A global perspective on decadal challenges and priorities in biodiversity informatics

Annals of Occupational and Environmental Medicine

A Townsend Peterson¹  Jorge Soberón¹  Leonard Krishtalka¹ 

[1] Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence 66045, KS, USA

关键词: Capacity-building;    Training;    Infrastructure;    Data;    Biodiversity informatics;   

Others  :  1210165
DOI  :  10.1186/s12898-015-0046-8

 received in 2014-09-09, accepted in 2015-04-24,  发布年份 2015

【 摘 要 】

Biodiversity informatics is a field that is growing rapidly in data infrastructure, tools, and participation by researchers worldwide from diverse disciplines and with diverse, innovative approaches. A recent ‘decadal view’ of the field laid out a vision that was nonetheless restricted and constrained by its European focus. Our alternative decadal view is global, i.e., it sees the worldwide scope and importance of biodiversity informatics as addressing five major, global goals: (1) mobilize existing knowledge; (2) share this knowledge and the experience of its myriad deployments globally; (3) avoid ‘siloing’ and reinventing the tools of knowledge deployment; (4) tackle biodiversity informatics challenges at appropriate scales; and (5) seek solutions to difficult challenges that are strategic.

【 授权许可】

   
2015 Peterson et al.

【 图 表 】

Figure1.

Figure2.

【 参考文献 】

• [1]Peterson AT, Knapp S, Guralnick R, Soberón J, Holder MT. The big questions for biodiversity informatics. Syst Biodivers. 2010; 8:159-168.
• [2]Hardisty A, Roberts D. A decadal view of biodiversity informatics: challenges and priorities. BMC Ecol. 2013; 13:16.
• [3]Bini LM, Diniz-Filho JAF, Rangel TF, Bastos RP, Pinto MP. Challenging Wallacean and Linnean shortfalls: knowledge gradients and conservation planning in a biodiversity hotspot. Divers Distrib. 2006; 12:475-482.
• [4]Whittaker RJ, Riddle BR, Hawkins BA, Ladle RJ. The geographical distribution of life and the problem of regionalization: 100 years after Alfred Russel Wallace. J Biogeogr. 2013; 40:2209-2214.
• [5]Gaston KJ, May RM. Taxonomy of taxonomists. Nature. 1992; 356:281-282.
• [6]Soberón JM, Sarukhán JK. A new mechanism for science-policy transfer and biodiversity governance? Environ Conserv. 2009; 36:265-267.
• [7]Buffetaut E. Tertiary ground birds from Patagonia (Argentina) in the Tournouër collection of the Muséum National d’Histoire Naturelle, Paris. Bull Soc Geol Fr. 2014; 185:207-214.
• [8]Den Tex R-J, Leonard J. The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala). Phylogenet Phylogenomics Syst. 2014; 2:16.
• [9]Boulangeat I, Gravel D, Thuiller W. Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances. Ecol Lett. 2012; 15(6):584-593.
• [10]Garcia RA, Cabeza M, Rahbek C, Araújo MB. Multiple dimensions of climate change and their implications for biodiversity. Science. 2014; 344:1247579.
• [11]Pignal M, Romaniuc-Neto S, Souza SD, Chagnoux S, Canhos DAL. Saint-Hilaire virtual herbarium, a new upgradeable tool to study Brazilian botany. Adansonia. 2012; 35:7-18.
• [12]Navarro-Sigüenza AG, Peterson AT, Gordillo-Martínez A. The big questions for biodiversity informatics. Bull Br Ornithol Club. 2003; 123A:207-225.
• [13]King N, Krishtalka L, Chavan V. Thoughts on implementation of the recommendations of the GBIF Task Group on a Global Strategy and Action Plan for Mobilisation of Natural History Collections Data. Biodivers Inform. 2010; 7:72-76.
• [14]Fontaine B, van Achterberg K, Alonso-Zarazaga MA, Araujo R, Asche M, Aspöck H et al.. New species in the old world: Europe as a frontier in biodiversity exploration, a test bed for 21st century taxonomy. PLoS One. 2012; 7:e36881.
• [15]Hobern D, Apostolico A, Arnaud E, Bello JC, Canhos D, Dubois G et al.. Global biodiversity informatics outlook: delivering biodiversity knowledge in the information age. Global Biodiversity Information Facility, Copenhagen; 2013.
• [16]Bafna S, Humphries J, Miranker DP. Schema driven assignment and implementation of life science identifiers (LSIDs). J Biomed Inform. 2008; 41:730-738.
• [17]Page RDM. LSID Tester, a tool for testing Life Science Identifier resolution services. Source Code Biol Med. 2008; 3:2.
• [18]Page RDM. Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Brief Bioinform. 2008; 9:345-354.
• [19]Roberts D, Chavan V. Standard identifier could mobilize data and free time. Nature. 2008; 453:449-450.
• [20]Chapman AD. Principles of data quality, version 1. Global Biodiversity Information Facility, Copenhagen; 2005.
• [21]Chapman AD. Principles and methods of data cleaning: primary species and species-occurrence data. Global Biodiversity Information Facility, Copenhagen; 2005.
• [22]Morris RA, Barve V, Carausu M, Chavan V, Cuadra J, Freeland C et al.. Discovery and publishing of primary biodiversity data associated with multimedia resources: the Audubon core strategies and approaches. Biodivers Inform. 2013; 8:185-197.
• [23]Beck J, Ballesteros-Mejia L, Nagel P, Kitching IJ. Online solutions and the ‘Wallacean shortfall’: what does GBIF contribute to our knowledge of species’ ranges? Divers Distrib. 2013; 19:1043-1050.
• [24]Graham C, Ferrier S, Huettman F, Moritz C, Peterson AT. New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol Evol. 2004; 19:497-503.
• [25]Soberón J, Arriaga L, Lara L. Issues of quality control in large, mixed-origin entomological databases. In: Towards a global biological information infrastructure. Saarenmaa H, Nielsen E, editors. European Environment Agency, Copenhagen; 2002: p.15-22.
• [26]Gaiji S, Chavan V, Ariño AH, Otegui J, Hobern D, Sood R et al.. Content assessment of the primary biodiversity data published through GBIF network: status, challenges and potentials. Biodivers Inform. 2013; 8:94-172.
• [27]Ballesteros-Mejia L, Kitching IJ, Jetz W, Nagel P, Beck J. Mapping the biodiversity of tropical insects: species richness and inventory completeness of African sphingid moths. Glob Ecol Biogeogr. 2013; 22:586-595.
• [28]Yesson C, Brewer PW, Sutton T, Caithness N, Pahwa JS, Burgess M et al.. How global is the global biodiversity information facility? PLoS One. 2007; 2:e1124.
• [29]GBIF annual report 2013. Global Biodiversity Information Facility, Copenhagen; 2014.
• [30]Vollmar A, Macklin JA, Ford L. Natural history specimen digitization: challenges and concerns. Biodivers Inform. 2010; 7:93-112.
• [31]Beaman RS, Cellinese N. Mass digitization of scientific collections: new opportunities to transform the use of biological specimens and underwrite biodiversity science. ZooKeys. 2012; 209:7.
• [32]Chalmers NR. Monitoring and inventorying biodiversity: collections, data and training. In: Biodiversity, science and development: towards a new partnership. Castri FD, Younes T, editors. CAB International, Wallingford; 1996: p.171-179.
• [33]Ariño AH. Approaches to estimating the universe of natural history collections data. Biodivers Inform. 2010; 7:81-92.
• [34]Smith GF, Steenkamp Y, Klopper RR, Siebert SJ, Arnold TH. The price of collecting life. Nature. 2003; 422:375-376.
• [35]Krishtalka L, Humphrey PS. Fiddling while the planet burns: the challenge for U.S. natural history museums. Mus News. 1998; 77:29-35.
• [36]Krishtalka L, Humphrey PS. Can natural history museums capture the future? Bioscience. 2000; 50:611-617.
• [37]Krishtalka L. Natural history museums as sentinel observatories of life on Earth: a public trust. In: Beyond the turnstile: making the case for museums and sustainable values. Holo S, Alvarez M-T, editors. AltaMira Press, London; 2009: p.12-15.
• [38]Freidman T. The world is flat. Farrar, Straus and Giroux, New York; 2005.
• [39]Crouch NR, Smith GF, Figuereido E. From checklists to an e-flora for southern Africa: past experiences and future prospects for meeting target 1 of the 2020 global strategy for plant conservation. Ann Mo Bot Gard. 2013; 99:153-160.
• [40]CONABIO (2012) CONABIO: two decades of history, 1992–2012. In: Mexico DF (ed) Mexico: Comision Nacional para el Conocimiento y Uso de la Biodiversidad, pp 1–36
• [41]Samper C. Linking science and policy: a research agenda for Colombian biodiversity. In: Nature and Human Society: the Quest for a Sustainable World. Press NA, editor. National Academy Press, Washington; 1997: p.483-491.
• [42]Sandlund OT. Costa Rica’s INBio: towards sustainable use of natural biodiversity. NINA Notat. 1991; 7:1-25.
• [43]Canhos DAL, Sousa-Baena MS, Souza S, Garcia LC, Giovanni RD, Maia LC et al.. Lacunas: a web interface to identify plant knowledge gaps to support informed decision-making. Biodivers Conserv. 2014; 23:109-131.
• [44]Chan LM, Brown JL, Yoder AD. Integrating statistical genetic and geospatial methods brings new power to phylogeography. Mol Phylogenet Evol. 2011; 59:523-537.
• [45]Harmon LJ, Baumes J, Hughes C, Soberón J, Specht CD, Turner W et al (2013) Arbor: comparative analysis workflows for the tree of life. PLoS Curr 5. doi:10.1371/currents.tol.099161de5eabdee073fd3d21a44518dc
• [46]Miller JT, Jolley-Rogers G. Correcting the disconnect between phylogenetics and biodiversity informatics. Zootaxa. 2014; 3754:195-200.
• [47]GBIF (2011) A Beginner’s guide to persistent identifiers, version 1.0: http://links.gbif.org/persistent_identifiers_guide_en_v1.pdf. Global Biodiversity Information Facility, Copenhagen
• [48]Paavola J, Gouldson A, Kluvánková-Oravská T. Interplay of actors, scales, frameworks and regimes in the governance of biodiversity. Environ Policy Gov. 2009; 19:148-158.
• [49]Folke C, Hahn T, Olsson P, Norberg J. Adaptive governance of social–ecological systems. Annu Rev Environ Resour. 2005; 30:441-473.
• [50]Beck J, Böller M, Erhardt A, Schwanghart W. Spatial bias in the GBIF database and its effect on modeling species’ geographic distributions. Ecol Inform. 2014; 19:10-15.
• [51]Purves D, Scharlemann JPW, Harfoot M, Newbold T, Tittensor DP, Hutton J et al.. Ecosystems: time to model all life on Earth. Nature. 2013; 493:295-297.
• [52]Edwards P (2010) A vast machine: computer models, climate data, and the politics of global warming. MIT Press, Cambridge. ISBN 978-0-262-01392-5
• [53]Pereira HM, Ferrier S, Walters M, Geller GN, Jongman RHG, Scholes RJ et al.. Essential biodiversity variables. Science. 2013; 339(6117):277-278.
• [54]Flock Together with CReATIVE-B (2015) A roadmap of global research data infrastructures supporting biodiversity and ecosystem science. http://tinyurl.com/qcbx92q. Accessed 24 Feb 2015
• [55]Health Level 7 (2015) HL7 Web site. http://www.hl7.org. Accessed 24 Feb 2015
• [56]Integrating the Healthcare Enterprise (2015) IHE Web site. http://www.ihe.net. Accessed 24 Feb 2015
• [57]Hardisty AR, Peirce SC, Preece A, Bolton CE, Conley EC, Gray WA et al.. Bridging two translation gaps: a new informatics research agenda for telemonitoring of chronic disease. Int J Med Inform. 2011; 80:734-744.
• [58]Biodiversity Virtual e-Laboratory (BioVeL) infrastructure. http://www.biovel.eu/. Accessed 24 Feb 2015
• [59]Mathew C, Güntsch A, Obst M, Vicario S, Haines R, Williams AR et al (2014) A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control. Biodivers Data J (2):e4221. doi:10.3897/bdj.2.e4221