Symbiota – A virtual platform for creating voucher-based biodiversity information communities

Abstract We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.

[1]  Anthony R. Brach,et al.  Why Are We Still Producing Paper Floras?1 , 2011 .

[2]  S. T. Buckland,et al.  An Introduction to the Bootstrap. , 1994 .

[3]  Nico M. Franz,et al.  Description of two new species and phylogenetic reassessment of Perelleschus O’Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013 , 2013 .

[4]  N. Grimm,et al.  Approaches to the study of urban ecosystems: The case of Central Arizona—Phoenix , 2004, Urban Ecosystems.

[5]  M. J. Dallwitz,et al.  A Flexible Computer Program for Generating Identification Keys , 1974 .

[6]  Anthony R. Brach,et al.  ActKey: a Web-based interactive identification key program , 2005 .

[7]  A. Townsend Peterson,et al.  Alternate Species Concepts as Bases for Determining Priority Conservation Areas , 1999 .

[8]  Q. Wheeler The New Taxonomy , 2008 .

[9]  Dagmar Triebel,et al.  An appraisal of megascience platforms for biodiversity information , 2012 .

[10]  James Hanken,et al.  Biodiversity Online: Toward a Network Integrated Biocollections Alliance , 2013 .

[11]  A. Townsend Peterson,et al.  An alternative species taxonomy of the birds of Mexico , 2004 .

[12]  S. J. Graves,et al.  Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity , 2012 .

[13]  Anne E. Thessen,et al.  Data issues in the life sciences , 2011, ZooKeys.

[14]  John Wieczorek,et al.  Darwin Core: An Evolving Community-Developed Biodiversity Data Standard , 2012, PloS one.

[15]  Daryl Lafferty,et al.  The SALIX Method: A semi-automated workflow for herbarium specimen digitization , 2013 .

[16]  Edward Baker,et al.  Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science , 2011, ZooKeys.

[17]  A. Peterson,et al.  New developments in museum-based informatics and applications in biodiversity analysis. , 2004, Trends in ecology & evolution.

[18]  A. Townsend Peterson,et al.  VertNet: A New Model for Biodiversity Data Sharing , 2010, PLoS biology.

[19]  Beth Baker New Push to Bring US Biological Collections to the World's Online Community , 2011 .

[20]  Mark Gahegan,et al.  Biodiversity data should be published, cited, and peer reviewed. , 2013, Trends in ecology & evolution.

[21]  A. Brach,et al.  eFloras: New directions for online floras exemplified by the Flora of China Project , 2006 .

[22]  James Cheney,et al.  Provenance in Databases: Why, How, and Where , 2009, Found. Trends Databases.

[23]  Malcolm J. Scoble Rationale and Value of Natural History Collections Digitisation , 2010 .

[24]  Alex Hardisty,et al.  UvA-DARE ( Digital Academic Repository ) A decadal view of biodiversity informatics : challenges and priorities , 2013 .

[25]  M. J. Dallwitz,et al.  A Comparison of Interactive Identification Programs , 2000 .

[26]  M. J. Dallwitz,et al.  A General System for Coding Taxonomic Descriptions , 1980 .

[27]  V. Marx Biology: The big challenges of big data , 2013, Nature.

[28]  Neil Beagrie,et al.  Business Models And Cost Estimation: Dryad Repository Case Study , 2010, iPRES.

[29]  A. Lister Natural history collections as sources of long-term datasets. , 2011, Trends in ecology & evolution.

[30]  R. Peet,et al.  Perspectives: Towards a language for mapping relationships among taxonomic concepts , 2009 .

[31]  Cherri M. Pancake,et al.  HyperSQL: web-based query interfaces for biological databases , 1997, Proceedings of the Thirtieth Hawaii International Conference on System Sciences.

[32]  Bertram Ludäscher,et al.  Semantic Annotation of Mutable Data , 2013, PloS one.

[33]  Henning Kroll,et al.  Policies to build research infrastructures in Europe: Following traditions or building new momentum? , 2013 .

[34]  Donat Agosti,et al.  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 , 2008 .

[35]  Linda O'Brien,et al.  Innovation and Information Infrastructure: Making Sound Investments for E-Research , 2010 .

[36]  M. Edwards,et al.  The potential for computer-aided identification in biodiversity research. , 1995, Trends in ecology & evolution.

[37]  Bertram Ludäscher,et al.  Euler/X: A Toolkit for Logic-based Taxonomy Integration , 2013, WFLP 2013.

[38]  Renato J. O. Figueiredo,et al.  A Computational- and Storage-Cloud for Integration of Biodiversity Collections , 2013, 2013 IEEE 9th International Conference on e-Science.

[39]  C. Marshall Encyclopedia of Life , 2008 .

[40]  Bertram Ludäscher,et al.  Names are not good enough: Reasoning over taxonomic change in the Andropogon complex , 2016, Semantic Web.

[41]  M. J. Dallwitz,et al.  A Comparison of Matrix-Based Taxonomic Identification Systems with Rule-Based Systems , 1992 .

[42]  Nico M. Franz,et al.  5 On the Use of Taxonomic Concepts in Support of Biodiversity Research and Taxonomy , 2006 .

[43]  A. Suarez,et al.  The Value of Museum Collections for Research and Society , 2004 .

[44]  Nico M. Franz,et al.  Assembling a Virtual Weevils of North America Checklist with Symbiota - Preliminary Insights , 2014 .

[45]  Malcolm J. Scoble NATURAL HISTORY COLLECTIONS DIGITIZATION: RATIONALE AND VALUE , 2010 .

[46]  Jennifer C Molloy,et al.  The Open Knowledge Foundation: Open Data Means Better Science , 2011, PLoS biology.