BioNoculars: Extracting protein-protein interactions from biomedical text

Amgad Madkour, Kareem Darwish, Hany Hassan, Ahmed Hassan, Ossama Emam

Research output: Contribution to conferencePaper

11 Citations (Scopus)

Abstract

The vast number of published medical documents is considered a vital source for relationship discovery. This paper presents a statistical unsupervised system, called BioNoculars, for extracting protein-protein interactions from biomedical text. BioNoculars uses graph-based mutual reinforcement to make use of redundancy in data to construct extraction patterns in a domain independent fashion. The system was tested using MEDLINE abstract for which the protein-protein interactions that they contain are listed in the database of interacting proteins and protein-protein interactions (DIPPPI). The system reports an F-Measure of 0.55 on test MEDLINE abstracts.

Original languageEnglish
Pages89-96
Number of pages8
Publication statusPublished - 1 Jan 2007
EventACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007 - Prague, Czech Republic
Duration: 29 Jun 2007 → …

Other

OtherACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007
CountryCzech Republic
CityPrague
Period29/6/07 → …

Fingerprint

Proteins
MEDLINE
Protein Databases
Protein
Interaction
Redundancy
Reinforcement

ASJC Scopus subject areas

  • Language and Linguistics
  • Information Systems
  • Software
  • Health Informatics
  • Computer Science Applications
  • Biomedical Engineering

Cite this

Madkour, A., Darwish, K., Hassan, H., Hassan, A., & Emam, O. (2007). BioNoculars: Extracting protein-protein interactions from biomedical text. 89-96. Paper presented at ACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007, Prague, Czech Republic.

BioNoculars : Extracting protein-protein interactions from biomedical text. / Madkour, Amgad; Darwish, Kareem; Hassan, Hany; Hassan, Ahmed; Emam, Ossama.

2007. 89-96 Paper presented at ACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007, Prague, Czech Republic.

Research output: Contribution to conferencePaper

Madkour, A, Darwish, K, Hassan, H, Hassan, A & Emam, O 2007, 'BioNoculars: Extracting protein-protein interactions from biomedical text', Paper presented at ACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007, Prague, Czech Republic, 29/6/07 pp. 89-96.
Madkour A, Darwish K, Hassan H, Hassan A, Emam O. BioNoculars: Extracting protein-protein interactions from biomedical text. 2007. Paper presented at ACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007, Prague, Czech Republic.
Madkour, Amgad ; Darwish, Kareem ; Hassan, Hany ; Hassan, Ahmed ; Emam, Ossama. / BioNoculars : Extracting protein-protein interactions from biomedical text. Paper presented at ACL 2007 Workshop on Biological, Translational, and Clinical Language Processing, BioNLP 2007, Prague, Czech Republic.8 p.
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