2017

  1. Egloff W, Agosti D, Kishor P, Patterson D, Miller JA 2016. Copyright and the Use of Images as Biodiversity Data. Research Ideas and Outcomes 3: e12502. doi: 10.3897/rio.3.e12502

 

2016

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. RDA-CODATA Legal Interoperability Interest Group. (2016). Legal Interoperability of Research Data: Principles and Implementation Guidelines. Zenodo. 10.5281/zenodo.162241
  7. Agosti D. (2016) Shuttleworth Fellowship Application 2016. Research Ideas and Outcomes 2: e11014. doi: 10.3897/rio.2.e11014 .  Video
  8. 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
  9. 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
  10. 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

Preprint

  1. 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
    1.  

2013

  1. 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.
  2. 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
  3. 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
  4. 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 
  5. 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
  6. 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

2012

  1. Penev L, Catapano T, Agosti D, et al. 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); 2012. Article
  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: http://dx.doi.org/10.3897/JHR.27.2961 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

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 Article
  2. Penev L, Roberts D, Smith VS, 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. 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
  2. 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
  3. 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 
  4. 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 doiI: 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

2002

  1. Agosti D, Johnson NF 2002. Taxonomists need better access to published data. Nature 417: 222 doi: 10.1038/417222b Article


 

Input

2013

  1. Hobern et al., 2013. Global Biodiversity Informatics Outlook: Delivering Biodiversity Knowledge in the Information Age, GBIF. PDFAbstract: 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.