A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules.

The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Library of Biological Macromolecules--JenaLib. Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data. Here, we briefly describe these resources from a user's point of view and from a comparative perspective. It is our aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources.     

MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data

Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level. Proteomics-based studies have also contributed to the ever-expanding array of data in modern biology, with many generating Web portals and online resources that contain incrementally expanding and updated information. Many of these resources reflect specialist research areas with significant and novel information that is not currently captured by centralized repositories. The Arabidopsis (Arabidopsis thaliana) community is well served by a number of online proteomics resources that hold an abundance of functional information. These sites can be difficult to locate among a multitude of online resources. Furthermore, they can be difficult to navigate in order to identify specific features of interest without significant technical knowledge. Recently, members of the Arabidopsis proteomics community involved in developing many of these resources decided to develop a summary aggregation portal that is capable of retrieving proteomics data from a series of online resources on the fly. The Web portal is known as the MASCP Gator and can be accessed at the following address: http://gator.masc-proteomics.org/. Significantly, proteomics data displayed at this site retrieve information from the data repositories upon each request. This means that information is always up to date and displays the latest data sets. The site also provides hyperlinks back to the source information hosted at each of the curated databases to facilitate more in-depth analysis of the primary data.     

The International Rice Information System. A platform for meta-analysis of rice crop data

Ambiguous germplasm identification; difficulty in tracing pedigree information; and lack of integration between genetic resources, characterization, breeding, evaluation, and utilization data are constraints in developing knowledge-intensive crop improvement programs. To address these constraints, the International Crop Information System (www.icis.cgiar.org), a database system for the management and integration of global information on genetic resources and crop improvement for any crop, was developed by genetic resource specialists, crop scientists, and information technicians associated with the Consultative Group for International Agricultural Research and collaborative partners. The International Rice Information System (www.iris.irri.org) is the rice (Oryza species) implementation of the International Crop Information System. New components are now being added to the International Rice Information System to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data, and proteomic information. Users access information in the database through stand-alone programs and Web interfaces, which offer specialized applications and customized views to researchers with different interests.     

Understanding investment in biodiversity conservation in Mexico

Documenting financial resources in biodiversity conservation is a key aspect worldwide in order to set priorities and use effectively the limited resources available. In Mexico, a megadiverse country, studies on financial resources invested in biodiversity conservation are scarce and do not address funding for conservation comprehensively. Using recent data from several sources and applying criteria based on the national priorities for conservation, we compiled, systematized and analyzed data at a national scale on financing sources, financial resources and conservation organizations and their projects. The information obtained is presented in various ways and part of it (case study) is already an information system that can be continuously up-dated. Some of the results show the following: a steady diversification of mechanisms and methods for raising funds for conservation; an increase in governmental budgets; the acknowledgment by the private sector of the importance of biodiversity conservation; a greater technical capacity in people and organizations working in conservation; a greater accessibility of financial resources to support and maintain conservation projects; yet a short term vision in conservation projects; among other. Although the results obtained through this study are a first approach, they can now be used as a baseline to continue gathering and analyzing information on conservation financing in Mexico.     

Path-based systems to guide scientists in the maze of biological data sources

Fueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer. Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data. In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.     

贵州省安顺市土地资源信息空间数据库的建立与应用

1　引　　言要制订不会危及环境的土地资源开发和保护计划 ,必须首先掌握可靠的、较新的有关土地资源的时空信息[3 ] .近年来 ,以ＧＩＳ和遥感技术为主的现代信息科学技术在土地覆盖/利用调查与填图[2 ,6] 、土地资源动态变化监测[13 ] 、土地质量退化与土壤侵蚀监测[5,8] 、土地资源评价[12 ] 与管理[10 ] 中得到了广泛应用 .这些技术可以较好地解决以往传统方法在获取、分析和处理大量、复杂土地信息中的众多限制 ,使我们得以动态地、综合地分析土地资源环境信息[4,7] .贵州省安顺市地处我国西南岩溶山区 ,生态环境脆弱 ,土地资源相对不足…     

糖类的生物信息学资源

生物信息学在推动遗传学和蛋白质科学的研究领域中,已发挥了举足轻重的作用.相比较而 言,糖科学产生的信息还比较有限,随着人们对糖类分子的关注,糖生物学的发展也出现新 的契机,其信息正在飞速地增长.对已经获得的糖类相关知识进行系统整合就显得越来越有 必要,许多研究型数据库和免费工具已应运而生,并且数目在不断扩大,正成为科学工作者 非常便利的工具.但到目前为止,许多数据库或者网络预测工具在文献中很少提及或难以找 到,给研究者带来了不少的麻烦.部分原因是数据库资源本身数据不断在更新,人机界面也 变得越方便和人性化,另外就是人们对于这些新型的研究工具了解较少.这篇综述介绍了 目前网络上最常用的糖类生物信息学资源,包括糖的一级结构,分析测试数据、构象,酶, 凝集素,糖蛋白等方面的各种数据库.     

Mahogany as a genetic resource

The development of a strategy for the sustainable management and conservation of mahogany is an urgent priority. Such a strategy should be based upon clear information about the extent of genetic differentiation within and between populations, and on an understanding of the processes maintaining this variation. At present, such information is very limited for mahogany. Preliminary data are presented from two genetic tests of Swietenia macrophylla King (Meliaceae), indicating significant differences between provenances and half-sib progenies in both growth and form characteristics. In addition, the use of molecular markers for the characterization of genetic resources of mahogany is discussed. On the basis of the results available, the impacts of deforestation and logging activities on genetic resources are evaluated. Although both deforestation and selective logging may deplete genetic resources, no quantitative information on the extent of such depletion in mahogany is currently available. Additional research is therefore required before clear guidelines can be provided for the sustainable management of mahogany.     

An Evaluation of Alternative Designs for a Grid Information Service

Computational grids consisting of large and diverse sets of distributed resources have recently been adopted by organizations such as NASA and the NSF. One key component of a computational grid is an information services that provides information about resources, services, and applications to users and their tools. This information is required to use a computational grid and therefore should be available in a timely and reliable manner. In this work, we describe the Globus information service, describe how this service is used, analyze its current performance, and perform trace-driven simulations to evaluate alternative implementations of this grid information service. We find that the majority of the transactions with the information service are changes to the data maintained by the service. We also find that of the three servers we evaluate, one of the commercial products provides the best performance for our workload and that the response time of the information service was not improved during the single experiment we performed with data distributed across two servers.     

Gene family matters: expanding the HGNC resource

The HUGO Gene Nomenclature Committee (HGNC) assigns approved gene symbols to human loci. There are currently over 33,000 approved gene symbols, the majority of which represent protein-coding genes, but we also name other locus types such as non-coding RNAs, pseudogenes and phenotypic loci. Where relevant, the HGNC organise these genes into gene families and groups. The HGNC website http://www.genenames.org/ is an online repository of HGNC-approved gene nomenclature and associated resources for human genes, and includes links to genomic, proteomic and phenotypic information. In addition to this, we also have dedicated gene family web pages and are currently expanding and generating more of these pages using data curated by the HGNC and from information derived from external resources that focus on particular gene families. Here, we review our current online resources with a particular focus on our gene family data, using it to highlight our new Gene Symbol Report and gene family data downloads.     

基于网络的杂草标本管理信息系统的设计与开发

杂草标本在一定程度上反映了杂草物种的区域多样性及其分布 ,对于农田杂草的生物生态学研究、杂草的综合治理以及杂草资源的保护和持续利用都具有重要意义 ,是进行杂草科学研究的宝贵资源。在对全国杂草区系进行全面深入的调查、标本采集和鉴定工作的基础上 ,南京农业大学建立了中国杂草标本室 ,收藏的杂草标本涵盖全国 30个省、市、自治区 ,共有标本 3万余份 ,是我国目前数量最多、覆盖最广、包罗最完备的专业杂草标本室[1] 。国内外许多生物标本馆利用计算机数据库技术开发了标本管理信息系统[2 7] 。这些系统的开发 ,极大地方便了标本信…     

江苏农业种质资源平台运行管理信息系统建设

为促进农业种质资源开放共享,江苏省于2005年启动农业种质资源保护与利用平台建设,经过十多年的努力,初步建成了“四位一体”“库圃结合”的农业种质资源保护与利用体系,涵盖农作物、林木、水产和家养动物4大类共计30个省级种质库(圃),有力地支撑了江苏现代农业品种创新与产业发展.由于平台跨学科、跨行业建设,种质库(圃)遍布全...     

Integrating epitope data into the emerging web of biomedical knowledge resources

The recognition of immune epitopes is an important molecular mechanism of the vertebrate immune system to discriminate between self and non-self. Increasing amounts of data on immune epitopes are becoming available due to technological advances in epitope-mapping techniques and the availability of genomic information for pathogens. Organizing this data poses a challenge that is similar to the successful effort that was required to organize genomic data, which needed the establishment of centralized databases that complement the primary literature to make the data readily accessible and searchable by researchers. As described in this Innovation article, the Immune Epitope Database and Analysis Resource aims to achieve the same for the more complex and context-dependent information on immune epitopes, and to integrate this data with existing and emerging knowledge resources.     

Review of Information Resources to Support Human Exposure Assessment Models

Efforts to model human exposures to chemicals are growing more sophisticated and encompass increasingly complex exposure scenarios. The scope of such analyses has increased, growing from assessments of single exposure pathways to complex evaluations of aggregate or cumulative chemical exposures occurring within a variety of settings and scenarios. In addition, quantitative modeling techniques have evolved from simple deterministic analyses using single point estimates for each necessary input parameter to more detailed probabilistic analyses that can accommodate distributions of input parameters and assessment results. As part of an overall effort to guide development of a comprehensive framework for modeling human exposures to chemicals, available information resources needed to derive input parameters for human exposure assessment models were compiled and critically reviewed. Ongoing research in the area of exposure assessment parameters was also identified. The results of these efforts are summarized and other relevant information that will be needed to apply the available data in a comprehensive exposure model is discussed. Critical data gaps in the available information are also identified. Exposure assessment modeling and associated research would benefit from the collection of additional data as well as by enhancing the accessibility of existing and evolving information resources.     

一种通用的、基于Agent的生物资源整合架构

众所周知,随着基因组测序工作的蓬勃发展和后基因组时代的到来,生物信息学数据呈指数级增长.生物界在享受着资源共享所带来便利的同时,也随着数据总量和复杂性的不断增加而变得异构化和分布化.目前,各种生物计算软件和数据库资源通常标准不一而且很难兼容.因此,如何在这些异构资源之间实现数据集成与软件共享是有效利用生物信息资源的关键.为解决以上问题,本文提出了一种新型的数据整合架构,该架构通过将web服务与并行计算相结合的方法,轻松地实现了对异地资源数据的访问、提取、转化以及整合.实验证明,本系统在处理异构、海量数据方面有着巨大的计算潜力.     

PatGen--a consolidated resource for searching genetic patent sequences

SUMMARY: Compared to the wealth of online resources covering genomic, proteomic and derived data the Bioinformatics community is rather underserved when it comes to patent information related to biological sequences. The current online resources are either incomplete or rather expensive. This paper describes, PatGen, an integrated database containing data from bioinformatic and patent resources. This effort addresses the inconsistency of publicly available genetic patent data coverage by providing access to a consolidated dataset. AVAILABILITY: PatGen can be searched at http://www.patgendb.com CONTACT: rjdrouse@patentinformatics.com.     

SPINE 2: a system for collaborative structural proteomics within a federated database framework

We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laboratory information management system (LIMS) for key bits of information related to the progress of the consortium in cloning, expressing and purifying proteins and then solving their structures by NMR or X-ray crystallography. Originally, SPINE focused on tracking constructs, but, in its current form, it is able to track target sample tubes and store detailed sample histories. The core database comprises a set of standard relational tables and a data dictionary that form an initial ontology for proteomic properties and provide a framework for large-scale data mining. Moreover, SPINE sits at the center of a federation of interoperable information resources. These can be divided into (i) local resources closely coupled with SPINE that enable it to handle less standardized information (e.g. integrated mailing and publication lists), (ii) other information resources in the NESG consortium that are inter-linked with SPINE (e.g. crystallization LIMS local to particular laboratories) and (iii) international archival resources that SPINE links to and passes on information to (e.g. TargetDB at the PDB).