EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature

This paper describes a set of guidelines for the citation of zoological and botanical specimens in the European Journal of Taxonomy. The guidelines stipulate controlled vocabularies and precise formats for presenting the specimens examined within a taxonomic publication, which allow for the rich data associated with the primary research material to be harvested, distributed and interlinked online via international biodiversity data aggregators. Herein we explain how the EJT editorial standard was defined and how this initiative fits into the journal's project to semantically enhance its publications using the Plazi TaxPub DTD extension. By establishing a standardised format for the citation of taxonomic specimens, the journal intends to widen the distribution of and improve accessibility to the data it publishes. Authors who conform to these guidelines will benefit from higher visibility and new ways of visualising their work. In a wider context, we hope that other taxonomy journals will adopt this approach to their publications, adapting their working methods to enable domain-specific text mining to take place. If specimen data can be efficiently cited, harvested and linked to wider resources, we propose that there is also the potential to develop alternative metrics for assessing impact and productivity within the natural science

Data hosting infrastructure for primary biodiversity data

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 12 Suppl. 15 (2011): S5, doi:10.1186/1471-2105-12-S15-S5.Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized

Envisaging a global infrastructure to exploit the potential of digitised collections

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in

Opportunities From the Digital Revolution: Implications for Researching, Publishing, and Consuming Qualitative Research

In the 1990s, the term 'online' research emerged as a new and vibrant suite of methods, focused on exploitation of sources not collected by traditional social science methods. Today, at least one part of the research life cycle is likely to be carried out 'online,' from data collection through to publishing. In this article, we seek to understand emergent modes of doing and reporting qualitative research 'online.' With a greater freedom now to term oneself a 'researcher,' what opportunities and problems do working with online data sources bring? We explore implications of emerging requirements to submit supporting data for social science journal articles and question whether these demands might disrupt the very nature of and identity of qualitative research. Finally, we examine more recent forms of publishing and communicating research that support outputs where data play an integral role in elucidating context and enhancing the reading experience

Assessment of biodiversity data holdings and user data needs for Ghana

Data on biodiversity are important to addressing the challenges of sustainable development, and for decision-making about natural resources and environments. Biodiversity information, when mobilized and shared openly, has the potential to impact science and conservation positively. However, biodiversity data mobilization is expensive, such that data mobilization and sharing activities must be prioritized to meet the needs of the user community. In this study, we undertook a detailed assessment of biodiversity data holdings and user needs in Ghana through semi-structured questionnaire interviews, and focus-group discussions in the form of a workshop. Most biodiversity data-holding organizations were at preliminary stages of digital biodiversity data mobilization and sharing. Taxonomic, checklist, and geographic data on plants and animals were identified as most needed. Priority thematic needs were as regards protected areas, invasive alien species, threatened species, economic species (timber and non-timber forest products), and pathogens and diseases. Human and infrastructural capacities, and sustainable coordination were identified as the major challenges to biodiversity data management. This study provides a detailed case study of how assessing biodiversity data holdings and user data needs can be used to strategize biodiversity data mobilization, data publication, and data use activities

The role of indigenous parataxonomists in botanical inventory: from Herbarium Amboinense to Herbarium Floresense

The enormous taxonomic scope of the Flora Malesiana Project is exacerbated by the extremely short supply of trained researchers and taxonomic experts available to undertake this task. The vast number of indigenous botanical experts resident in Malesia represents a potentially valuable, yet largely unrecognised and untapped, resource. By engaging in collaborative research with indigenous parataxonomists, Flora Malesiana researchers can develop field methodologies that enable a more comprehensive and accurate assessment of the botanical resources of the region while simultaneously enrolling local communities in the sustainable, long-term conservation of native biocultural diversity. This paper outlines a number of projects involving indigenous research associates, discusses the advantages of developing a network of parataxonomists, and details ways in which botanists and ecologists can incorporate indigenous expertise into biological inventory and conservation

The future of botanical monography : report from an international workshop, 12–16 March 2012, Smolenice, Slovak Republic

Monographs are fundamental for progress in systematic botany. They are the vehicles for circumscribing and naming taxa, determining distributions and ecology, assessing relationships for formal classification, and interpreting long-term and short-term dimensions of the evolutionary process. Despite their importance, fewer monographs are now being prepared by the newer generation of systematic botanists, who are understandably involved principally with DNA data and analysis, especially for answering phylogenetic, biogeographic, and population genetic questions. As monographs provide hypotheses regarding species boundaries and plant relationships, new insights in many plant groups are urgently needed. Increasing pressures on biodiversity, especially in tropical and developing regions of the world, emphasize this point. The results from a workshop (with 21 participants) reaffirm the central role that monographs play in systematic botany. But, rather than advocating abbreviated models for monographic products, we recommend a full presentation of relevant information. Electronic publication offers numerous means of illustration of taxa, habitats, characters, and statistical and phylogenetic analyses, which previously would have been prohibitively costly. Open Access and semantically enhanced linked electronic publications provide instant access to content from anywhere in the world, and at the same time link this content to all underlying data and digital resources used in the work. Resources in support of monography, especially databases and widely and easily accessible digital literature and specimens, are now more powerful than ever before, but interfacing and interoperability of databases are much needed. Priorities for new resources to be developed include an index of type collections and an online global chromosome database. Funding for sabbaticals for monographers to work uninterrupted on major projects is strongly encouraged. We recommend that doctoral students be assigned smaller genera, or natural portions of larger ones (subgenera, sections, etc.), to gain the necessary expertise for producing a monograph, including training in a broad array of data collection (e.g., morphology, anatomy, palynology, cytogenetics, DNA techniques, ecology, biogeography), data analysis (e.g., statistics, phylogenetics, models), and nomenclature. Training programs, supported by institutes, associations, and agencies, provide means for passing on procedures and perspectives of challenging botanical monography to the next generation of young systematists.Appreciation is expressed to: the Andrew W. Mellon Foundation for financial support that allowed the workshop to be convened; the International Association for Plant Taxonomy (IAPT) for additional financial support for the workshop.http://www.botanik.univie.ac.at/iapt/s_taxon.phpam201

The future of botanical monography : report from an international workshop, 12–16 March 2012, Smolenice, Slovak Republic

Monographs are fundamental for progress in systematic botany. They are the vehicles for circumscribing and naming taxa, determining distributions and ecology, assessing relationships for formal classification, and interpreting long-term and short-term dimensions of the evolutionary process. Despite their importance, fewer monographs are now being prepared by the newer generation of systematic botanists, who are understandably involved principally with DNA data and analysis, especially for answering phylogenetic, biogeographic, and population genetic questions. As monographs provide hypotheses regarding species boundaries and plant relationships, new insights in many plant groups are urgently needed. Increasing pressures on biodiversity, especially in tropical and developing regions of the world, emphasize this point. The results from a workshop (with 21 participants) reaffirm the central role that monographs play in systematic botany. But, rather than advocating abbreviated models for monographic products, we recommend a full presentation of relevant information. Electronic publication offers numerous means of illustration of taxa, habitats, characters, and statistical and phylogenetic analyses, which previously would have been prohibitively costly. Open Access and semantically enhanced linked electronic publications provide instant access to content from anywhere in the world, and at the same time link this content to all underlying data and digital resources used in the work. Resources in support of monography, especially databases and widely and easily accessible digital literature and specimens, are now more powerful than ever before, but interfacing and interoperability of databases are much needed. Priorities for new resources to be developed include an index of type collections and an online global chromosome database. Funding for sabbaticals for monographers to work uninterrupted on major projects is strongly encouraged. We recommend that doctoral students be assigned smaller genera, or natural portions of larger ones (subgenera, sections, etc.), to gain the necessary expertise for producing a monograph, including training in a broad array of data collection (e.g., morphology, anatomy, palynology, cytogenetics, DNA techniques, ecology, biogeography), data analysis (e.g., statistics, phylogenetics, models), and nomenclature. Training programs, supported by institutes, associations, and agencies, provide means for passing on procedures and perspectives of challenging botanical monography to the next generation of young systematists.Appreciation is expressed to: the Andrew W. Mellon Foundation for financial support that allowed the workshop to be convened; the International Association for Plant Taxonomy (IAPT) for additional financial support for the workshop.http://www.botanik.univie.ac.at/iapt/s_taxon.phpam201

Electrical impedance spectroscopy for potassium content analysis and botanical origin identification of honey

Minerals are reported to dominate the electrical properties of honey and indicate its botanical and geographical origins. In this study, Electrochemical Impedance Spectroscopy (EIS) was used to assess the relation between mineral elements, electrical properties and botanical origin using three honey varieties - Citrus sp., Eucalyptus sp., and Erica sp. These varieties are identified through pollen analysis and market labelling. Flame atomic absorption and emission spectroscopies were used to quantify the concentrations of eight elements (potassium, sodium, calcium, magnesium, manganese, zinc, copper, and iron). Among all the mineral elements, potassium showed a consistent correlation with impedance. The potassium estimation in honey and standard solutions (calibration curve) had similar sensitivities of 153.43 nF/mM and 132.68 nF/mM, respectively. Additionally, the analysis revealed that potassium dominates the mineral composition, with the other species present in minimal quantities. The EIS technique showed high sensitivity to potassium and other ionisable species, making it possible to classify the botanical origin of these three honey types. The EIS technique proved to be both time and cost effective, yielding a classification rate higher than that achieved by analysing mineral composition.We acknowledge support from the Portuguese Foundation for Science and Technology (FCT/MCTES), through national funds and when applicable co-funded EU funds by FEDER under the PT 2020 Partnership Agreement. The project contributing to this work was the institutional projects UIDB/EEA/50008/2020 (Instituto de Telecomunicaç˜oes, IT). MED (https://doi.org/10.54499/UIDB/05183/2020; https://doi. org/10.54499/UIDP/05183/2020) and CHANGE (https://doi.org/10.5 4499/LA/P/0121/2020). FCT/MCTES (PIDDAC) to CIMO (UIDB/ 00690/2020 and UIDP/00690/2020) and SusTEC (LA/P/0007/2021). Youssef Elamine was funded by the Instituto de Telecomunicaç˜oes in the scope of the “CEEC Institucional” program funded by FCT (DOI 10.54499/CEECINST/00058/2021/CP2816/CT0001).info:eu-repo/semantics/publishedVersio