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Sesión 2 : Bioinformatics – Literature + GENE Databases

Sesión 2 : Bioinformatics – Literature + GENE Databases. Please play with the following tools using your research theme/gene/author We will use: prostate cancer bioinformatics, slit2, Trevino V. Bioinformatics - Literature Databases. PubMed (Medline) / Entrez

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Sesión 2 : Bioinformatics – Literature + GENE Databases

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  1. Sesión 2 : Bioinformatics – Literature + GENE Databases

  2. Please play with the following tools using your research theme/gene/author We will use: prostate cancer bioinformatics, slit2, Trevino V Bioinformatics - Literature Databases

  3. PubMed (Medline) / Entrez • National Center for Biological Information USA Literature Databases and Information Prostate Cancer http://www.ncbi.nlm.nih.gov/

  4. On-Line View http://www.ncbi.nlm.nih.gov/

  5. Searches are “AND” by default • Queries using … are more powerful • AND • OR • NOT Pubmed

  6. Use MyNCBIandhighlightsquerywords • Fields • [TI] • [TIAB] • [AB] • Authors[AU] • Journal[TA] • http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip • MeshTerms PubmedSearchimprovement help

  7. "Software" Mesh Terms

  8. We wanted all software "published" so we query: • software=88448 • *Software[MH] = 88448 • "*Software"[MH] = 64315 • Software[MH] =64315 *Software Mesh Term Query Issue

  9. MAIN abstracts source from published papers in the WORLD about biosciences. • Versatile query and search engine • Access to specific fields, e. g. 'prostate "bmc"[TA]', 'Trevino V[AU]' • Several data formats • Citations EndNote • Links to paper • Clipboard, History • User-Specific Features PubMed Summary

  10. EBI (European Bioinformatics Institute) http://www.ebi.ac.uk/http://www.ebi.ac.uk/citexplore(similar to PubMed) EBIMed – Related to Geneshttp://www.ebi.ac.uk/Rebholz-srv/ebimed CiteXplorehttp://www.ebi.ac.uk/citexplore/newSimpleSearch.do EBI - Literature Databases/Services

  11. 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 BiotecnologíaparalasAméricas • http://biblioteca.ibt.unam.mx/vcba/articulos.php I need a paper… Now what?

  12. Patents

  13. XplorMedhttp://www.ogic.ca/projects/xplormed eTBLASThttp://invention.swmed.edu/etblast/ HubMedhttp://www.hubmed.org Richer Literature Mining Services

  14. HubMedhttp://www.hubmed.org(is it working at the moment?, but as seen in http://www.touchgraph.com/TGGoogleBrowser.html) HubMed has TouchGraph™ Technology

  15. GoPubMedhttp://www.gopubmed.org/

  16. Text/Literature Mining Research is very active

  17. Trends…Separated?

  18. Try as many tools/services as you can • Remember/SAVE your favorites • Use PubMed/CiteXploreuser 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 Text/Literature Mining/Searching

  19. Bioinformatics Databases and WebServices Paper http://bioinformatics.ca/links_directory/narweb2007 Original Paper published in 2005, then updated in 2006 and 2007

  20. AIM: Common repository/links to Free Tools, Free Databases, and Free Resources for Bioinformatics and Molecular Biology Research.

  21. Materials and Methods: • Published in NAR • Includes NAR WebServer Issue • Done by British Columbia Univ & NAR

  22. 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

  23. Results (cont): • 2006: More than 1000 links

  24. Results (cont): • 2006: More than 1000 links

  25. Results (Cont)2008:

  26. Results (Cont)2007:

  27. The Bioinformatics Links Directory is a growing rich source of searchable, and browsable bioinformatics tools, services, and databases. Conclusion • http://bioinformatics.ca/links_directory/narweb2007 http://bioinformatics.ca/links_directory/index.php

  28. Disadvantages: • ONLY NAR PAPERS • Wish List • FAVORITES? • BOOKMARKS? • AUTOSARCHES?

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