WholeCellKB: model organism databases for comprehensive whole-cell models

Details

• Alternative Title:
  Nucleic Acids Res
• Personal Author:
  Karr, Jonathan R. ; Sanghvi, Jayodita C. ; Macklin, Derek N. ; Arora, Abhishek ; Covert, Markus W.
• Description:
  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.
• Subjects:
  • Bacterial Proteins
  • Chromosomes, Bacterial
  • Databases, Genetic
  • Genes, Bacterial
  • Internet
  • Models, Biological
  • Mycoplasma genitalium
  • RNA, Bacterial
  • Software
  • User-Computer Interface
• Source:
  Nucleic Acids Res. 2012; 41(Database issue):D787-D792.
• Pubmed ID:
  23175606
• Pubmed Central ID:
  PMC3531061
• Document Type:
  Journal Article
• Funding:
  5DP1LM01150-05/DP/NCCDPHP CDC HHS/United States ; DP1 LM011510/LM/NLM NIH HHS/United States ; DP1 OD006413/OD/NIH HHS/United States
• Volume:
  41
• Download URL:
  https://stacks.cdc.gov/view/cdc/22629/cdc_22629_DS1.pdf
• File Type:
  [PDF - 2.49 MB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:84403743df26c136961426a4b85de9e6f65369f0d0358375818e50516e8345c8