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Page R. Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people. Biodivers Data J 2023; 11:e107914. [PMID: 37745899 PMCID: PMC10514697 DOI: 10.3897/bdj.11.e107914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
A major gap in the biodiversity knowledge graph is a connection between taxonomic names and the taxonomic literature. While both names and publications often have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs) or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to DOIs for publications. This article describes efforts to make those connections across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI) and the Index of Organism Names (ION). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications. This represents approximately 36% of names for which publication data are available. The mappings between LSIDs and publication PIDs are made available through ChecklistBank. Applications of this mapping are discussed, including a web app to locate the citation of a taxonomic name and a knowledge graph that uses data on researcher ORCID ids to connect taxonomic names and publications to authors of those names.
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Affiliation(s)
- Roderic Page
- University of Glasgow, Glasgow, United KingdomUniversity of GlasgowGlasgowUnited Kingdom
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2
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Agosti D, Benichou L, Addink W, Arvanitidis C, Catapano T, Cochrane G, Dillen M, Döring M, Georgiev T, Gérard I, Groom Q, Kishor P, Kroh A, Kvaček J, Mergen P, Mietchen D, Pauperio J, Sautter G, Penev L. Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e97374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon names, material citations, gene sequences, specimens, scientific collections) in taxonomy and biodiversity publishing. The paper proposes best practices on how identifiers should be used in the different cases and on how they can be minted, cited, and expressed in the backend article XML to facilitate conversion to and further re-use of the article content as FAIR data. The paper also discusses several specific routes for post-publication re-use of semantically enhanced content through large biodiversity data aggregators such as the Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence Database Collaboration (INSDC) and others, and proposes specifications of both identifiers and XML tags to be used for that purpose. A summary table provides an account and overview of the recommendations. The guidelines are supported with examples from the existing publishing practices.
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Ramon GD, Green BJ, Levetin E, Makra L, Bielory L. The Importance of Binomial Nomenclature for the Identification of Pollen Aeroallergens. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:2642-2644. [PMID: 33741508 DOI: 10.1016/j.jaip.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/23/2021] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
The diagnosis and treatment of atopic disorders associated with specific aerobiological triggers require basic botanical training. However, the identification of specific pollen can often be confounded by broad naming conventions that range from categorized colloquial to scientific names based on either higher taxonomic levels or, in some cases, binomial nomenclature. Physicians specializing in allergy often lack a comprehensive understanding with respect to plant taxonomy and botanical nomenclature that are critical skills required for clinical practice and research programs evaluating pollen and airborne fungal spores. In addition, binomial and current family designation and synonyms, including author citation are often misused, causing a misinterpretation of existing plants species or pollen types. It is critical that the correct botanical name is linked to a validated specimen and scientific naming conventions are used where possible by the clinician and researcher. In relation to pollen identification, we propose that clinicians and researchers should provide the currently accepted binomial nomenclature, offer relevant synonyms, and use the Angiosperm Phylogeny Group names.
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Affiliation(s)
- German Dario Ramon
- Instituto de Alergia e Inmunología del Sur, Hospital Italiano Regional del Sur, Bahía Blanca, Buenos Aires, Argentina.
| | - Brett James Green
- Office of the Director, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, Va
| | - Estelle Levetin
- Department of Biological Science, University of Tulsa, Tulsa, Okla
| | - László Makra
- University of Szeged, Faculty of Agriculture, Institute of Economics and Rural Development, Hódmezővásárhely, Hungary
| | - Leonard Bielory
- Department of Medicine and Ophthalmology, Hackensack Meridian School of Medicine, Seton Hall University, Nutley Center for Environmental Prediction, Department of Environmental Sciences, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
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Bates ST, Miller AN, the Macrofungi Collections and Microfungi Collections Consor . The protochecklist of North American nonlichenized Fungi. Mycologia 2018. [DOI: 10.1080/00275514.2018.1515410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Scott T. Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, Indiana 46391
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, Illinois 61820
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Kress WJ, Knapp S, Stoev P, Penev L. PhytoKeys at 100: progress in sustainability, innovation, and speed to enhance publication in plant systematics. PHYTOKEYS 2018; 100:1-9. [PMID: 29962889 PMCID: PMC6023950 DOI: 10.3897/phytokeys.100.27591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
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Affiliation(s)
- W. John Kress
- National Museum of Natural History, Smithsonian Institution, Washington DC, USA
| | - Sandra Knapp
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Pavel Stoev
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Pensoft Publishers, Sofia, Bulgaria
| | - Lyubomir Penev
- Pensoft Publishers, Sofia, Bulgaria
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Franz NM, Zhang C, Lee J. A logic approach to modelling nomenclatural change. Cladistics 2018; 34:336-357. [PMID: 34645079 DOI: 10.1111/cla.12201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2017] [Indexed: 11/27/2022] Open
Abstract
We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case, with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature, including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species-level epithets. Permutations of this child-to-parent reassignment action lead to 36 alternative scenarios, where each scenario requires a set of 1-14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code-mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic-based nomenclatural change optimization and validation services, which could be applied in global nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and can therefore inform the design of future, big data-compatible identifier systems that recognize and mitigate these constraints.
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Affiliation(s)
- Nico M Franz
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA
| | - Chao Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, PO Box 878809, Tempe, AZ, 85287-8809, USA
| | - Joohyung Lee
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, PO Box 878809, Tempe, AZ, 85287-8809, USA
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Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S. Strategies and guidelines for scholarly publishing of biodiversity data. RESEARCH IDEAS AND OUTCOMES 2017. [DOI: 10.3897/rio.3.e12431] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Abstract
The first few words of the title of this symposium are “Anchoring Biodiversity Information”. In order to properly anchor anything for a long-lasting future, a solid foundation needs to have been laid. For the zoological portion of biodiversity information, that firm foundation is best exemplified in the works of Charles Davies Sherborn. This man, like others of his ilk, was intimately focused on indexing names. This incredible focus was a life-long passion for him and culminated in his 9500-page Index Animalium of over 400,000 names of animals. This Index represents not only one of the most prodigious efforts in publication by a single man and the single most important reference to names in zoology, but a permanent legacy to the efforts of an indexer that proved to be an inspiration to many.
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Affiliation(s)
- Neal L Evenhuis
- Bishop Museum, 1525 Bernice Street, Honolulu, Hawaii 96817, USA
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Alonso-Zarazaga MA, Fautin DG, Michel E. The List of Available Names (LAN): A new generation for stable taxonomic names in zoology? Zookeys 2016; 550:225-32. [PMID: 26877661 PMCID: PMC4741223 DOI: 10.3897/zookeys.550.10043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 05/25/2015] [Indexed: 11/23/2022] Open
Abstract
The List of Available Names in Zoology (LAN) is an inventory of names with specific scope in time and content, presented and approved in parts, and constituted as a cumulative index of names available for use in zoological nomenclature. It was defined in Article 79 in the fourth edition of the International Code of Zoological Nomenclature. The LAN is likely to gain importance with the development of the online Official Registry for Zoological Nomenclature (ZooBank) as it is potentially a source of many nomenclaturally certified names. Article 79 describes the deliberative process for adding large numbers of names to the LAN simultaneously, detailing steps and chronology for submission of a candidate Part to the LAN and consideration of a candidate Part by the public and Commission, but it is largely mute about the contents of a candidate Part. It does make clear that a name within the scope of a Part but not on the LAN has no nomenclatural standing, even if it had previously been considered available, thereby preventing long-forgotten names from displacing accepted ones and the accumulation of nomina dubia. Thus, for taxa on the LAN, nomenclatural archaeology - the resurrecting of old unused names to replace by priority names in current usage - will not be worthwhile. Beyond that, it has been unclear if Article 79 is intended to document every available name known within the scope of the Part, or if its intention is to pare the inventory of available names within the scope of the Part. Consideration by the Commission and two committees to deal with the LAN have defined steps to implement Article 79 with the latter intent. Procedures for consideration of a candidate Part are defined in a manual, published as an appendix in this volume.
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Affiliation(s)
- Miguel A. Alonso-Zarazaga
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias, Naturales (MNCN-CSIC), Madrid, Spain
| | - Daphne Gail Fautin
- Department of Ecology and Evolutionary Biology, and Natural History Museum (Biodiversity Institute), University of Kansas, Lawrence, Kansas USA & International Commission on Zoological Nomenclature
| | - Ellinor Michel
- Department of Life Sciences, The Natural History Museum, Cromwell Road London SW7 5BD, UK
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Erwin T, Stoev P, Georgiev T, Penev L. ZooKeys 500: traditions and innovations hand-in-hand servicing our taxonomic community. Zookeys 2015:1-8. [PMID: 25987868 PMCID: PMC4432237 DOI: 10.3897/zookeys.500.9844] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/22/2022] Open
Affiliation(s)
- Terry Erwin
- Hyper-diversity Group, Department of Entomology, MRC-187, National Museum of Natural History, Smithsonian Institution, Washington, P.O. Box 37012, DC 20013-7012, USA
| | - Pavel Stoev
- Pensoft Publishers, Sofia, Bulgaria ; National Museum of Natural History, Sofia, Bulgaria
| | | | - Lyubomir Penev
- Pensoft Publishers, Sofia, Bulgaria ; Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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