ArticleJournal of biomedical semantics2013
Query enhancement through the practical application of ontology: the IEDB and OBI.
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 12 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
12 citing papers in PubMed.
- VO: The Vaccine Ontology.Scientific data · 2026Article
- The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook.Immunogenetics · 2020Review
- The Immune Epitope Database (IEDB): 2018 update.Nucleic acids research · 2019Article
- Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection.PloS one · 2019Article
- CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.BMC bioinformatics · 2018Article
- The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.Journal of biomedical semantics · 2018Review
- Identification of errors in the IEDB using ontologies.Database : the journal of biological databases and curation · 2018Article
- FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.Database : the journal of biological databases and curation · 2018Article
- Robotic crowd biology with Maholo LabDroids.Nature biotechnology · 2017Article
- Better living through ontologies at the Immune Epitope Database.Database : the journal of biological databases and curation · 2017Article
- Perspectives on next steps in classification of oro-facial pain - Part 3: biomarkers of chronic oro-facial pain - from research to clinic.Journal of oral rehabilitation · 2015Review
- Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.Journal of biomedical semantics · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. The Immune Epitope Database (IEDB, http://www.iedb.org) utilizes the Ontology for Biomedical Investigations (OBI) and several additional ontologies to represent immune epitope mapping experiments. Here, we describe our experiences utilizing this representation in order to provide enhanced database search functionality. We applied a simple approach to incorporate the benefits of the information captured in a formal ontology directly into the user web interface, resulting in an improved user experience with minimal changes to the database itself. The integration is easy to maintain, provides standardized terms and definitions, and allows for subsumption queries. In addition to these immediate benefits, our long-term goal is to enable true semantic integration of data and knowledge in the biomedical domain. We describe our progress towards that goal and what we perceive as the main obstacles.
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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.