Reference : PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from Pu...
Scientific journals : Article
Life sciences : Biotechnology
Systems Biomedicine
http://hdl.handle.net/10993/26645
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
English
Barbosa Da Silva, Adriano mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Fontaine, Jean-Fred [> >]
Donnard, Elisa R. [> >]
Stussi, Fernanda [> >]
Ortega, J. Miguel [> >]
Andrade-Navarro, Miguel A. [> >]
2011
BMC bioinformatics
12
435
Yes (verified by ORBilu)
1471-2105
1471-2105
England
[en] Colorectal Neoplasms/genetics/metabolism ; Data Mining ; Humans ; Internet ; Neurodegenerative Diseases/genetics/metabolism ; Proteins/genetics/metabolism ; PubMed ; Software
[en] BACKGROUND: Biological function is greatly dependent on the interactions of proteins with other proteins and genes. Abstracts from the biomedical literature stored in the NCBI's PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-occurrences of their terms. Often, the amount of interactions obtained through such an approach is large and may mix processes occurring in different contexts. Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation. RESULTS: To help the concept-oriented exploration of such data we developed PESCADOR, a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts. We illustrate its use in exploring protein aggregation in neurodegenerative disease and in the expansion of pathways associated to colon cancer. CONCLUSIONS: PESCADOR is a platform independent web resource available at: http://cbdm.mdc-berlin.de/tools/pescador/
http://hdl.handle.net/10993/26645

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Open access
1471-2105-12-435.pdfPublisher postprint963.72 kBView/Open

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.