MEDLINE摘要本地下载与更新及癌基因表达数据的文本挖掘(英文)

近年来对生物医学文献的文本挖掘在功能基因组学研究中得到了广泛开展。为了更好的检索MEDLINE摘要,本文介绍利用Unix文本过滤命令实现了对摘要的自动下载和更新。同时,对癌基因表达数据,如癌的种类,癌基因表达情况,及与p53基因的关联等进行了初步的文本挖掘分析。     

中文生物医学文献信息数据库分析

本文从生物医学数据库用户角度,浅析了中文生物医学文献信息服务的特点和数据库建库的一些要求。     

中文生物医学文献信息数据库分析

本文从生物医学数据库用户角度,浅析了中文生物医学文献信息服务的特点和数据库建库的一些要求。     

生命与健康大数据中心资源

生命与健康多组学数据是生命科学研究和生物医学技术发展的重要基础。然而,我国缺乏生物数据管理和共享平台,不但无法满足国内日益增长的生物医学及相关学科领域的研究发展需求,而且严重制约我国生物大数据整合共享与转化利用。鉴于此,中国科学院北京基因组研究所于2016年初成立生命与健康大数据中心(BIG Data Center, BIGD),围绕国家人口健康和重要战略生物资源,建立生物大数据管理平台和多组学数据资源体系。本文重点介绍BIGD的生命与健康大数据资源系统,主要包括组学原始数据归档库、基因组数据库、基因组变异数据库、基因表达数据库、甲基化数据库、生物信息工具库和生命科学维基知识库,提供生物大数据汇交、整合与共享服务,为促进我国生命科学数据管理、推动国家生物信息中心建设奠定重要基础。     

基因表达谱微阵列网络数据库在肿瘤研究中的应用

基因表达谱微阵列数据库是一类可提供存储、查询、下载分析的在线网络数据库,在肿瘤相关领域的研究中提供了大量的数据来源。由于微阵列分析对于无生物/医学信息学专业背景的研究人员仍然有较多困难,致使该数据库的使用尚未普及。本文从数据查询、下载分析和使用方法等方面对常用基因表达谱微阵列数据库进行概述,并对现阶段基因表达微阵列数据库的应用策略进行总结,旨在帮助该领域研究的初学工作者了解数据库的基本知识并推动其在科研工作中的应用。     

NCBI的数据库资源及其应用

NCBI是美国的一个大型生物信息学系统,它主要通过NCBI网站为全世界的科学家服务,它拥有GenBank,RefSeq,UniGene,dbSNP等等多种大型生物学数据库,并且提供了多种数据库查询工具,如：Entrez,PubMed,LocusLink,TaxonomyBrowser等等,以及多种数据库分析资源,对于我们查询文献,人类基因组信息、基因表达、蛋白质结构、肿瘤遗传信息,以及不同种属遗传信息等等有非常大的帮助。是一个非常重要的生物医学资源。     

全国中文核心期刊 中国农业核心期刊

<正>《生物技术通报》是中国农业部主管、中国农业科学院农业信息研究所主办的综合性学术期刊。是美国化学文摘(CA)、中国生物医学文献服务系统(SinoMed)中的《中国生物医学文献数据库》(CBM)、中国科学引文数据库(CSCD)、中国核心期刊遴选数据库     

MetaGen: 从KEGG建模代谢网络的新工具

为便于大规模代谢网络的计算,发展了一款方便实用的工具:MetaGen,对Kyoto Encyclopedia of Genesand Genomes(KEGG)中物种特异的各层次代谢系统进行建模,生成的代谢网络以酶图和通路图的方式表示.利用该工具,对人类代谢系统的bow-tie结构进行了初步研究,并以此为例展示了该工具广阔的应用前景.MetaGen利用KEGGweb服务保证建模数据的可靠性,依靠本地关系数据库加速网络建模过程并提供更多的数据管理和利用方式,并结合高级JAVA技术提高代码的可扩展性.MetaGen完全开源,可直接从http://bnct.sourceforge.net/下载.     

全国中文核心期刊 中国农业核心期刊

<正>《生物技术通报》是中国农业部主管、中国农业科学院农业信息研究所主办的学术期刊。被美国化学文摘(CA)、中国生物医学文献服务系统(SinoMed)中的《中国生物医学文献数据库》(CBM)、中国科学引文数据库(CSCD)、中国科技论文与引文数据库(CSTPCD)、中国核心期刊遴选数据库、中国学术期刊综合评价数据库等国内外重要数据库收录。入选全国中文核心期刊,中国农业核心期刊,RCCSE中国核心学术期刊(扩展版)。     

本刊被《中国生物医学文献数据库》收录

[本刊讯]近日本刊接到通知,《四川动物》杂志被中国生物医学文献服务系统(SinoMed)中的《中国生物医学文献数据库》(CBM)收录。中国生物医学文献数据库(CBM)是由中国医学科学院医学信息研究所于1994年研制开发的综合性中文医学文献数据库,是国内最专业、权威的医学、生物学数据库之一,作为国家查新必备库,已在国内各医学领域得到了广泛的应用和认可。CBM收录1978年以来1600多种中国生物医学     

The EBI SRS server-new features

MOTIVATION: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. AVAILABILITY: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.     

The EBI SRS server--recent developments

MOTIVATION: The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform interface--representing the domain knowledge. The SRS has become an integration system for both data retrieval and applications for data analysis. It provides capabilities to search multiple databases by shared attributes and to query across databases fast and efficiently. RESULTS: Here we present recent developments at the EBI SRS server (http://srs.ebi.ac.uk). The EBI SRS server contains today more than 130 biological databases and integrates more than 10 applications. It is a central resource for molecular biology data as well as a reference server for the latest developments in data integration. One of the latest additions to the EBI SRS server is the InterPro database-Integrated Resource of Protein Domains and Functional Sites. Distributed in XML format it became a turning point in low level XML-SRS integration. We present InterProScan as an example of data analysis applications, describe some advanced features of SRS6, and introduce the SRSQuickSearch JavaScript interfaces to SRS.     

Protein structure topological comparison, discovery and matching service

We describe a fold level fast protein comparison and motif matching facility based on the TOPS representation of structure. This provides an update to a previous service at the EBI, with a better graph matching with faster results and visualization of both the structures being compared against and the common pattern of each with the target domain. AVAILABILITY: Web service at http://balabio.dcs.gla.ac.uk/tops or via the main TOPS site at http://www.tops.leeds.ac.uk. Software is also available for download from these sites.     

The EMBL Nucleotide Sequence Database: major new developments

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization. Webin is the preferred web-based submission system for individual submitters, while automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, Email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases plus many other specialized molecular biology databases. For sequence similarity searching, a variety of tools (e.g. Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

DBcat: a catalog of 500 biological databases

The DBcat (http://www.infobiogen.fr/services/dbcat ) is a comprehensive catalog of biological databases, maintained and curated at Infobiogen. It contains 500 databases classified by application domains. The DBcat is a structured flat-file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for download from Infobiogen anonymous ftp server.     

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database

The submission of multiple sequence alignment data to EMBL has grown 30-fold in the past 10 years, creating a problem of archiving them. The EBI has developed a new public database of multiple sequence alignments called EMBL-Align. It has a dedicated web-based submission tool, Webin-Align. Together they represent a comprehensive data management solution for alignment data. Webin-Align accepts all the common alignment formats and can display data in CLUSTALW format as well as a new standard EMBL-Align flat file format. The alignments are stored in the EMBL-Align database and can be queried from the EBI SRS (Sequence Retrieval System) server. AVAILABILITY: Webin-Align: http://www.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align, http://srs.ebi.ac.uk/     

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl.html) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. While automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO), the preferred submission tool for individual submitters is Webin (WWW). Through all stages, dataflow is monitored by EBI biologists communicating with the sequencing groups. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI). Database releases are produced quarterly and are distributed on CD-ROM. Network services allow access to the most up-to-date data collection via Internet and World Wide Web interface. EBI's Sequence Retrieval System (SRS) is a Network Browser for Databanks in Molecular Biology, integrating and linking the main nucleotide and protein databases, plus many specialised databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, Blast etc) are available for external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.     

The EMBL nucleotide sequence database

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.     

The EMBL Nucleotide Sequence Database

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

The EMBL nucleotide sequence database

The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http://www.ebi.ac. uk/embl/index.html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. WEBIN is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via Internet and WWW interfaces. EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology, integrating and linking the main nucleotide and protein databases plus many specialised databases. For sequence similarity searching a variety of tools (e.g., BLITZ, FASTA, BLAST) are available which allow external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.