Assisted Curation: Does Text Mining Really Help?

Beatrice Alex; Claire Grover; Barry Haddow; Mijail Kabadjor; Ewan Klein; Michael Matthews; Stuart Roebuck; Richard 	Tobin; Xinglong Wang

Assisted Curation: Does Text Mining Really Help?

Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjor, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, Xinglong Wang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract / Description of output

Although text mining shows considerable promise as a tool for supporting the curation of biomedical text, there is little concrete evidence as to its effectiveness. We report on three experiments measuring the extent to which curation can be speeded up with assistance from Natural Language Processing (NLP), together with subjective feedback from curators on the usability of a curation tool that integrates NLP hypotheses for protein-protein interactions (PPIs). In our curation scenario, we found that a maximum speed-up of 1/3 in curation time can be expected if NLP output is perfectly accurate. The preference of one curator for consistent NLP output and output with high recall needs to be confirmed in a larger study with several curators.

Original language	English
Title of host publication	Proceedings of the Pacific Symposium on Biocomputing (Biocomputing 2008)
Editors	Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein
Publisher	World Scientific
Pages	556-567
Number of pages	12
Publication status	Published - 2008

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Alex Grover et al 2008 Assisted Curation Does Text Mining Really HelpAccepted author manuscript, 152 KB

http://psb.stanford.edu/psb-online/proceedings/psb08/alex.pdf

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Alex, B., Grover, C., Haddow, B., Kabadjor, M., Klein, E., Matthews, M., Roebuck, S., Tobin, R., & Wang, X. (2008). Assisted Curation: Does Text Mining Really Help? In R. B. Altman, A. K. Dunker, L. Hunter, T. Murray, & T. E. Klein (Eds.), Proceedings of the Pacific Symposium on Biocomputing (Biocomputing 2008) (pp. 556-567). World Scientific. http://psb.stanford.edu/psb-online/proceedings/psb08/alex.pdf

@inproceedings{f3e3a7321bc340c8b8156a16b23f3fd0,

title = "Assisted Curation: Does Text Mining Really Help?",

abstract = "Although text mining shows considerable promise as a tool for supporting the curation of biomedical text, there is little concrete evidence as to its effectiveness. We report on three experiments measuring the extent to which curation can be speeded up with assistance from Natural Language Processing (NLP), together with subjective feedback from curators on the usability of a curation tool that integrates NLP hypotheses for protein-protein interactions (PPIs). In our curation scenario, we found that a maximum speed-up of 1/3 in curation time can be expected if NLP output is perfectly accurate. The preference of one curator for consistent NLP output and output with high recall needs to be confirmed in a larger study with several curators.",

author = "Beatrice Alex and Claire Grover and Barry Haddow and Mijail Kabadjor and Ewan Klein and Michael Matthews and Stuart Roebuck and Richard Tobin and Xinglong Wang",

year = "2008",

language = "English",

pages = "556--567",

editor = "Altman, {Russ B.} and Dunker, {A. Keith} and Lawrence Hunter and { Murray}, Tiffany and Klein, {Teri E.}",

booktitle = "Proceedings of the Pacific Symposium on Biocomputing (Biocomputing 2008)",

publisher = "World Scientific",

}

Alex, B , Grover, C , Haddow, B, Kabadjor, M, Klein, E, Matthews, M, Roebuck, S, Tobin, R & Wang, X 2008, Assisted Curation: Does Text Mining Really Help? in RB Altman, AK Dunker, L Hunter, T Murray & TE Klein (eds), Proceedings of the Pacific Symposium on Biocomputing (Biocomputing 2008). World Scientific, pp. 556-567. <http://psb.stanford.edu/psb-online/proceedings/psb08/alex.pdf>

Assisted Curation: Does Text Mining Really Help? / Alex, Beatrice ; Grover, Claire ; Haddow, Barry et al.
Proceedings of the Pacific Symposium on Biocomputing (Biocomputing 2008). ed. / Russ B. Altman; A. Keith Dunker; Lawrence Hunter; Tiffany Murray; Teri E. Klein. World Scientific, 2008. p. 556-567.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Assisted Curation

T2 - Does Text Mining Really Help?

AU - Alex, Beatrice

AU - Grover, Claire

AU - Haddow, Barry

AU - Kabadjor, Mijail

AU - Klein, Ewan

AU - Matthews, Michael

AU - Roebuck, Stuart

AU - Tobin, Richard

AU - Wang, Xinglong

PY - 2008

Y1 - 2008

N2 - Although text mining shows considerable promise as a tool for supporting the curation of biomedical text, there is little concrete evidence as to its effectiveness. We report on three experiments measuring the extent to which curation can be speeded up with assistance from Natural Language Processing (NLP), together with subjective feedback from curators on the usability of a curation tool that integrates NLP hypotheses for protein-protein interactions (PPIs). In our curation scenario, we found that a maximum speed-up of 1/3 in curation time can be expected if NLP output is perfectly accurate. The preference of one curator for consistent NLP output and output with high recall needs to be confirmed in a larger study with several curators.

AB - Although text mining shows considerable promise as a tool for supporting the curation of biomedical text, there is little concrete evidence as to its effectiveness. We report on three experiments measuring the extent to which curation can be speeded up with assistance from Natural Language Processing (NLP), together with subjective feedback from curators on the usability of a curation tool that integrates NLP hypotheses for protein-protein interactions (PPIs). In our curation scenario, we found that a maximum speed-up of 1/3 in curation time can be expected if NLP output is perfectly accurate. The preference of one curator for consistent NLP output and output with high recall needs to be confirmed in a larger study with several curators.

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M3 - Conference contribution

SP - 556

EP - 567

BT - Proceedings of the Pacific Symposium on Biocomputing (Biocomputing 2008)

A2 - Altman, Russ B.

A2 - Dunker, A. Keith

A2 - Hunter, Lawrence

A2 - Murray, Tiffany

A2 - Klein, Teri E.

PB - World Scientific

ER -

Assisted Curation: Does Text Mining Really Help?

Abstract / Description of output

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