ArticleBMC systems biology2011
Integrating systems biology models and biomedical ontologies.
Article in BMC systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 63 citations in OpenAlex.
- Evaluating completeness, coherence, and consistency of genome-scale function annotations.Briefings in bioinformatics · 2026Review
- Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.Scientific reports · 2019Article
- Recent advances in biomedical simulations: a manifesto for model engineering.F1000Research · 2019Review
- OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.Scientific reports · 2018Article
- The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.Journal of biomedical semantics · 2017Article
- Ontological interpretation of biomedical database content.Journal of biomedical semantics · 2017Article
- Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.Journal of biomedical informatics · 2016Article
- The role of ontologies in biological and biomedical research: a functional perspective.Briefings in bioinformatics · 2015Article
- Diverse array-designed modes of combination therapies in Fangjiomics.Acta pharmacologica Sinica · 2015Review
- Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT.Journal of the American Medical Informatics Association : JAMIA · 2015Article
- Mining Electronic Health Records using Linked Data.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2015Article
- Combining computational models, semantic annotations and simulation experiments in a graph database.Database : the journal of biological databases and curation · 2015Article
- BioModels linked dataset.BMC systems biology · 2014Article
- Genome scale modeling in systems biology: algorithms and resources.Current genomics · 2014Article
- The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.Journal of biomedical semantics · 2014Article
- Thematic series on biomedical ontologies in JBMS: challenges and new directions.Journal of biomedical semantics · 2014Review
- CSEO - the Cigarette Smoke Exposure Ontology.Journal of biomedical semantics · 2014Article
- An empirically derived taxonomy of errors in SNOMED CT.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2014Article
- Evaluation of research in biomedical ontologies.Briefings in bioinformatics · 2013Article
- Ontology-Based Querying with Bio2RDF's Linked Open Data.Journal of biomedical semantics · 2013Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundSystems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology.
resultsWe provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models.
conclusionsWe establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.
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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.