WholeCellKB: Model organism databases for comprehensive whole-cell models

Jonathan R. Karr; Jayodita C. Sanghvi; Derek N. Macklin; Abhishek Arora; Markus W. Covert

doi:10.1093/nar/gks1108

WholeCellKB: Model organism databases for comprehensive whole-cell models

Jonathan R. Karr
, Jayodita C. Sanghvi
, Derek N. Macklin
, Abhishek Arora
, Markus W. Covert

Research output: Contribution to journal › Article › peer-review

41 Scopus citations

Abstract

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 functionofeach 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.

Original language	English
Pages (from-to)	D787-D792
Journal	Nucleic Acids Research
Volume	41
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gks1108
State	Published - 1 Jan 2013
Externally published	Yes

Access to Document

10.1093/nar/gks1108

Cite this

@article{047fa279ffee460485af34be145e2d25,

title = "WholeCellKB: Model organism databases for comprehensive whole-cell models",

abstract = "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 functionofeach 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.",

author = "Karr, \{Jonathan R.\} and Sanghvi, \{Jayodita C.\} and Macklin, \{Derek N.\} and Abhishek Arora and Covert, \{Markus W.\}",

note = "Funding Information: NIH Director{\textquoteright}s Pioneer Award [5DP1LM01150-05] and a Hellman Faculty Scholarship (to M.W.C.); NDSEG, NSF and Stanford Graduate Fellowships (to J.R.K.); NSF and Bio-X Graduate Student Fellowships (to J.C.S.) and a Stanford Graduate Fellowship (to D.N.M.). Funding for open access charge: NIH Director{\textquoteright}s Pioneer Award [5DP1LM01150-05].",

year = "2013",

month = jan,

day = "1",

doi = "10.1093/nar/gks1108",

language = "English",

volume = "41",

pages = "D787--D792",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

TY - JOUR

T1 - WholeCellKB

T2 - Model organism databases for comprehensive whole-cell models

AU - Karr, Jonathan R.

AU - Sanghvi, Jayodita C.

AU - Macklin, Derek N.

AU - Arora, Abhishek

AU - Covert, Markus W.

N1 - Funding Information: NIH Director’s Pioneer Award [5DP1LM01150-05] and a Hellman Faculty Scholarship (to M.W.C.); NDSEG, NSF and Stanford Graduate Fellowships (to J.R.K.); NSF and Bio-X Graduate Student Fellowships (to J.C.S.) and a Stanford Graduate Fellowship (to D.N.M.). Funding for open access charge: NIH Director’s Pioneer Award [5DP1LM01150-05].

PY - 2013/1/1

Y1 - 2013/1/1

N2 - 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 functionofeach 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.

AB - 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 functionofeach 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.

UR - https://www.scopus.com/pages/publications/84876554105

U2 - 10.1093/nar/gks1108

DO - 10.1093/nar/gks1108

M3 - Article

C2 - 23175606

AN - SCOPUS:84876554105

SN - 0305-1048

VL - 41

SP - D787-D792

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

WholeCellKB: Model organism databases for comprehensive whole-cell models

Abstract

Access to Document

Fingerprint

Cite this