NDLI: iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology

Content Provider	IEEE Xplore Digital Library
Author	Zhang-Zhi Hu Cohen, K.B. Hirschman, L. Valencia, A. Hongfang Liu Giglio, M.G. Wu, C.H.
Copyright Year	2008
Description	Author affiliation: Protein Inf. Resource, Georgetown Univ. Med. Center, Washington, DC (Zhang-Zhi Hu; Wu, C.H.) \|\| Spanish Nat. Cancer Res. Centre (CNIO) (Valencia, A.) \|\| Inf. Technol. Center, MITRE Corp., MA (Cohen, K.B.; Hirschman, L.) \|\| Dept. of Biostat., Biomath. & Bioinf., Georgetown Univ. Med. Center, Washington, DC (Hongfang Liu) \|\| Sch. of Med., Univ. of Maryland, Baltimore, MD (Giglio, M.G.)
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 bio-ontologies 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.
Starting Page	467
Ending Page	472
File Size	1415353
Page Count	6
File Format	PDF
ISBN	9780769534527
DOI	10.1109/BIBM.2008.73
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-11-03
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Text mining systems biology Data analysis Ontologies protein network Proteins Databases Systems biology User interfaces community workshop text mining protein-protein interaction Large-scale systems Joining processes Software tools ontology
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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