ArticleNucleic acids research2013
WholeCellKB: model organism databases for comprehensive whole-cell models.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 47 citations in OpenAlex.
- A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms.Nucleic acids research · 2024Article
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.Biomolecules · 2022Review
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- Bayesian metamodeling of complex biological systems across varying representations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior.Nucleic acids research · 2021Article
- A biochemical network modeling of a whole-cell.Scientific reports · 2020Article
- Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation.MolVa : Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020 · 2020Article
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- Emerging whole-cell modeling principles and methods.Current opinion in biotechnology · 2018Review
- Automated visualization of rule-based models.PLoS computational biology · 2017Article
- Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions.Briefings in functional genomics · 2017Review
- Evolvix BEST Names for semantic reproducibility across code2brain interfaces.Annals of the New York Academy of Sciences · 2017Review
- Toward Community Standards and Software for Whole-Cell Modeling.IEEE transactions on bio-medical engineering · 2016Article
- Guidelines for Reproducibly Building and Simulating Systems Biology Models.IEEE transactions on bio-medical engineering · 2016Article
- Potentials of single-cell biology in identification and validation of disease biomarkers.Journal of cellular and molecular medicine · 2016Review
- Databases for Microbiologists.Journal of bacteriology · 2015Review
- Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.Journal of molecular graphics & modelling · 2015Article
- The future of whole-cell modeling.Current opinion in biotechnology · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
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 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.