SESIÓN 2 : BIOINFORMATICS – LITERATURE + GENE DATABASES [email protected] BIOINFORMATICS - LITERATURE DATABASES Please play with the following tools using your research theme/gene/author We will use: prostate cancer bioinformatics, slit2, Trevino V [email protected] LITERATURE DATABASES AND INFORMATION PubMed (Medline) / Entrez National Prostate Cancer Center for Biological Information USA http://www.ncbi.nlm.nih.gov/ [email protected] [email protected] ON-LINE VIEW http://www.ncbi.nlm.nih.gov/ [email protected] PUBMED Searches are “AND” by default Queries using … are more powerful AND OR NOT [email protected] PUBMED SEARCH IMPROVEMENT Use MyNCBI and highlights query words Fields [TI] [TIAB] [AB] Authors[AU] Journal[TA] help http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppu bmed.section.pubmedhelp.Search_Field_Descrip Mesh Terms [email protected] "SOFTWARE" MESH TERMS [email protected] *SOFTWARE MESH TERM QUERY ISSUE We wanted all software "published" so we query: software=88448 *Software[MH] = 88448 "*Software"[MH] = 64315 Software[MH] =64315 [email protected] PUBMED SUMMARY MAIN abstracts source from published papers in the WORLD about biosciences. Versatile query and search engine Several data formats Access to specific fields, e. g. 'prostate "bmc"[TA]', 'Trevino V[AU]' Citations EndNote Links to paper Clipboard, History User-Specific Features [email protected] EBI - LITERATURE DATABASES/SERVICES EBI (European Bioinformatics Institute) http://www.ebi.ac.uk/ http://www.ebi.ac.uk/citexplore (similar to PubMed) EBIMed – Related to Genes http://www.ebi.ac.uk/Rebholz-srv/ebimed CiteXplore http://www.ebi.ac.uk/citexplore/newSimpleSearch. do [email protected] I NEED A PAPER… NOW WHAT? PubMed Central Free Papers Tec: http://biblioteca.itesm.mx CiteSeer: http://citeseer.ist.psu.edu/ (Ingeniería) Google Scholar http://scholar.google.com.mx/ email authors (normally corresponding author) Friends (but not so many nor so often) Your Tutor/Supervisor Springer Books from ITESM: http://www.springerlink.com Biblioteca Virtual de Biotecnología para las Américas http://biblioteca.ibt.unam.mx/vcba/articulos.php [email protected] PATENTS País MX Nombre BD Liga http://www.impi.gob.mx/impi/jsp/indice.jsp BANAPANET http://siga.impi.gob.mx/ http://vidoc.impi.gob.mx USA USPTO JP JPDL AL depatisnet http://www.ipdl.inpit.go.jp/homepg_e.ipdl http://depatisnet.dpma.de/DepatisNet/depatisnet?window=1 &space=unknown&content=index&action=index&session=c23 b66f330d986fd2581bfdf4e20939cdc40df8949e5&stamp=1 03011 OMPI OMPI http://www.wipo.int/pctdb/en/ Canada CIPO http://patents1.ic.gc.ca/srch_adv-e.html Taiwan IPO http://patents1.ic.gc.ca/srch_adv-e.html http://www.uspto.gov/patft/index.html http://es.espacenet.com/search97cgi/s97_cgi.exe?Action=For ES ESPACENET mGen&Template=es/ES/home.hts http://www.oepm.es/basesAm Latina latipat documentales/latipat_sp?ACTION=RETOUR [email protected] RICHER LITERATURE MINING SERVICES XplorMed http://www.ogic.ca/projects/xplormed eTBLAST http://invention.swmed.edu/etblast/ HubMed http://www.hubmed.org [email protected] HUBMED HAS TOUCHGRAPH™ TECHNOLOGY HubMed http://www.hubmed.org (is it working at the moment?, but as seen in http://www.touchgraph.com/TGGoogleBrowser. html) [email protected] GOPUBMED HTTP://WWW.GOPUBMED.ORG/ [email protected] TEXT/LITERATURE MINING RESEARCH IS VERY ACTIVE [email protected] TRENDS…SEPARATED? [email protected] TEXT/LITERATURE MINING/SEARCHING Try as many tools/services as you can Remember/SAVE your favorites Use PubMed/CiteXplore user features Save your research queries, so systems keep you updated Search and try NEW TOOLS Use EndNoteWeb http://biblioteca.mty.itesm.mx/bases-de-datos BIOINFORMATICS Databases and WebServices Paper http://bioinformatics.ca/links_directory/narweb2007 Original Paper published in 2005, then updated in 2006 and 2007 AIM: Common repository/links to Free Tools, Free Databases, and Free Resources for Bioinformatics and Molecular Biology Research. [email protected] Materials and Methods: Published in NAR Includes NAR WebServer Issue Done by British Columbia Univ & NAR [email protected] Results: http://bioinformatics.ca/links_directory/narweb2007 Links with descriptive biological categories PubMed citations Searchable Browsable RSS feeds Done by British Columbia Univ & NAR Community-driven [email protected] Results (cont): 2006: More than 1000 links [email protected] Results (cont): 2006: More than 1000 links Results (Cont) 2008: Results (Cont) 2007: [email protected] CONCLUSION The Bioinformatics Links Directory is a growing rich source of searchable, and browsable bioinformatics tools, services, and databases. –http://bioinformatics.ca/links_directory/narweb2007 http://bioinformatics.ca/links_directory/index.php [email protected] Disadvantages: ONLY NAR PAPERS Wish List FAVORITES? BOOKMARKS? AUTOSARCHES?
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