Community Structure and Patterns of Tropical and Subtropical Forest in China
Although biodiversity of marine remains high, it increasingly suffers from human interference and destruction. The world’s largest open, online, georeferenced database is the Ocean Biogeographic Information System (OBIS); it has information on a total of 120,000 species with 37 million records. The World Register of Marine Species (WoRMS) has collected taxonomic information on 220,000 global marine species. Besides these two large databases, three single-taxa databases were established for marine organisms—FishBase, AlgaeBase, and Hexacorallians of the World. Many databases on organisms are cross-taxa and include both terrestrial and marine species, such as Encyclopedia of Life (EOL), CoL (Species 2000) , Integrated Taxonomic Information System (ITIS), Wikispecies, ETI Bioinformatics, Barcode of Life (BOL), GenBank, Biodiversity Heritage Library (BHL), SeaLifeBase, Marine Species Identification Portal, and FAO Fisheries and Aquaculture Fact Sheets. Above databases were mainly established to focus on taxonomy and species descriptions. The Global Biodiversity Information Facility (GBIF), Discover Life, AquaMaps, etc. can provide integrated ecological distribution data, user customized maps, and data for download. By changing the values of environmental factors such as water temperature and salinity in an established distribution model, the distribution of a species can be predicted with different parameters. Websites of other organizations, such as Google Earth Ocean, National Geographic, and NGOs such as ReefBase, aim to raise public awareness on ocean conservation with rich and diversified content. Google Images and Google Scholar are very useful in cooperating with keywords provided by marine biodiversity websites to complement the lack of images or references. Most of the above websites are linked to each other, and thus users can access and query data conveniently. To be useful for conservation, biodiversity databases need both to promote public usage in addition to the integration and sharing of data. In this article, we build on a speech by Rainer Froese in Paris to demonstrate how to use marine biodiversity data to conduct research on the impact of climate change on fish distribution. Finally, we also briefly introduce the status of marine biodiversity databases in Mainland China and Taiwan, including the Cross-Strait collaboration, as well as recommendations for how to link to global databases.
Biodiversity research, conservation practices, natural resource management, and scientific decision-making increasingly depend on the sharing and integration of large amounts of primary data. In recent years, there has been an appeal increased sharing of biodiversity data, however, many scientists actively or passively resist sharing data. Some major cultural and technological obstacles exist among scientists, such as keeping data private to conduct other analyses, conflicts of interests with colleagues, lack of benefits, unfamiliarity with public databases, lack of user-friendly data submission tools, and lack of time and funding. One solution to improve the culture of data sharing is to provide benefits to scientists who share data (e.g. data citations). Recently, some organizations and scientists have advocated data publishing under peer review as a reward mechanism for individuals involved in data creation, management and sharing, and as a way to effectively increase the use and reuse of data. New data journals have been launched to fulfill the function of publishing data. In fact, besides the advocate of scholarly publication of data, an improved joint data archiving policy by databases and scientific journals may be more practically feasible to improve data sharing in a broader sense. In this article we review recent progress in data sharing and publishing and discuss to what extent data papers can boost data sharing and how to define ‘data sharing’ and ‘data publishing’. We also provide suggestions for improving data sharing by individual scientists, data repositories, journals, and funding agencies/institutions.
DNA barcoding technology provides an opportunity for rapid, accurate, and standardized species-level identification using short DNA sequences. This method speeds up species identification and classification, and presents a new tool for the management, conservation and sustainable development of biodiversity at a global level. Due to improvements in plant barcode database availability and functionality, it is becoming feasible to meet increasing demands for biodiversity information. A framework is needed for a barcoding server platform that utilizes, integrates, and shares among different data types. Such a platform would be an important step towards enabling the public to rapidly identify species and acquire species-related digital information. In this paper, we review current progress on plant DNA barcoding. Secondly, we summarize the current status of, and identify bottlenecks for, plant DNA barcode reference libraries specifically. Thirdly, in the Big Data era, it is indispensable to manage and make good use of massive amounts of plant information. We provide the following suggestions for the framework of server platform: (1) metadata should be substantial, accurate and correlative; (2) data should be normalized; (3) query entrance is convenient, efficient, easy to manage, and available for large-scale data sharing and global communication.
We describe key features of the Scratchpads 2.0 Virtual Research Environment (VRE), which supports the creation, management and reuse of biodiversity data. This paper provides an introduction to recent developments and status of the Scratchpads 2.0 system, including its technical architecture. Key features include mechanisms to integrate individual research data and online resources, creation and management of multilingual content, license and authorization of system and data content, dynamic tracing of data editing history, research team cooperation, and methods of data paper publication. Important technical features include effective maintenance and installation of the system, ability to build distributed architecture, modularized function and development, and implementation of related information standards. These are put into a context with related biodiversity informatics tools. Scratchpads was designed with accurate role orientation, a deep understanding of taxonomic research requirements, and excellent technical solutions. All of these attributes contribute to Scratchpads’ importance to e-infrastrature in the Internet era for taxonomy, thereby providing us with a promising tool to complete ambitious projects like World Online Flora.
A scientific workflow system is designed specifically to organize, manage and execute a series of research steps, or a workflow, in a given runtime environment. The vision for scientific workflow systems is that the scientists around the world can collaborate on designing global-scaled experiments, sharing the data sets, experimental processes, and results on an easy-to-use platform. Each scientist can create and execute their own workflows and view results in real-time, and then subsequently share and reuse workflows among other scientists. Two case studies, using the Kepler system and BioVeL, are introduced in this paper. Ecological niche modeling process, which is a specialized form of scientific workflow system included in both Kepler system and BioVeL, was used to describe and discuss the features, developmental trends, and problems of scientific workflows.
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