Sabine von Mering

The Global Caryophyllales Initiative: Towards an updated taxonomic backbone and a dynamic monograph of a major plant group

Publisher: Pensoft Publishers

Date: 13-06-2019

DOI: 10.3897/BISS.3.35357

Abstract: The ongoing paradigm shift in taxonomy from in idual contributions to a truly collaborative and forward-looking endeavour results in a number of challenges related to distributed data management. Examination of physical specimens remains a key task, but searching for specimen data, literature, and name information is now mostly done online. In the past, these research steps involved many physical visits to collections and libraries. Although these infrastructures were and are still freely accessible and supportive for research carried out by in iduals, the amount of characters, specimens, and the complexity of current analytical approaches limit what can be achieved by in idual workers. Monographing is challenged because: larger genera remain unstudied and become fragmented in regional treatments long-term availability of detailed (unpublished) primary research data is often not addressed cross-disciplinary interoperability and open data principles are needed and highly specialised techniques used in phylogenetic and genomic analyses require teamwork by specialists. larger genera remain unstudied and become fragmented in regional treatments long-term availability of detailed (unpublished) primary research data is often not addressed cross-disciplinary interoperability and open data principles are needed and highly specialised techniques used in phylogenetic and genomic analyses require teamwork by specialists. The process towards generating truly community-based integrative dynamic taxonomic treatments is ongoing. In botany, specialist communities and networks have formed for certain plant groups, for ex le in the families Solanaceae, Brassicaceae, Fabaceae, Poaceae, Melastomataceae-Miconieae, Asteraceae-Cichorieae, and in the order Caryophyllales. Their common aim is to create sustainable information systems according to the FAIR principles, making the information Findable, Accessible, Interoperable and Reusable. At the same time, the information system is meant to support and document ongoing taxonomic research as an iterative process with tracking of changes, and backlinks to original data sources. This represents a big step forward with respect to the efficiency of the entire field of taxonomy. The Global Caryophyllales Initiative aims at creating a global synthesis of species ersity in this group (Borsch et al. 2015) encompassing about 12,500 species in more than 30 families or about 6% of flowering plants (Fig. 1). Caryophyllales include ecologically erse, economically important, invasive, and threatened species. The Caryophyllales Network was initiated in 2011 and unites specialists from across the world (to date, 150 scientists from 37 countries). The network is recognized by the World Flora Online (WFO) Council as its Taxonomic Expert Network for Caryophyllales. Advances by the network are presented in the open-access Caryophyllales Portal (caryophyllales.org/), aiming to provide up-to-date phylogenetic and taxonomic information. The systematic treatment is powered by the EDIT Platform for Cybertaxonomy (cybertaxonomy.eu/), with the generic checklist (caryophyllales.org/Checklist) and some family treatments already publicly available (e.g. Cactaceae). The checklist is regularly updated in consultation with family editors. A species-level taxonomic backbone incorporating all names and pertinent nomenclatural acts and evaluations is being compiled. A compilation of the Nepenthaceae (Berendsohn et al. 2018) served as a case study for the accommodation of descriptive and other factual data, and for demonstrating the feasibility of the workflow contributing to the WFO initiative. The taxonomic treatment of Iresine (Borsch et al. 2018) is another ex le. These studies are fundamental in establishing a general workflow for collaborative online monographs. Several challenges remain, inter alia the genomics perspective in bio ersity informatics, proper attribution and unique identification of taxonomic concepts, review and impact assessment of in idual contributions, possibilities to simultaneously display contrasting taxonomical concepts and classifications, and engaging both the wider taxonomic community and the public. The ongoing implementation shows that a dynamic online monograph requires rethinking of editorial workflows. Based on experiences with the Caryophyllales network, the taxonomic and bio ersity informatics communities are ready to meet this challenge.

The disambiguation of people names in biological collections

Publisher: Pensoft Publishers

Date: 10-10-2022

DOI: 10.3897/BDJ.10.E86089

Abstract: 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 in iduals 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 in iduals, 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 in iduals, natural history collections, institutions, learned societies, government agencies and data aggregators.

Collections do not have to Remain Ambiguous Forever: Seven steps to getting the correct people into your data

Publisher: Pensoft Publishers

Date: 03-08-2022

DOI: 10.3897/BISS.6.91194

Abstract: People are involved with the collection and curation of all bio ersity data, whether they are researchers, members of the public, taxonomists, conservationists, collection managers or wildlife managers. Knowing who those people are and connecting their biographical information to the bio ersity data they collect helps us contextualise their scientific work. We are particularly concerned with those people and communities involved in the collection and identification of biological specimens. People from herbaria and natural science museums have been collecting and preserving specimens from all over the world for more than 200 years. The problem is that many of these people are only known by unstandardized names written on specimen labels, often with only initials and without any biographical information. The process of identifying and linking in iduals to their biographies enables us to improve the quality of the data held by collections while also quantifying the contributions of the often underappreciated people who collected and identified these specimens. This process improves our understanding of the history of collecting, and addresses current and future needs for maintaining the provenance of specimens so as to comply with national and international practices and regulations. In this talk we will outline the steps that collection managers, data scientists, curators, software engineers, and collectors can take to work towards fully disambiguated collections. With ex les, we can show how they can use these data to help them in their work, in the evaluation of their collections, and in measuring the impact of in iduals and organisations, local to global.

Is Your Collection Ambiguous?

Publisher: Pensoft Publishers

Date: 31-08-2021

DOI: 10.3897/BISS.5.73702

Abstract: The natural history specimens of the world have been documented on paper labels, often physically attached to the specimen itself. As we transcribe these data to make them digital and more useful for analysis, we make interpretations. Sometimes these interpretations are trivial, because the label is unambiguous, but often the meaning is not so clear, even if it is easily read. One key element that suffers from considerable ambiguity is people’s names. Though a person is in isible, their name can change, is rarely unique and can be written in many ways. Yet knowing the people associated with data is incredibly useful. Data on people can be used to validate other data, simplify data capture, link together data across domains, reduce duplication-of-effort and facilitate data-gap-analysis. In addition, people data enable the discovery of in iduals unique to our collections, the collective charting of the history of scientific researchers and the provision of credit to the people who deserve it (Groom et al. 2020). We foresee a future where the people associated with collections are not ambiguous, are shared globally, and data of all kinds are linked through the people who generate them. The TDWG People in Bio ersity Data Task Group is therefore working on a guide to the disambiguation of people in natural history collections. The ultimate goal is to connect the various strings of characters on specimen labels and other documentation to persistent identifiers (PIDs) that unambiguously link a name “string” to the identity of a person. In working towards this goal, 150 volunteers in the Bionomia project have linked 21 million specimens to persistent identifiers for their collectors and determiners. An additional 2 million specimens with links to identifiers for people have already emerged directly from collections that make use of the recently ratified Darwin Core terms recordedByID and identifiedByID. Furthermore, the CETAF Botany Pilot conducted among a group of European herbaria and museums has connected over 1.4 million specimens to disambiguated collectors (Güntsch et al. 2021). Still, given the estimated 2 billion (Ariño 2010) natural history specimens globally, there is much more disambiguation to be done. The process of disambiguation starts with a trigger, which is often the transcription of a specimen’s label data. Unambiguous identification of the collector may facilitate this transcription, as it offers knowledge of their biographical details and collecting habits, allowing us to infer missing information such as collecting date or locality. Another trigger might be the flagging of inconsistent data during data entry or resulting from data quality processes, revealing for instance that multiple collectors have been conflated. A disambiguation trigger is followed by the gathering of data, then the evaluation of the results and finally by the documentation of the new information. Disambiguation is not always straightforward and there are many pitfalls. It requires access to biographical data, and identifiers to be minted. In the case of living people, they have to cooperate with being disambiguated and we have to follow legal and ethical guidelines. In the case of dead people, particularly those long dead, disambiguation may require considerable research. We will present the progress made by the People in Bio ersity Data Task Group and their recommendations for disambiguation in collections. We want to encourage other institutions to engage with a global effort of linking people to persistent identifiers to collaboratively improve all collection data.

Museum Für Naturkunde

Location: Germany

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Universität Hamburg

Location: Germany

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Loughborough University Loughborough Sport

Location: United Kingdom of Great Britain and Northern Ireland

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Johannes Gutenberg-Universität Mainz

Location: No location found

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Julius Kühn-Institut Federal Research Centre For Cultivated Plants

Location: Germany

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Friedrich-Schiller-Universität Jena

Location: Germany

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Johannes Gutenberg Universität Mainz

Location: Germany

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Freie Universität Berlin Botanischer Garten Und Botanisches Museum Berlin-Dahlem

Location: Germany

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