• Joe Miller, GBIF Executive Secretary

Digital Extended Specimens: A second community consultation

Biodiversity data is not static. Digitization of legacy natural history specimens and collection of new data broadens our knowledge. ­When digitization is combined with other improvements and advances in biodiversity informatics new opportunities arise.


Specimens collected a hundred years or more ago are often limited to basic data about their origins: What is it? Where and when was it collected? And by whom? A specimen is often housed in a part of the world distant from its collection place. But global data integration now makes it increasingly possible for anyone, anywhere to enhance record-level data, thereby increasing the value of a collection. A Brazilian plant specimen held in a European herbarium can be enhanced through contributions of Australian taxonomists, Chinese biogeographers and Kenyan geneticists.


Many components needed to develop a global system for annotating and adding value to the digital representation of physical specimens are now available. And the global community around scientific collections is working together to design a road map for building out what’s needed to make these advances happen.


Throughout February and March the alliance for biodiversity knowledge coordinated a first phase of a virtual consultation with the world’s biodiversity informatics, collections and research communities which helped to converge the ideas behind two related but distinct concepts: the Digital Specimen, proposed by the European-based Distributed System of Scientific Collections (DiSSCo), and the Extended Specimen, which emerged from the Biological Collections Network (BCoN).


The large group of organizers and moderators, over 20 people in all, were delighted with the participation in the first phase over 300 people attended the introductory sessions and viewed and participated in the online discussion.


This first phase focused on the value streams enabled by the digital and extended specimen concepts through discussions of the following topics:

  1. Digitizing and mobilizing FAIR data for specimens

  2. Extending, enriching and integrating data

  3. Annotating specimens and related data

  4. Crediting and attributing tasks like data and material curation

  5. Analysing and mining specimen data for novel applications

The first phase discussions indicate considerable consensus among members of the global community, signalling the potential for converging the Digital Specimen and Extended Specimen ideas into a shared approach, now renamed as Digital Extended Specimens, or ‘DeS’.


Building on these efforts, the alliance will convene a second phase of the discussion starting on 15 June and running through 27 July. Phase 2 will focus on capturing the infrastructure capabilities needed to support Digital Extended Specimens, and topics will include:

  1. Access points and data infrastructure alignment

  2. Persistent identifier (PID) schemes

  3. Meeting legal/regulatory, ethical and sensitive data obligations

  4. Workforce capacity development and inclusion

  5. Transactional mechanisms and provenance

  6. Partnerships to collaborate more effectively

Consultation Format

Similar to phase 1, phase 2 of the virtual global consultation will involve two components:

  • Two opening webinar sessions on 15 June, scheduled nine time zones apart at UTC 05:00 and UTC 15:00 to support wider global participation, to introduce the topics to be discussed.

  • An open, facilitated online consultation running between 15 June and 27 July 2021, consisting of multiple online discussion threads hosted on the GBIF community forum.

The organizer’s working document provides an early glimpse of the possible directions for these conversations.

The consultation aims to expand participation in the process, build support for further collaboration, identify key use cases, and develop an initial roadmap for community adoption and implementation.

Who should participate?

Anyone with an interest in natural history collections can join the consultation as a contributor at any time and ensure that they receive regular updates on the process. We want to hear from you, especially if you:

  • Are a collections professional

  • Work with living, preserved, or geological specimens

  • Work for a data provider or aggregator

  • Participate in collections data management or data publishing

  • Are a researcher or end-user of collections data, including graduate students, postdocs, and faculty

  • Are a bioinformatician or data scientist

  • Work for a standards organization

  • Work for a technology vendor or CMS developer

  • Work as an educator

  • Work for a publisher or journal

  • Possess expertise on legal, regulatory or ethical issues related to data management

Following the second phase, participants from the community will focus on summarizing the consultation for a session at the Biodiversity Information Standards (TDWG) conference in October 2021, where additional community members can contribute to drafting and reviewing a road map for the newly aligned Digital Extended Specimens.

A previous blog post highlighted a number of groups that signed a Letter of Intent to collaborate on the topics. The alliance for biodiversity knowledge invites other parties to participate in this process. If you have ideas, want to ask questions, or would like to co-moderate a topic, please contact us at

alliance@gbif.org.

Australian golden wattle, Acacia pycnantha, collected in Australia. Photo from Royal Botanic Gardens, Kew, licensed under CC BY 4.0.