ReviewBiomolecules2021
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.
Review in Biomolecules, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- metagRoot: a comprehensive database of protein families associated with plant root microbiomes.Nucleic acids research · 2026Article
- Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions.Briefings in bioinformatics · 2025Article
- Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data.Molecular systems biology · 2025Review
- Spectral divergence prioritizes key classes, genes, and pathways shared between substance use disorders and cardiovascular disease.Frontiers in neuroscience · 2025Article
- Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations.Computational and structural biotechnology journal · 2025Article
- mFusion: a multiscale fusion method bridging neuroimages to genes through neurotransmissions in mental health disorders.Communications biology · 2024Article
- Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes.Genomics, proteomics & bioinformatics · 2024Review
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.Bioinformatics (Oxford, England) · 2023Article
- Arena3DNAR genomics and bioinformatics · 2023Article
- SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.BMC bioinformatics · 2023Article
- Potential role of the regulatoryFrontiers in plant science · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- A roadmap for the functional annotation of protein families: a community perspective.Database : the journal of biological databases and curation · 2022Article
- Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining.Biomolecules · 2022Article
- PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types.Microorganisms · 2022Article
- The network makeup artist (NORMA-2.0): distinguishing annotated groups in a network using innovative layout strategies.Bioinformatics advances · 2022Article
- Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY.Frontiers in physiology · 2022Article
- Text Mining for Building Biomedical Networks Using Cancer as a Case Study.Biomolecules · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.
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.