iProLINK: A framework for linking text mining with ontology and systems biology

Zhang Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

The ever-increasing scientific literature and the exponential growth of large-scale molecular data have prompted active research in biological text mining to facilitate literature-based curation of molecular databases. Meanwhile, systems biology and bioontologies are emerging as critical tools in biological research where complex data in disparate resources are generated, integrated and analyzed. Both rely on literature for data annotation and analysis. The challenges facing us are to develop broadly utilized text mining tools and systems, and to bring together developer and user communities for system development and evaluation. We describe a framework for linking text mining tools with ontology and systems biology, extending from a previously developed text mining resource, iProLINK. We focus on molecular and ontological resources, including genes/proteins, protein-protein interaction (PPI), and Protein Ontology. The framework consists of two major components: a user interface for text mining of PPI from an integrated tool server and software modules to allow text mining outputs to be created, ranked, and used by the community. Use cases are presented for assessing the gaps and making recommendations for future development.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages467-472
Number of pages6
DOIs
StatePublished - Dec 1 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

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ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

Cite this

Hu, Z. Z., Cohen, K. B., Hirschman, L., Valencia, A., Liu, H., Giglio, M. G., & Wu, C. H. (2008). iProLINK: A framework for linking text mining with ontology and systems biology. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 467-472). [4684941] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.73