Designing a state-of-the-art taxonomic research workstation integrating digital and physical resources

Lead Research Organisation: Royal Botanic Garden Edinburgh
Department Name: Royal Botanic Garden Edinburgh

Abstract

The science of naming, classifying and identifying species, known as taxonomy, is absolutely fundamental to building scientific research programmes on biodiversity. Without knowing what an organism is and being able to refer to it unambiguously, scientists would be unable to make the scientific progress required in food security, medical research and resilience to climate change. However, as we develop more knowledge the science of taxonomy becomes increasingly complex. Between 1753 and 2016, the number of known plant species has risen from 6,000 to 390,000, an average increase of nearly 1,500 species each year. Over 2,000 new species were discovered in 2015. The number of specimens held globally in herbaria has also increased. There are now over 3,000 herbaria around the world holding nearly 400 million specimens. Any taxonomist working now therefore has an immense and expensive task of gathering information about the species that they are studying, involving travel to various herbaria or the risk of damage or loss to specimens if they are sent on loan. With about 10-20% of flowering plant species still to be described, it is estimated that about half of these have already been collected and are held in herbaria around the world.

Herbarium collections are vital to taxonomy and biodiversity research so we need to find solutions to making the information more widely accessible in order to speed up the research process given the scale of the challenges we are facing. In many cases, a high resolution digital image of the specimen with electronic collection data attached will enable researchers to carry out much of the basic work. By digitising the herbarium collections we can provide these resources to taxonomists in every part of the world. However, digitisation is only one step of the process. We also need to create an environment where taxonomic researchers can bring all the digital resources together with the physical specimens, using tools and equipment to make working with massive amounts of complex information easy and intuitive. This kind of workstation is most famously seen in television programmes such as CSI, but we need to be implementing the technology and data management in our institutes if we are going to have a chance to produce the taxonomic basis for global biodiversity in time to help its survival.

Publications

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Description Digital resources created during the mass digitisation of herbarium collections are currently underused. This partly due to the difficulties in making the digital specimens accessible and discoverable as well as providing the tools for their use.

Herbaria do not currently have adequate facilities in place to enable researchers to use the physical and digital collections together. There is frequently limited access to computing equipment including digital image viewers, particularly in areas where physical specimens can be laid out and compared to digital specimens. In addition, there is often limited power and internet availability for researchers to use their own equipment in these spaces.

The identification of herbarium specimens is a major part of many taxonomists' work. This is usually based on a manual process, frequently requiring extensive knowledge from the taxonomist and often using a form of "gestalt". This process can take up to half a day and this was often cited as the time limit that would be given to a single identification by taxonomists. Use of genetic data or automated artificial intelligence is becoming more used, but still plays a relatively small part in the current identification of herbarium specimens.

Low-cost options are available for increased use of digital images within herbarium collections. These options include adaptors for researchers to use their own equipment to capture more detailed images and view them alongside digital specimens held in other institutes. Low-cost options have the potential to increase uptake, reduce security requirements and enable updating more easily.

The management of herbarium collections to include additional equipment for taxonomic research using digital specimens is a major challenge for the future. The maintenance of equipment and software as well as managing online access for visitors requires additional resources for many institutes and should not be underestimated. It is not clear if maintaining certain equipment is feasible given the issues of software updates, cyber security and limited life-span of the technology involved.

The design of herbarium collection space in the future will need to consider the relationship of accessing the specimens for research alongside the researchers' own computer equipment and additional technological tools.
Exploitation Route The outcomes from this research are being used in the current process of planning the reorganisation of the Herbarium building at the Royal Botanic Garden Edinburgh.

In addition, the key findings will feed into the Consortium of European Taxonomic Facilities (CETAF) Collections Group which is currently creating a Task Group for Collection Space.
Sectors Digital/Communication/Information Technologies (including Software),Culture, Heritage, Museums and Collections

 
Description The findings from this project have more recently fed into the planning of the reorganisation of the Herbarium Building at the Royal Botanic Garden Edinburgh. As part of the planning, a clear vision of the requirements for taxonomic research workstations for the future was requested by the architects during the Space Requirements Survey. The information is currently feeding into the Options Appraisal process. The findings are therefore impacting the future design of the collection building at RBGE.
First Year Of Impact 2020
Sector Culture, Heritage, Museums and Collections
Impact Types Cultural,Policy & public services

 
Description Collaboration with Smithsonian National Museum of Natural History 
Organisation Smithsonian Institution
Country United States 
Sector Public 
PI Contribution The support from AHRC enabled me to work at the Smithsonian Museum of Natural History for 3 months. During this time I interviewed a number of staff at the Smithsonian about their current practices in taxonomic research. I was then able to take this information and combine it with information gained from my personal experience as a taxonomist and information gained from interviews with research staff at RBGE, to determine the physical and technological requirements for a taxonomic workstation. I investigated the options available for supplying the requirements: hardware, software as well as workspace and workflows. I then purchased equipment and developed a prototype taxonomic research workstation for testing. I gave a demonstration to staff at the Smithsonian and provided training in the use of the equipment. The following staff at RBGE contributed time, knowledge and experience in participating in the interviews about their current practices in taxonomic research. Individuals were able to contribute specific technical expertise in microscope and imaging technology as well as software solutions for various taxonomic research tasks. Hannah Atkins, Elspeth Haston, David Harris, Mark Hughes, Peter Moonlight, Mark Newman, Carmen Puglisi, Peter Wilkie.
Collaborator Contribution Staff at the Smithsonian contributed time, knowledge and experience in participating in the interviews about their current practices in taxonomic research. Individuals were able to contribute specific technical expertise in microscope and imaging technology as well as software solutions for various taxonomic research tasks. The main point of contact at the Smithsonian was Sylvia Orli, Information Manager for the Department of Botany, and leading the digitisation programme for the Herbarium. She provided the facilities for my work, including a space to set up the prototype workstation for demonstrations. The following staff and research visitors at the Smithsonian contributed to the data gathering and interviews: Pedro Acevedo, Chris Campbell, Marcos Caraballo-Ortiz, Larry Dorr, Robin Everly, Vidal de Freitas Mansano, Sylvia Orli, Paul Peterson, Mauricio Posada, Harold Robinson, Mark Strong, Warren Wagner, Alex White, John Wiersema, Stanley Yankowski
Impact Knowledge sharing between staff at the two institutes Design of a prototype taxonomic research workstation Prototype of a taxonomic research workstation at the Smthsonian and RBGE. OSF wiki (proof of concept)
Start Year 2019
 
Description Demonstration of prototype taxonomic workstation to school pupils 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact A Taxonomy Day for advanced higher school pupils from across Scotland included a demonstration of a prototype taxonomic research workstation in the Herbarium of the Royal Botanic Garden Edinburgh
Year(s) Of Engagement Activity 2019
 
Description Publication of article in Smithsonian Institution newsletter. 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact An article describing the project was published in The Plant Press, a quarterly newsletter from the Botany Dept (NMNH) and the U.S. National Herbarium. This triggered discussion with a wider audience in the institute.
Year(s) Of Engagement Activity 2019
URL https://nmnh.typepad.com/files/vol22no3.pdf