PubMed-EX
TL;DR: UNLABELLED PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information that can help researchers to quickly focus on key terms and provide additional information on them.
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Abstract: Summary: PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources.
Availability: PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.
Contact: thtsai@saturn.yzu.edu.tw
Supplementary information:Supplementary data are available at Bioinformatics online.
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References
GoPubMed : exploring pubMed with the Gene Ontology
Andreas Doms,Michael Schroeder +1 more
TL;DR: GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology, gives an overview of the literature abstracts by categorizing abstracts according to the GO and thus allowing users to quickly navigate through the Abstracts by category.
PASBio: predicate-argument structures for event extraction in molecular biology.
TL;DR: The hypothesis is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions, as well as outlining the major issues that require consideration in their construction.
125
BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features
Richard Tzong-Han Tsai,Wen-Chi Chou,Ying-Shan Su,Ying-Shan Su,Yu-Chun Lin,Cheng-Lung Sung,Hong-Jie Dai,Irene Tzu-Hsuan Yeh,Irene Tzu-Hsuan Yeh,Wei Ku,Ting-Yi Sung,Wen-Lian Hsu +11 more
TL;DR: A biomedical SRL system called BIOSMILE is constructed that uses a maximum entropy (ME) machine-learning model to extract biomedical relations and is trained on BioProp, the authors' semi-automatic, annotated biomedical proposition bank, demonstrating the necessity of using a biomedical propositions bank for training SRL systems in the biomedical domain.
Using contextual information to clarify Gene Normalization ambiguity
Po-Ting Lai,Yue-Yang Bow,Chi-Hsin Huang,Hong-Jie Dai,Richard Tzong-Han Tsai,Wen-Lian Hsu +5 more
- 10 Aug 2009
TL;DR: A method to exploit contextual information in an abstract, like tissue type, chromosome location, etc., to tackle inter-species gene ambiguity in Gene Normalization is introduced.
10