Transcript Sesión 1 : Bioinformatics

SESIÓN 2 : BIOINFORMATICS –
LITERATURE + GENE DATABASES
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BIOINFORMATICS - LITERATURE
DATABASES
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Please play with the following tools using your
research theme/gene/author
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We will use: prostate cancer bioinformatics,
slit2, Trevino V
[email protected]
LITERATURE DATABASES AND INFORMATION
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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/
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PUBMED
Searches are “AND” by default
 Queries using … are more powerful
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 AND
 OR
 NOT
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PUBMED SEARCH IMPROVEMENT
Use MyNCBI and highlights query words
 Fields
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[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
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Mesh Terms
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"SOFTWARE" MESH TERMS
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*SOFTWARE MESH TERM QUERY ISSUE
We wanted all software "published" so we query:
 software=88448
 *Software[MH] = 88448
 "*Software"[MH] = 64315
 Software[MH] =64315
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PUBMED SUMMARY
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MAIN abstracts source from published papers
in the WORLD about biosciences.
Versatile query and search engine
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Several data formats
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Access to specific fields, e. g. 'prostate "bmc"[TA]',
'Trevino V[AU]'
Citations  EndNote
Links to paper
Clipboard, History
User-Specific Features
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EBI - LITERATURE DATABASES/SERVICES
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EBI (European Bioinformatics Institute)
http://www.ebi.ac.uk/
http://www.ebi.ac.uk/citexplore
(similar to PubMed)
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EBIMed – Related to Genes
http://www.ebi.ac.uk/Rebholz-srv/ebimed
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CiteXplore
http://www.ebi.ac.uk/citexplore/newSimpleSearch.
do
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I NEED A PAPER… NOW WHAT?
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PubMed Central
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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
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RICHER LITERATURE MINING SERVICES
XplorMed http://www.ogic.ca/projects/xplormed
 eTBLAST http://invention.swmed.edu/etblast/
 HubMed http://www.hubmed.org
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[email protected]
HUBMED HAS TOUCHGRAPH™
TECHNOLOGY
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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/
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TEXT/LITERATURE MINING RESEARCH IS
VERY ACTIVE
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TRENDS…SEPARATED?
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TEXT/LITERATURE MINING/SEARCHING
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Try as many tools/services as you can
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Remember/SAVE your favorites
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Use PubMed/CiteXplore user features
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Save your research queries, so systems keep you updated
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Search and try NEW TOOLS
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Use EndNoteWeb
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http://biblioteca.mty.itesm.mx/bases-de-datos
BIOINFORMATICS
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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]
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Materials and Methods:
 Published
in NAR
 Includes NAR WebServer Issue
 Done by British Columbia Univ & NAR
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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]
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Results (cont):
 2006:
More than 1000 links
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Results (cont):
 2006:
More than 1000 links
Results (Cont)
2008:
Results (Cont)
2007:
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CONCLUSION
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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]
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Disadvantages:
 ONLY
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NAR PAPERS
Wish List
 FAVORITES?
 BOOKMARKS?
 AUTOSARCHES?