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Blohm, P. ; Frishman, G. ; Smialowski, P. ; Goebels, F.* ; Wachinger, B. ; Ruepp, A. ; Frishman, D.

Negatome 2.0: A database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis.

Nucleic Acids Res. 42, D396-D400 (2014)
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Knowledge about non-interacting proteins (NIPs) is important for training the algorithms to predict protein-protein interactions (PPIs) and for assessing the false positive rates of PPI detection efforts. We present the second version of Negatome, a database of proteins and protein domains that are unlikely to engage in physical interactions (available online at http://mips.helmholtz-muenchen.de/proj/ppi/negatome). Negatome is derived by manual curation of literature and by analyzing three-dimensional structures of protein complexes. The main methodological innovation in Negatome 2.0 is the utilization of an advanced text mining procedure to guide the manual annotation process. Potential non-interactions were identified by a modified version of Excerbt, a text mining tool based on semantic sentence analysis. Manual verification shows that nearly a half of the text mining results with the highest confidence values correspond to NIP pairs. Compared to the first version the contents of the database have grown by over 300%.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Interaction Datasets; Extraction; Resource; Negation; Domain; Pdb
Language english
Publication Year 2014
Prepublished in Year 2013
HGF-reported in Year 2013
ISSN (print) / ISBN 0305-1048
e-ISSN 1362-4962
Journal Nucleic Acids Research
Quellenangaben Volume: 42, Issue: D1, Pages: D396-D400 Article Number: , Supplement: ,
Publisher Oxford University Press
Publishing Place Oxford
Reviewing status Peer reviewed
Institute(s) Institute of Bioinformatics and Systems Biology (IBIS)
POF-Topic(s) 30505 - New Technologies for Biomedical Discoveries
Research field(s) Enabling and Novel Technologies
PSP Element(s) G-503700-001
PubMed ID 24214996
DOI 10.1093/nar/gkt1079
WOS ID WOS:000331139800059
Scopus ID 84891773554
Erfassungsdatum 2013-11-15
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