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

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: Origin and Evolution of an Exhibition

Two hundred years after his birth, Darwin, originated by the American Museum of Natural History in New York, is the most important exhibition about the English scientist ever organized for the general public. This traveling exhibition has appeared in many versions worldwide, and a study of the relationships between local developers of the various editions of the exhibition underlines how a scientific exhibition and, more generally, science communication can succeed in striking a good equilibrium between universal content and cultural determinants.     

Liposuction abdominoplasty: an evolving concept

Liposuction abdominoplasty-liposuction of abdominal subcutaneous tissue deep and superficial to Scarpa's fascia, with excision of excess abdominal skin and, when indicated, plication of the anterior rectus sheath without undermining-is an effective, low-risk approach to minimizing abdominal flap undermining. The technique allows aggressive thinning and "sculpting" of full-thickness abdominal subcutaneous tissue and achieves a natural (not featureless) abdominal contour. It minimizes the creation of "dead space," which often leads to postoperative complications, as well as preserves sensory nerve and blood supply to the abdominal skin. The operation may be performed with the patient under local anesthesia, which probably diminishes the risk for deep vein thrombosis. Moreover, additional procedures can be conducted safely and the postoperative course is short, uneventful, and without restrictions; patients return to normal activity within a week or so. New evaluation criteria for abdominoplasty are discussed in this article, the most important of which is the assessment of intraabdominal fat content and its impact on surgical outcome and the decision to perform anterior rectus sheath plication. The concept of a sliding, mobile, sensate abdominal flap, created by liposuction and sustained by multiple neurovascular mesenteries, is also offered.     

The establishment of China's core biodiversity metadata standard

Biodiversity metadata provide service to query, management and use of actual data sets. The progress of the development of metadata standards in China was analyzed, and metadata required and/or produced based on the Convention on Biological Diversity were reviewed. A biodiversity metadata standard was developed based on the characteristics of biodiversity data and in line with the framework of international metadata standards. The content of biodiversity metadata is divided into two levels. The first level consists of metadata entities and elements that are necessary to exclusively identify a biodiversity data set, and is named as Core Metadata. The second level comprises metadata entities and elements that are necessary to describe all aspects of a biodiversity data set. The standard for core biodiversity metadata is presented in this paper, which is composed of 51 elements belonging to 6 categories (entities), i.e. inventory information, collection information, information on the content of the data set, management information, access information, and metadata management information. The name, definition, condition, data type, and field length of metadata elements in these six categories (entities) are also described.     

Amazonian biodiversity: assessing conservation priorities with taxonomic data

Data from 3991 records of museum collections representing 421 species of plants, arthropods, amphibians, fish, and primates were analyzed with GIS to identify areas of high species diversity and endemism in Amazonia. Of the 472 1 × 1° grid cells in Amazonia, only nine cells are included in the highest species diversity category (43–67 total species) and nine in the highest endemic species diversity category (4–13 endemic species). Over one quarter of the grid cells have no museum records of any of the organisms in our study. Little correspondence exists between the centers of species diversity identified by our collections-based data and those areas recommended for conservation in an earlier qualitative study of Amazonian biodiversity. Museum collections can play a vital role in identifying species-rich areas for potential conservation in Amazonia, but a concerted and structured effort to increase the number and distribution of collections is needed to take maximum advantage of the information they contain.     

Biodiversity informatics: managing and applying primary biodiversity data

Recently, advances in information technology and an increased willingness to share primary biodiversity data are enabling unprecedented access to it. By combining presences of species data with electronic cartography via a number of algorithms, estimating niches of species and their areas of distribution becomes feasible at resolutions one to three orders of magnitude higher than it was possible a few years ago. Some examples of the power of that technique are presented. For the method to work, limitations such as lack of high-quality taxonomic determination, precise georeferencing of the data and availability of high-quality and updated taxonomic treatments of the groups must be overcome. These are discussed, together with comments on the potential of these biodiversity informatics techniques not only for fundamental studies but also as a way for developing countries to apply state of the art bioinformatic methods and large quantities of data, in practical ways, to tackle issues of biodiversity management.     

Emergency room coverage: an evolving crisis

Historically, a newly graduated plastic surgeon in the United States could build a practice from his or her emergency room coverage. The historical cliche was for the surgeon to be affable, able, and available, and from that basis one's practice would grow. Emergency room exposure was an avenue for starting a practice, developing recognition, and, after that, building a referral pattern. Recently, the cross-shifting influence of management care, rising malpractice insurance costs, and risk ratio are changing this cliche to a crisis. An evaluation of a 2 1/2-year exposure to emergency room coverage has revealed a completely different profile. A total of 300 patient visits resulting in 69 surgical operations were evaluated for insurance and remuneration history. The findings indicated a significant remuneration dilemma for emergency room coverage. Interestingly, a remuneration problem exists in a market different from what one would expect. In this study, a sample from a suburban hospital, rather than an inner-city university hospital, is the greater problem.     

Unconventional protein secretion: an evolving mechanism

The process by which proteins are secreted without entering the classical endoplasmic reticulum (ER)–Golgi complex pathway, in eukaryotic cells, is conveniently called unconventional protein secretion. Recent studies on one such protein called Acb1 have revealed a number of components involved in its secretion. Interestingly, conditions that promote the secretion of Acb1 trigger the biogenesis of a new compartment called CUPS (Compartment for Unconventional Protein Secretion). CUPS form near the ER exit site but lack ER‐specific proteins. Other proteins that share some of the features common with the secretion of Acb1 are interleukin‐1β and tissue transglutaminase. Here I will review recent advances made in the field and propose a new model for unconventional protein secretion.     

Towards recommending visualizations for biodiversity data

To address the critical challenges of biodiversity conservation and study its impact on the ecosystem, over the last decade, scientists have been producing a large amount of highly heterogeneous and distributed data. For managing, processing, and visualizing this data, requires informatics skills. While many biologists lack these skills, informaticians are limited in their understanding of biological domain requirements and the context of the data. The focus of our research study is to assist scientists with the suggestion of possible visualizations for exploring and understanding their data. To be useful, such suggestions need to be based on the visualization knowledge of domain experts. We intend to gather such knowledge and use in the development of a visualization recommendation framework serving the biodiversity research community. Therefore, the authors want to encourage readers to share their domain knowledge on the biodiversity data visualization usage by participating in an online survey.     

Southeast Asian biodiversity: an impending disaster

Southeast Asia has the highest relative rate of deforestation of any major tropical region, and could lose three quarters of its original forests by 2100 and up to 42% of its biodiversity. Here, we report on the current state of its biota and highlight the primary drivers of the threat of extinction now faced by much of the unique and rich fauna and flora of the region. Furthermore, the known impacts on the biodiversity of Southeast Asia are likely to be just the tip of the iceberg, owing to the paucity of research data. The looming Southeast Asian biodiversity disaster demands immediate and definitive actions, yet such measures continue to be constrained by socioeconomic factors, including poverty and lack of infrastructure. Any realistic solution will need to involve a multidisciplinary strategy, including political, socioeconomic and scientific input, in which all major stakeholders (government, non-government, national and international organizations) must participate.     

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012)

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27-29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database.     

TRiDaS 1.1: The tree-ring data standard

Tree-ring research and collaboration are currently being hampered by the lack of a suitable data-transfer standard for both data and metadata. This paper highlights the issues currently being faced and proposes a solution that, if adopted by the global dendro community, will open up the possibility of exciting new research collaborations. The solution consists of a data model for dendrochronological data and metadata, and an eXtensible Markup Language (XML) schema as a technical vehicle to exchange this data and metadata. The technology and structure of the standard enable future versions to be developed that will satisfy evolving requirements whilst remaining backwards compatible.     

Darwin would have loved DNA: celebrating Darwin 200

Analysis of DNA sequences now plays a key role in evolutionary biology research. If Darwin were to come back today, I think he would be absolutely delighted with molecular evolutionary genetics, for three reasons. First, it solved one of the greatest problems for his theory of evolution by natural selection. Second, it gives us a tool that can be used to investigate many of the questions he found the most fascinating. And third, DNA data confirm Darwin''s grand view of evolution.     

Eosinophils in innate immunity: an evolving story

Eosinophils are innate immune leukocytes found in relatively low numbers within the blood. Terminal effector functions of eosinophils, deriving from their capacity to release their content of tissue-destructive cationic proteins, have historically been considered primary effector mechanisms against specific parasites, and are likewise implicated in tissue damage accompanying allergic responses such as asthma. However, the past decade has seen dramatic advancements in the field of eosinophil immunobiology, revealing eosinophils to also be key participants in many other facets of innate immunity, from bridging innate and adaptive immune responses to orchestrating tissue remodeling events. Here, we review the multifaceted functions of eosinophils in innate immunity that are currently known, and discuss new avenues in this evolving story.