ArticleJournal of biomedical semantics2011
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.
Article in Journal of biomedical semantics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 66 citations in OpenAlex.
- Real-World Use of Controlled Terminologies, Ontologies, and Vocabularies for Evidence Generation Across a Large International Observational Network: Challenges and Lessons Learned From a Mixed Method Study.JMIR medical informatics · 2026Article
- Immune biomarkers, profiles, and responses: a vaccine ontology perspective.Journal of biomedical semantics · 2026Article
- BERTopic-driven term extraction from biomedical texts toward ontology population: evaluating vaccine ontology with Plotkin's vaccines corpus.Journal of biomedical semantics · 2026Article
- Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase.Frontiers in cellular and infection microbiology · 2025Article
- CanVaxKB: a web-based cancer vaccine knowledgebase.NAR cancer · 2024Article
- A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Journal of biomedical semantics · 2022Article
- Alignment of vaccine codes using an ontology of vaccine descriptions.Journal of biomedical semantics · 2022Article
- Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs.Journal of biomedical semantics · 2022Article
- COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.Briefings in bioinformatics · 2022Article
- Profiling COVID-19 Vaccine Adverse Events by Statistical and Ontological Analysis of VAERS Case Reports.Frontiers in pharmacology · 2022Article
- Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base.Vaccine: X · 2021Article
- CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature.Journal of biomedical semantics · 2021Article
- Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research.Briefings in functional genomics · 2021Article
- VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms.Frontiers in immunology · 2021Article
- CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.Scientific data · 2020Article
- VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.BMC bioinformatics · 2019Article
- A systematic review on literature-based discovery workflow.PeerJ. Computer science · 2019Article
- Standards-based Semantic Integration of Manufacturing Information: Past, Present, and Future.Journal of manufacturing systems · 2019Article
- Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.Journal of biomedical semantics · 2018Article
- The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.Journal of biomedical semantics · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundInterferon-gamma (IFN-γ) is vital in vaccine-induced immune defense against bacterial and viral infections and tumor. Our recent study demonstrated the power of a literature-based discovery method in extraction and comparison of the IFN-γ and vaccine-mediated gene interaction networks. The Vaccine Ontology (VO) contains a hierarchy of vaccine names. It is hypothesized that the application of VO will enhance the prediction of IFN-γ and vaccine-mediated gene interaction network.
resultsIn this study, 186 specific vaccine names listed in the Vaccine Ontology (VO) and their semantic relations were used for possible improved retrieval of the IFN-γ and vaccine associated gene interactions. The application of VO allows discovery of 38 more genes and 60 more interactions. Comparison of different layers of IFN-γ networks and the example BCG vaccine-induced subnetwork led to generation of new hypotheses. By analyzing all discovered genes using centrality metrics, 32 genes were ranked high in the VO-based IFN-γ vaccine network using four centrality scores. Furthermore, 28 specific vaccines were found to be associated with these top 32 genes. These specific vaccine-gene associations were further used to generate a network of vaccine-vaccine associations. The BCG and LVS vaccines are found to be the most central vaccines in the vaccine-vaccine association network.
conclusionOur results demonstrate that the combined usages of biomedical ontologies and centrality-based literature mining are able to significantly facilitate discovery of gene interaction networks and gene-concept associations. AVAILABILITY: VO is available at: http://www.violinet.org/vaccineontology; and the SVM edit kernel for gene interaction extraction is available at: http://www.violinet.org/ifngvonet/int_ext_svm.zip.
Identifiers
What OpenQuestion holds
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.