ArticleDatabase : the journal of biological databases and curation2019
Enabling semantic queries across federated bioinformatics databases.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Interactive network visualization of opioid crisis research: a tool for reinforcing data linkage skills for public health policy researchers.Frontiers in artificial intelligence · 2024Pooled it
- Improving annotation, access, and comparison of nutritional composition data for underutilized crops.Database : the journal of biological databases and curation · 2026Article
- An epidemiological knowledge graph extracted from the World Health Organization's Disease Outbreak News.Scientific data · 2025Article
- A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.GigaScience · 2025Article
- A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.Integrative organismal biology (Oxford, England) · 2025Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- An ontology-based knowledge graph for representing interactions involving RNA molecules.Scientific data · 2024Article
- The SIB Swiss Institute of Bioinformatics Semantic Web of data.Nucleic acids research · 2024Article
- Article
- Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.GigaScience · 2022Article
- Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation.Distributed and parallel databases · 2022Article
- Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects.Frontiers in bioinformatics · 2022Review
- Accessing scientific data through knowledge graphs withPatterns (New York, N.Y.) · 2021Review
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication.Trends in biochemical sciences · 2021Review
- OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.Nucleic acids research · 2021Article
- The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.Nucleic acids research · 2021Article
- Querying knowledge graphs in natural language.Journal of big data · 2021Article
- Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface.JMIR medical informatics · 2020Article
- A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.F1000Research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationData integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.
resultsWe introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.
Indexed as
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.