Biobanking for Europe

Biobanks are well-organized resources comprising biological samples and associated information that are accessible to scientific investigation. Across Europe, millions of samples with related data are held in different types of collections. While individual collections can be well organized and accessible, the resources are subject to fragmentation, insecurity of funding and incompleteness. To address these issues, a Biobanking and BioMolecular Resources Infrastructure (BBMRI) is to be developed across Europe, thereby implementing a European 'roadmap' for research infrastructures that was developed by a forum of EU member states and that has been received by the European Commission. In this review, we describe the work involved in preparing for the construction of BBMRI in a European and global context.     

Absolute and relational control of a sequential auditory discrimination by pigeons (Columba livia)

Recent evidence indicates that pigeons can readily learn visual discriminations based on both absolute and relational stimulus factors. To examine how these two types of control function in their non-dominant auditory modality, we tested four pigeons in a go/no-go sequential auditory discrimination in which both absolute and relational cues were redundantly available. In this task, sequences of different sounds created from one set of pitches were reinforced, while different sequences created from another set of pitches and any same sequences made from either set of pitches were not. Across three experiments, we independently varied the relative discriminability of the absolute and relational components. The pigeons were consistently and primarily controlled by the absolute fundamental pitch of our notes in all of the experiments, although this was influenced by the range and arrangement of the pitches used in each set. A majority of the pigeons also demonstrated relational control when this component was made more salient. The more robust control exhibited by absolute factors is consistent with the comparative hypothesis that birds in general may have a well-developed aptitude for processing absolute pitch in many auditory settings. The relational control is consistent with our recent evidence of same/different auditory learning by pigeons.     

A brute‐force approach to vegetation classification

Aim: Introduction of a novel approach to the classification of vegetation data (species by plot matrices). This approach copes with a large amount of noise, groups irregularly shaped in attribute space and species turnover within groups. Method: The proposed algorithm (Isopam) is based on the classification of ordination scores from isometric feature mapping. Ordination and classification are repeated in a search for either high overall fidelity of species to groups of sites, or high quantity and quality of indicator species for groups of sites. The classification is performed either as a hierarchical, divisive method or as non‐hierarchical partitioning. In divisive clustering, resulting groups are subdivided until a stopping criterion is met. Isopam was tested on 20 real‐world data sets. The resulting classifications were compared with solutions from eight widely used clustering algorithms. Results: When looking at the significance of species fidelities to groups of sites, and at quantity and quality of indicator species, Isopam often achieved high ranks as compared with other algorithms.     

InterStoreDB:A Generic Integration Resource for Genetic and Genomic Data

Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research.InterStoreDB is a suite of integrated databases designed to assist in this process.The individual databases are species independent and generic in design,providing access to curated datasets relating to plant populations,phenotypic traits,genetic maps,marker loci and QTL,with links to functional gene annotation and genomic sequence data.Each component database provides access to associated metadata,including data provenance and parameters used in analyses,thus providing users with information to evaluate the relative worth of any associations identified.The databases include CropStoreDB,for management of population,genetic map,QTL and trait measurement data,SeqStoreDB for sequence-related data and AlignStoreDB,which stores sequence alignment information,and allows navigation between genetic and genomic datasets.Genetic maps are visualized and compared using the CMAP tool,and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal.We demonstrate the value of InterStoreDB as a tool for Brassica research.InterStoreDB is available from:http://www.interstoredb.org     

BASECO: a floristic and ecological database of Mediterranean French flora

The French Mediterranean zone is one of the richest of the country, with 3200 species and many endemics. Because of its interest as a synthetic tool to store and manage data, an ecological Mediterranean flora database was created. Built around five tables, BASECO allows several queries about the botanical and ecological characteristics of about 1800 plants. The database was implemented in Access, which is a relational database management system. Each species is identified by a code and is characterised by several qualitative traits relating to morphology, reproduction, life forms and biogeographical distribution, including several modalities. Each trait is informed from one or two pre-defined reference botanical handbooks as much as possible. There are many different possible uses of this database, even at a huge scale, allowing to reveal patterns hard to detect with the taxonomic approach alone.     

A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development.

Using methods for database screening with individual protein sequences and alignment blocks, a conserved domain is delineated in a group of proteins including several FAD-dependent oxidases. Two motifs within this domain resemble phosphate-binding loops and may be directly involved in FAD binding. These motifs can be readily distinguished from previously described nucleotide-binding sites using a method for database screening with position-dependent weight matrices derived from alignment blocks. Unexpectedly, this group of known and predicted FAD-dependent oxidases includes the product of the DIMINUTO gene, which is involved in Arabidopsis development, and its homologues from man and Mycobacterium leprae.     

一个中药信息系统原型的初步设计与实现

中药信息系统是实现中药信息科学管理最有效的技术系统。我们以国内权威中药学论著和《中华人民共和国药典》1995年版(一部)为蓝本,综合其他20余部中药论著及文献资料,应用关系型数据库FoxProforWindows研制了一个中药信息系统的原型(中文版)1),主要内容如下。1　系统设计要点11　数据项与系统结构本系统选择的数据项为:本草考证、文献查考、资源调查、分类学鉴定、性状鉴定、显微鉴定、商品鉴定、理化分析、化学成分、药理实验、野生药源的开发利用、引种栽培或驯化研究、生物技术应用、新药开发、有效成分的合成和结构改造、综合利用、…