EURASIP Journal on Bioinformatics and Systems Biology
International Journal of Data Mining and Bioinformatics
International Journal of Data Mining and Bioinformatics
Detecting Protein-Protein Interactions in Biomedical Texts Using a Parser and Linguistic Resources
CICLing '09 Proceedings of the 10th International Conference on Computational Linguistics and Intelligent Text Processing
Semantic enrichment of journal articles using chemical named entity recognition
ACL '07 Proceedings of the 45th Annual Meeting of the ACL on Interactive Poster and Demonstration Sessions
@Note: A workbench for Biomedical Text Mining
Journal of Biomedical Informatics
Mining the biomedical literature for genic information
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Identification of Chemical Entities in Patent Documents
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Slicing through the Scientific Literature
DILS '09 Proceedings of the 6th International Workshop on Data Integration in the Life Sciences
Assigning roles to protein mentions: The case of transcription factors
Journal of Biomedical Informatics
Support tools for literature-based information access in molecular biology
Proceedings of the 3rd International Universal Communication Symposium
Syntactic Parsing for Bio-molecular Event Detection from Scientific Literature
EPIA '09 Proceedings of the 14th Portuguese Conference on Artificial Intelligence: Progress in Artificial Intelligence
Measuring prediction capacity of individual verbs for the identification of protein interactions
Journal of Biomedical Informatics
Semantic techniques for the web
Recognizing biomedical named entities using skip-chain conditional random fields
BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
A comparison of machine learning techniques for detection of drug target articles
Journal of Biomedical Informatics
Biomedical publication knowledge acquisition, processing and dissemination with CORAAL
OTM'10 Proceedings of the 2010 international conference on On the move to meaningful internet systems: Part II
Prediction of Similarities Among Rheumatic Diseases
Journal of Medical Systems
A consensus method for prioritising drug-associated target proteins
International Journal of Data Mining and Bioinformatics
Relation mining experiments in the pharmacogenomics domain
Journal of Biomedical Informatics
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
The Medical Semantic Web: Opportunities and Issues
International Journal of Information Technology and Web Engineering
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Summary: To allow efficient and systematic retrieval of statements from Medline we have developed EBIMed, a service that combines document retrieval with co-occurrence-based analysis of Medline abstracts. Upon keyword query, EBIMed retrieves the abstracts from EMBL-EBI's installation of Medline and filters for sentences that contain biomedical terminology maintained in public bioinformatics resources. The extracted sentences and terminology are used to generate an overview table on proteins, Gene Ontology (GO) annotations, drugs and species used in the same biological context. All terms in retrieved abstracts and extracted sentences are linked to their entries in biomedical databases. We assessed the quality of the identification of terms and relations in the retrieved sentences. More than 90% of the protein names found indeed represented a protein. According to the analysis of four protein--protein pairs from the Wnt pathway we estimated that 37% of the statements containing such a pair mentioned a meaningful interaction and clarified the interaction of Dkk with LRP. We conclude that EBIMed improves access to information where proteins and drugs are involved in the same biological process, e.g. statements with GO annotations of proteins, protein--protein interactions and effects of drugs on proteins. Availability: Available at http://www.ebi.ac.uk/Rebholz-srv/ebimed Supplementary Data: Supplementary Data are available at Bioinformatics online. Contact: Rebholz@ebi.ac.uk