Pathway curation: Application of text-mining tools eGIFT and RLIMS-P

Author

Schmidt, C.J. ; Liang Sun ; Arighi, Cecilia N. ; Decker, K. ; Vijay-Shanker, K. ; Torii, Manabu ; Tudor, C.O. ; Wu, Chunlin ; D´Eustachio, P.

Author_Institution

Dept. of Animal & Food Sci., Univ. of Delaware, Newark, DE, USA

fYear

2012

fDate

4-7 Oct. 2012

Firstpage

523

Lastpage

528

Abstract

Gallus Reactome provides a manually curated reference database for chicken signaling and metabolic pathways. Providing such a high-quality reference database requires significant time input from both curators and pathway experts. This paper describes the application of orthology prediction, computational linguistic tools including text mining and information extraction applications, along with resources available from the Protein Information Resource, to facilitate pathway curation. In this paper, we describe these methods in the context of curating the chicken TGF beta signaling pathway.

Keywords

biology computing; data mining; database management systems; genetics; molecular biophysics; text analysis; RLIMS-P tool; chicken TGF beta signaling pathway; computational linguistic tool; eGIFT tool; information extraction; manually curated reference database; metabolic pathway; orthology prediction; pathway curation; protein information resource; text mining; Bioinformatics; Biological cells; Databases; Genomics; Humans; Proteins; Substrates; computational linguistics; orthology prediction; pathway curation;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on

Conference_Location

Philadelphia, PA

Print_ISBN

978-1-4673-2746-6

Electronic_ISBN

978-1-4673-2744-2

Type

conf

DOI

10.1109/BIBMW.2012.6470377

Filename

6470377