The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
A survey of visualization tools for biological network analysis
Open accessAbstract
The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Karp, P. D., Paley, S., & Romero, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s225 · Cited by 661
CellML: its future, present and past
Lloyd, C. M., Halstead, M. D. B., & Nielsen, P. F. (2004) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2004.01.004 · Cited by 499
Systems biology markup language: Level 2 and beyond
Finney, A., & Hucka, M. (2003) · Biochemical Society Transactions · doi:10.1042/bst0311472 · Cited by 187
Cited by
Kell, D. B. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-2 · Cited by 554
Gaiteri, C., Ding, Y., French, B., Tseng, G. C., & Sibille, E. (2014) · Genes, Brain and Behavior · doi:10.1111/gbb.12106 · Cited by 289
Modeling formalisms in Systems Biology
Machado, D., Costa, R. S., Rocha, M., Ferreira, E. C., Tidor, B., & Rocha, I. (2011) · AMB Express · doi:10.1186/2191-0855-1-45 · Cited by 189
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data
(2018) · doi:10.1093/nar/gky466 · Cited by 169
A Six‐Stage Workflow for Robust Application of Systems Pharmacology
Gadkar, K., Kirouac, D., Mager, D., van der Graaf, P., & Ramanujan, S. (2016) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12071 · Cited by 93
Metadata
- Authors
- Pavlopoulos, G. A., Wegener, A.-L., & Schneider, R.
- Venue
- BioData Mining
- Published
- 2008-11-28
- Volume
- 1
- Issue
- 1
- Pages
- 12-12
- ISSN
- 1756-0381 (ISSN-L)
- OpenAlex
- W2153490111
- Cited by
- 218
- References
- 4
- FWCI
- 4.59
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A survey of visualization tools for biological network analysis. https://app.cochat.ai/papers/10.1186/1756-0381-1-12
- The paper
- Pavlopoulos, G. A., Wegener, A.-L., & Schneider, R. (2008). A survey of visualization tools for biological network analysis. BioData Mining. https://doi.org/10.1186/1756-0381-1-12
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
