WholeCellKB: model organism databases for comprehensive whole-cell models

Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors. Whole-cell model development requires comprehensive model organism databases. WholeCellKB (http://wholecellkb.stanford.edu) is an open-source web-based software program for constructing model organism databases. WholeCellKB provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction and pathway. We used WholeCellKB to create WholeCellKB-MG, a comprehensive database of the Gram-positive bacterium Mycoplasma genitalium using over 900 sources. WholeCellKB-MG is extensively cross-referenced to existing resources including BioCyc, KEGG and UniProt. WholeCellKB-MG is freely accessible through a web-based user interface as well as through a RESTful web service.

[1]  Lei Shi,et al.  SABIO-RK—database for biochemical reaction kinetics , 2011, Nucleic Acids Res..

[2]  C. Woese,et al.  The chemical composition and submicroscopic morphology of Mycoplasma gallisepticum, avian PPLO 5969. , 1962, Journal of molecular biology.

[3]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Peter D. Karp,et al.  EcoCyc: a comprehensive database of Escherichia coli biology , 2010, Nucleic Acids Res..

[5]  R. Herrmann,et al.  Transcription in Mycoplasma pneumoniae. , 2000, Nucleic acids research.

[6]  Antje Chang,et al.  BRENDA, the enzyme information system in 2011 , 2010, Nucleic Acids Res..

[7]  J. Silberg,et al.  A transposase strategy for creating libraries of circularly permuted proteins , 2012, Nucleic acids research.

[8]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[9]  M. Suyama,et al.  Transcriptome Complexity in a Genome-Reduced Bacterium , 2009, Science.

[10]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[11]  Erin Beck,et al.  The comprehensive microbial resource , 2000, Nucleic Acids Res..

[12]  L. Peil.  Ribosome assembly factors in Escherichia coli , 2009 .

[13]  David S. Wishart,et al.  The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli , 2004, Nucleic Acids Res..

[14]  Vinay Satish Kumar,et al.  A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189 , 2009, PLoS Comput. Biol..

[15]  John M. Walker,et al.  The Proteomics Protocols Handbook , 2005, Humana Press.

[16]  Peter D. Karp,et al.  Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology , 2015, Briefings Bioinform..

[17]  J. Rabinowitz,et al.  Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli , 2009, Nature chemical biology.

[18]  David S. Wishart,et al.  DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs , 2010, Nucleic Acids Res..

[19]  Hinrich W. H. Göhlmann,et al.  Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures. , 2003, Nucleic acids research.

[20]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[21]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[22]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[23]  Jonathan R. Karr,et al.  A Whole-Cell Computational Model Predicts Phenotype from Genotype , 2012, Cell.

[24]  The UniProt Consortium,et al.  Reorganizing the protein space at the Universal Protein Resource (UniProt) , 2011, Nucleic Acids Res..

[25]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[26]  Kenta Nakai,et al.  DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information , 2007, Nucleic Acids Res..

[27]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[28]  Bernhard O. Palsson,et al.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions , 2010, BMC Bioinformatics.

[29]  C. Hutchison,et al.  Essential genes of a minimal bacterium. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Yanli Wang,et al.  PubChem: Integrated Platform of Small Molecules and Biological Activities , 2008 .