Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal

Vincent Smith; Teodor Georgiev; Pavel Stoev; Jordan Biserkov; Jeremy Miller; Laurence Livermore; Edward Baker; Daniel Mietchen; Thomas Couvreur; Gregory Mueller; Torsten Dikow; Kristofer M. Helgen; Jiři Frank; Donat Agosti; David Roberts; Lyubomir Penev

doi:10.3897/BDJ.1.e995

Adrian Glover, Helena Wiklund, Muriel Rabone, Diva Amon, Craig Smith, Tim O'Hara, Christopher Mah, Thomas Dahlgren (2016)
Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata. Biodiversity Data Journal 4: e7251.

DOI: 10.3897/BDJ.4.e7251

Scott E. Miller, Axel Hausmann, Winnie Hallwachs, Daniel H. Janzen (2016)
Advancing taxonomy and bioinventories with DNA barcodes. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150339.

DOI: 10.1098/rstb.2015.0339

Scott C Edmunds, Chris I Hunter, Vincent Smith, Pavel Stoev, Lyubomir Penev (2013)
Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description. GigaScience 2: .

DOI: 10.1186/2047-217X-2-14

Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Donald Hobern, Olaf Banki, Wouter Addink, Urmas Kõljalg, Kyle Copas, Patricia Mergen, Anton Güntsch, Laurence Benichou, Jose Benito Gonzalez Lopez, Patrick Ruch, Corinne Martin, Boris Barov, Iliyana Demirova, Kristina Hristova (2022)
Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: .

DOI: 10.3897/rio.8.e81136

Pavel Stoev, Ana Komerički, Nesrine Akkari, Shanlin Liu, Xin Zhou, Alexander Weigand, Jeroen Hostens, Christopher Hunter, Scott Edmunds, David Porco, Marzio Zapparoli, Teodor Georgiev, Daniel Mietchen, David Roberts, Sarah Faulwetter, Vincent Smith, Lyubomir Penev (2013)
Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodiversity Data Journal 1: e1013.

DOI: 10.3897/BDJ.1.e1013

Lyubomir Penev, Teodor Georgiev, Peter Geshev, Seyhan Demirov, Viktor Senderov, Iliyana Kuzmova, Iva Kostadinova, Slavena Peneva, Pavel Stoev (2017)
ARPHA-BioDiv: A toolbox for scholarly publication and dissemination of biodiversity data based on the ARPHA Publishing Platform. Research Ideas and Outcomes 3: e13088.

DOI: 10.3897/rio.3.e13088

Willi Egloff, Donat Agosti, Puneet Kishor, David Patterson, Jeremy Miller (2017)
Copyright and the Use of Images as Biodiversity Data. Research Ideas and Outcomes 3: .

DOI: 10.3897/rio.3.e12502

Yde de Jong, Melina Verbeek, Verner Michelsen, Per de Place Bjørn, Wouter Los, Fedor Steeman, Nicolas Bailly, Claire Basire, Przemek Chylarecki, Eduard Stloukal, Gregor Hagedorn, Florian Wetzel, Falko Glöckler, Alexander Kroupa, Günther Korb, Anke Hoffmann, Christoph Häuser, Andreas Kohlbecker, Andreas Müller, Anton Güntsch, Pavel Stoev, Lyubomir Penev (2014)
Fauna Europaea – all European animal species on the web. Biodiversity Data Journal 2: e4034.

DOI: 10.3897/BDJ.2.e4034

Jinfa Wong, Maosheng Foo, Hugh Tan, Rudolf Meier (2017)
Whitefly predation and extensive mesonotum color polymorphism in an Acletoxenus population from Singapore (Diptera, Drosophilidae). ZooKeys 725: 49.

DOI: 10.3897/zookeys.725.13675

Torsten Dikow, Donat Agosti (2015)
Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae). Biodiversity Data Journal 3: e5707.

DOI: 10.3897/BDJ.3.e5707

Daniel Mietchen, Lyubomir Penev, Teodor Georgiev, Boriana Ovcharova, Iva Kostadinova (2021)
Open science in practice: 300 published research ideas and outcomes illustrate how RIO Journal facilitates engagement with the research process. Research Ideas and Outcomes 7: .

DOI: 10.3897/rio.7.e68595

Christian Thompson, Thomas Pape (2016)
Sherborn’s influence on Systema Dipterorum. ZooKeys 550: 135.

DOI: 10.3897/zookeys.550.9447

Adrian Glover, Thomas Dahlgren, Helena Wiklund, Inga Mohrbeck, Craig Smith (2015)
An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss. Journal of Marine Science and Engineering 4: 2.

DOI: 10.3390/jmse4010002

Adam Tofilski (2018)
DKey software for editing and browsing dichotomous keys. ZooKeys 735: 131.

DOI: 10.3897/zookeys.735.21412

M. Andrew Johnston, Rolf Aalbu, Nico Franz (2018)
An updated checklist of the Tenebrionidae sec. Bousquet et al. 2018 of the Algodones Dunes of California, with comments on checklist data practices. Biodiversity Data Journal 6: e24927.

DOI: 10.3897/BDJ.6.e24927

Nico M Franz, Beckett W Sterner (2018)
To increase trust, change the social design behind aggregated biodiversity data. Database 2018: .

DOI: 10.1093/database/bax100

Leonardo Candela, Donatella Castelli, Paolo Manghi, Alice Tani (2015)
Data journals: A survey. Journal of the Association for Information Science and Technology 66: 1747.

DOI: 10.1002/asi.23358

Jeremy Miller, Donat Agosti, Lyubomir Penev, Guido Sautter, Teodor Georgiev, Terry Catapano, David Patterson, David King, Serrano Pereira, Rutger Vos, Soraya Sierra (2015)
Integrating and visualizing primary data from prospective and legacy taxonomic literature. Biodiversity Data Journal 3: e5063.

DOI: 10.3897/BDJ.3.e5063

Yde de Jong, Juliana Kouwenberg, Louis Boumans, Charles Hussey, Roger Hyam, Nicola Nicolson, Paul Kirk, Alan Paton, Ellinor Michel, Michael Guiry, Phillip Boegh, Henrik Pedersen, Henrik Enghoff, Eckhard von Raab-Straube, Anton Güntsch, Marc Geoffroy, Andreas Müller, Andreas Kohlbecker, Walter Berendsohn, Ward Appeltans, Christos Arvanitidis, Bart Vanhoorne, Joram Declerck, Leen Vandepitte, Francisco Hernandez, Róisín Nash, Mark Costello, David Ouvrard, Pascale Bezard-Falgas, Thierry Bourgoin, Florian Wetzel, Falko Glöckler, Günther Korb, Caroline Ring, Gregor Hagedorn, Christoph Häuser, Nihat Aktaç, Ahmet Asan, Adorian Ardelean, Paulo Borges, Dhimiter Dhora, Hasmik Khachatryan, Michael Malicky, Shaig Ibrahimov, Alexander Tuzikov, Aaike De Wever, Snejana Moncheva, Nikolai Spassov, Karel Chobot, Alexi Popov, Igor Boršić, Spyros Sfenthourakis, Urmas Kõljalg, Pertti Uotila, Olivier Gargominy, Jean-Claude Dauvin, David Tarkhnishvili, Giorgi Chaladze, Michael Tuerkay, Anastasios Legakis, László Peregovits, Gudmundur Gudmundsson, Erling Ólafsson, Liam Lysaght, Bella Galil, Francesco Raimondo, Gianniantonio Domina, Fabio Stoch, Alessandro Minelli, Voldermars Spungis, Eduardas Budrys, Sergej Olenin, Armand Turpel, Tania Walisch, Vladimir Krpach, Marie Gambin, Laurentia Ungureanu, Gordan Karaman, Roy Kleukers, Elisabeth Stur, Kaare Aagaard, Nils Valland, Toril Moen, Wieslaw Bogdanowicz, Piotr Tykarski, Jan Węsławski, Monika Kędra, Antonio M. de Frias Martins, António Abreu, Ricardo Silva, Sergei Medvedev, Alexander Ryss, Smiljka Šimić, Karol Marhold, Eduard Stloukal, Davorin Tome, Marian Ramos, Benito Valdés, Francisco Pina, Sven Kullander, Anders Telenius, Yves Gonseth, Pascal Tschudin, Oleksandra Sergeyeva, Volodymyr Vladymyrov, Volodymyr Rizun, Chris Raper, Dan Lear, Pavel Stoev, Lyubomir Penev, Ana Rubio, Thierry Backeljau, Hannu Saarenmaa, Sandrine Ulenberg (2015)
PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: .

DOI: 10.3897/BDJ.3.e5848

Florian T. Wetzel, Hannu Saarenmaa, Eugenie Regan, Corinne S. Martin, Patricia Mergen, Larissa Smirnova, Éamonn Ó Tuama, Francisco A. García Camacho, Anke Hoffmann, Katrin Vohland, Christoph L. Häuser (2015)
The roles and contributions of Biodiversity Observation Networks (BONs) in better tracking progress to 2020 biodiversity targets: a European case study. Biodiversity 16: 137.

DOI: 10.1080/14888386.2015.1075902

Hervé Sauquet, Susana Magallón (2018)
Key questions and challenges in angiosperm macroevolution. New Phytologist 219: 1170.

DOI: 10.1111/nph.15104

Lyubomir Penev (2017)
From Open Access to Open Science from the viewpoint of a scholarly publisher. Research Ideas and Outcomes 3: e12265.

DOI: 10.3897/rio.3.e12265

Lyubomir Penev, Daniel Mietchen, Vishwas Chavan, Gregor Hagedorn, Vincent Smith, David Shotton, Éamonn Ó Tuama, Viktor Senderov, Teodor Georgiev, Pavel Stoev, Quentin Groom, David Remsen, Scott Edmunds (2017)
Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431.

DOI: 10.3897/rio.3.e12431

Larissa Smirnova, Patricia Mergen, Quentin Groom, Aaike De Wever, Lyubomir Penev, Pavel Stoev, Israel Pe’er, Veljo Runnel, Antonio Camacho, Timothy Vincent, Donat Agosti, Christos Arvanitidis, Francisco Bonet, Hannu Saarenmaa (2016)
Data sharing tools adopted by the European Biodiversity Observation Network Project. Research Ideas and Outcomes 2: e9390.

DOI: 10.3897/rio.2.e9390

Thomas Horn (2016)
Integrating Biodiversity Data into Botanic Collections. Biodiversity Data Journal 4: e7971.

DOI: 10.3897/BDJ.4.e7971

Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A. Morris, Lyubomir Penev (2018)
OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system. Journal of Biomedical Semantics 9: .

DOI: 10.1186/s13326-017-0174-5

Daniela Gigante, Gianni Bacchetta, Simonetta Bagella, Daniele Viciani (2020)
Does an open access journal about vegetation still make sense in 2020?. Plant Sociology 57: 85.

DOI: 10.3897/pls2020571/09

Axel Hausmann, Scott E. Miller, Jeremy D. Holloway, Jeremy R. deWaard, David Pollock, Sean W.J. Prosser, Paul D.N. Hebert, John-James Wilson (2016)
Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae). Genome 59: 671.

DOI: 10.1139/gen-2015-0197

Jeremy Miller, Teodor Georgiev, Pavel Stoev, Guido Sautter, Lyubomir Penev (2015)
Corrected data re-harvested: curating literature in the era of networked biodiversity informatics. Biodiversity Data Journal 3: e4552.

DOI: 10.3897/BDJ.3.e4552

Robert P. Guralnick, Nico Cellinese, John Deck, Richard L. Pyle, John Kunze, Lyubomir Penev, Ramona Walls, Gregor Hagedorn, Donat Agosti, John Wieczorek, Terry Catapano, Roderic Page (2015)
Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data. ZooKeys 494: 133.

DOI: 10.3897/zookeys.494.9352

Viktor Senderov, Lyubomir Penev (2016)
The Open Biodiversity Knowledge Management System in Scholarly Publishing. Research Ideas and Outcomes 2: e7757.

DOI: 10.3897/rio.2.e7757

Aurélien Miralles, Teddy Bruy, Katherine Wolcott, Mark D Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim W Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne S Renner, Miguel Vences, Matt Friedman (2020)
Repositories for Taxonomic Data: Where We Are and What is Missing. Systematic Biology 69: 1231.

DOI: 10.1093/sysbio/syaa026

Jose Fernandez-Triana, Lyubomir Penev, Sujeevan Ratnasingham, M. Alex Smith, Jayme Sones, Angela Telfer, Jeremy deWaard, Paul Hebert (2014)
Streamlining the use of BOLD specimen data to record species distributions: a case study with ten Nearctic species of Microgastrinae (Hymenoptera: Braconidae). Biodiversity Data Journal 2: e4153.

DOI: 10.3897/BDJ.2.e4153

Daniel Mietchen, Ross Mounce, Lyubomir Penev (2015)
Publishing the research process. Research Ideas and Outcomes 1: .

DOI: 10.3897/rio.1.e7547

Astrid Schmidt-Kloiber, Aaike De Wever (2018)
Riverine Ecosystem Management. Chapter 20: 391.

DOI: 10.1007/978-3-319-73250-3_20