ArticleBMC immunology2011
Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network.
Article in BMC immunology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.
- Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates.BMC bioinformatics · 2013Pooled it
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- Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base.Vaccine: X · 2021Article
- Genetic Determinants in Salmonella enterica Serotype Typhimurium Required for OvercomingMicrobiology spectrum · 2021Article
- A Word Graph-based Method for Disease Topic Identification in Biomedical Literature.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2020Article
- Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels.BMC bioinformatics · 2019Article
- Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.Journal of biomedical semantics · 2018Article
- Identification of Cross-Protective Potential Antigens against PathogenicJournal of immunology research · 2018Article
- Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China.Scientific reports · 2017Article
- Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.Journal of biomedical semantics · 2017Article
- Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research.Current pharmacology reports · 2016Article
- Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches.Global vaccines and immunology · 2016Article
- The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.BioData mining · 2016Article
- Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over.Frontiers in genetics · 2016Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundVaccine literature indexing is poorly performed in PubMed due to limited hierarchy of Medical Subject Headings (MeSH) annotation in the vaccine field. Vaccine Ontology (VO) is a community-based biomedical ontology that represents various vaccines and their relations. SciMiner is an in-house literature mining system that supports literature indexing and gene name tagging. We hypothesize that application of VO in SciMiner will aid vaccine literature indexing and mining of vaccine-gene interaction networks. As a test case, we have examined vaccines for Brucella, the causative agent of brucellosis in humans and animals.
resultsThe VO-based SciMiner (VO-SciMiner) was developed to incorporate a total of 67 Brucella vaccine terms. A set of rules for term expansion of VO terms were learned from training data, consisting of 90 biomedical articles related to Brucella vaccine terms. VO-SciMiner demonstrated high recall (91%) and precision (99%) from testing a separate set of 100 manually selected biomedical articles. VO-SciMiner indexing exhibited superior performance in retrieving Brucella vaccine-related papers over that obtained with MeSH-based PubMed literature search. For example, a VO-SciMiner search of "live attenuated Brucella vaccine" returned 922 hits as of April 20, 2011, while a PubMed search of the same query resulted in only 74 hits. Using the abstracts of 14,947 Brucella-related papers, VO-SciMiner identified 140 Brucella genes associated with Brucella vaccines. These genes included known protective antigens, virulence factors, and genes closely related to Brucella vaccines. These VO-interacting Brucella genes were significantly over-represented in biological functional categories, including metabolite transport and metabolism, replication and repair, cell wall biogenesis, intracellular trafficking and secretion, posttranslational modification, and chaperones. Furthermore, a comprehensive interaction network of Brucella vaccines and genes were identified. The asserted and inferred VO hierarchies provide semantic support for inferring novel knowledge of association of vaccines and genes from the retrieved data. New hypotheses were generated based on this analysis approach.
conclusionVO-SciMiner can be used to improve the efficiency for PubMed searching in the vaccine domain.
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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.