Editing Portal:Life Sciences (section)

=== Perl, databases, and biological records ===

Bioinformatics is inseparable from databases. GenBank, EMBL, DDBJ, SwissProt, UniProt, Ensembl, FlyBase, WormBase, model-organism databases, laboratory information systems, and local genome-center databases all shaped the field.

Perl was useful because it could bridge flat files, relational databases, web forms, APIs, and command-line tools. A Perl script could parse a GenBank file, extract gene features, load them into MySQL or PostgreSQL, compare them with local annotations, and generate a web page or report.

This database role was especially important during the early genomics era. Biology had many public databases, but formats and identifiers were inconsistent. Perl helped researchers map between accession numbers, clone names, gene symbols, protein IDs, transcript IDs, and laboratory sample names.

Perl’s DBI database interface made it possible to work with many relational databases using a common Perl programming style. In bioinformatics, this meant Perl could connect laboratory pipelines to MySQL, PostgreSQL, Oracle, SQLite, and other database systems.