order to provide, track and make use of the linked digital specimens in the collection-holding institutions the community might need to think of digital specimens as standalone virtual collections that originate from physical collections. However, new versions of a digital specimen still derive from changes of the physical specimen as the (meta)data is being updated in collection management systems to document the state and treatment of the physical objects. Consequently, there is a challenge to enable the management of both: linked digital specimens in the World Wide Web and the local data of physical specimens in databases of collection-holding institutions and other tools and services.

In this session central questions on the requirements, obstacles and chances of implementing the concepts of digital specimens and extended specimens in software tools are being discussed. The aim is to identify the major tasks and priorities regarding the transformation of tools and services from multiple perspectives: local collection data management, international data infrastructures like DiSSCo and GBIF, data usage outside of domain specific subject areas.

Last updated 23 July 2020