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Dietrich CH, Dmitriev DA. Insect phylogenetics in the digital age. CURRENT OPINION IN INSECT SCIENCE 2016; 18:48-52. [PMID: 27939710 DOI: 10.1016/j.cois.2016.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Insect systematists have long used digital data management tools to facilitate phylogenetic research. Web-based platforms developed over the past several years support creation of comprehensive, openly accessible data repositories and analytical tools that support large-scale collaboration, accelerating efforts to document Earth's biota and reconstruct the Tree of Life. New digital tools have the potential to further enhance insect phylogenetics by providing efficient workflows for capturing and analyzing phylogenetically relevant data. Recent initiatives streamline various steps in phylogenetic studies and provide community access to supercomputing resources. In the near future, automated, web-based systems will enable researchers to complete a phylogenetic study from start to finish using resources linked together within a single portal and incorporate results into a global synthesis.
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Affiliation(s)
- Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S Oak St., Champaign, IL 61820, USA.
| | - Dmitry A Dmitriev
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S Oak St., Champaign, IL 61820, USA
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Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M. EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e10445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Affiliation(s)
- Marco Sigovini
- CNR – National Research Council of Italy ISMAR – Marine Sciences Institute Arsenale Tesa 104 Castello 2737/F I‐30122 Venice Italy
| | - Erica Keppel
- CNR – National Research Council of Italy ISMAR – Marine Sciences Institute Arsenale Tesa 104 Castello 2737/F I‐30122 Venice Italy
- Smithsonian Environmental Research Center (SERC) 647, Contees Wharf Road Edgewater MD 21037 USA
| | - Davide Tagliapietra
- CNR – National Research Council of Italy ISMAR – Marine Sciences Institute Arsenale Tesa 104 Castello 2737/F I‐30122 Venice Italy
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Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M. EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e9774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Pilsk SC, Kalfatovic MR, Richard JM. Unlocking Index Animalium: From paper slips to bytes and bits. Zookeys 2016:153-71. [PMID: 26877657 PMCID: PMC4741219 DOI: 10.3897/zookeys.550.9673] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022] Open
Abstract
In 1996 Smithsonian Libraries (SIL) embarked on the digitization of its collections. By 1999, a full-scale digitization center was in place and rare volumes from the natural history collections, often of high illustrative value, were the focus for the first years of the program. The resulting beautiful books made available for online display were successful to a certain extent, but it soon became clear that the data locked within the texts needed to be converted to more usable and re-purposable form via digitization methods that went beyond simple page imaging and included text conversion elements. Library staff met with researchers from the taxonomic community to understand their path to the literature and identified tools (indexes and bibliographies) used to connect to the library holdings. The traditional library metadata describing the titles, which made them easily retrievable from the shelves of libraries, was not meeting the needs of the researcher looking for more detailed and granular data within the texts. The result was to identify proper print tools that could potential assist researchers in digital form. This paper outlines the project undertaken to convert Charles Davies Sherborn’s Index Animalium into a tool to connect researchers to the library holdings: from a print index to a database to eventually a dataset. Sherborn’s microcitation of a species name and his bibliographies help bridge the gap between taxonomist and literature holdings of libraries. In 2004, SIL received funding from the Smithsonian’s Atherton Seidell Endowment to create an online version of Sherborn’s Index Animalium. The initial project was to digitize the page images and re-key the data into a simple data structure. As the project evolved, a more complex database was developed which enabled quality field searching to retrieve species names and to search the bibliography. Problems with inconsistent abbreviations and styling of his bibliographies made the parsing of the data difficult. Coinciding with the development of the Biodiversity Heritage Library (BHL) in 2005, it became obvious there was a need to integrate the database converted Index Animalium, BHL’s scanned taxonomic literature, and taxonomic intelligence (the algorithmic identification of binomial, Latinate name-strings). The challenges of working with legacy taxonomic citation, computer matching algorithms, and making connections have brought us to today’s goal of making Sherborn available and linked to other datasets. Partnering with others to allow machine-to-machine communications the data is being examined for possible transformation into RDF markup and meeting the standards of Linked Open Data. SIL staff have partnered with Thomson Reuters and the Global Names Initiative to further enhance the Index Animalium data set. Thomson Reuters’ staff is now working on integrating the species microcitation and species name in the ION: Index to Organism Names project ; Richard Pyle (The Bishop Museum) is also working on further parsing of the text. The Index Animalium collaborative project’s ultimate goal is to successful have researchers go seamlessly from the species name in either ION or the scanned pages of Index Animalium to the digitized original description in BHL - connecting taxonomic researchers to original authored species descriptions with just a click.
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Dickinson EC. Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn's and Richmond's historical legacy of bibliographic exploration. Zookeys 2016:107-34. [PMID: 26877655 PMCID: PMC4741217 DOI: 10.3897/zookeys.550.10170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 11/13/2022] Open
Abstract
Due to its public popularity, ornithology has a huge corpus of scientific publication for a relatively small number of species. Although there are global checklists of currently recognised taxa, there has been only limited, mainly individual, effort to build a nomenclatural database that the science of ornithology deserves. This is especially true in relation to concise synonymies. With the arrival of ZooBank and the Biodiversity Heritage Library, the time has come to develop synonymies and to add fuller bibliographic detail to databases. The preparation for both began at the start of the 20th century with extensive work by Sherborn and Richmond. I discuss their legacy, offer notes on significant work since then, and provide suggestions for what remains to be done. To make solid the foundations for ornithological nomenclature and taxonomy, especially for synonymies, ornithologists will need to collaborate much more and contribute to the digital infrastructure.
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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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Penev L, Paton A, Nicolson N, Kirk P, Pyle RL, Whitton R, Georgiev T, Barker C, Hopkins C, Robert V, Biserkov J, Stoev P. A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank). Zookeys 2016; 550:233-46. [PMID: 26877662 PMCID: PMC4741224 DOI: 10.3897/zookeys.550.9551] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/10/2015] [Indexed: 11/30/2022] Open
Abstract
Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.
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Affiliation(s)
- Lyubomir Penev
- Institute for Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Pensoft Publishers, Sofia, Bulgaria
| | - Alan Paton
- International Plant Name Index (IPNI) and Index Fungorum (IF), Royal Botanic Gardens Kew, UK
| | - Nicola Nicolson
- International Plant Name Index (IPNI) and Index Fungorum (IF), Royal Botanic Gardens Kew, UK
| | - Paul Kirk
- International Plant Name Index (IPNI) and Index Fungorum (IF), Royal Botanic Gardens Kew, UK
| | | | | | | | - Christine Barker
- International Plant Name Index (IPNI) and Index Fungorum (IF), Royal Botanic Gardens Kew, UK
| | - Christopher Hopkins
- International Plant Name Index (IPNI) and Index Fungorum (IF), Royal Botanic Gardens Kew, UK
| | - Vincent Robert
- Mycobank, CBS Fungal Biodiversity Centre, Utrecht, The Netherlands
| | | | - Pavel Stoev
- Pensoft Publishers, Sofia, Bulgaria
- National Museum of Natural History, Sofia, Bulgaria
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