Publications

All our publications are published under open licenses. If you are unable to locate a copy, please contact us and we will be happy to send it to you.

2023
  1. Agosti D, Penev L, Ruch P, Benichou L, Ioannidis-Pantopikos A (2023) The Ecosystem of Linked Biodiversity Publications: General Picture of Tools and Services Created by Plazi, Pensoft, MNHN, CETAF, Zenodo, and SIBiLS. Biodiversity Information Science and Standards 7: e110681. https://doi.org/10.3897/biss.7.110681
  2. Benichou L, Agosti D, Egloff W, Hermann E, Kageyama M, Mergen P, Rinaldo C, Buschbom J (2023) Joint statement by CETAF, SPNHC and BHL on DATA within scientific publications: clarification of [non]copyrightability. Research Ideas and Outcomes 9: e115466. https://doi.org/10.3897/rio.9.e115466>
  3. Caucheteur D, Pendlington ZM, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P 2000., COVoc and COVTriage: novel resources to support literature triage, Bioinformatics, 39 (1): btac800, doi: https://doi.org/10.1093/bioinformatics/btac800
  4. Cornwell P (2023) Progress with Repository-based Annotation Infrastructure for Biodiversity Applications. Biodiversity Information Science and Standards 7: e112707. https://doi.org/10.3897/biss.7.112707
  5. Giora J, Agosti D, Ruschel T, Castro JB (2023) Engaging the Scientific Community, Authors and Publishers in FAIR Taxonomic Data Liberation: An Overview of Training Resources at Plazi. Biodiversity Information Science and Standards 7: e110695. https://doi.org/10.3897/biss.7.110695
  6. Pasche E, Gobeill J, Agosti D, Penev L, Groom Q, Georgiev T, Gaillac E, Flament A, Caucheteur D, Michel P-A, Ruch P (2023) From SIBiLS to Biodiversity PMC: Foundations for the One Health Library. Biodiversity Information Science and Standards 7: e111660. https://doi.org/10.3897/biss.7.111660
  7. Pasche E, Agosti D, Penev L, Groom Q, Flament A, Gobeill J, Ruch P (2023) Towards "Biodiversity PMC". Biodiversity Information Science and Standards 7: e111647. https://doi.org/10.3897/biss.7.111647
  8. Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Cochrane G, Pauperio J, Bánki O, Addink W, Kõljalg U, Ruch P, Hristova K, Barov B, Madeira Scauri M, Montinaro S, Vaira L, Fiore N, Bamford E, Arvanitidis C (2023) The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data. Biodiversity Information Science and Standards 7: e111482. https://doi.org/10.3897/biss.7.111482
  9. Sautter G, Agosti D (2023) Bidirectional Linking: Benefits, challenges, pitfalls, and solutions. Biodiversity Information Science and Standards 7: e112344. https://doi.org/10.3897/biss.7.112344
  10. Simoes F, Agosti D, Alvares DJ, Castro JB, Giora J, da Rosa Gonçalves V, Ruschel TP, Sokolowicz C, Wingert JM (2023) Post-Publication Linking. Biodiversity Information Science and Standards 7: e110692. https://doi.org/10.3897/biss.7.110692
  11. Baskauf SJ, Girón Duque JC, Nielsen M, Cobb NS, Singer R, Seltmann KC, Kachian Z, Pérez M, Agosti D, Klompen AML (2023) Implementation Experience Report for Controlled Vocabularies Used with the Audubon Core Terms subjectPart and subjectOrientation. Biodiversity Information Science and Standards 7: e94188. doi: 10.3897/biss.7.94188
2022
  1. 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 (2022) Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing. Research Ideas and Outcomes 8: e97374. doi: 10.3897/rio.8.e97374
  2. Meeus S, Addink W, Agosti D, Arvanitidis C, Balech B, Dillen M, Dimitrova M, González-Aranda JM, Holetschek J, Islam S, Jeppesen TS, Mietchen D, Nicolson N, Penev L, Robertson T, Ruch P, Trekels M, Groom Q (2022) Recommendations for interoperability among infrastructures. Research Ideas and Outcomes 8: e96180. doi: 10.3897/rio.8.e96180
  3. Egloff W 2022. FAIR Works – Eckpunkte eines Urheberrechts für die digitale Welt. Sic!, 2022, 405–424. doi: 10.5281/zenodo.7184216
  4. Egloff W 2022. FAIR Works - Cornerstones for a Copyright in the Digital World. Sic!, 2022, 405–424. doi: 10.5281/zenodo.7181457 (english translation of doi: 10.5281/zenodo.7184216)
  5. Benichou L, Buschbom J, Campbell M, Hermann E, Kvacek J, Mergen P, Mitchell L, Rinaldo C, Agosti D (2022) Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL. Research Ideas and Outcomes 8: e94338. doi: 10.3897/rio.8.e94338
  6. Agosti D, Ioannidis-Pantopikos A (2022) Taxonomic Treatments as Open FAIR Digital Objects. Research Ideas and Outcomes 8: e93709. doi: 10.3897/rio.8.e93709
  7. Gmür R, Agosti D, Sautter G (2022) Synospecies, a Linked Data Application to Explore Taxonomic Names. Biodiversity Information Science and Standards 6: e93707. doi: 10.3897/biss.6.93707
  8. Agosti D, Benichou L, Penev L, Hyam R (2022) A Possible Workflow from New and Legacy Publications to keep the World Flora Online up to date with New Species and Augmenting Taxonomic Treatments. Biodiversity Information Science and Standards 6: e91241. doi: 10.3897/biss.6.91241
  9. Agosti D, Ruch P, Benito Gonzalez Lopez J, Penev L (2022) Enabling Published Taxonomic Data to be used to Address the Biodiversity Crisis: Biodiversity Literature Repository and TreatmentBank. Biodiversity Information Science and Standards 6: e91167. doi: 10.3897/biss.6.91167
  10. Fawcett S, Agosti D, Cole SR, Wright CF 2022. Digital accessible knowledge: Mobilizing legacy data and the future of taxonomic publishing. Bulletin of the Society of Systematic Biologists 1(1): 1-12. doi: 10.18061/bssb.v1i1.8296
  11. Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. doi: 10.3897/rio.8.e81136
2021
  1. Guidoti M, Simões FL, Ruschel TP, DA Rosa Gonçalves V, Sokolowicz C, Agosti D. 2021. Using taxonomic treatments to assess an author's career: the impactful Jocélia Grazia. Zootaxa 4958 (1): 12-33 doi: 10.11646/zootaxa.4958.1.4. BLR: Zenodo Record 4692727
  2. Bénichou, L., Guidoti, M., Gérard, I., Agosti, D., Robillard, T., & Cianferoni, F. (2021). European Journal of Taxonomy: a deeper look into a decade of data. European Journal of Taxonomy, 782(1), 173-196. doi: 10.5852/ejt.2021.782.1597
  3. Abrahamse T, Andrade-Correa MG, Arida C, Galsim R, Häuser C, Price M, Sommerwerk N 2021. The Global Taxonomy Initiative in Support of the Post-2020 Global Biodiversity Framework. CBD Technical Series No. 96. Secretariat of the Convention on Biological Diversity, Montreal, 103 pages. (Plazi: participant) doi: 10.5281/zenodo.5728812
  4. Agosti D, Cornwell P, Bénichou L, Gonzalez J, Herren M, Ruch P 2021. Progress with improving preservation and reuse of scientific research data. iPRES 2021 - 17th International Conference on Digital Preservation, October 19-22, 2021, Beijing, China. manuscript
  5. Waterhouse RM, Adam-Blondon AF, Agosti D et al. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR [version 1; peer review: awaiting peer review]. F1000Research 2021, 10(ELIXIR):1238. doi: 10.12688/f1000research.73825.1
  6. Souza JLP, Fernandes IO, Agosti D, Johnson NF, Baccaro FB 2021. Assessing the efficacy of higher-taxon approach for ant species surveys to improve biodiversity inventories. Animal Conservation 24 (early view) doi: 10.1111/acv.12758. doi: 10.1111/acv.12758
  7. Miller JA, Agosti D, Guidoti M, Rivera Quiroz FA. 2021. Linking and the Role of the Material Citation. Biodiversity Information Science and Standards 5: e75543. doi: 10.3897/biss.5.75543
  8. Agosti D, Egloff W. 2021. Herausfinden, was wir schon wissen. Gfbs Newsletter, 39, 24–31. doi: 10.5281/zenodo.5168465
  9. Guidoti M, Sokolowicz C, Simoes F, Gonçalves V, Ruschel T, Alvares DJ, Agosti D 2021. TreatmentBank: Plazi’s strategies and its implementation to most efficiently liberate data from scholarly publications. Biodiversity Information Science and Standards 5: e75690. doi: 10.3897/biss.5.75690
  10. Van der Jeucht L, Groom Q, Agosti D, Phelps K, Reeder DM, Simmons NB 2021. Using iNaturalist to monitor adherence to best practices in bat handling. Biodiversity Data Journal 9: e68052. doi: 10.3897/BDJ.9.e68052
  11. Upham NS, Poelen JH, Paul D, Groom QJ, Simmons NB, Vanhove MPM, Bertolino S, Reeder DM, Bastos-Silveira C, Sen A, Sterner B, Franz NM, Guidoti M, Penev L, Agosti D 2021. Liberating host–virus knowledge from biological dark data. The Lancet Planetary Health. doi: 10.1016/S2542-5196(21)00196-0
  12. Alvares DJ, Guidoti M, Simoes F, Sokolowicz C, Agosti D 2021. The BHL-Plazi Partnership: Getting data from the 1800s directly into 21st century, reused digital accessible knowledge. Biodiversity Information Science and Standards 5: e75604. doi: 10.3897/biss.5.75604
  13. Gmür R, Agosti D 2021. Synospecies, an application to reflect changes in taxonomic names based on a triple store based on taxonomic data liberated from publication. Biodiversity Information Science and Standards 5: e75641. doi: 10.3897/biss.5.75641
  14. Agosti D 2021. (Re)Discovering Known Biodiversity: Introduction. Biodiversity Information Science and Standards 5: e75491. doi: 10.3897/biss.5.75491
  15. Simoes F, Agosti D, Guidoti M 2021. Delivering Fit-for-Use Data: Quality control. Biodiversity Information Science and Standards 5: e75432. doi: 10.3897/biss.5.75432
  16. Ioannidis-Pantopikos A, Agosti D 2021. Biodiversity Literature Repository: Building the customized FAIR repository by using custom metadata. Biodiversity Information Science and Standards 5: e75147. doi: 10.3897/biss.5.75147
  17. Sokolowicz C, Guidoti M, Agosti D 2021. Discovering Known Biodiversity: Digital accessible knowledge — Getting the community involved. Biodiversity Information Science and Standards 5: e74369. doi: 10.3897/biss.5.74369
  18. Meeus S, Addink W, Agosti D, Arvanitidis C, Dimitrova M, González-Aranda JM, Holetschek J, Islam S, Jeppesen TS, Mietchen D, Robertson T, Sanchez Cano FM, Trekels M, Groom Q (2021) Hacking Infrastructures Together: Towards better interoperability of infrastructures. Biodiversity Information Science and Standards 5: e74325. doi: 10.3897/biss.5.74325
  19. Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Barov B, Hobern D, Banki O, Addink W, Köljalg U, Ruch P, Copas K, Mergen P, Güntsch A, Benichou L, Gonzalez Lopez JB 2021. Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective. Biodiversity Information Science and Standards 5: e74233. doi: 10.3897/biss.5.74233
2020
  1. Mottin L, Ruch P, Mottaz A, Naderi N, Caucheteur D, Agosti D, Matentzoglu N, Michel PA, Pendlington Z, Roncaglia P 2020. CoVoc Coronavirus Vocabulary
  2. Rivera-Quiroz A, Petchaard B, Miller JA 2020. Mining data from legacy taxonomic literature and application for sampling spiders of the Teutamus group (Araneae; Liocranidae) in Southeast Asia. Scientific Reports 10: 15787. doi: 10.1038/s41598-020-72549-8
  3. Dimitrova M, Poelen J, Zhelezov G, Georgiev T, Agosti D, Penev L 2020. Semantic publishing enables text mining of biotic interactions. Biodiversity Information Science and Standards 4: e95036. doi: 10.3897/biss.4.59036
  4. Agosti D, Guidoti M, Sautter G 2020. Liberating the Richness of Facts implicit in taxonomic Publication: The Plazi Workflow . Biodiversity Information Science and Standards 4: e59179. doi: 10.3897/biss.4.59179
  5. Agosti D, Guidoti M, Catapano T, Ioannidis-Pantopikos A, Sautter G 2020. The Standards behind the Scenes: Explaining data from the Plazi workflow. Biodiversity Information Science and Standards 4: e59178. doi: 10.3897/biss.4.59178
  6. Upham NS, Agosti D, Poelen J, Penev L, Paul D, Reeder DM, Simmons NB, Csorba G, Groom Q, Dimitrova M, Miller JT 2020. Liberating Biodiversity Data From COVID-19 Lockdown: Toward a knowledge hub for mammal host-virus information. Biodiversity Information Science and Standards 4: e59199. doi: 10.3897/biss.4.59199
2019
  1. Swiss Academies of Arts and Sciences (2019) Open Science in Switzerland: Opportunities and Challenges. Swiss Academies Factsheets 14 (2). PDF
  2. Chester C, Agosti D, Sautter G, Catapano T, Martens K, Gérard I, Bénicou L 2019. EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature. European Journal of Taxonomy 586: 1-22. doi: 10.5852/ejt.2019.586
  3. Saarenma H, Agosti D, Dillen M, Egloff W, Gagnier P-Y, Groom Q, Hardisty A, Raes N. 2019. Open access implementation guidelines for DiSSCo. Deliverable D6.5. ICEDIG, Helsinki. doi: 10.5281/zenodo.3465285
  4. Agosti D, Nielsen LH, Dillen M, Groom Q. 2019. Digitisation infrastructure design for Zenodo. Deliverable D6.3. ICEDIG, Helsinki. doi: 10.5281/zenodo.3346782
  5. Plazi. 2019. Policy Component of ICEDIG Project Website. Deliberable D7.1. ICEDIG, Helsinki. doi: 10.5281/zenodo.3484047
  6. Bénichou L, Gerard I, Chester C, Agosti D. 2019. The European Journal of Taxonomy: Enhancing taxonomic publications for dynamic data exchange and navigation. Biodiversity Information Science and Standards 3: e37199. doi: 10.3897/biss.3.37199
  7. Agosti D, Catapano T, Sautter G, Kishor P, Nielsen L, Ioannidis-Pantopikos A, Bigarella C, Georgiev T, Penev L, Egloff W. 2019. Biodiversity Literature Repository (BLR), a repository for FAIR data and publications. Biodiversity Information Science and Standards 3: e37197. doi: 10.3897/biss.3.37197
  8. Nieva de la Hidalga A, Cazenave N, Agosti D, Wu Z, Dillen M, Nielsen L. 2019. Use of European Open Science Cloud and National e-Infrastructures for the Long-Term Storage of Digitised Assets from Natural History Collections. Biodiversity Information Science and Standards 3: e37164. doi: 10.3897/biss.3.37164
  9. Dillen M, Groom Q, Agosti D, Nielsen L. 2019. Zenodo, an Archive and Publishing Repository: A tale of two herbarium specimen pilot projects. Biodiversity Information Science and Standards 3: e37080. doi: 10.3897/biss.3.37080
  10. Miller JA, Braumuller Y, Kishor P, Shorthouse DP, Dimitrova M, Sautter G, Agosti A. 2019. Mobilizing Data from Taxonomic Literature for an Iconic Species (Dinosauria, Theropoda, Tyrannosaurus rex). Biodiversity Information Science and Standards 3: e37078. doi: 10.3897/biss.3.37078
  11. Agosti D, Catapano T, Sautter G, Egloff W. 2019. The Plazi Workflow: The PDF prison break for biodiversity data. Biodiversity Information Science and Standards 3: e37046. doi: 10.3897/biss.3.37046
  12. Hardisty AR, Michener WK, Agosti D,Alonso García, E, Bastine L, Belbin L, Bowserg A, Buttigieg PL, Canhos DAL, Egloff W, De Giovanni R, Figueira R, Groomk Q, Guralnick, RP, Hobern D, Hugo W,Koureas D, Ji L, Kissling WD 2018. The Bari Manifesto: An interoperability framework for essential biodiversity variables. Ecological Informatics 49: 22-31. doi: 10.1016/j.ecoinf.2018.11.003
2018
  1. Agosti D 2018. Bezahlschranken für Schnappschüsse? Neue Zürcher Zeitung, Gastkommentar, 29.11.2018. link
  2. Penev L, Agosti D, Georgiev T, Senderov V, Sautter G, Catapano T, Stoev P 2018. The Open Biodiversity Knowledge Management (eco-)System: Tools and services for extraction, mobilization, handling and re-use of data from the published literature. Biodiversity Information Science and Standards 2: e25748. doi: 10.3897/biss.2.25748
  3. Hardisty AR, Michener WK, Agosti D, .. Egloff W, … (26 authors) 2018. The Bari Manifesto: An interoperability framework for essential biodiversity variables. Ecological Informatics 49: 23-31. doi: 10.1016/j.ecoinf.2018.11.003
  4. Egloff W 2018. Copyright stories: Sketches on the political economy of copyright. Advocomplex, Bern, Switzerland. English translation of Geschichten vom Urheberrecht oder: Skizzen zur politischen Ökonomie des Copyright" by Stämpfli Verlag AG Bern ISBN 978-3-033-06835-3. doi: 10.5281/zenodo.1412365
  5. Kissling WD, Walls R, … Agosti D, .. Egloff W, … (29 authors) 2018. Towards global data products of Essential Biodiversity Variables on species traits. Nature Ecology and Evolution 2018DA. doi: 10.1038/s41559-018-0667-3
  6. Senderov V, Simov K, Franz N, Stoev P, Catapano T, Agosti D, Sautter G, Morris RA, Penev L 2018. OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system. Journal of Biomedical Semantics 9: 5. doi: 10.1186/s13326-017-0174-5
  7. Esterman B, Agosti D, Cretton F, Cochard J-L, Gmür R, Hellstern M, Hladky D, Mabbett A, Mastrandrea E, Plitzker M, Prongué N, Stinson A, Weinberg B 2018. eCH-0205 Linked Open Data. eCH E-Government Standards publication eCH-0205. doi: 10.5281/zenodo.2641710
  8. Côtez E, Mabille A, Chester C, Rocklin M, Deroin T, Desutter-Grandcolas L, Lesur J Merle D, Robillard R, Bénichou 2018. 1802-2018: a 220-year history of the Muséum periodicals. Adansonia 40(1): 1-42. (description of Plazi involvement on p.28 onwards) PDF , doi: 10.5252/adansonia2018v40a1
2017
  1. Bingham H, Doudin M, Weatherdon LV, Despot-Belmonte K, Wetzel FT, Groom Q, Lewis E, Appeltrans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K Kim H, Archambeau AS, Häuser C, Schmeller DS, Ilse Geijzendorffer, Camacho AG, Guerra C, Robertson T, Runnel V, Valland N, Martin CS 2017. The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcome 3: e14059. doi: 10.3897/rio.3.e14059
  2. Despot-Belmonte K, Doudin M, Groom Q, Wetzel FT, Agosti D, Jacobsen K, Smirnova L, Weatherdon LV, Robertson T, Penev L, Regan E, Hoffmann A, MacSharry Y, Martin CS 2017. EU BON’s contributions towards meeting Aichi Biodiversity Target 19. Research Ideas and Outcome 3: e14013. doi: 10.3897/rio.3.e14013
  3. Senderov V, Georgiev TA, Agosti D, Catapano T, Sautter G, Ó Tuama É, Franz N, Simov K, Stoev P, Penev L 2017. OpenBiodiv Computer Demo: an Implementation of a Semantic System Running on top of the Biodiversity Knowledge Graph. Proceedings of TDWG 1: e20193. doi: 10.3897/tdwgproceedings.1.20193
  4. Kissling D (and 35 coauthors) 2017. Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biological Reviews. doi: 10.1111/brv.12359
  5. Despot-Belmonte K, Doudin M, Groom Q, Wetzel FT, Agosti D, Jacobsen K, Smirnova L, Weatherdon LV, Robertson T, Penev L, Regan E, Hoffmann A, MacSharry B, Shennan-Farpon Y, Martin CS 2017. EU BON’s contributions towards meeting Aichi Biodiversity Target 19. Research Ideas and Outcomes 3: e14013. doi: 10.3897/rio.3.e14013
  6. Despot-Belmonte K, Bingham Heather, Doudin M, Weatherdon L, Regan E, Lewis E, Scrimgeour R, Bubb Ph, Pan X, Martin C, Wetzel F, Hoffmann A, Häuser Ch, Penner J, Vohland K, Geijzendorffer I, Schmeller D, Agosti D, Arvanitidis Ch, Thalmann A, Underwood E, Tucker G, Grace M, Rose D, Penev L, Jacobsen K 2017. Deliverable 7.4 (D7.4). Strategies and business plan for regional and global biodiversity information infrastructures. M52. EU BON, Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin Germany. doi: 10.5281/zenodo.569819
2016
  1. Senderov V, Georgiev TA, Agosti D, Catapano T, Sautter G, Ó Tuama É, Franz N, Simov K, Stoev P, Penev L 2016. The Open Biodiversity Knowledge Management System: A Semantic Suite Running on top of the Biodiversity Knowledge Graph. TDWG 2016 conference presentation abstract. doi: 10.5281/zenodo.841648
  2. Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvantidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel, Senderov V, Teaca A, Tsompanou M 2016. EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. doi: 10.3897/rio.2.e9774
  3. Koureas D, Hardisty A, Vos R, Agosti D, Arvanitidis C, Bogatencov P, Buttigieg P, de Jong Y, Horvath F, Gkoutos G, Groom Q, Kliment T, Kõljalg U, Manakos I, Marcer A, Marhold K, Morse D, Mergen P, Penev L, Pettersson L, Svenning J, van de Putte A, Smith V 2016. Unifying European Biodiversity Informatics (BioUnify). Research Ideas and Outcomes 2: e7787. doi: 10.3897/rio.2.e7787
  4. Egloff W, Agosti D, Patterson D, Hoffmann A, Mietchen D, Kishor P, Penev L 2016. Data Policy Recommendations for Biodiversity Data. EU BON Project Report. Research Ideas and Outcomes 2: e8458. doi: 10.3897/rio.2.e8458
  5. Alonso LA, Agosti D 2016. Ants. In: Larsen TH (ed.) 2016. Core Standardized Methods for Rapid Biological Field Assessment. Conservation International, Arlington, VA. pp. doi: 10.5281/zenodo.50824
  6. Smirnova L, Mergen P, Groom QJ, De Wever, A, Penev L, Stoev P, Pe’er I, Runnel V, Camacho AC, Vincent T, Agosti D, Arvanitidis C, García FJB, Saarenmaa H 2016. Data sharing tools adopted by the European Biodiversity Observation Network Project. Research Ideas and Outcomes 2: 2: e9390 doi: 10.3897/rio.2.e9390
  7. RDA-CODATA Legal Interoperability Interest Group. 2016. Legal Interoperability of Research Data: Principles and Implementation Guidelines. Zenodo. 10.5281/zenodo.162241
  8. Agosti D. (2016) Shuttleworth Fellowship Application 2016. Research Ideas and Outcomes 2: e11014. doi: 10.3897/rio.2.e11014 . Video
  9. Agosti D, Sautter G, Catapano T, Kishor P, Penev L 2016. Deliverable 3.3 (D3.3): Updated release and report on publication data-mining software. EU BON, Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin Germany. doi: 10.5281/zenodo.187446
  10. Kohlbecker A, Güntsch A, Müller A, von Raab-Straube E, Wetzel F, Ring C, Kempa M, Stoev P, De Wever A, Sautter G, Agosti D 2016. Deliverable 1.4 (D1.4): Summary report of operational EU BON services and data provision for the European taxonomic backbone. EU BON, Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin Germany. doi: 10.5281/zenodo.182122
  11. Ronquist F, Skyttner M, Kõljalg U, Röppert D, Penev L, Stoev P, Peer I, Stein M, Calabuig I, Agosti D, Kempa M 2016. Deliverable 1.3 (D1.3): Systems for mobilizing and managing collection-based data (specimen + DNA-data) fully integrated. EU BON, Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin Germany. doi: 10.5281/zenodo.189960
  12. Egloff W, Agosti D, Kishor P, Patterson D, Miller JA 2016. Copyright and the Use of Images as Biodiversity Data. bioRxiv doi: 10.1101/087015 (preprint submitted Nov 12; article submitted to PLoS Biology Nov 12; resubmitted Dec 3 to Rio Journal; accepted article doi: 10.3897/rio.3.e12502)
2015
  1. Dikow T, Agosti D. 2015. Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae). Biodiversity Data Journal 3: e5707 (06 Oct 2015. doi: 10.3897/BDJ.3.e5707
  2. Egloff W, Agosti D, Patterson D, Penev L 2015. EU BON Policy Brief on Open Data. Website, doi: 10.5281/zenodo.188391
  3. Guralnick RP, Cellinese N, Deck J, Pyle RL, Kunze J, Penev L, Walls R, Hagedorn G, Agosti D, Wieczorek J, Catapano T, Page R. 2015 Community next steps for making globally unique identifiers work for biocollections data. ZooKeys 494: 133-154 doi: 10.3897/zookeys.494.9352
  4. Miller JA, Georgiev T, Stoev P, Sautter G, Penev L 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
  5. Miller JA, Agosti D, Penev L, Sautter G, Georgiev T, Catapano T, Patterson D, King D, Pereira S, Vos RA, Sierra S 2015. Integrating and visualizing primary data from prospective and legacy taxonomic literature. Biodiversity Data Journal 3: e5063 (12 May 2015) doi: 10.3897/BDJ.3.e5063
2014
  1. Egloff W 2014. Access to scientific and technical information - between social needs and private interests. In: Gartska,H., und Coy,W. (Hg.), Wovon –für wen -wozu. Systemdenken wider die Diktatur der Daten.Helmholtz-Zentrum für Kulturtechnik und Humboldt-Universität Berlin 2014, S. 349 –373. doi: 10.5281/zenodo.10597
  2. Agosti D 2014. Some thoughts after the Cusco meeting. Hamuli 5 (2): 4-5. doi: 10.5281/zenodo.11671
  3. Egloff W, Patterson D, Agosti D, Hagedorn G 2014. Open exchange of scientific knowledge and European copyright: The case of biodiversity information. ZooKeys 414, 109-135. doi: 10.3897/zookeys.414.7717
  4. Egloff W, 2014. Der Zugang zu Fachinformationen – zwischen gesellschaftlicher Notwendigkeit und privatem Verwertungsinteresse In: Hansjürgen Garstka, Wolfgang Coy (Hg.), Wovon - für wen - wozu. Systemdenken wider die Diktatur der Daten, Helmholtz-Zentrum für Kulturtechnik, Humboldt-Universität zu Berlin, S. 349-373, ISBN 978-3-86004-298-4. doi: 10.5281/zenodo.10378
  5. Interview. Donat Agosti on big data, copyright and attribution in taxonomy. BIOME April 9, 2014 (This is a followup of the Patterson et al. paper. Though it is credited to Donat (because of his role as editor of BMC research notes?), it has a major input from Paddy and Willi.
  6. Patterson DJ, Egloff W, Agosti D, Eades D, Franz N, Hagedorn G, Rees J, Remsen DP 2014. Scientific names of organisms: attribution, rights, and licensing . BMC Research Notes 2014, 7:79 doi: 10.1186/1756-0500-7-79, most viewed.
  7. Vos R and 37 co-authors 2014. Enriched biodiversity data as a resource and service. Biodiversity Data Journal 2, e1125 doi: 10.3897/bdj.2.e1125
  8. Sautter G, Böhm K 2014. Improved bibliographic reference parsing based on repeated patterns. International Journal on Digital Libraries 14.1-2: 59-80. doi: 10.1007/s00799-014-0110-6
  9. pro-iBiosphere 2014. Open Biodiversity Knowledge Management System (OBKMS). Final OBKMS brochure. doi: 10.5281/zenodo.191785
  10. Saarenmaa H, Camacho A G, Ó Tuama É, Agosti D, Bailly N, Calderisi M, Drucker D, Güntsch A, Jacobsen K, Kempa M, Kõljalg U, Mergen P, Peer I, Penev L, Valland N, de Wever A 2014. Deliverable 2.1 (D2.1): Architectural design, review and guidelines for using standards. M14. EU BON FP7-308454. doi: 10.5281/zenodo.292208
  11. Egloff W, Agosti D, Morris RA, Groom Q, Güntsch A, Hovenkamp P, Mantel J-W, Sierra S, Mietchen D, Paton A, Patterson D, Stoev P, Macklin J 2014. D2.4.2 Draft policy on Open Access for data and information. Pro-iBiosphere. doi: 10.5281/zenodo.10879
2013
  1. Karol Marhold, Tod Stuessy, Mariam Agababian, Donat Agosti, Mac H. Alford, Ana Crespo, Jorge V. Crisci, Laurence J. Dorr, Zuzana Ferencová, David Frodin, Dmitry V. Geltman, Norbert Kilian, H. Peter Linder, Lucia G. Lohmann, Christoph Oberprieler, Lyubomir Penev, Gideon F. Smith, Wayt Thomas, Melissa Tulig, Nicholas Turland, Xian-Chun Zhang (2013) The Future of Botanical Monography: Report from an international workshop, 12–16 March 2012, Smolenice, Slovak Republic. doi: 10.1002/tax.621003
  2. Agosti D, Catapano T, Cora J, Güntsch A, Groom Q, Hagedorn G, Kirkup D, Macklin J, Mietchen Da, Miller J, Morris R, Patton A, Penev L, Patterson D, Sierra S 2013. D3.2.2 Report on the state and quality of biosystematics documents and survey reports. pro-IBiosphere. doi
  3. Groom Q, Agosti D, Güntsch A, Hovenkamp P, Kralt E, Mietchen D, Paton A, Sierra S 2013. D2.3 The Use of e-Tools among Producers of Taxonomic Knowledge (Proof of concept report on the use of e-tools) Deliverable. pro-iBiosphere. doi
  4. Hardisty A, Roberts D. and The Biodiversity Informatics Community, 2013. A decadal view of biodiversity informatics: challenges and priorities. BMC Ecology 2013, 13:16 doi: 10.1186/1472-6785-13-16. Abstract: Biodiversity informatics plays a central enabling role in the research community’s efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species. It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible. This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens’ science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.
  5. Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T L P , Mueller G, Dikow T, Helgen K M, Frank J, Agosti D, Roberts D, Penev L. 2013. Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal. 09/2013; 1. doi: 10.3897/BDJ.1.e995
  6. King D, Sautter G, Morse D, Penev L, Biserkov J, Georgiev T, Roberts D, Smith V 2013. Bibliography of live: a freely accessible bibliography of every paper ever published. Poster, TDWG 2013, Florence, Italy, October 28 - November 1, 2013. doi: 10.5281/zenodo.181364
  7. Tschöppe O, Macklin JA, Morris RA, Suhrbier L, Berendsohn WG 2013. Annotating biodiversity data via the Internet. Taxon, 62(2): 1248-1258. doi: 10.12705/626.4
  8. Sautter G, Böhm K 2013. High-throughput crowdsourcing mechanisms for complex tasks. Social Network Analysis and Mining, 3(4): 873-888. doi: 10.1007/s13278-013-0114-z; doi (preprint): 10.5281/zenodo.188564
  9. Morris RA, Barve V, Carausu M, Chavan V, Cuadra J, Freeland C, Hagedorn G, Leary P, Mozzherin D, Olson A, Riccardi G, Teage I, Whitebread G 2013. Discovery and publishing of primary biodiversity data associated with multimedia resources: The Audubon Core strategies and approaches. Biodiversity Informatics 8(2): 185-197. doi: 10.17161/bi.v8i2.4117
  10. Sautter G, various 2013. D7.3 - Literature search. ViBRANT project deliverable d7.3, http://wiki.scratchpads.eu/w/D73report
  11. Hobern et al., 2013. Global Biodiversity Informatics Outlook: Delivering Biodiversity Knowledge in the Information Age, GBIF. PDF . Abstract: Much progress has been made in the past ten years to fulfil the potential of biodiversity informatics. However, it is dwarfed by the scale of what is still required. The Global Biodiversity Informatics Outlook (GBIO) offers a framework for reaching a much deeper understanding of the world’s biodiversity, and through that understanding the means to conserve it better and to use it more sustainably. The GBIO identifies four major focal areas, each with a number of core components, to help coordinate efforts and funding. The co-authors, from a wide range of disciplines, agree these are the essential elements of a global strategy to harness biodiversity data for the common good.
2012
  1. Penev L, Catapano T, Agosti D, Georgiev T, Sautter, G, Stoev P (2012). Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2012 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US). doi: [10.5281/zenodo.804247](https://doi.org/10.5281/zenodo.804247); [Article](http://www.ncbi.nlm.nih.gov/books/NBK100351/)
  2. Miller J, Dikow T, Agosti D, Sautter G, Catapano T, Penev L, Zhang Z-Q, Pentcheff D, Pyle R, Blum S, Parr C, Freeland C, Garnett T, Ford LS, Muller B, Smith L, Strader G, Georgiev T & Bénichou L 2012. From taxonomic literature to cybertaxonomic content. BMC Biology, 10: 87. doi: 10.1186/1741-7007-10-87
  3. Seltman KC, … Agosti D., Johnson N and 35 co-authors. 2012. A hymenopterist’s guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. doi: 10.3897/jhr.27.2961

  4. Thessen AE, Patterson DJ, Murray SA 2012. The taxonomic significance of species that have only been observed once: The genus Gymnodinium (Dinoflagellata) as an Example. PLoS One 7 (8): e44015. doi: 10.1371/journal.pone.0044015

2011
  1. Catapano T, Hobern D, Lapp H, Morris RA, Morrison N, Noy N, Schildhauer M, Thau D 2011. Recommendations for the Use of Knowledge Organisation Systems by GBIF. Report
  2. Chavan V, Penev L 2011. The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics, 12 (Suppl 15): S2. doi: 10.1186/1471-2105-12-S15-S2 highly accessed
  3. Hagedorn G, Mietchen D, Morris RA, Agosti D, Penev L, Berendsohn W, Hobern D 2011. Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information. ZooKeys 150: 127-149. doi: 10.3897/zookeys.150.2189
  4. Kress W, Penev L 2011. Innovative electronic publication in plant systematics: PhytoKeys and the changes to the “Botanical Code” accepted at the XVIII International Botanical Congress in Melbourne. PhytoKeys 6: 1-4. doi: 10.3897/phytokeys.6.2063
  5. Lapp H, Morris RA, Catapano T, Hobern D, Morrison N 2011. Organizing Our Knowledge of Biodiversity. ASIST Bulletin, 37:38-42. Article
  6. Moritz T, Krishnan S, Roberts D, Ingwersen P, Agosti D, Penev L, Cockerill M, Chavan V 2011. Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group. BMC Bioinformatics 2011, 12(Suppl 15):S1. doi: 10.1186/1471-2105-12-S15-S1
  7. Penev L, Lyal CHC, Weitzman A, Morse DR, King D, Sautter G, Georgiev T, Morris RA, Catapano T, Agosti D 2011. XML schemas and mark-up practices of taxonomic literature. ZooKeys 01/2011. doi: 10.3897/zookeys.150.2213
  8. Penev L, Hagedorn G, Mietchen D, Georgiev T, Stoev P, Sautter G, Agosti D, Plank A, Balke M, Hendrich L, Erwin T 2011. Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID. Zookeys 90: 1-12, doi: 10.3897/zookeys.90.1369
  9. Thessen AE, Patterson DJ 2011. Data issues in the life sciences. ZooKeys 150: 15-51 doi: 10.3897/zookeys.150.1766
  10. Sautter G.2011. Efficient Conversion of Scientific Legacy Documents into Semantic Web Resources using biosystematics as a working example. PhD Thesis, Karlsruher Intitut für Technologie. 10.5281/zenodo.11066341
2010
  1. Catapano T 2010. TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. Proceedings of the Journal Article Tag Suite Conference 2010 doi: 10.5281/zenodo.3484285 Article
  2. Penev L, Roberts D, Smith VS, Agosti D, Erwin T. 2010. Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research. ZooKeys 50: i-iv. doi: 10​.3897/zookeys.50.543
  3. Penev L, Agosti D, Georgiev T, Catapano T, Miller J, Blagoderov V, Roberts D, Smith VS, Brake I, Ryrcroft S, Scott B, Johnson NF, Morris RA, Sautter G, Chavan V, Robertson T, Remsen D, Stoev P, Parr C, Knapp S, Kress WJ, Thompson FC, Erwin T. 2010. Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. ZooKeys 50: 1-16. doi: 10​.3897/zookeys.50.538
  4. Sautter G, Böhm K, Kühne C, Mathäss T 2010. Process Tron: Efficient semi-automated markup generation for scientific documents. Proceedings of the 10th Annual Joint Conference on Digital Libraries, 21-28. doi (preprint): 10.5281/zenodo.55638
2009
  1. Agosti D, Egloff W 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, [2:53]. doi: 10.1186/1756-0500-2-53, hihgly accessed
  2. Sautter G, Böhm K, Agosti D, Klingenber C 2009. Creating digital resources from legacy documents: An experience report from the biosystematics domain. pp 738-752 in: The Semantic Web: Research and Applications. Lecture Notes in Computer Science 5554. Aroyo L et al. (eds). Springer Links. doi: 10.1007/978-3-642-02121-3_54 Article
2008
  1. Penev L, Erwin T, Thompson CF, Sues H-D, Engel M, Agosti D, Pyle R, Ivie M, Assmann T, Henry T, Miller J, Ananjeva N, Casale A, Lourenco W, Golocatch S, Fagerholm H-P, Taili S, Alonso-Zarazaga M, Nieukerken E von 2008. ZooKeys, unlocking Earth’s incredible biodiversity and building a sustainable bridge into the public domain: From “print-based” to “web-based” taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper. ZooKeys 1: 1-7. doi: 10.3897/zookeys.1.11
2007
  1. Catapano T, Agosti D, Sautter G 2007. Plazi.org: Using DSpace as a repository for species descriptions. Dspace User Group Meeting in Rome, Rome, Italy, 17-19 October 2007 doi: 10.5281/zenodo.3552076
  2. Agosti D, Klingenberg C, Sautter G, Johnson N, Stephenson C, Catapano T 2007. Why not let the computer save you time by reading the taxonomic papers for you? Biológico, São Paulo, 69, suplemento 2, 545-548, 2007. doi: 10.5281/zenodo.15584
  3. Sautter G, Böhm K, Agosti D 2007. A quantitative comparison of XML schemas for taxonomic publications. Biodiversity Informatics 4: 1-13. doi: 10.17161/bi.v4i0.36
  4. Sautter G, Böhm K, Padberg F, Tichy W. 2007. Empirical Evaluation of Semi-automated XML Annotation of Text Documents with the GoldenGATE Editor. In. Kovacs L, Fuhr N, Meghini c (eds). Research and Advanced Technology for Digital Libraries: 11th European Conference, ECDL 2007, Budapest, Hungary, September 16-21, 2007. Proceedings. Spinger Berlin, Heidelberg, pp 357-367. doi: 10.1007/978-3-540-74851-9_30. Preprint
  5. Sautter G, Böhm K, Agosti D 2007. Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor. Pacific Symposium on Biocomputing 12: 391-402. doi (preprint): 10.5281/zenodo.55665
2006
  1. Agosti D 2006. Biodiversity data are out of local taxonomists' reach. Nature 439, 392. doi: 10.1038/439392a Article
  2. Sautter G, Böhm K, Agosti D 2006. A combining approach to find all taxon names (FAT) in legacy biosisystematics literature. Biodiversity Informatics 3, 41-53. doi: 10.17161/bi.v3i0.34
  3. Agosti, D 2006. ‘Free’ access to research should not be limited. SicDev.Net. Article
2005
  1. Polaszek A, Agosti D, 24 co-authors 2005. A universal register for animal names. Nature, 437: 477 doi: 10.1038/437477a, Article
2003
  1. Agosti D 2003. Encyclopedia of life: should species description equal gene sequence? Trends in Ecology and Evolution 18(6): 273. doi: 10.1016/S0169-5347(03)00099-5 Article
  2. Moritz T (PI) 2003. Collaborative Research: Development of new digital library applications in the context of a basic ontology for biosystematics information using the literature of entomology (ants). Proposal to US NSF Division of Information and Intelligent Systems (IIS). Award IIS-0241229, submitted April 15, 2003; start date April 1, 2004. doi: 10.5281/zenodo.580296
2002
  1. Agosti D, Johnson NF 2002. Taxonomists need better access to published data. Nature 417: 222 doi: 10.1038/417222b Article