Introducing meta-services for biomedical information extraction

Martin Krallinger; Florian Leitner; Carlos Rodriguez-Penagos; Jörg Hakenberg; Conrad Plake; Cheng-Ju Kuo; Chun-Nan Hsu; Richard Tsai; Hsi-Chuan Hung; William W. Lau; Calvin A. Johnson; Rune Sætre; Kazuhiro Yoshida; Yan Chen; Sun Kim; Soo-Yong Shin; Byoung-Tak Zhang; William A. Baumgartner; Lawrence Hunter; Barry Haddow; Michael Matthews; Xinglong Wang; Patrick Ruch; Frédéric Ehrler; Arzucan Özgür; Güne Erkan; Dragomir R. Radev; Michael Krauthammer; ThaiBinh Luong; Robert Hoffmann; Chris Sander; Alfonso Valencia

doi:10.1186/gb-2008-9-s2-s6

Introducing meta-services for biomedical information extraction

Martin Krallinger, Florian Leitner, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tsai, Hsi-Chuan Hung, William W. Lau, Calvin A. Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A. Baumgartner, Lawrence Hunter, Barry HaddowMichael Matthews, Xinglong Wang, Patrick Ruch, Frédéric Ehrler, Arzucan Özgür, Güne Erkan, Dragomir R. Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander, Alfonso Valencia

Research output: Contribution to journal › Article › peer-review

Abstract

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.

Original language	English
Pages (from-to)	1-11
Number of pages	11
Journal	Genome Biology
Volume	9
Issue number	2
DOIs	https://doi.org/10.1186/gb-2008-9-s2-s6
Publication status	Published - 2008

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Krallinger, M., Leitner, F., Rodriguez-Penagos, C., Hakenberg, J., Plake, C., Kuo, C.-J., Hsu, C.-N., Tsai, R., Hung, H.-C., Lau, W. W., Johnson, C. A., Sætre, R., Yoshida, K., Chen, Y., Kim, S., Shin, S.-Y., Zhang, B.-T., Baumgartner, W. A., Hunter, L., ... Valencia, A. (2008). Introducing meta-services for biomedical information extraction. Genome Biology, 9(2), 1-11. https://doi.org/10.1186/gb-2008-9-s2-s6

@article{614349a515ab447b97d33b8779e95602,

title = "Introducing meta-services for biomedical information extraction",

abstract = "We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.",

author = "Martin Krallinger and Florian Leitner and Carlos Rodriguez-Penagos and J{\"o}rg Hakenberg and Conrad Plake and Cheng-Ju Kuo and Chun-Nan Hsu and Richard Tsai and Hsi-Chuan Hung and Lau, {William W.} and Johnson, {Calvin A.} and Rune S{\ae}tre and Kazuhiro Yoshida and Yan Chen and Sun Kim and Soo-Yong Shin and Byoung-Tak Zhang and Baumgartner, {William A.} and Lawrence Hunter and Barry Haddow and Michael Matthews and Xinglong Wang and Patrick Ruch and Fr{\'e}d{\'e}ric Ehrler and Arzucan {\"O}zg{\"u}r and G{\"u}ne Erkan and Radev, {Dragomir R.} and Michael Krauthammer and ThaiBinh Luong and Robert Hoffmann and Chris Sander and Alfonso Valencia",

year = "2008",

doi = "10.1186/gb-2008-9-s2-s6",

language = "English",

volume = "9",

pages = "1--11",

journal = "Genome Biology",

issn = "1465-6906",

publisher = "BioMed Central",

number = "2",

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Krallinger, M, Leitner, F, Rodriguez-Penagos, C, Hakenberg, J, Plake, C, Kuo, C-J, Hsu, C-N, Tsai, R, Hung, H-C, Lau, WW, Johnson, CA, Sætre, R, Yoshida, K, Chen, Y, Kim, S, Shin, S-Y, Zhang, B-T, Baumgartner, WA, Hunter, L, Haddow, B, Matthews, M, Wang, X, Ruch, P, Ehrler, F, Özgür, A, Erkan, G, Radev, DR, Krauthammer, M, Luong, T, Hoffmann, R, Sander, C & Valencia, A 2008, 'Introducing meta-services for biomedical information extraction', Genome Biology, vol. 9, no. 2, pp. 1-11. https://doi.org/10.1186/gb-2008-9-s2-s6

TY - JOUR

T1 - Introducing meta-services for biomedical information extraction

AU - Krallinger, Martin

AU - Leitner, Florian

AU - Rodriguez-Penagos, Carlos

AU - Hakenberg, Jörg

AU - Plake, Conrad

AU - Kuo, Cheng-Ju

AU - Hsu, Chun-Nan

AU - Tsai, Richard

AU - Hung, Hsi-Chuan

AU - Lau, William W.

AU - Johnson, Calvin A.

AU - Sætre, Rune

AU - Yoshida, Kazuhiro

AU - Chen, Yan

AU - Kim, Sun

AU - Shin, Soo-Yong

AU - Zhang, Byoung-Tak

AU - Baumgartner, William A.

AU - Hunter, Lawrence

AU - Haddow, Barry

AU - Matthews, Michael

AU - Wang, Xinglong

AU - Ruch, Patrick

AU - Ehrler, Frédéric

AU - Özgür, Arzucan

AU - Erkan, Güne

AU - Radev, Dragomir R.

AU - Krauthammer, Michael

AU - Luong, ThaiBinh

AU - Hoffmann, Robert

AU - Sander, Chris

AU - Valencia, Alfonso

PY - 2008

Y1 - 2008

N2 - We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.

AB - We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.

U2 - 10.1186/gb-2008-9-s2-s6

DO - 10.1186/gb-2008-9-s2-s6

M3 - Article

SN - 1465-6906

VL - 9

SP - 1

EP - 11

JO - Genome Biology

JF - Genome Biology

IS - 2

ER -

Introducing meta-services for biomedical information extraction

Abstract

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