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Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJF, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Overview of the gene ontology task at BioCreative IV. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau086. [PMID: 25157073 PMCID: PMC4142793 DOI: 10.1093/database/bau086] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation. Database URL:http://www.biocreative.org/tasks/biocreative-iv/track-4-GO/.
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Affiliation(s)
- Yuqing Mao
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Kimberly Van Auken
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Donghui Li
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Cecilia N Arighi
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Peter McQuilton
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - G Thomas Hayman
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Susan Tweedie
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Mary L Schaeffer
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Stanley J F Laulederkind
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Shur-Jen Wang
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Julien Gobeill
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Patrick Ruch
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Anh Tuan Luu
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Jung-Jae Kim
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Jung-Hsien Chiang
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Yu-De Chen
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Chia-Jung Yang
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Hongfang Liu
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Dongqing Zhu
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Yanpeng Li
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Hong Yu
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Ehsan Emadzadeh
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Graciela Gonzalez
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Jian-Ming Chen
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Hong-Jie Dai
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20817, USA WormBase, Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA, TAIR, Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, HES-SO, HEG, Library and Information Sciences, 7 route de Drize, CH-1227 Carouge, Switzerland, SIBtex, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva 4, Switzerland, School of Computer Engineering, Nanyang Technological University, Block N4, #02a-32, Nanyang Avenue, Singapore 639798, Department of Computer Science and Information Engineering, National Cheng-Kung University, No. 1, University Rd., Tainan 701, Taiwan, Republic of China, Department of Radiology, Mackay Memorial Hospital, Taitung Branch, Lane 303 Chang Sha St. Taitung, Taiwan, Republic of China, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA, Department of Computer Science, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA, Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue North (AC7-059), Worcester, MA 01655 USA, Department of Biomedical Informatics, Arizona State University, 13212 East Shea Boulevard Scottsdale, AZ 85259 USA, Institute of Information Science, Academia Sinica, 128 Academia Road, Secti
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Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJF, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z. BC4GO: a full-text corpus for the BioCreative IV GO task. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau074. [PMID: 25070993 PMCID: PMC4112614 DOI: 10.1093/database/bau074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gene function curation via Gene Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this task is considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification of GO terms and supporting information from full text. However, few systems have delivered an accuracy that is comparable with humans. One recognized challenge in developing such systems is the lack of marked sentence-level evidence text that provides the basis for making GO annotations. We aim to create a corpus that includes the GO evidence text along with the three core elements of GO annotations: (i) a gene or gene product, (ii) a GO term and (iii) a GO evidence code. To ensure our results are consistent with real-life GO data, we recruited eight professional GO curators and asked them to follow their routine GO annotation protocols. Our annotators marked up more than 5000 text passages in 200 articles for 1356 distinct GO terms. For evidence sentence selection, the inter-annotator agreement (IAA) results are 9.3% (strict) and 42.7% (relaxed) in F1-measures. For GO term selection, the IAAs are 47% (strict) and 62.9% (hierarchical). Our corpus analysis further shows that abstracts contain ∼10% of relevant evidence sentences and 30% distinct GO terms, while the Results/Experiment section has nearly 60% relevant sentences and >70% GO terms. Further, of those evidence sentences found in abstracts, less than one-third contain enough experimental detail to fulfill the three core criteria of a GO annotation. This result demonstrates the need of using full-text articles for text mining GO annotations. Through its use at the BioCreative IV GO (BC4GO) task, we expect our corpus to become a valuable resource for the BioNLP research community. Database URL:http://www.biocreative.org/resources/corpora/bc-iv-go-task-corpus/.
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Affiliation(s)
- Kimberly Van Auken
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Mary L Schaeffer
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Peter McQuilton
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stanley J F Laulederkind
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Donghui Li
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Shur-Jen Wang
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - G Thomas Hayman
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Susan Tweedie
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Cecilia N Arighi
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - James Done
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Hans-Michael Müller
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Paul W Sternberg
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USAWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Yuqing Mao
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Chih-Hsuan Wei
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Zhiyong Lu
- WormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA
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Comeau DC, Batista-Navarro RT, Dai HJ, Doğan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RTH, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC interoperability track overview. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau053. [PMID: 24980129 PMCID: PMC4074764 DOI: 10.1093/database/bau053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format. This promotes the development of interoperable tools for natural language processing (NLP) of biomedical text. The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format. These contributions included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format. The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format. Database URL:http://bioc.sourceforge.net/
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Affiliation(s)
- Donald C Comeau
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Riza Theresa Batista-Navarro
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Hong-Jie Dai
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Rezarta Islamaj Doğan
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Antonio Jimeno Yepes
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Ritu Khare
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Hernani Marques
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Carolyn J Mattingly
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Mariana Neves
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USANational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Univers
| | - Yifan Peng
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Rafal Rak
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Fabio Rinaldi
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Richard Tzong-Han Tsai
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Karin Verspoor
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USANational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Univers
| | - Thomas C Wiegers
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Cathy H Wu
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USANational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Univers
| | - W John Wilbur
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
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