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

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 585-598, doi: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.We gratefully acknowledge support from the Global Biodiversity Information Facility (GBIF), from the Global Genome Biodiversity Network (GGBN), from the EU 7FP Biodiversity, Bioinformatics, Biotechnology project (Micro B3), and from the US National Science Foundation (NSF) through the following grants: DBI-0840989 [Research Coordination Network for the Ge-nomic Standards Consortium (RCN4GSC)], IIS-1255035 [EAGER: An Interoperable Information Infrastructure for Biodiversity Research (I3BR)], ABI Development: Collaborative Research: VertNet, a New Model for Bio-diversity Networks (DBI-1062193), and Collaborative Research: BiSciCol Tracker: Towards a tagging and tracking infrastructure for biodiversity science collec-tions (DBI-0956426)

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

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

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

Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations

Random-phase approximation and its applications in computational chemistry and materials science

The random-phase approximation (RPA) as an approach for computing the electronic correlation energy is reviewed. After a brief account of its basic concept and historical development, the paper is devoted to the theoretical formulations of RPA, and its applications to realistic systems. With several illustrating applications, we discuss the implications of RPA for computational chemistry and materials science. The computational cost of RPA is also addressed which is critical for its widespread use in future applications. In addition, current correction schemes going beyond RPA and directions of further development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012

Resolution-of-identity approach to Hartree-Fock, hybrid density functionals, RPA, MP2, and \textit{GW} with numeric atom-centered orbital basis functions

Efficient implementations of electronic structure methods are essential for first-principles modeling of molecules and solids. We here present a particularly efficient common framework for methods beyond semilocal density-functional theory, including Hartree-Fock (HF), hybrid density functionals, random-phase approximation (RPA), second-order M{\o}ller-Plesset perturbation theory (MP2), and the $GW$ method. This computational framework allows us to use compact and accurate numeric atom-centered orbitals (popular in many implementations of semilocal density-functional theory) as basis functions. The essence of our framework is to employ the "resolution of identity (RI)" technique to facilitate the treatment of both the two-electron Coulomb repulsion integrals (required in all these approaches) as well as the linear density-response function (required for RPA and $GW$). This is possible because these quantities can be expressed in terms of products of single-particle basis functions, which can in turn be expanded in a set of auxiliary basis functions (ABFs). The construction of ABFs lies at the heart of the RI technique, and here we propose a simple prescription for constructing the ABFs which can be applied regardless of whether the underlying radial functions have a specific analytical shape (e.g., Gaussian) or are numerically tabulated. We demonstrate the accuracy of our RI implementation for Gaussian and NAO basis functions, as well as the convergence behavior of our NAO basis sets for the above-mentioned methods. Benchmark results are presented for the ionization energies of 50 selected atoms and molecules from the G2 ion test set as obtained with $GW$ and MP2 self-energy methods, and the G2-I atomization energies as well as the S22 molecular interaction energies as obtained with the RPA method.Comment: 58 pages, 15 figures, and 7 table