Modular Semantic Tagging of Medline Abstracts and its Use in Inferring Regulatory Networks

Conference · Mon Sep 19 00:00:00 EDT 2011

DOI:https://doi.org/10.1109/ICSC.2011.78· OSTI ID:1030882

Verhagen, Marc; Pustejovsky, James; Taylor, Ronald C; Sanfilippo, Antonio P

We describe MedstractPlus, a resource for mining relations from the Medline bibliographic database that is currently under construction. It was built on the remains of Medstract, a previously created resource that included a biorelation server and an acronym database. MedstractPlus uses simple and scalable natural language processing modules to structure text, is designed with reusability and extendibility in mind, and adheres to the philosophy of the Linguistic Annotation Framework. We show how MedstractPlus has been used to provide seeds for a novel approach to inferring transcriptional regulatory networks from gene expression data.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1030882
• Report Number(s): PNNL-SA-81610; 400412000; TRN: US201124%%513
• Resource Relation: Conference: Proceedings of the 5th IEEE International Conference on Semantic Computing (ICSC 2011), September 18-21, 2011, Palo Alto, California, 498-505
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
CONSTRUCTION
GENES
MINING
PROCESSING
SEEDS
semantic tagging
Medline
regulatory networks
cross-ontological analytics