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SESIÓN 2 : BIOINFORMATICS – LITERATURE + GENE DATABASES
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 Center for Biological Information USA
http://www.ncbi.nlm.nih.gov/
Prostate Cancer
PUBMED SEARCH IMPROVEMENT
Use MyNCBI and highlights query words Fields
[TI] [TIAB] [AB] Authors[AU] Journal[TA] http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=
helppubmed.section.pubmedhelp.Search_Field_Descrip
Mesh Terms
help
*SOFTWARE MESH TERM QUERY ISSUE
We wanted all software "published" so we query:
software=88448 *Software[MH] = 88448 "*Software"[MH] = 64315 Software[MH] =64315
PUBMED SUMMARY
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
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 Geneshttp://www.ebi.ac.uk/Rebholz-srv/ebimed
CiteXplore http://www.ebi.ac.uk/citexplore/newSimpleSearch.do
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
PATENTS
PaísNombre BD Liga
MXBANAPANET
http://www.impi.gob.mx/impi/jsp/indice.jsphttp://siga.impi.gob.mx/ http://vidoc.impi.gob.mx
USA USPTO http://www.uspto.gov/patft/index.html
ESESPACENET http://es.espacenet.com/search97cgi/s97_cgi.exe?Ac
tion=FormGen&Template=es/ES/home.htsAm Latina latipat http://www.oepm.es/bases-documentales/latipat_sp?
ACTION=RETOURJP JPDL http://www.ipdl.inpit.go.jp/homepg_e.ipdl
ALdepatisnet http://depatisnet.dpma.de/DepatisNet/depatisnet?wi
ndow=1&space=unknown&content=index&action=index&session=c23b66f330d986fd2581bfdf4e20939cdc40df8949e5&stamp=103011
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
RICHER LITERATURE MINING SERVICES XplorMed
http://www.ogic.ca/projects/xplormed eTBLAST
http://invention.swmed.edu/etblast/ HubMed http://www.hubmed.org
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)
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.
Materials and Methods: Published in NAR Includes NAR WebServer Issue Done by British Columbia Univ & NAR
Results: http://bioinformatics.ca/links_directory/nar
web2007 Links with descriptive biological categories PubMed citations Searchable Browsable RSS feeds Done by British Columbia Univ & NAR Community-driven
Results (Cont)2008:
Results (Cont)2007:
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
