The Australasian Virtual Herbarium: Tracking data usage and benefits for biological collections

Data mobilisation in the LWS Herbarium: success and prospects

Background

Digitisation of hosted specimens is a crucial task for all herbaria worldwide and is one of the main streams for today. By digitising their collections and publishing the datasets, the herbaria grant access to essential data to a wide research audience and, as a result, involve their collections in scientific work more actively. Digitisation also allows virtual preservation of the collections, which is especially important in conditions of hostilities, when the entire collection can be destroyed or damaged in one moment. This paper describes two datasets recently published in GBIF in the framework of the LWS herbarium digitisation initiative. It also contains some considerations about further digitisation priorities and plans in the LWS Herbarium in the context of complicated war conditions and limited facilities.

New information

In total, 2,419 occurrence records from Ukraine mobilised from LWS Herbarium were published. These datasets are planned to be dynamic with the addition of new records along with progress of digitisation work at LWS. At least 6,000 more records are planned to be published through these datasets in 2024.

Endemic vascular plants in the Ukrainian Carpathians

Background

This dynamic dataset aims to gather all available data, extracted mostly from the preserved material deposited at the leading Ukrainian herbaria on the distribution of the endemic vascular plants in the Ukrainian Carpathians and adjacent territories. This dataset is created in the framework of mapping the distribution of the endemic plants and is aimed to unveil the patterns of their spatial distribution, ecological preferences and temporal trends in the flora of the Ukrainian Carpathians. A total of 76 species and subspecies of vascular plants belonging to 49 genera and 27 families are reported herein to occur in the Ukrainian Carpathians and close regions. Amongst the total number of reported 6,427 occurrence records, 1,961 records are georeferenced and supported with a translation of Cyrillic information into English. The remaining occurrence records will be georeferenced and translated into English in the near future, as well as the dataset being completed with new records obtained from the new sources.

New information

In total, 6,427 occurrence records of the endemic vascular plants distributed in the Ukrainian Carpathians were published.

A data management workflow of biodiversity data from the field to data users

PREMISE

Heterogeneity of biodiversity data from the collections, research, and management communities presents challenges for data findability, accessibility, interoperability, and reusability. Workflows designed with data collection, standards, dissemination, and reuse in mind will generate better information across geopolitical, administrative, and institutional boundaries. Here, we present our data workflow as a case study of how we collected, shared, and used data from multiple sources.

METHODS

In 2012, we initiated the collection of biodiversity data relating to Michigan prairie fens, including data on plant communities and the federally endangered Poweshiek skipperling (Oarisma poweshiek).

RESULTS

Over 23,000 occurrence records were compiled in a database following Darwin Core standards. The records were linked with media and biological, chemical, and geometric measurements. We published the data as Global Biodiversity Information Facility data sets and in Symbiota SEINet portals.

DISCUSSION

We highlight data collection techniques that optimized transcription time, including the use of predetermined and controlled vocabulary, Darwin Core terms, and data dictionaries. The validity and longevity of our data were supported by voucher specimens, metadata with measurement records, and published manuscripts detailing methods and data sets. Key to our data dissemination was cooperation among partners and the utilization of dynamic tools. To increase data interoperability, we need flexible and customizable data collection templates, coding, and enhanced communication among communities using biodiversity data.

Enhancement of conservation knowledge through increased access to botanical information

Herbarium specimens are increasingly recognized as an important resource for conservation science and virtual herbaria are making specimens freely available to a wider range of users than ever before. Few virtual herbaria are designed with conservation use as a primary driver. Exceptionally, Brazil's Reflora Virtual Herbarium (RVH) was created to increase knowledge and conservation of the Brazilian flora. The RVH is closely integrated with the Flora of Brazil 2020 platform on which Brazil's new national Flora is under construction. Both resources are accessible via the Reflora home page and thousands of users move seamlessly between these Reflora resources. To understand how the Reflora resources are currently used and their impact on conservation science, we conducted a literature review and an online survey. We searched for publications of studies in which Reflora resources were used and publications resulting from Brazilian researchers who were part of Reflora's research and mobility program. The survey contained multiple choice questions and questions that required a written response. We targeted Reflora webpage visitors with the survey to capture a wider range of Reflora users than the literature review. Reflora resources were used for a variety of conservation-relevant purposes. Half the 806 scientific publications in which Reflora was cited and 81% of the 1069 survey respondents accessing Reflora resources mentioned conservation-relevant research outputs. Most conservation-relevant uses of the Reflora resources in scientific publications were research rather than implementation focused. The survey of Reflora users showed conservation uses and impacts of virtual herbaria were more numerous and diverse than the uses captured in the literature review. Virtual herbaria are vital resources for conservation science, but they must document use and impacts more comprehensively to ensure sustainability.

Improved standardization of transcribed digital specimen data

There are more than 1.2 billion biological specimens in the world's museums and herbaria. These objects are particularly important forms of biological sample and observation. They underpin biological taxonomy but the data they contain have many other uses in the biological and environmental sciences. Nevertheless, from their conception they are almost entirely documented on paper, either as labels attached to the specimens or in catalogues linked with catalogue numbers. In order to make the best use of these data and to improve the findability of these specimens, these data must be transcribed digitally and made to conform to standards, so that these data are also interoperable and reusable. Through various digitization projects, the authors have experimented with transcription by volunteers, expert technicians, scientists, commercial transcription services and automated systems. We have also been consumers of specimen data for taxonomical, biogeographical and ecological research. In this paper, we draw from our experiences to make specific recommendations to improve transcription data. The paper is split into two sections. We first address issues related to database implementation with relevance to data transcription, namely versioning, annotation, unknown and incomplete data and issues related to language. We then focus on particular data types that are relevant to biological collection specimens, namely nomenclature, dates, geography, collector numbers and uniquely identifying people. We make recommendations to standards organizations, software developers, data scientists and transcribers to improve these data with the specific aim of improving interoperability between collection datasets.

The history and impact of digitization and digital data mobilization on biodiversity research

The first two decades of the twenty-first century have seen a rapid rise in the mobilization of digital biodiversity data. This has thrust natural history museums into the forefront of biodiversity research, underscoring their central role in the modern scientific enterprise. The advent of mobilization initiatives such as the United States National Science Foundation's Advancing Digitization of Biodiversity Collections (ADBC), Australia's Atlas of Living Australia (ALA), Mexico's National Commission for the Knowledge and Use of Biodiversity (CONABIO), Brazil's Centro de Referência em Informação (CRIA) and China's National Specimen Information Infrastructure (NSII) has led to a rapid rise in data aggregators and an exponential increase in digital data for scientific research and arguably provide the best evidence of where species live. The international Global Biodiversity Information Facility (GBIF) now serves about 131 million museum specimen records, and Integrated Digitized Biocollections (iDigBio) in the USA has amassed more than 115 million. These resources expose collections to a wider audience of researchers, provide the best biodiversity data in the modern era outside of nature itself and ensure the primacy of specimen-based research. Here, we provide a brief history of worldwide data mobilization, their impact on biodiversity research, challenges for ensuring data quality, their contribution to scientific publications and evidence of the rising profiles of natural history collections.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.