The Functional Genomics Software Suite

The Functional Genomics Production Team at the European Bioinformatics Institute have produced a large suite of software for data submissions, working with the MAGE-TAB format, annotating data against the Experimental Factor Ontology and automating curation processes of microarray and high throughput sequencing data. Here we present an overview of our publicly available tools. Tab2MAGE is a series of Perl modules that facilitate data submissions to ArrayExpress. It includes support for parsing and validating a variety of formats, including MAGE-TAB, MAGE-ML and MIAMExpress. It also contains a lightweight process tracking system and taxon specific template generation system implemented in Ruby on Rails with a MySQL backend. Limpopo is a MAGE-TAB parser written in Java. It provides functionality for validating MAGE-TAB with custom rules and exporting MAGE-TAB data to any other format (including your own database). OntoCAT is a Java library that abstracts a number of common ontology-related tasks for interacting with ontology resources, including local files and public repositories. OntoCAT R is an R-package designed to enable ontology traversal and search in R environment. ZOOMA is a tool that provides optimal ontology mappings for user supplied terms, facilitating automatic data annotation to preferred ontologies. OntologyMapper is a Perl package providing fuzzy concept recognition and lexical matching based on a list of terms and any target ontology. Bubastis is an ontology diff tool used to compare two ontologies (typically versions of the same ontology) in OWL or OBO format for logical differences in classes and identifying new or deleted classes.