Yet Another Perl Biology Toolkit

Yet Another Perl Biology Toolkit

By Guillaume Rousse (‎guillomovitch‎) from Paris.pm
Date: Thursday, 24 July 2003 17:40
Duration: 20 minutes
Language:

Everyone already heard of BioPerl, a wonderful Perl toolkit designed by
skillful hackers for efficiently solving different problems in molecular
biology. This talk is absolutely not about BioPerl. This talk is about another
toolkit, dedicated to another biology subdomain: systematics.

This toolkit is composed of two parts:
- Data::Knowledge, a domain-agnostic knowledge representation framework
- Bio::Systematics::OSIS, a systematics-dedicated model built upon Data::Knowledge

Data::Knowledge provides several generic services for managing complex data:
- knowledge representation
- UML-based object-oriented model
- declarative-based property management
- arbitrary constraint support
- runtime model discovery
- classes, associations, constraints descriptors
- fully localised
- persistence management
- backend abstraction (relational, XML, ...)
- almost transparent persistence
Moreover, it provides a few generic CGI applications.

Bio::Systematics::OSIS is a set of classes modeling major systematics concepts
(names, taxons, specimens) structure and behaviour, based on Data::Knowledge. The
goal is to define the semantic once, and to quickly create specific applications from
this common code base.

The talk will first present the two modules, then present effective use to manage
reference databases hosted at Laboratory of Informatics and Systematics (University Paris 6).