ArticleJournal of biomedical semantics2013
Ontology-Based Querying with Bio2RDF's Linked Open Data.
Article in Journal of biomedical semantics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Visualization and exploration of linked data using virtual reality.Database : the journal of biological databases and curation · 2024Article
- Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets.Journal of biomedical semantics · 2023Article
- Towards FAIR protocols and workflows: the OpenPREDICT use case.PeerJ. Computer science · 2020Article
- 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
- How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM).Methods in molecular biology (Clifton, N.J.) · 2019Article
- Article
- Consolidating drug data on a global scale using Linked Data.Journal of biomedical semantics · 2017Article
- KaBOB: ontology-based semantic integration of biomedical databases.BMC bioinformatics · 2015Article
- Computational approaches for pharmacovigilance signal detection: toward integrated and semantically-enriched frameworks.Drug safety · 2015Article
- Mining Electronic Health Records using Linked Data.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2015Article
- Design and development of a linked open data-based health information representation and visualization system: potentials and preliminary evaluation.JMIR medical informatics · 2014Article
- The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.Journal of biomedical semantics · 2014Article
- BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.Journal of biomedical semantics · 2014Article
- SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques.Journal of biomedical semantics · 2014Article
- Evolving BioAssay Ontology (BAO): modularization, integration and applications.Journal of biomedical semantics · 2014Article
- Automatically exposing OpenLifeData via SADI semantic Web Services.Journal of biomedical semantics · 2014Article
- Desiderata for an authoritative Representation of MeSH in RDF.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2014Article
- linkedISA: semantic representation of ISA-Tab experimental metadata.BMC bioinformatics · 2014Article
- Semantic Web repositories for genomics data using the eXframe platform.Journal of biomedical semantics · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA key activity for life scientists in this post "-omics" age involves searching for and integrating biological data from a multitude of independent databases. However, our ability to find relevant data is hampered by non-standard web and database interfaces backed by an enormous variety of data formats. This heterogeneity presents an overwhelming barrier to the discovery and reuse of resources which have been developed at great public expense.To address this issue, the open-source Bio2RDF project promotes a simple convention to integrate diverse biological data using Semantic Web technologies. However, querying Bio2RDF remains difficult due to the lack of uniformity in the representation of Bio2RDF datasets.
resultsWe describe an update to Bio2RDF that includes tighter integration across 19 new and updated RDF datasets. All available open-source scripts were first consolidated to a single GitHub repository and then redeveloped using a common API that generates normalized IRIs using a centralized dataset registry. We then mapped dataset specific types and relations to the Semanticscience Integrated Ontology (SIO) and demonstrate simplified federated queries across multiple Bio2RDF endpoints.
conclusionsThis coordinated release marks an important milestone for the Bio2RDF open source linked data framework. Principally, it improves the quality of linked data in the Bio2RDF network and makes it easier to access or recreate the linked data locally. We hope to continue improving the Bio2RDF network of linked data by identifying priority databases and increasing the vocabulary coverage to additional dataset vocabularies beyond SIO.
Identifiers
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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.