Editing Portal:Life Sciences (section)

=== Ensembl and genome annotation infrastructure ===

'''Ensembl''' is one of the major genome browser and genome annotation resources in biology. It provides genome assemblies, gene annotations, comparative genomics data, variation data, and programmatic access to biological databases.

Ensembl has long provided a Perl API. Ensembl’s own documentation states that for each Ensembl database, the project provides a specific Perl API, and that Ensembl also uses code provided by BioPerl.<ref>Ensembl, “Perl API Installation,” https://www.ensembl.org/info/docs/api/api_installation.html, accessed July 3, 2026.</ref>

Ensembl data are stored in relational databases, especially MySQL, and the Perl API became an important way for researchers and developers to query genome features programmatically. This allowed users to retrieve genes, transcripts, exons, regulatory features, variation data, comparative-genomics data, and related annotations.

A 2017 paper on Ensembl core software resources described the Ensembl REST API as building on the Perl API, giving the REST service a stable platform for development and data transfer.<ref>Matthew Ruffier et al., “Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation,” Database, 2017, https://academic.oup.com/database/article/doi/10.1093/database/bax020/3074789, accessed July 3, 2026.</ref>

This is a major part of Perl’s bioinformatics legacy. Perl was not merely used by individual researchers. It was part of the infrastructure of major public genome resources.