ArticleBMC bioinformatics2009
BioGateway: a semantic systems biology tool for the life sciences.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Annotation of biological samples data to standard ontologies with support from large language models.Computational and structural biotechnology journal · 2025Article
- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- APPINetwork: an R package for building and computational analysis of protein-protein interaction networks.PeerJ · 2022Article
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- A National, Semantic-Driven, Three-Pillar Strategy to Enable Health Data Secondary Usage Interoperability for Research Within the Swiss Personalized Health Network: Methodological Study.JMIR medical informatics · 2021Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- BioHackathon 2015: Semantics of data for life sciences and reproducible research.F1000Research · 2020Article
- The Cytoscape BioGateway App: explorative network building from the BioGateway triple store.Bioinformatics (Oxford, England) · 2019Article
- PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.Journal of biomedical semantics · 2017Article
- Harnessing Big Data for Systems Pharmacology.Annual review of pharmacology and toxicology · 2017Review
- BioSearch: a semantic search engine for Bio2RDF.Database : the journal of biological databases and curation · 2017Article
- KaBOB: ontology-based semantic integration of biomedical databases.BMC bioinformatics · 2015Article
- Implementation of linked data in the life sciences at BioHackathon 2011.Journal of biomedical semantics · 2015Review
- A framework for ontology-based question answering with application to parasite immunology.Journal of biomedical semantics · 2015Article
- Finding gene regulatory network candidates using the gene expression knowledge base.BMC bioinformatics · 2014Article
- Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives.BioMed research international · 2014Review
- The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.Journal of biomedical semantics · 2013Article
- Ontology for vector surveillance and management.Journal of medical entomology · 2013Article
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.Journal of biomedical semantics · 2012Article
- Gauging triple stores with actual biological data.BMC bioinformatics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLife scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance.
resultsWe implemented a semantically integrated resource named BioGateway, comprising the entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single entry point to query these resources through SPARQL. It constitutes a key component for a Semantic Systems Biology approach to generate new hypotheses concerning systems properties. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse representations. We present a detailed analysis of the obstacles that had to be overcome in creating BioGateway. We demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data.
conclusionThe time is ripe for launching a community effort aimed at a wider acceptance and application of Semantic Web technologies in the life sciences. We call for the creation of a forum that strives to implement a truly semantic life science foundation for Semantic Systems Biology. Access to the system and supplementary information (such as a listing of the data sources in RDF, and sample queries) can be found at http://www.semantic-systems-biology.org/biogateway.
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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.