Blum Stan D.
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ArticleMeeting report : GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)(Genomic Standards Consortium, 2014) Wieczorek, John ; Banki, Olaf ; Blum, Stan D. ; Deck, John ; Doring, Markus ; Droge, Gabriele ; Endresen, Dag ; Goldstein, Philip ; Leary, Patrick R. ; Krishtalka, Leonard ; O'Tuama, Eamonn ; Robbins, Robert J. ; Robertson, Tim ; Yilmaz, PelinThe workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a “Biodiversity Data Archive”. A wide variety of use cases were assembled and discussed in order to inform further developments.
ArticleRCN4GSC Workshop Report : managing data at the interface of biodiversity and (meta)genomics, March 2011(Genomic Standards Consortium, 2012-07-28) Robbins, Robert J. ; Amaral-Zettler, Linda A. ; Bik, Holly M. ; Blum, Stan D. ; Edwards, James ; Field, Dawn ; Garrity, George M. ; Gilbert, Jack A. ; Kottmann, Renzo ; Krishtalka, Leonard ; Lapp, Hilmar ; Lawrence, Carolyn ; Morrison, Norman ; O Tuama, Eamonn ; Parr, Cynthia Sims ; San Gil, Inigo ; Schindel, David ; Schriml, Lynn M. ; Vieglas, David ; Wooley, JohnBuilding on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.
ArticleMapping the biosphere : exploring species to understand the origin, organization and sustainability of biodiversity(Taylor & Francis, 2012-03-27) Wheeler, Q. D. ; Knapp, Sandra ; Stevenson, D. W. ; Stevenson, J. ; Blum, Stan D. ; Boom, B.. M. ; Borisy, Gary G. ; Buizer, James L. ; De Carvalho, M. R. ; Cibrian, A. ; Donoghue, M. J. ; Doyle, V. ; Gerson, E. M. ; Graham, C. H. ; Graves, P. ; Graves, Sara J. ; Guralnick, Robert P. ; Hamilton, A. L. ; Hanken, J. ; Law, W. ; Lipscomb, D. L. ; Lovejoy, T. E. ; Miller, Holly ; Miller, J. S. ; Naeem, Shahid ; Novacek, M. J. ; Page, L. M. ; Platnick, N. I. ; Porter-Morgan, H. ; Raven, Peter H. ; Solis, M. A. ; Valdecasas, A. G. ; Van Der Leeuw, S. ; Vasco, A. ; Vermeulen, N. ; Vogel, J. ; Walls, R. L. ; Wilson, E. O. ; Woolley, J. B.The time is ripe for a comprehensive mission to explore and document Earth's species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.