Library

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Authors: Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes, Anna Sandionigi, Monica Santamaria, Wouter Addink, Jiri Vohradsky, Amandine Nunes-Jorge, Nils Peder Willassen, Jerry Lanfear

Status: Published
Year: 2021
Journal: F1000Research
Publisher: F1000 Research Ltd

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Enabling Published Taxonomic Data to be used to Address the Biodiversity Crisis: Biodiversity Literature Repository and TreatmentBank

Authors: Donat Agosti, Patrick Ruch, Jose Benito Gonzalez Lopez, Lyubomir Penev

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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Delivering Fit-for-Use Data: Quality control

Authors: Felipe Simoes, Donat Agosti, Marcus Guidoti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective

Authors: Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Boris Barov, Donald Hobern, Olaf Banki, Wouter Addink, Urmas Kõljalg, Patrick Ruch, Kyle Copas, Patricia Mergen, Anton Güntsch, Laurence Benichou, Jose Benito Gonzalez Lopez

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Publisher: Pensoft Publishers

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Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

Authors: Kessy Abarenkov, Allan Zirk, Kadri Põldmaa, Timo Piirmann, Raivo Pöhönen, Filipp Ivanov, Kristjan Adojaan, Urmas Kõljalg

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Towards Connecting Molecular Data and the Biodiversity Research Community: An ENA and ELIXIR biodiversity community perspective

Authors: Joana Paupério, Josephine Burgin, Toni Gabaldón, Jerry Lanfear, Robert M Waterhouse, Guy Cochrane

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data

Authors: Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane

Status: Published
Year: 2022
Journal: F1000Research
Volume/Issue: 11
Publisher: F1000 Research Ltd

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The BHL-Plazi Partnership: Getting data from the 1800s directly into 21st century, reused digital accessible knowledge

Authors: Diego Janisch Alvares, Marcus Guidoti, Felipe Simoes, Carolina Sokolowicz, Donat Agosti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Synospecies, an application to reflect changes in taxonomic names based on a triple store based on taxonomic data liberated from publication

Authors: Reto Gmür, Donat Agosti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Semantic Search in Legacy Biodiversity Literature: Integrating data from different data infrastructures

Authors: Adrian Pachzelt, Gerwin Kasperek, Andy Lücking, Giuseppe Abrami, Christine Driller

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Biodiversity Information Science and Standards 5: e74251

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Robust Integration of Biodiversity Data by Process- and State-based Representation of Object Histories and Modular Application Architecture

Authors: Christian Bölling, Satpal Bilkhu, Christian Gendreau, Falko Glöckler, James Macklin, David Shorthouse

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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(Re)Discovering Known Biodiversity: Introduction

Authors: Donat Agosti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Linking and the Role of the Material Citation

Authors: Jeremy A. Miller, Donat Agosti, Marcus Guidoti, Francisco Andres Rivera Quiroz

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Discovering Known Biodiversity: Digital accessible knowledge — Getting the community involved

Authors: Carolina Sokolowicz, Marcus Guidoti, Donat Agosti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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A Possible Workflow from New and Legacy Publications to keep the World Flora Online up to date with New Species and Augmenting Taxonomic Treatments

Authors: Donat Agosti, Laurence Benichou, Lyubomir Penev, Roger Hyam

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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Biodiversity Literature Repository: Building the customized FAIR repository by using custom metadata

Authors: Alexandros Ioannidis-Pantopikos, Donat Agosti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Connecting the Dots: Joint development of best practices between infrastructures in support of bidirectional data linking

Authors: Wouter Addink, Niki Kyriakopoulou

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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The OpenBiodiv Knowledge Graph Rebuilt: A semantic hub on top of the ARPHA-published content and the Biodiversity Literature Repository

Authors: Lyubomir Penev, Mariya Dimitrova, Georgi Zhelezov, Teodor Georgiev

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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The ENA Source Attribute Helper: An API for improved biological source data

Authors: Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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Beyond the print and PDF prisons: Data about biodiversity want to be free

Authors: Donat Agosti

Status: Published
Year: 2022
Journal: Zenodo
Publisher: Zenodo

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TreatmentBank: Plazi's strategies and its implementation to most efficiently liberate data from scholarly publications

Authors: Marcus Guidoti, Carolina Sokolowicz, Felipe Simoes, Valdenar Gonçalves, Tatiana Ruschel, Diego Janisch Alvares, Donat Agosti

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Stakeholder input into the network graph provided by Third Global Biodiversity Informatics Conference (GBIC3)

Authors: Kyle Copas, Joe Miller

Status: Published
Year: 2022
Deliverable number: D2.2

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Best practice manual for findability, re-use and accessibility of infrastructures

Authors: Wouter Addink, Niki Kyriakopoulou, Lyubomir Penev, David Fichtmueller, Ben Norton, David Shorthouse

Status: Published
Year: 2022
Deliverable number: D1.3

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Recommendations for interoperability among infrastructures

Authors: Sofie Meeus, Wouter Addink, Donat Agosti, Christos Arvanitidis, Bachir Balech, Mathias Dillen, Mariya Dimitrova, Juan Miguel González-Aranda, Jörg Holetschek, Sharif Islam, Thomas S. Jeppesen, Daniel Mietchen, Nicky Nicolson, Lyubomir Penev, Tim Robertson, Patrick Ruch, Maarten Trekels, Quentin Groom

Status: Published
Year: 2022
Deliverable number: D1.2

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User Requirements Analysis Report

Authors: Christos Arvanitidis, Cristina Huertas Olivares, Quentin Groom, Elizabeth Bamford, Lucia Vaira, Sara Montinaro, Ana Casino, Donat Agosti, Boris Barov, Kristina Hristova, Lyubomir Penev

Status: Published
Year: 2022
Deliverable number: D1.1

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Relational network graph for the Biodiversity Knowledge Hub (BKH)

Authors: Kyle Copas, Joe Miller

Status: Published
Year: 2022
Deliverable number: D2.1

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Hacking Infrastructures Together: Towards better interoperability of infrastructures

Authors: Sofie Meeus, Wouter Addink, Donat Agosti, Christos Arvanitidis, Mariya Dimitrova, Juan Miguel González-Aranda, Jörg Holetschek, Sharif Islam, Thomas S. Jeppesen, Daniel Mietchen, Tim Robertson, Francisco Manuel Sanchez Cano, Maarten Trekels, Quentin Groom

Status: Published
Year: 2021
Journal: Biodiversity Information Science and Standards
Volume/Issue: 5
Publisher: Pensoft Publishers

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Network analysis of specimen co-collection

Authors: Sofie Meeus, Tom August, Maarten Trekels, Lien Reyserhove, Quentin Groom

Status: Published
Year: 2021
Publisher: BioHackrXiv Preprints

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Zen and the Art of Persistent Identifier Service Development for Digital Specimen

Authors: Sharif Islam, Soulaine Theocharides, Wouter Addink

Status: Published
Year: 2022
Journal: Biodiversity Information Science and Standards
Volume/Issue: 6
Publisher: Pensoft Publishers

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The European Nucleotide Archive in 2021

Authors: Carla Cummins, Alisha Ahamed, Raheela Aslam, Josephine Burgin, Rajkumar Devraj, Ossama Edbali, Dipayan Gupta, Peter W Harrison, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Kadhirvelu, Simon Kay, Manish Kumar, Ankur Lathi, Rasko Leinonen, Fabio Madeira, Nandana Madhusoodanan, Milena Mansurova, Colman O’Cathail, Matt Pearce, Stéphane Pesant, Nadim Rahman, Jeena Rajan, Gabriele Rinck, Sandeep Selvakumar, Alexey Sokolov, Swati Suman, Ross Thorne, Prabhat Totoo, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Rodrigo Lopez, Tony Burdett, Guy Cochrane

Status: Published
Year: 2022
Journal: Nucleic Acids Research
Volume/Issue: 50
Publisher: Oxford University Press

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Architecture Design for a pan-European PID system for Digital Specimens

Authors: Wouter Addink, Sharif Islam, Mathias Dillen, Anton Güntsch, Soulaine Theocharides

Status: Published
Year: 2022
Deliverable number: D7.1

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Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

Authors: Laurence Benichou, Jutta Buschbom, Mariel Campbell, Elisa Hermann, Jiří Kvaček, Patricia Mergen, Lorna Mitchell, Constance Rinaldo, Donat Agosti

Status: Published
Year: 2022
Journal: Research Ideas and Outcomes
Volume/Issue: 10
Publisher: Pensoft Publishers

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The TreatmentBank factory: Data access

Authors: Donat Agosti, Jeremy Miller

Status: Published
Year: 2022
Journal: Zenodo
Publisher: Zenodo

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The significance of taxonomic publications to understand biodiversity in the digital world

Authors: Donat Agosti

Status: Published
Year: 2022
Journal: Zenodo
Publisher: Zenodo

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Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing

Authors: 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

Status: Published
Year: 2022
Journal: Research Ideas and Outcomes
Volume/Issue: 8
Publisher: Pensoft Publishers

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Discovering known biodiversity

Authors: Donat Agosti

Status: Published
Year: 2022
Publisher: Zenodo

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Nothing in (taxonomic) publishing makes sense except in the light of treatments

Authors: Donat Agosti

Status: Published
Year: 2022
Journal: Zenodo
Publisher: Zenodo

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Plan for Dissemination and Exploitation of Results

Authors: Ana Casino, Laura Tilley

Status: Published
Year: 2021
Deliverable number: D3.2

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Project call definition and execution plan, published via BiCIKL website

Authors: Jerry Lanfear

Status: Published
Year: 2021
Deliverable number: D4.1

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A workflow for bidirectional linking of data from literature to external resources

Authors: Donat Agosti, Terry Catapano, Reto Gmür, Puneet Kishor, Conny Naseband, Guido Sautter, Alexandre Flament, Emilie Pasche, Patrick Ruch, Alexandros Ioannidis-Pantopikos, Jose Benito Gonzalez Lopez Donat Agosti, Jose Benito Gonzalez Lopez

Status: Published
Year: 2022
Deliverable number: D6.3

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Validation tool open-source software release

Authors: Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane

Status: Published
Year: 2023
Deliverable number: D8.2

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Web interface for ELIXIR Contextual Data ClearingHouse

Authors: Kessy Abarenkov, Allan Zirk, Guy Cochrane, Vishnukumar Kadhirvelu, Suran Jayathilaka, Joana Paupério, Olaf Banki, Jerry Lanfear, Filipp Ivanov, Timo Piirmann, Raivo Pöhönen, Urmas Kõljalg

Status: Published
Year: 2022
Deliverable number: D8.3

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Validation and Curation Workbench for Taxonomic Data

Authors: Olaf Bánki, Joe Miller, Donald Hobern, Peter Schalk, Thomas Stjernegaard Jeppesen, Markus Döring

Status: Published
Year: 2022
Deliverable number: D10.3

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Search and link association services: A RESTful API, which will input a link/accession number and return a ranked list of neighbours links with a confidence score

Authors: Soulaine Theocharides, Niki Kyriakopoulou

Status: Published
Year: 2022
Deliverable number: D11.2

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Passage retrieval services: A RESTful API, which will input a set of keywords and return a set of articles/ passages ranked by relevance

Authors: Emilie Pasche, Julien Gobeill, Alexandre Flament, Jeevanthi Liyanapathirana, Pierre-André Michel, Déborah Caucheteur, Esteban Gaillac, Nona Naderi, Patrick Ruch

Status: Published
Year: 2022
Deliverable number: D11.3

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Data Management Plan

Authors: Lyubomir Penev, Teodor Georgiev, Boris Barov, Pavel Stoev, Kristina Hristova

Status: Published
Year: 2021
Deliverable number: D12.9

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Applications for interoperable access to OpenBiodiv through semantically enhanced queries

Authors: Lyubomir Penev, Mariya Dimitrova, Georgi Zhelezov, Teodor Georgiev

Status: Published
Year: 2022
Deliverable number: D6.4

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Project logo, marketing pack and website design and development

Authors: Slavena Peneva, Kristina Hristova, Anna Sapundzhieva, Boris Barov, Pavel Stoev, Margarita Grudova, Iva Kostadinova

Status: Published
Year: 2021
Deliverable number: D3.1

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Web visualisation of mappings between CoL and other checklists

Authors: Olaf Bánki, Joe Miller, Donald Hobern, Thomas Stjernegaard Jeppesen, Markus Döring

Status: Published
Year: 2022
Deliverable number: D10.4

Download (4.33 MB)