Can Natural History Museums Capture the Future?

This is the publisher's version, also available electronically from http://bioscience.oxfordjournals.org/content/50/7/611.See article for abstract

Thoughts on implementation of the recommendeds of the GBIF task force on a global strategy and action plan for mobilization of natural history collections data

This is the publisher's version, also available electronically from https://journals.ku.edu/index.php/jbi/article/view/4019The Global Biodiversity Information Facility (GBIF) has a mandate to facilitate free and open access to primary biodiversity data worldwide. This Special Issue of Biodiversity Informatics publishes the findings of the recent GBIF Task Group on a Global Strategy and Action Plan for Mobilisation of Natural History Collections Data (GSAP-NHC). The GSAP-NHC Task Group has made three primary recommendations dealing with discovery, capture, and publishing of natural history collections data. This overview article provides insight on various activities initiated by GBIF to date to assist with an early uptake and implementation of these recommendations. It calls for proactive participation by all relevant players and stakeholder communities. Given recent technological progress and growing recognition and attention to biodiversity science worldwide, we think rapid progress in discovery, publishing and access to large volumes of useful collection data can be achieved for the immediate benefit of science and society

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

The Global Biodiversity Information Facility (GBIF) has a mandate to facilitate free and open access to primary biodiversity data worldwide. This Special Issue of Biodiversity Informatics publishes the findings of the recent GBIF Task Group on a Global Strategy and Action Plan for Mobilisation of Natural History Collections Data (GSAP-NHC). The GSAP-NHC Task Group has made three primary recommendations dealing with discovery, capture, and publishing of natural history collections data. This overview article provides insight on various activities initiated by GBIF to date to assist with an early uptake and implementation of these recommendations. It calls for proactive participation by all relevant players and stakeholder communities. Given recent technological progress and growing recognition and attention to biodiversity science worldwide, we think rapid progress in discovery, publishing and access to large volumes of useful collection data can be achieved for the immediate benefit of science and society

A global perspective on decadal challenges and priorities in biodiversity informatics

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

Advances in biodiversity: metagenomics and the unveiling of biological dark matter

BACKGROUND: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones. RESULTS: Biology, like physics, has a fundamental duality—the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm—with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life. Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet’s biomass and most of its genetic diversity. The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology. CONCLUSION: Classical genetics one held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string. Similarly, classical biology asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life. Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

This is the published version, also available at http://dx.doi.org/10.4056/sigs.4898640.The 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

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

This is the published version, also available at http://dx.doi.org/10.4056/sigs.4898640.The 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