Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.

Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species.

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.

Background: Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability, the utility lies dormant.

Results: In this article, we discuss several approaches to boost interoperability depending on the interoperable parts.

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g.

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

Background: In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses.