The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Implementing the iHOP concept for navigation of biomedical literature
Abstract
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.
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Cites
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566
Carlson, H., Ota, S., Song, Y., Chen, Y., & Hurlin, P. J. (2002) · Oncogene · doi:10.1038/sj.onc.1205476 · Cited by 102
Life cycles of successful genes
Hoffmann, R., & Valencia, A. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(02)00014-8 · Cited by 69
Self-citation
Cited by
Rouillard, A. D., Gundersen, G. W., Fernandez, N. F., Wang, Z., Monteiro, C. D., McDermott, M. G., & Ma’ayan, A. (2016) · Database · doi:10.1093/database/baw100 · Cited by 1,515
Corpus annotation for mining biomedical events from literature
Kim, J.-D., Ohta, T., & Tsujii, J. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-10 · Cited by 395
Özgür, A., Vu, T., Erkan, G., & Radev, D. R. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn182 · Cited by 373
Text mining and its potential applications in systems biology
Ananiadou, S., Kell, D. B., & Tsujii, J.-I. (2006) · Trends in Biotechnology · doi:10.1016/j.tibtech.2006.10.002 · Cited by 324
Bravo, À., Piñero, J., Queralt-Rosinach, N., Rautschka, M., & Furlong, L. I. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0472-9 · Cited by 264
Metadata
- Authors
- Hoffmann, R., & Valencia, A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-09-01
- Volume
- 21
- Issue
- suppl_2
- Pages
- ii252-ii258
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2148395543
- Cited by
- 236
- References
- 4
- FWCI
- 7.49
- Type
- journal article
- Language
- en
- Open access
- closed
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