XML在生物信息学中的应用Application of XML in Bioinformatics
张秀格;翁梅;
摘要(Abstract)：
[目的]阐明XML在生物信息学研究中的重要地位与作用。[方法]通过详细阐述XML的基本原理,系统地比较和分析XML与其他应用于生物数据管理的标记语言包括HTML、BSML、BioML等的利与弊,以期阐明XML作为一种数据语言在生物信息学中的重要作用。[结果]XML是一个很有前途的扩展性标准语言,是生物信息学数据库内部数据交换的重要枢纽。[结论]XML是用于生物信息学的各个领域中生物数据管理最有效的标记语言。
关键词(KeyWords)： XML;生物信息;数据整合;应用
基金项目(Foundation): 河南省科技厅河南重点保护植物资源信息管理系统及评价体系(0624050020)
作者(Author): 张秀格;翁梅;
Email:
DOI: 10.13989/j.cnki.0517-6611.2009.30.165
参考文献(References)：
- [1]LAWRENCE S,GILES C L.Accessibility of information on the web[J].Nature,1999,400:107-109.
- [2]张咏.XML及其在图书馆和情报检索中的应用[J].现代图书情报技术,2001(2):30-34.
- [3]CIANCARINI P,VITALI F,MASCOLOC.Managingcomplexdocuments o-verthe WWW:a case studyforXML.IEEETrans[J].Knowledge and DataEngineering,1999,11:629-638.
- [4]MURRAY-RUSTP,RZEPAHS.Chemical markup,XML,and the World-wide Web.l.Basic principles[J].Journal of Chemical Information and Compution Sciences,1999,39:928-942.
- [5]FENYOD.The biopolymer markup language[J].Bioinformatics,1999,15:339-340.
- [6]GILMOUR R.Taxonomic markup language:applying XML to systematic data[J].Bioinformatics,2000,16:406-407.
- [7]LEWISSE,HARRISNL,HELTGA,etal.Anintelligentsystemforinter-pretation of sequence alignment results[M].The Institute for Genomic Re-search:Second Annual Conference on Computational Genomics.Reston,Virginia,1998:9.
- [8]EDITORIAL.Arraydata gopublic[J].Nature Genetics,1999,22(3):211-212.
- [9]ROBBINS R J.Report of the invitational DOE workshop on genome infor-matics,26-27April1993,Baltimore,Maryland.genome informatics I:com-munity database[J].Journal of Computational Biology,1994(1):73-190.
- [10]LETOVSKYSI.Beyond the informationmaze[J].Journal ofComputation-al Biology,1995(2):539-546.
- [11]DISCALAC,NINNINM,ACHARDF,etal.DBcat:a catalogof biological databases[J].Nucleic Acids Research,1999,27:10-11.
- [12]MARKOWITZ V M,RITTER O.Characterizing heterogeneous molecular biology database systems[J].Journal of Computational Biology,1995(2):547-556.
- [13]ETZOLDT,ULYANOVA,ARGOSP.SRS:Informationretrieval systemfor molecular biology data banks[J].Methods in Enzymology,1996,266:114-128.
- [14]MEDIGUE C,RECHENMANN F,DANCHIN A,et al.Imagene:an inte-grated computer environment for sequence annotation and analysis[J].Bioinformatics,1999,15:2-15.
- [15]STEEDMAND.ASN.I the tutorial and reference[M].Twickenham,UK:Technology Appraisals,1993.
- [16]ACHARD F,BARILLOTE.Ubiquitous distributed objects with CORBA[M]//ALTMAN R,DUNKER K,HUNTER,et al.Pacific symposium on Biocomputing’97.Singapore:World Scientific,1997:39-50.
- [17]CATTELL R G.The object database standard:ODMG-93[M].Morgan Kaufman,San Francisco,1996.
- [18]MOLLER S,LESER U,FLEISCHMANNW,et al.DITto TrEMBL:a dis-tributed approach to high-quality automated protein sequence annotation[J].Bioinformatics,1999,15:219-227.
- [19]ABERER K.The use of object-oriented data models in biomolecular data-bases[M].Heidelberg Germany:Conference on Object-Oriented Compu-ting in the Natural Sciences,1994:3-13.
- [20]The Gene Ontology Consortium.Gene ontology:tool for the unification of biology[J].Nature Genetics,2000,25:25-29.