FRINK Linked Data Fragments server

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• W2103679300 abstract "We are proud to present the fourth Database Issue of Plant and Cell Physiology (PCP) (available online at http://pcp.oxfordjour nals.org/). As we have introduced in previous years (Matsuoka and Yano 2010, Obayashi and Yano 2013), the ultimate goal of PCP’s annual Database Issue is to provide a useful online resource and forum for discussion of bioinformatics research, and in particular the development and maintenance of the infrastructure of web databases for plant science. Recently, largescale biological data sets, such as those for DNA polymorphisms and gene expression, have been obtained using next-generation sequencing technology. In addition, website and database construction has also become easier due to the many commercial and non-commercial types of software that have been recently released and widely distributed. This has resulted in the creation of many diverse web-based tools and databases that house and/or analyze large-scale data. However, it is not always easy for researchers to extract data efficiently from such databases, since their concept, contents and/or functions may sometimes be unclear. Therefore, to promote discussion and develop bioinformatics approaches and omics/knowledge information specifically for the plant sciences, databases ought to be designed with particular specifications in mind, for instance to include user-friendly interfaces, search functions and manuals. To ensure that a common consensus is reached in this and future Database Issues, PCP has updated its Instructions for Authors and implemented standard key features and descriptions of databases and online tools (see http://www.oxfordjournals.org/our_journals/pcp/pcp_2013_ call_for_paper.html), which will aid researchers in extracting relevant data. This year’s collection of Database articles promises to provide useful omics data to plant researchers, and comprise descriptions of nine sophisticated web databases. On pages 1–9 (e3), Kiefer et al. (2014) report on a new Brassica database—BrassiBase (http://brassibase.cos.uni-heidelberg.de/). The authors aim to develop an online database system of cross-referenced information and resources on Brassicaceae taxonomy, systematics, evolution, traits and germplasm resources. Biological material and resources, either collected directly in the wild or held in germplasm collections, are often taxonomically misidentified and are very rarely further characterized and documented. BrassiBase will close these various gaps and provide the full potential of research focusing on the adaptive characters and character trait evolution in the Brassicaceae. MEGANTE (https://megante.dna.affrc.go.jp/) is a web-based annotation system that makes plant genome annotation easy for non-bioinformaticians (Numa and Itoh 2014; see pp. 1–8 (e2)). Users can submit a sequence of up to 10 Mb in length and save up to 100 sequences on the server. The annotation is visualized with a genome browser and the results can be downloaded in a Microsoft Excel format. Yonemaru et al. (2014; see pp. 1–12 (e9)) introduce the HapRice database, which provides information about single nucleotide polymorphisms (SNPs) in different rice genomes. The SNP haplotypes were determined by the allele frequencies in two populations consisting of 3,334 SNPs within 76 world accessions and 3,252 SNPs within 177 Japanese accessions, and will aid marker-assisted breeding and provide useful additional markers for geneticists. The SNP information is available from the HapRice database (http://qtaro.abr.affrc.go.jp/). To allow a comprehensive understanding of the interactions between an organism’s metabolites and the chemical-level contribution of metabolites to human health, Nakamura et al. (2014; see pp. 1–9 (e7)) constructed a metabolite activity database known as the KNApSAcK Metabolite Activity DB (http://kanaya.naist.jp/MetaboliteActivity/top. jsp). The KNApSAcK Metabolite Activity DB is integrated within the KNApSAcK Family DBs (Afendi et al. 2012, Nakamura et al. 2013) to facilitate further systematized research in various omics fields, especially metabolomics, nutrigenomics and foodomics. The KNApSAcK Metabolite Activity DB could also be utilized for developing novel drugs and materials, as well as for identifying viable drug resources and other useful compounds. On pages 1–9 (e5), Fukami-Kobayashi et al. (2014) also describe the integration of omics information and resources in plant science. The original SABRE (Systematic consolidation of Arabidopsis and other Botanical Resources) database (Yamazaki et al. 2010), retrieved TAIR (The Arabidopsis Information Resource) gene models and their annotations, together with homologous gene clones from various species, and" @default.
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• W2103679300 title "Plant and Cell Physiology 2014 Online Database Issue" @default.
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