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 Please play with the following tools using your research theme/gene/author  We will use: prostate cancer bioinformatics, slit2, Trevino.

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Presentation on theme: " Please play with the following tools using your research theme/gene/author  We will use: prostate cancer bioinformatics, slit2, Trevino."— Presentation transcript:

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2 vtrevino@itesm.mx  Please play with the following tools using your research theme/gene/author  We will use: prostate cancer bioinformatics, slit2, Trevino V

3 vtrevino@itesm.mx  PubMed (Medline) / Entrez  National Center for Biological Information USA http://www.ncbi.nlm.nih.gov/ Prostate Cancer

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5 http://www.ncbi.nlm.nih.gov/

6 vtrevino@itesm.mx  Searches are “AND” by default  Queries using … are more powerful  AND  OR  NOT

7 vtrevino@itesm.mx  Use MyNCBI and highlights query words  Fields  [TI]  [TIAB]  [AB]  Authors[AU]  Journal[TA]  http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppu bmed.section.pubmedhelp.Search_Field_Descrip http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppu bmed.section.pubmedhelp.Search_Field_Descrip  Mesh Terms help

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9 We wanted all software "published" so we query:  software=88448  *Software[MH] = 88448  "*Software"[MH] = 64315  Software[MH] =64315

10 vtrevino@itesm.mx  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

11 vtrevino@itesm.mx  EBI (European Bioinformatics Institute) http://www.ebi.ac.uk/ http://www.ebi.ac.uk/citexplore (similar to PubMed) http://www.ebi.ac.uk/ http://www.ebi.ac.uk/citexplore  EBIMed – Related to Genes http://www.ebi.ac.uk/Rebholz-srv/ebimed http://www.ebi.ac.uk/Rebholz-srv/ebimed  CiteXplore http://www.ebi.ac.uk/citexplore/newSimpleSearch. do http://www.ebi.ac.uk/citexplore/newSimpleSearch. do

12 vtrevino@itesm.mx  PubMed Central  Free Papers  Tec: http://biblioteca.itesm.mxhttp://biblioteca.itesm.mx  CiteSeer: http://citeseer.ist.psu.edu/ (Ingeniería)http://citeseer.ist.psu.edu/  Google Scholar http://scholar.google.com.mx/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 http://www.springerlink.com  Biblioteca Virtual de Biotecnología para las Américas  http://biblioteca.ibt.unam.mx/vcba/articulos.php

13 vtrevino@itesm.mx PaísNombre BDLiga MXBANAPANET http://www.impi.gob.mx/impi/jsp/indice.jsp http://siga.impi.gob.mx/http://www.impi.gob.mx/impi/jsp/indice.jsp http://siga.impi.gob.mx/ http://vidoc.impi.gob.mxhttp://vidoc.impi.gob.mx USAUSPTOhttp://www.uspto.gov/patft/index.html ESESPACENET http://es.espacenet.com/search97cgi/s97_cgi.exe?Action=For mGen&Template=es/ES/home.hts Am Latinalatipat http://www.oepm.es/bases- documentales/latipat_sp?ACTION=RETOUR JPJPDLhttp://www.ipdl.inpit.go.jp/homepg_e.ipdl ALdepatisnet http://depatisnet.dpma.de/DepatisNet/depatisnet?window=1 &space=unknown&content=index&action=index&session=c23 b66f330d986fd2581bfdf4e20939cdc40df8949e5&stamp=1 03011 OMPI http://www.wipo.int/pctdb/en/ CanadaCIPOhttp://patents1.ic.gc.ca/srch_adv-e.html TaiwanIPOhttp://patents1.ic.gc.ca/srch_adv-e.html

14 vtrevino@itesm.mx  XplorMed http://www.ogic.ca/projects/xplormed http://www.ogic.ca/projects/xplormed  eTBLAST http://invention.swmed.edu/etblast/ http://invention.swmed.edu/etblast/  HubMed http://www.hubmed.org http://www.hubmed.org

15 vtrevino@itesm.mx  HubMed http://www.hubmed.org (is it working at the moment?, but as seen in http://www.touchgraph.com/TGGoogleBrowser. html) http://www.hubmed.org http://www.touchgraph.com/TGGoogleBrowser. html

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19  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 http://biblioteca.mty.itesm.mx/bases-de-datos

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

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

22 vtrevino@itesm.mx  Materials and Methods:  Published in NAR  Includes NAR WebServer Issue  Done by British Columbia Univ & NAR

23 vtrevino@itesm.mx  Results:  http://bioinformatics.ca/links_directory/narweb2007 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

24 vtrevino@itesm.mx  Results (cont):  2006: More than 1000 links

25 vtrevino@itesm.mx  Results (cont):  2006: More than 1000 links

26 Results (Cont) 2008:

27 Results (Cont) 2007:

28 vtrevino@itesm.mx  The Bioinformatics Links Directory is a growing rich source of searchable, and browsable bioinformatics tools, services, and databases. –http://bioinformatics.ca/links_directory/narweb2007http://bioinformatics.ca/links_directory/narweb2007 http://bioinformatics.ca/links_directory/index.php

29 vtrevino@itesm.mx  Disadvantages:  ONLY NAR PAPERS  Wish List  FAVORITES?  BOOKMARKS?  AUTOSARCHES?


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