ArticleNucleic acids research2015
BioModels: ten-year anniversary.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers, 1 of them a synthesis that pooled it.
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
164 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Synthetic Microbial Cocultivation for Targeted Production of Odd-Chain Carboxylates and Alcohols from Carbon Monoxide.Environmental science & technology · 2025Article
- A semi-mechanistic mathematical framework for simulating multi-hormone dynamics in reproductive endocrinology.Computational and structural biotechnology journal · 2025Article
- Acetate is a beneficial nutrient for E. coli at low glycolytic flux.The EMBO journal · 2023Article
- High throughputMicrobial cell factories · 2023Article
- CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.Frontiers in bioinformatics · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE).F1000Research · 2023Article
- Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives.Molecular metabolism · 2022Review
- Reconstructed Genome-Scale Metabolic Model Characterizes Adaptive Metabolic Flux Changes in Peripheral Blood Mononuclear Cells in Severe COVID-19 Patients.International journal of molecular sciences · 2022Article
- Article
- Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum.Microbial cell factories · 2022Article
- A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability.Bulletin of mathematical biology · 2022Article
- NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.Frontiers in physiology · 2022Article
- Path to improving the life cycle and quality of genome-scale models of metabolism.Cell systems · 2021Review
- Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment.Cancers · 2021Review
- SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.Briefings in bioinformatics · 2021Article
- Review
104 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors.
Funding
Abstract
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140,000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels' first release a decade ago. This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form. We also outline planned improvements to cope with a diverse array of new challenges.
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.