A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways

Sine Zambach, Tine Lassen

Research output: Contribution to conferencePaperResearchpeer-review

Abstract

Knowledge of regulation relations is widely applied by biomedical researchers in for example experiment design
on regulatory pathways and in systems biology. Such knowledge has typically been represented very roughly as
simple graphs or very expressively in simulations of pathways.
In the work presented here, we analyze 6 frequently used verbs denoting the regulation relations regulates,
positively regulates and negatively regulates through corpus analysis, and propose a formal representation of the
acquired knowledge as domain speci¯c semantic frames. The acquired knowledge patterns can thus be used to
identify and reason over knowledge represented in texts from the biomedical domain.
Original languageEnglish
Publication date25 Oct 2011
Number of pages6
Publication statusPublished - 25 Oct 2011
Event4th International Symposium on Semantic Mining in Biomedicine - European Bioinformatics Institute (EBI) , Hinxton, United Kingdom
Duration: 25 Oct 201026 Oct 2010
http://www.smbm.eu/Home

Conference

Conference4th International Symposium on Semantic Mining in Biomedicine
LocationEuropean Bioinformatics Institute (EBI)
CountryUnited Kingdom
CityHinxton
Period25/10/201026/10/2010
Internet address

Cite this

Zambach, S., & Lassen, T. (2011). A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways. Paper presented at 4th International Symposium on Semantic Mining in Biomedicine, Hinxton, United Kingdom.
Zambach, Sine ; Lassen, Tine. / A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways. Paper presented at 4th International Symposium on Semantic Mining in Biomedicine, Hinxton, United Kingdom.6 p.
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Zambach, S & Lassen, T 2011, 'A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways' Paper presented at, Hinxton, United Kingdom, 25/10/2010 - 26/10/2010, .

A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways. / Zambach, Sine; Lassen, Tine.

2011. Paper presented at 4th International Symposium on Semantic Mining in Biomedicine, Hinxton, United Kingdom.

Research output: Contribution to conferencePaperResearchpeer-review

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T1 - A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways

AU - Zambach, Sine

AU - Lassen, Tine

PY - 2011/10/25

Y1 - 2011/10/25

N2 - Knowledge of regulation relations is widely applied by biomedical researchers in for example experiment designon regulatory pathways and in systems biology. Such knowledge has typically been represented very roughly assimple graphs or very expressively in simulations of pathways.In the work presented here, we analyze 6 frequently used verbs denoting the regulation relations regulates,positively regulates and negatively regulates through corpus analysis, and propose a formal representation of theacquired knowledge as domain speci¯c semantic frames. The acquired knowledge patterns can thus be used toidentify and reason over knowledge represented in texts from the biomedical domain.

AB - Knowledge of regulation relations is widely applied by biomedical researchers in for example experiment designon regulatory pathways and in systems biology. Such knowledge has typically been represented very roughly assimple graphs or very expressively in simulations of pathways.In the work presented here, we analyze 6 frequently used verbs denoting the regulation relations regulates,positively regulates and negatively regulates through corpus analysis, and propose a formal representation of theacquired knowledge as domain speci¯c semantic frames. The acquired knowledge patterns can thus be used toidentify and reason over knowledge represented in texts from the biomedical domain.

M3 - Paper

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Zambach S, Lassen T. A Lexical Framework for Semantic Annotation of Positive and Negative Regulation Relations in Biomedical Pathways. 2011. Paper presented at 4th International Symposium on Semantic Mining in Biomedicine, Hinxton, United Kingdom.