ArticlePloS one2015
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A proteome-driven strategy to discover novel therapeutic targets in Orientia tsutsugamushi.Antonie van Leeuwenhoek · 2026Article
- BioHackathon 2015: Semantics of data for life sciences and reproducible research.F1000Research · 2020Article
- MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.Nucleic acids research · 2019Article
- A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.F1000Research · 2019Article
- SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.BMC bioinformatics · 2017Article
- The Orthology Ontology: development and applications.Journal of biomedical semantics · 2016Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.
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