databases > DOI:10.25504/FAIRsharing.4dfs3p

ready Whole-Cell Knowledge Base

Abbreviation:WholeCellKB

General Information
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.

Homepage http://www.wholecellkb.org

Countries that developed this resource United States

Created in 2013

Taxonomic range

Knowledge Domains 





How to cite this record FAIRsharing.org: WholeCellKB; Whole-Cell Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.4dfs3p; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Aug 19 2019 8:45 a.m.


This record is maintained by jonrkarr  ORCID

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

Show edit history


Support

General

help http://www.wholecellkb.org/tutorial/Mgen ...
Mailing List None
online documentation http://www.wholecellkb.org/about/Mgenita ...
twitter @jonrkarr

Additional Information

Contact Jonathan Karr   ORCID

Tools

    No tools defined


Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Versioning

versioning on a per entry basis http://www.wholecellkb.org/about

Data Curation

manual curation http://www.wholecellkb.org/about

Data Access

browse http://www.wholecellkb.org/Mgenitalium
download http://www.wholecellkb.org/export/Mgenitalium

REST Web Services

RESTful API http://www.wholecellkb.org/about/Mgenitalium#api


Publications

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

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

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined



Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

Funds

Maintains

Grant Number(s)