Modular semantic tagging of medline abstracts and its use in inferring regulatory networks

Marc Verhagen, James Pustejovsky, Ronald Taylor, Antonio Sanfilippo

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

Abstract

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.

Original languageEnglish
Title of host publicationProceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011
Pages498-505
Number of pages8
DOIs
Publication statusPublished - 2011
Externally publishedYes
Event5th Annual IEEE International Conference on Semantic Computing, ICSC 2011 - Palo Alto, CA
Duration: 18 Sep 201121 Sep 2011

Other

Other5th Annual IEEE International Conference on Semantic Computing, ICSC 2011
CityPalo Alto, CA
Period18/9/1121/9/11

Fingerprint

Regulatory Networks
Tagging
Semantics
Acronym
Resources
Reusability
Gene Expression Data
Gene expression
Linguistics
Natural Language
Annotation
Seed
Mining
Servers
Server
Module
Processing
Text
Philosophy
Framework

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Computer Science Applications
  • Theoretical Computer Science

Cite this

Verhagen, M., Pustejovsky, J., Taylor, R., & Sanfilippo, A. (2011). Modular semantic tagging of medline abstracts and its use in inferring regulatory networks. In Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011 (pp. 498-505). [6061506] https://doi.org/10.1109/ICSC.2011.78

Modular semantic tagging of medline abstracts and its use in inferring regulatory networks. / Verhagen, Marc; Pustejovsky, James; Taylor, Ronald; Sanfilippo, Antonio.

Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011. 2011. p. 498-505 6061506.

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

Verhagen, M, Pustejovsky, J, Taylor, R & Sanfilippo, A 2011, Modular semantic tagging of medline abstracts and its use in inferring regulatory networks. in Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011., 6061506, pp. 498-505, 5th Annual IEEE International Conference on Semantic Computing, ICSC 2011, Palo Alto, CA, 18/9/11. https://doi.org/10.1109/ICSC.2011.78
Verhagen M, Pustejovsky J, Taylor R, Sanfilippo A. Modular semantic tagging of medline abstracts and its use in inferring regulatory networks. In Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011. 2011. p. 498-505. 6061506 https://doi.org/10.1109/ICSC.2011.78
Verhagen, Marc ; Pustejovsky, James ; Taylor, Ronald ; Sanfilippo, Antonio. / Modular semantic tagging of medline abstracts and its use in inferring regulatory networks. Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011. 2011. pp. 498-505
@inproceedings{f95c994747f9409da60b920a03f63f08,
title = "Modular semantic tagging of medline abstracts and its use in inferring regulatory networks",
abstract = "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.",
author = "Marc Verhagen and James Pustejovsky and Ronald Taylor and Antonio Sanfilippo",
year = "2011",
doi = "10.1109/ICSC.2011.78",
language = "English",
isbn = "9780769544922",
pages = "498--505",
booktitle = "Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011",

}

TY - GEN

T1 - Modular semantic tagging of medline abstracts and its use in inferring regulatory networks

AU - Verhagen, Marc

AU - Pustejovsky, James

AU - Taylor, Ronald

AU - Sanfilippo, Antonio

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=81255205452&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=81255205452&partnerID=8YFLogxK

U2 - 10.1109/ICSC.2011.78

DO - 10.1109/ICSC.2011.78

M3 - Conference contribution

AN - SCOPUS:81255205452

SN - 9780769544922

SP - 498

EP - 505

BT - Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011

ER -