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ready Whole-Cell Knowledge Base


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WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. genitalium database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. The M. genitalium database was curated from over 900 primary research articles, reviews, books, and databases. The M. genitalium database is extensively cross-referenced to external resources including BioCyc, KEGG, and UniProt. WholeCellKB is also an open-source web-based software program for constructing model organism databases. The WholeCellKB software 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. WholeCellKB is freely accessible via a web-based user interface as well as via a RESTful web service.


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Created in 2013

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How to cite this record WholeCellKB; Whole-Cell Knowledge Base; DOI:; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Oct 27 2021 4:54 p.m.

This record is maintained by jonrkarr  ORCID

Record updated: Sept. 8, 2016, 3:13 p.m. by The FAIRsharing Team.

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WholeCellKB: model organism databases for comprehensive whole-cell models.

Karr JR,Sanghvi JC,Macklin DN,Arora A,Covert MW
Nucleic Acids Res 2012

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