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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: 3.1] [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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Keseler IM, Skrzypek M, Weerasinghe D, Chen AY, Fulcher C, Li GW, Lemmer KC, Mladinich KM, Chow ED, Sherlock G, Karp PD. Curation accuracy of model organism databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau058. [PMID: 24923819 PMCID: PMC4207230 DOI: 10.1093/database/bau058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Manual extraction of information from the biomedical literature-or biocuration-is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org//
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Affiliation(s)
- Ingrid M Keseler
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Marek Skrzypek
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Deepika Weerasinghe
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Albert Y Chen
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Carol Fulcher
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Gene-Wei Li
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Kimberly C Lemmer
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Katherine M Mladinich
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Edmond D Chow
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Gavin Sherlock
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
| | - Peter D Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, CA, USA, Department of Genetics, Stanford University, CA 94305, USA, Department of Bacteriology, University of Wisconsin, WI 53706-1521, USA, Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA 94158-2140, USA, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, WI 53726, USA and Department of Medical Microbiology and Immunology, University of Wisconsin, WI 53706-1521, USA
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