Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity

Antonio Sanfilippo, Christian Posse, Banu Gopalan, Stephen Tratz, Michelle Gregory

Research output: Contribution to conferencePaper

1 Citation (Scopus)

Abstract

With the rising influence of the Gene Ontology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associated with them. So far, these approaches have solely relied on the knowledge encoded in the Gene Ontology and the gene annotations associated with the Gene Ontology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

Original languageEnglish
Pages25-32
Number of pages8
Publication statusPublished - 1 Jan 2006
EventHLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006 - New York, United States
Duration: 8 Jun 2006 → …

Other

OtherHLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006
CountryUnited States
CityNew York
Period8/6/06 → …

Fingerprint

Gene Ontology
Genes
Ontology
Molecular Sequence Annotation
Databases
Ontological
Gene

ASJC Scopus subject areas

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

Cite this

Sanfilippo, A., Posse, C., Gopalan, B., Tratz, S., & Gregory, M. (2006). Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity. 25-32. Paper presented at HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006, New York, United States.

Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity. / Sanfilippo, Antonio; Posse, Christian; Gopalan, Banu; Tratz, Stephen; Gregory, Michelle.

2006. 25-32 Paper presented at HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006, New York, United States.

Research output: Contribution to conferencePaper

Sanfilippo, A, Posse, C, Gopalan, B, Tratz, S & Gregory, M 2006, 'Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity' Paper presented at HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006, New York, United States, 8/6/06, pp. 25-32.
Sanfilippo A, Posse C, Gopalan B, Tratz S, Gregory M. Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity. 2006. Paper presented at HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006, New York, United States.
Sanfilippo, Antonio ; Posse, Christian ; Gopalan, Banu ; Tratz, Stephen ; Gregory, Michelle. / Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity. Paper presented at HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006, New York, United States.8 p.
@conference{5adf816fce114405b2e67f7f2f0c7c2d,
title = "Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity",
abstract = "With the rising influence of the Gene Ontology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associated with them. So far, these approaches have solely relied on the knowledge encoded in the Gene Ontology and the gene annotations associated with the Gene Ontology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.",
author = "Antonio Sanfilippo and Christian Posse and Banu Gopalan and Stephen Tratz and Michelle Gregory",
year = "2006",
month = "1",
day = "1",
language = "English",
pages = "25--32",
note = "HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006 ; Conference date: 08-06-2006",

}

TY - CONF

T1 - Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity

AU - Sanfilippo, Antonio

AU - Posse, Christian

AU - Gopalan, Banu

AU - Tratz, Stephen

AU - Gregory, Michelle

PY - 2006/1/1

Y1 - 2006/1/1

N2 - With the rising influence of the Gene Ontology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associated with them. So far, these approaches have solely relied on the knowledge encoded in the Gene Ontology and the gene annotations associated with the Gene Ontology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

AB - With the rising influence of the Gene Ontology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associated with them. So far, these approaches have solely relied on the knowledge encoded in the Gene Ontology and the gene annotations associated with the Gene Ontology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

UR - http://www.scopus.com/inward/record.url?scp=33947171096&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33947171096&partnerID=8YFLogxK

M3 - Paper

AN - SCOPUS:33947171096

SP - 25

EP - 32

ER -