ReviewBriefings in bioinformatics2019
Harmonizing semantic annotations for computational models in biology.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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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.
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Who cites it
37 citing papers in PubMed.
- TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.bioRxiv : the preprint server for biology · 2026Article
- A standardized workflow for kinetic metabolic model curation and dissemination.PLoS computational biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- Genome-scale metabolic model ofmSystems · 2025Article
- Metabolic modeling elucidates phenformin and atpenin A5 as broad-spectrum antiviral drugs against RNA viruses.Communications biology · 2025Article
- FAIRification of computational models in biology.bioRxiv : the preprint server for biology · 2025Article
- Article
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- Making PBPK models more reproducible in practice.Briefings in bioinformatics · 2024Article
- Genome-scale model ofMicrobiology spectrum · 2024Article
- BioKC: a collaborative platform for curation and annotation of molecular interactions.Database : the journal of biological databases and curation · 2024Article
- Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.Journal of integrative bioinformatics · 2024Article
- An automated model annotation system (AMAS) for SBML models.Bioinformatics (Oxford, England) · 2023Article
- New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells.PLoS computational biology · 2023Article
- Bayesian estimation reveals that reproducible models in Systems Biology get more citations.Scientific reports · 2023Article
- CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.Frontiers in bioinformatics · 2023Article
- A pathway model of glucose-stimulated insulin secretion in the pancreaticFrontiers in endocrinology · 2023Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- Article
Corrections and comments
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Authors and funding
28 authors.
Funding
Abstract
Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.
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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.