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1、UsingWeb-Services:NCBIEUtils, onlineBLASTBCHB524 2008 Lecture1011/5/2008BCHB524-2008-EdwardsOutlineNCBIEUtils…fromascript,viatheinternetNCBIBlast…fromascript,viatheinternetExercisesLecture8exercises11/5/20082BCHB524-2008-EdwardsNCBIEntrezPowerfulweb-portalforNC
2、BI'sonlinedatabasesNucleotideProteinPubMedGeneStructureTaxonomyOMIMetc…11/5/20083BCHB524-2008-EdwardsNCBIEntrezWecandoalotusingaweb-browserLookupaspecificrecordnucleotide,protein,mRNA,EST,PubMed,structure,…SearchformatchestoageneordiseasenameDownloadsequenceand
3、otherdataassociatedwithanucleotideorproteinSometimesweneedtoautomatetheprocessUseEntreztoselectandreturntheitemsofinterest,ratherthandownload,parse,andselect.11/5/20084BCHB524-2008-EdwardsNCBIEUtilsUsedtoautomatetheuseofEntrezcapabilities.Google:EUtilsHelphttp:
4、//www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.htmlSeealso,Chapter7oftheBioPythontutorialPlaynicewiththeEntrezresources!Atmost100requestsduringthedaySupplyyouremailaddressUsehistoryforlargerequests…otherwiseyouoryourcomputercouldbebanned!11/5/20085BCHB5
5、24-2008-EdwardsNCBIEUtilsNoneedtousePython,BioPythonCanformurlsandparseXMLdirectly.EInfoPubMedInfo11/5/20086BCHB524-2008-EdwardsBioPythonandEntrezEUtilsAsyoumightexpectBioPythonprovidessomenicetoolstosimplifythisprocessfromBioimportEntrezEntrez.email='netid@geo
6、rgetown.edu'handle=Entrez.einfo()result=Entrez.read(handle)printresult["DbList"]handle=Entrez.einfo(db='pubmed')result=Entrez.read(handle)printresult["DbInfo"]["Description"]printresult["DbInfo"]["Count"]printresult["DbInfo"].keys()11/5/20087BCHB524-2008-Edward
7、sBioPythonandEntrezEUtils"Thin"wrapperaroundEUtilsweb-servicesUseEUtilsargumentnamesdbfordatabasename,forexampleUseEntrez.readtomakeasimpledictionaryfromtheXMLresults.CouldalsoparseXMLdirectly(ElementTree),orgetresultsingenbankformat(forsequence)Useresult.keys(
8、)to"discover"structureofreturnedresults.11/5/20088BCHB524-2008-EdwardsEUtilsWeb-ServicesEInfoDiscoverdatabasenamesandfieldsESearchSearchwithinaparticulardatabaseReturns"prim
