Biodiversity Community Integrated Knowledge Library (BiCIKL)

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

doi:10.3897/rio.8.e81136

Donat Agosti, Laurence Bénichou, Ana Casino, Lars Nielsen, Patrick Ruch, Puneet Kishor, Lyubomir Penev, Patricia Mergen, Christos Arvanitidis (2024)
Liberate the power of biodiversity literature as FAIR digital objects. Research Ideas and Outcomes 10: .

DOI: 10.3897/rio.10.e126586

Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane (2022)
The ENA Source Attribute Helper: An API for improved biological source data. Biodiversity Information Science and Standards 6: .

DOI: 10.3897/biss.6.91118

Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Guy Cochrane, Joana Pauperio, Olaf Bánki, Wouter Addink, Urmas Kõljalg, Patrick Ruch, Kristina Hristova, Boris Barov, Madeira Madeira Scauri, Sara Montinaro, Lucia Vaira, Nicola Fiore, Elizabeth Bamford, Christos Arvanitidis (2023)
The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data. Biodiversity Information Science and Standards 7: .

DOI: 10.3897/biss.7.111482

Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane (2022)
ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data. F1000Research 11: 1042.

DOI: 10.12688/f1000research.123934.1

Joana Paupério, Vikas Gupta, Josephine Burgin, Suran Jayathilaka, Jerry Lanfear, Kessy Abarenkov, Urmas Kõljalg, Lyubomir Penev, Guy Cochrane (2023)
Improving FAIRness of eDNA and Metabarcoding Data: Standards and tools for European Nucleotide Archive data deposition. Biodiversity Information Science and Standards 7: .

DOI: 10.3897/biss.7.111835

Lyubomir Penev, Georgi Zhelezov, Mariya Dimitrova, Iva Boyadzhieva, Teodor Georgiev (2023)
OpenBiodiv for Users: Applications and Approaches to Explore a Biodiversity Knowledge Graph. Biodiversity Information Science and Standards 7: .

DOI: 10.3897/biss.7.110724

Wouter Addink, Soulaine Theocharides, Sharif Islam (2023)
A Novel Part in the Swiss Army Knife for Linking Biodiversity Data: The digital specimen identifier service. Biodiversity Information Science and Standards 7: .

DOI: 10.3897/biss.7.112283

Josephine Burgin, Alisha Ahamed, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan Gupta, Vikas Gupta, Muhammad Haseeb, Maira Ihsan, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Ankur Lathi, Rasko Leinonen, Milena Mansurova, Jasmine McKinnon, Colman O’Cathail, Joana Paupério, Stéphane Pesant, Nadim Rahman, Gabriele Rinck, Sandeep Selvakumar, Swati Suman, Senthilnathan Vijayaraja, Zahra Waheed, Peter Woollard, David Yuan, Ahmad Zyoud, Tony Burdett, Guy Cochrane (2023)
The European Nucleotide Archive in 2022. Nucleic Acids Research 51: D121.

DOI: 10.1093/nar/gkac1051

Laurence Benichou, Donat Agosti, Willi Egloff, Elisa Hermann, Mariko Kageyama, Patricia Mergen, Constance Rinaldo, Jutta Buschbom (2023)
Joint statement by CETAF, SPNHC and BHL on DATA within scientific publications: clarification of [non]copyrightability. Research Ideas and Outcomes 9: .

DOI: 10.3897/rio.9.e115466

Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Bachir Balech, Endre Barta, Physilia Ying Shi Chua, Valeria Di Cola, Katharina F. Heil, Graham M. Hughes, Lars S. Jermiin, Matúš Kalaš, Jerry Lanfear, Evangelos Pafilis, Patricia M. Palagi, Aristotelis C. Papageorgiou, Joana Paupério, Fotis Psomopoulos, Niels Raes, Josephine Burgin, Toni Gabaldón (2024)
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. F1000Research 12: 499.

DOI: 10.12688/f1000research.133724.2

Joana Paupério, Josephine Burgin, Toni Gabaldón, Jerry Lanfear, Robert Waterhouse, Guy Cochrane (2022)
Towards Connecting Molecular Data and the Biodiversity Research Community: An ENA and ELIXIR biodiversity community perspective. Biodiversity Information Science and Standards 6: .

DOI: 10.3897/biss.6.91204

Savvas Paragkamian, Georgia Sarafidou, Dimitra Mavraki, Christina Pavloudi, Joana Beja, Menashè Eliezer, Marina Lipizer, Laura Boicenco, Leen Vandepitte, Ruben Perez-Perez, Haris Zafeiropoulos, Christos Arvanitidis, Evangelos Pafilis, Vasilis Gerovasileiou (2022)
Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow. Frontiers in Marine Science 9: .

DOI: 10.3389/fmars.2022.940844

Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Guy Cochrane, Olaf Bánki, Urmas Kõljalg, Patrick Ruch, Anton Güntsch, Jose Benito Gonzalez Lopez, Patricia Mergen, Joana Pauperio, Tobias Kuhn, Nikos Minadakis, Vincent Smith, Christos Arvanitidis (2024)
Beyond BiCIKL: Towards Building an AI-Assisted “Biodiversity Supergraph”. Biodiversity Information Science and Standards 8: .

DOI: 10.3897/biss.8.135550

Samuli Lehtonen, Kevin R. Thiele (2023)
Report of the Special‐purpose Committee on DNA Sequences as Types, established at the XIX International Botanical Congress in Shenzhen, China. TAXON 72: 1137.

DOI: 10.1002/tax.13055

Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen Parkinson, Patrick Ruch, Alfonso Valencia (2023)
COVoc and COVTriage: novel resources to support literature triage. Bioinformatics 39: .

DOI: 10.1093/bioinformatics/btac800

Sharif Islam, Soulaine Theocharides, Wouter Addink (2022)
Zen and the Art of Persistent Identifier Service Development for Digital Specimen. Biodiversity Information Science and Standards 6: .

DOI: 10.3897/biss.6.91168

Donat Agosti, Laurence Benichou, Wouter Addink, Christos Arvanitidis, Terence Catapano, Guy Cochrane, Mathias Dillen, Markus Döring, Teodor Georgiev, Isabelle Gérard, Quentin Groom, Puneet Kishor, Andreas Kroh, Jiří Kvaček, Patricia Mergen, Daniel Mietchen, Joana Pauperio, Guido Sautter, Lyubomir Penev (2022)
Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing. Research Ideas and Outcomes 8: .

DOI: 10.3897/rio.8.e97374

Lyubomir Penev, Quentin Groom, Ana Casino, Boris Barov (2024)
Uniting FAIR data through interlinked, machine-actionable infrastructures. Research Ideas and Outcomes 10: .

DOI: 10.3897/rio.10.e126588

Joana Paupério, Vikas Gupta, Vishnukumar Balavenkataraman Kadhirvelu, Kessy Abarenkov, Wouter Addink, Donat Agosti, Olaf Bánki, Josephine Burgin, Marcus Ernst, Tobias Frøslev, Quentin Groom, Anton Güntsch, Suran Jayathilaka, Sam Leeflang, Urmas Kõljalg, Joe Miller, Guido Sautter, Lyubomir Penev, Guy Cochrane (2024)
Linking Between Molecular and Biodiversity Data: A BiCIKL Perspective. Biodiversity Information Science and Standards 8: .

DOI: 10.3897/biss.8.135646

Sofie Meeus, Wouter Addink, Donat Agosti, Christos Arvanitidis, Bachir Balech, Mathias Dillen, Mariya Dimitrova, Juan Miguel González-Aranda, Jörg Holetschek, Sharif Islam, Thomas Jeppesen, Daniel Mietchen, Nicky Nicolson, Lyubomir Penev, Tim Robertson, Patrick Ruch, Maarten Trekels, Quentin Groom (2022)
Recommendations for interoperability among infrastructures. Research Ideas and Outcomes 8: .

DOI: 10.3897/rio.8.e96180

Alex Borisenko, Robert Young, Robert Hanner (2024)
A lab-centric, workflow-based data management system for environmental DNA research. Research Ideas and Outcomes 10: .

DOI: 10.3897/rio.10.e120483