ArticleMolecular systems biology2011
Retrieval, alignment, and clustering of computational models based on semantic annotations.
Article in Molecular systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- An automated model annotation system (AMAS) for SBML models.Bioinformatics (Oxford, England) · 2023Article
- Model comparison via simplicial complexes and persistent homology.Royal Society open science · 2021Article
- BioModels-15 years of sharing computational models in life science.Nucleic acids research · 2020Article
- Harmonizing semantic annotations for computational models in biology.Briefings in bioinformatics · 2019Review
- Notions of similarity for systems biology models.Briefings in bioinformatics · 2018Article
- Identifying frequent patterns in biochemical reaction networks: a workflow.Database : the journal of biological databases and curation · 2018Article
- Semantic biomedical resource discovery: a Natural Language Processing framework.BMC medical informatics and decision making · 2015Article
- Article
- BioModels: Content, Features, Functionality, and Use.CPT: pharmacometrics & systems pharmacology · 2015Article
- Combining computational models, semantic annotations and simulation experiments in a graph database.Database : the journal of biological databases and curation · 2015Article
- Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.PloS one · 2015Article
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
- Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM).Interface focus · 2013Article
- Propagating semantic information in biochemical network models.BMC bioinformatics · 2012Article
- Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).Standards in genomic sciences · 2011Article
- Controlled vocabularies and semantics in systems biology.Molecular systems biology · 2011Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The exploding number of computational models produced by Systems Biologists over the last years is an invitation to structure and exploit this new wealth of information. Researchers would like to trace models relevant to specific scientific questions, to explore their biological content, to align and combine them, and to match them with experimental data. To automate these processes, it is essential to consider semantic annotations, which describe their biological meaning. As a prerequisite for a wide range of computational methods, we propose general and flexible similarity measures for Systems Biology models computed from semantic annotations. By using these measures and a large extensible ontology, we implement a platform that can retrieve, cluster, and align Systems Biology models and experimental data sets. At present, its major application is the search for relevant models in the BioModels Database, starting from initial models, data sets, or lists of biological concepts. Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data.
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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.