The Catalogue of Life Data Package (CoLDP) and the Taxon Concept Standard (TCS): A Comparison

The Catalogue of Life Data Package (CoLDP; Catalogue of Life 2022) is the preferred mechanism for getting data in and out of the ChecklistBank. A CoLDP is a ZIP file containing files with delimiter-separated values, similar to the Darwin Core Archive (DwC-A; Global Biodiversity Information Facility 2023), but does not enforce the DwC-A star schema requiring a single Core file and zero or more Extension files. This makes it preferable for exchanging taxonomic data in tabular format as taxonomic data contains at least three different types of objects—taxa, names and references—that are all interlinked.TCS (currently still Taxon Concept Schema) is the TDWG (Biodiversity Information Standards) standard for dealing with taxonomic data specifically. An effort is currently underway (TCS 2 Task Group 2023) to free TCS from its XML schema and turn it into a TDWG vocabulary standard that is maintainable under the TDWG Vocabulary Maintenance Specification (VMS; Vocabulary Maintenance Specification Task Group 2017). For a domain standard like TCS, it is essential that it supports an important warehouse of taxonomic information like ChecklistBank and an exchange format like CoLDP. Therefore, as part of the Implementation Experience Report that has to accompany a major update to an existing TDWG standard, a comparison has been undertaken between TCS and the data model behind CoLDP.While some of the terms CoLDP uses are different from the ones used by TCS, the two specifications are completely compatible. This presentation will highlight some of the key similarities and differences. It is heartening to see that different groups of people independently chose to make the same departure from the existing specification. As TCS will be maintainable—and, in fact, still has to undergo public review—and CoLDP presumably can evolve as well, there are opportunities for TCS and CoLDP to come even closer together than they already are

VicFlora: a dynamic, service-based Flora

VicFlora (https://vicflora.rbg.vic.gov.au), launched in September 2016, combines the Flora of Victoria and the Census of Vascular Plants of Victoria. VicFlora is used by government agencies, conservation agencies and consultancies: analytics indicate that on weekdays VicFlora is used by between 200 and 250 people. Content of VicFlora can be updated inside the system, so changes will be live as soon as they are made, the keys coming from KeyBase and the maps using data from the Australasian Virtual Herbarium (AVH) and the Victorian Biodiversity Atlas (VBA), both obtained through Atlas of Living Australia (ALA) web services. Corrections and value-adding to the maps are done through annotations. There have been requests from government and consultancies for the ability to use content from VicFlora in their own applications. Therefore, web services have been created that give access to all content. New versions of VicFlora will use these same services. It is the intention that names and taxon concepts for VicFlora will be managed in the National Species Lists (NSL) and accessed through NSL web services

The Australasian Virtual Herbarium (AVH) and the Changing Role of Herbaria

Australia's Virtual Herbarium (AVH) was created in 2001 and developed between 2001 and 2006 with the databasing of the label data of specimens from the Australian Commonwealth, state and territory herbaria. The success of AVH ultimately led to funding for the Atlas of Living Australia (ALA) and in October 2012 AVH was re-launched as part of the ALA infrastructure (http://avh.chah.org.au). Since 2012, some university herbaria have also joined AVH and in June 2017 the New Zealand Virtual Herbarium (NZVH) was integrated, giving rise to the Australasian Virtual Herbarium. The AVH currently holds almost 6.3 million records from 23 Australian and New Zealand herbaria and comprises over 80 per cent of the vouchered occurrence records of Australian plants, algae and fungi in ALA. While no longer at the forefront of the digitisation wave, having been around for so long, AVH can provide valuable insights into how and to what extent herbarium data is used and into the benefits of digitisation for herbaria and natural history collections. Six years of download statistics shows an ever-increasing use of AVH data and a widening of the user base. A far greater proportion of downloaded records is ostensibly used for new uses like ecological research and conservation, than for the traditional uses of herbarium specimen data, systematics and collections management. The last few years have also seen an increase in the use of AVH data in education. Over the years many research articles based on AVH data have been written, mostly at the interface between ecology and systematics, i.e. biogeography and conservation science. With the increase of the types of uses for herbarium data, it becomes important, also for the herbaria themselves, to consider the fitness for purpose of AVH data for uses other than the purpose for which it was collected. It has become apparent that the uncertainty of the latitudes and longitude provided with herbarium specimens is often too great for use in ecological research or conservation and there is a bias in collection density at the bioregion level, which is likely to be more severe at smaller spatial scales. Also, while the demand for vouchered occurrence records is increasing, we have seen a steady decrease in the intake of new specimens by Australian herbaria since the 1980s. This presentation will cover how Australian herbaria use AVH, how other users use AVH and what being part of AVH has meant to Australian herbaria

The disambiguation of people names in biological collections

Scientific collections have been built by people. For hundreds of years, people have collected, studied, identified, preserved, documented and curated collection specimens. Understanding who those people are is of interest to historians, but much more can be made of these data by other stakeholders once they have been linked to the people’s identities and their biographies. Knowing who people are helps us attribute work correctly, validate data and understand the scientific contribution of people and institutions. We can evaluate the work they have done, the interests they have, the places they have worked and what they have created from the specimens they have collected. The problem is that all we know about most of the people associated with collections are their names written on specimens. Disambiguating these people is the challenge that this paper addresses. Disambiguation of people often proves difficult in isolation and can result in staff or researchers independently trying to determine the identity of specific individuals over and over again. By sharing biographical data and building an open, collectively maintained dataset with shared knowledge, expertise and resources, it is possible to collectively deduce the identities of individuals, aggregate biographical information for each person, reduce duplication of effort and share the information locally and globally. The authors of this paper aspire to disambiguate all person names efficiently and fully in all their variations across the entirety of the biological sciences, starting with collections. Towards that vision, this paper has three key aims: to improve the linking, validation, enhancement and valorisation of person-related information within and between collections, databases and publications; to suggest good practice for identifying people involved in biological collections; and to promote coordination amongst all stakeholders, including individuals, natural history collections, institutions, learned societies, government agencies and data aggregators

(276–279) Proposals to provide for registration of new names and nomenclatural acts

The Melbourne Congress of 2011 authorized a Special Committee on Registration of Algal and Plant Names (including fossils), which was established the following year (Wilson in Taxon 61: 878–879. 2012). Its explicit mandate was “to consider what would be involved in registering algal and plant names (including fossils), using a procedure analogous to that for fungal names agreed upon in Melbourne and included in the Code as Art. 42”, but expectations at the Nomenclature Section in Melbourne went farther than that. There was the hope that registration systems for at least some of the main groups would soon be set up, to be used and tested on a voluntary basis and, if found to be generally accepted, would persuade the subsequent Congress in Shenzhen, in 2017, to declare registration of new names an additional requirement for valid publication. The Melbourne Congress also approved mandatory registration of nomenclatural novelties in fungi, starting on 1 Jan 2013. The new Art. 42 of the Code (McNeill & al. in Regnum Veg. 154. 2012) requires authors to register any fungal nomenclatural novelty, prior to publication, with a recognized repository, whereupon they are provided with a unique identifier for each name, to be included in the protologue along with other Code-mandated information. Years before registration became mandatory, mycologists had been encouraged, often prompted by journal editors, to register their nomenclatural novelties prior to publication. Most complied. Consequently, when mandatory registration was proposed, it had strong support from the mycological community. There are currently three recognized repositories for fungal names. They vary somewhat in how they operate, but they share records of their registered novelties as soon as publication has been effected. One consequence of implementing mandatory registration is that locating new fungal names and combinations and associated protologue information is much simpler now than it was before. This makes it easier to incorporate the information into taxonomic studies and to update taxonomic treatments, inventories, and indices. A corollary is that, no matter what publication outlet an author chooses, the name cannot fail to be noticed. The positive experience in mycology makes extension of the registration concept to plants and algae a compelling idea. That experience shows that the best way to make mandatory registration of nomenclatural novelties palatable to botanists and phycologists is the establishment of trial registration at repositories with a history of involvement in and commitment to the indexing of names. Trial registration enables users to acquaint themselves with registration procedures, make suggestions on how they might be improved, and appreciate, by personal experience, the benefits of registration. Unfortunately, the task of establishing such repositories proved to be more complex and time-consuming than had been foreseen. Substantial progress has been made in the establishment of such centres (Barkworth & al., in this issue, pp. 670–672) but the Committee is not in a position to make firm proposals to regulate registration procedures, even less to make registration mandatory from a concrete future date. Nevertheless, the Committee sees it as imperative that the Shenzhen Congress be offered the opportunity to move forward with registration without having to wait six more years. In this spirit, we offer the proposals below. Proposal (276) would declare registration an ongoing concern of the botanical, mycological, and phycological community and provide the basic structure for making it possible. Proposal (277) and Prop. (278) would, in addition, define a flexible framework within which a system of voluntary registration could be developed for various categories of organisms. Proposal (279) would provide for future mandatory registration in a way that does not depend on the six-year intervals between International Botanical Congresses. Presentation of each proposal is followed by a summary of the support received from members of the Committee.Fil: Barkworth, Mary E.. State University of Utah; Estados UnidosFil: Watson, Mark. Royal Botanic Gardens; Reino UnidoFil: Barrie, Fred R.. Missouri Botanical Garden; Estados Unidos. Field Museum Of Natural History; Estados UnidosFil: Belyaeva, Irina V.. Royal Botanic Gardens; Reino UnidoFil: Chung, Richard C. K.. Forest Research Institute ; MalasiaFil: Dasková, Jirina. Národní Muzeum; República ChecaFil: Davidse, Gerrit. Missouri Botanical Garden; Estados UnidosFil: Dönmez, Ali A.. Hacettepe Üniversitesi; TurquíaFil: Doweld, Alexander B.. National Institute Of Carpology; RusiaFil: Dressler, Stefan. Senckenberg Forschungsinstitut Und Naturmuseum; AlemaniaFil: Flann, Christina. Naturalis Biodiversity Center; Países BajosFil: Gandhi, Kanchi. Harvard University; Estados UnidosFil: Geltman, Dmitry. Russian Academy of Science; RusiaFil: Glen, Hugh F.. Forest Hills; SudáfricaFil: Greuter, Werner. Freie Universität Berlin; AlemaniaFil: Head, Martin J.. Brock University; CanadáFil: Jahn, Regine. Freie Universität Berlin; AlemaniaFil: Janarthanam, Malapati K.. Goa University; IndiaFil: Katinas, Liliana. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División de Plantas Vasculares; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Kirk, Paul M.. Royal Botanic Gardens; Reino UnidoFil: Klazenga, Niels. Royal Botanic Gardens Victoria; AustraliaFil: Kusber, Wolf-Henning. Freie Universität Berlin; AlemaniaFil: Kvacek, Jirí. Národní Muzeum; República ChecaFil: Malécot, Valéry. Universite D'angers; FranciaFil: Mann, David G.. Royal Botanic Gardens; Reino UnidoFil: Marhold, Karol. Charles University; República ChecaFil: Nagamasu, Hidetoshi. Kyoto University; JapónFil: Nicolson, Nicky. Royal Botanic Gardens; Reino UnidoFil: Paton, Alan. Royal Botanic Gardens; Reino UnidoFil: Patterson, David J.. The University Of Sydney; AustraliaFil: Price, Michelle J.. Conservatoire et Jardin botaniques de la Ville de Genève; SuizaFil: van Reine, Willem F Prud' Homme. Naturalis Biodiversity Center; Países BajosFil: Schneider, Craig W.. Trinity College Hartford; Estados UnidosFil: Sennikov, Alexander. Russian Academy Of Sciences; RusiaFil: Smith, Gideon F.. Nelson Mandela Metropolitan University; Sudáfrica. Universidad de Coimbra; PortugalFil: Stevens, Peter F.. Missouri Botanical Garden; Estados Unidos. University of Missouri; Estados UnidosFil: Yang, Zhu-Liang. Kunming Institute Of Botany Chinese Academy Of Sciences; ChinaFil: Zhang, Xian-Chun. Chinese Academy of Sciences; República de ChinaFil: Zuccarello, Giuseppe C.. Victoria University Of Wellington; Nueva Zeland

Report of the Special Committee on Registration of Algal and Plant Names (including fossils)

The Special Committee on Registration of Algal and Plant Names (including fossils) was established at the XVIII International Botanical Congress (IBC) in Melbourne in 2011, its mandate being to consider what would be involved in registering algal and plant names (including fossils), using a procedure analogous to that for fungal names agreed upon in Melbourne and included as Art. 42 in the International Code of Nomenclature for algae, fungi, and plants. Because experience with voluntary registration was key to persuading mycologists of the advantages of mandatory registration, we began by asking institutions with a history of nomenclatural indexing to develop mechanisms that would permit registration. The task proved more difficult than anticipated, but considerable progress has been made, as is described in this report. It also became evident that the Nomenclature Section needs a structure that will allow ongoing discussion of registration and associated issues. Simultaneously with this report we are submitting four proposals that would provide such a structure