Journal of Biomedical Informatics
@Note: A workbench for Biomedical Text Mining
Journal of Biomedical Informatics
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Mining the biomedical literature for genic information
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Supporting Literature Exploration with Granular Knowledge Structures
RSFDGrC '07 Proceedings of the 11th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
Knowledge management in biomedical libraries: A semantic web approach
Information Systems Frontiers
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Measuring prediction capacity of individual verbs for the identification of protein interactions
Journal of Biomedical Informatics
Summarizing biological literature with BioSumm
CIKM '10 Proceedings of the 19th ACM international conference on Information and knowledge management
A comparison of machine learning techniques for detection of drug target articles
Journal of Biomedical Informatics
Visual Exploration across Biomedical Databases
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A hybrid methodology for pattern recognition in signaling cervical cancer pathways
MCPR'10 Proceedings of the 2nd Mexican conference on Pattern recognition: Advances in pattern recognition
DDIExtractor: a web-based java tool for extracting drug-drug interactions from biomedical texts
NLDB'11 Proceedings of the 16th international conference on Natural language processing and information systems
BOSS: a biomedical object search system
Proceedings of the ACM fifth international workshop on Data and text mining in biomedical informatics
Enabling enrichment analysis with the Human Disease Ontology
Journal of Biomedical Informatics
Firework visualization: a model for local citation analysis
Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium
Enhancing search results with semantic annotation using augmented browsing
IJCAI'11 Proceedings of the Twenty-Second international joint conference on Artificial Intelligence - Volume Volume Three
A consensus method for prioritising drug-associated target proteins
International Journal of Data Mining and Bioinformatics
Methodological Review: Biomedical text mining and its applications in cancer research
Journal of Biomedical Informatics
P-Biblio-MetReS, a parallel data mining tool for the reconstruction of molecular networks
Proceedings of the 20th European MPI Users' Group Meeting
PIMiner: a web tool for extraction of protein interactions from biomedical literature
International Journal of Data Mining and Bioinformatics
Hi-index | 3.84 |
Motivation: The World Wide Web has profoundly changed the way in which we access information. Searching the internet is easy and fast, but more importantly, the interconnection of related contents makes it intuitive and closer to the associative organization of human memory. However, the information retrieval tools currently available to researchers in biology and medicine lag far behind the possibilities that the layman has come to expect from the internet. Results: By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource. iHOP (Information Hyperlinked over Proteins) is an online service that provides this gene-guided network as a natural way of accessing millions of PubMed abstracts and brings all the advantages of the internet to scientific literature research. Navigating across interrelated sentences within this network is closer to human intuition than the use of conventional keyword searches and allows for stepwise and controlled acquisition of information. Moreover, this literature network can be superimposed upon experimental interaction data to facilitate the simultaneous analysis of novel and existing knowledge. The network presented in iHOP currently contains5 million sentences and 40 000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. Availability: iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/ Contact: hoffmann@cbio.mskcc.org Supplementary Information: Supplementary data are available at Bioinformatics online.