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

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

doi:10.3115/1567619.1567624

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

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

Pacific Northwest National Laboratory

Research output: Contribution to conference › Paper › peer-review

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 language	English
Pages	25-32
Number of pages	8
DOIs	https://doi.org/10.3115/1567619.1567624
Publication status	Published - 2006
Externally published	Yes
Event	HLT-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 → …

Conference

Conference	HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006
Country/Territory	United States
City	New York
Period	8/06/06 → …

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10.3115/1567619.1567624

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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. https://doi.org/10.3115/1567619.1567624

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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",

note = "Publisher Copyright: {\textcopyright} 2006 Association for Computational Linguistics.; HLT-NAACL 2006 Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, BioNLP 2006 ; Conference date: 08-06-2006",

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doi = "10.3115/1567619.1567624",

language = "English",

pages = "25--32",

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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, 8/06/06 pp. 25-32. https://doi.org/10.3115/1567619.1567624

Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity. / Sanfilippo, Antonio; Posse, Christian; Gopalan, Banu et al.
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 conference › Paper › peer-review

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

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AU - Posse, Christian

AU - Gopalan, Banu

AU - Tratz, Stephen

AU - Gregory, Michelle

PY - 2006

Y1 - 2006

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.

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DO - 10.3115/1567619.1567624

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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. doi: 10.3115/1567619.1567624

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

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