Sesión 1 : Bioinformatics - Literature Databases

educationafflictedΒιοτεχνολογία

4 Οκτ 2013 (πριν από 4 χρόνια και 8 μέρες)

91 εμφανίσεις

SESIÓN 2 :
BIOINFORMATICS


LITERATURE + GENE DATABASES


vtrevino@itesm.mx

BIOINFORMATICS
-

LITERATURE
DATABASES



Please play with the following tools using your
research theme/gene/author



We will use: prostate cancer bioinformatics,
slit2, Trevino
V

vtrevino@itesm.mx

LITERATURE DATABASES AND INFORMATION


PubMed (Medline) / Entrez




National Center for Biological Information USA

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

Prostate Cancer

vtrevino@itesm.mx

vtrevino@itesm.mx

ON
-
LINE VIEW


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


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PUBMED


Searches are “AND” by default


Queries using … are more powerful


AND


OR


NOT

vtrevino@itesm.mx

P
UBMED

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
=
helppu
bmed.section.pubmedhelp.Search_Field_Descrip


Mesh

Terms

help

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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

vtrevino@itesm.mx

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


vtrevino@itesm.mx

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


vtrevino@itesm.mx

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

vtrevino@itesm.mx

PATENTS

País

Nombre BD

Liga

MX

BANAPANET

http://www.impi.gob.mx/impi/jsp/indice.
jsp

http://siga.impi.gob.mx/

http://vidoc.impi.gob.mx


USA

USPTO

http://www.uspto.gov/patft/index.html

ES

ESPACENET

http://es.espacenet.com/search97cgi/s97_cgi.exe?Action=For
mGen&Template=es/ES/home.hts

Am Latina

latipat

http://www.oepm.es/bases
-
documentales/latipat_sp?ACTION=RETOUR

JP

JPDL

http://www.ipdl.inpit.go.jp/homepg_e.ipdl

AL

depatisnet

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

vtrevino@itesm.mx

RICHER LITERATURE MINING SERVICES


XplorMed

http://www.ogic.ca/projects/xplormed



eTBLAST

http://invention.swmed.edu/etblast/



HubMed

http://www.hubmed.org


vtrevino@itesm.mx

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
)




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GOPUBMED

HTTP://WWW.GOPUBMED.ORG/


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TEXT/LITERATURE MINING RESEARCH IS
VERY ACTIVE

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TRENDS…SEPARATED?

vtrevino@itesm.mx

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.


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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



vtrevino@itesm.mx


Results (cont):


2006: More than 1000 links



vtrevino@itesm.mx


Results (cont):


2006: More than 1000 links



Results (Cont)

2008:

Results (Cont)

2007:

vtrevino@itesm.mx

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

vtrevino@itesm.mx


Disadvantages:


ONLY NAR PAPERS



Wish List


FAVORITES?


BOOKMARKS?


AUTOSARCHES?