ArticleBriefings in bioinformatics2021
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- Causal network analysis of omics data using prior knowledge databases.Briefings in bioinformatics · 2025Pooled it
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- SIGNOR 4.0: the 2025 update with focus on phosphorylation data.Nucleic acids research · 2026Article
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.Frontiers in immunology · 2023Article
- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism.Frontiers in molecular biosciences · 2022Article
- Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.Molecular systems biology · 2021Article
- Assembling Disease Networks From Causal Interaction Resources.Frontiers in genetics · 2021Review
- Data Integration Challenges for Machine Learning in Precision Medicine.Frontiers in medicine · 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
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical regulatory networks can be used to predict biological and cellular behaviors by system perturbations and in silico simulations. Today, broad sets of causal interactions are available in a variety of biological knowledge resources. However, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data. This review lists the different types of public resources with causal interactions, the different views on biological processes that they represent, the various data formats they use for data representation and storage, and the data exchange and conversion procedures that are available to extract and download these interactions. This may further raise awareness among the targeted audience, i.e. logical modelers and other scientists interested in molecular causal interactions, but also database managers and curators, about the abundance and variety of causal molecular interaction data, and the variety of tools and approaches to convert them into one interoperable resource.
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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.