Using Web-Services NCBI EUtils lec10.pptVIP

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Using Web-Services NCBI EUtils lec10.ppt

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Using Web-Services NCBI EUtils lec10.ppt

11/5/2008 BCHB524 - 2008 - Edwards Using Web-Services: NCBI EUtils, online BLAST BCHB5242008Lecture 10 Outline NCBI EUtils …from a script, via the internet NCBI Blast …from a script, via the internet Exercises Lecture 8 exercises NCBI Entrez Powerful web-portal for NCBIs online databases Nucleotide Protein PubMed Gene Structure Taxonomy OMIM etc… NCBI Entrez We can do a lot using a web-browser Look up a specific record nucleotide, protein, mRNA, EST, PubMed, structure,… Search for matches to a gene or disease name Download sequence and other data associated with a nucleotide or protein Sometimes we need to automate the process Use Entrez to select and return the items of interest, rather than download, parse, and select. NCBI EUtils Used to automate the use of Entrez capabilities. Google: EUtils Help /entrez/query/static/eutils_help.html See also, Chapter 7 of the BioPython tutorial Play nice with the Entrez resources! At most 100 requests during the day Supply your email address Use history for large requests …otherwise you or your computer could be banned! NCBI EUtils No need to use Python, BioPython Can form urls and parse XML directly. EInfo PubMed Info BioPython and Entrez EUtils As you might expect BioPython provides some nice tools to simplify this process BioPython and Entrez EUtils Thin wrapper around EUtils web-services Use EUtils argument names db for database name, for example Use Entrez.read to make a simple dictionary from the XML results. Could also parse XML directly (ElementTree), or get results in genbank format (for sequence) Use result.keys() to discover structure of returned results. EUtils Web-Services EInfo Discover database names and fields ESearch Search within a particular database Returns primary ids EFetch Download database entries Others: ELink, EPost, ESummary, EGQuery Using ESearch By default only get back some of the ids: Use retmax to get back more… Meaning of returned id is database specific… Using EFetch ESearch and