The Functional Genomics Production Team 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. Our publicly available tools are listed below.
All tools are open source and available under the European Molecular Biology Software License.
If you have any general questions or comments about these tools, please contact the team by emailing firstname.lastname@example.org. If you have more specific questions, bug reports or feature requests for an individual tool, please see the page for that tool to find out how best to direct your enquiry to us.
The latest versions of these tools are available for download.
Curation and Annotation Tools
Annotare is a tool for annotating biomedical investigations and resulting data. It is designed to help a bench biologist construct a MIAME-compliant annotation file based on the MAGE-TAB format.
Conan is an extremely light-weight workflow management application. It is designed for "script-chaining" types of operations that are typical in most bioinformatics workflows. It does not attempt to provide a solution for data analysis workflow problems - you are far better off using Galaxy or Taverna for this. However, if you want to chain scripts together quickly and easily, in an automated fashion, whilst retaining provenance information about them, Conan is a good choice.
Corona is a web interface for interacting with the Gene Expression Atlas curation API. It allows users to annotate sample and assay description for experiments in the Atlas. It also uses BioPortal services to assist in annotating Atlas data with ontologies such as EFO. Corona requires access to an Atlas database instance.
Limpopo MAGE-TAB Validation Service
Limpopo is a Java library for parsing MAGE-TAB and SampleTab documents, supporting submissions to ArrayExpress and the BioSamples Databases. It can both parse, validate write MAGE-TAB and SampleTab documents and provides easy support for adding validation rules or format converters.
MAGE-TAB Perl Libraries
Our MAGE-TAB Perl libraries are a series of modules that facilitate data manipulation, modification, parsing and creation of MAGE-TAB documents and other similar formats. This is extremely useful in support of data submissions to ArrayExpress, or other repositories of gene expression data.
SampleTab Accessioner Service
Ontology Powered Tools
The EFO Browser is an online tool that shows an up to date view of the most recent version of the Experimental Factor Ontology that can be searched and explored, whilst at the same time serving stable URLs for ontology concepts according to Linked Data principles.
GWAS Diagram Browser
The GWAS Diagram Browser is an online tool that visualises the known associations between Single Nucleotide Polymorphisms (SNPs) and observable traits in the NHGRI Genome Wide Association Study catalog.
MageComet is an online tool that facilitates curation of MAGE-TAB. It combines text-mining and the Experimental Factor Ontology (EFO) to create a semi-automatic environment for faster annotation, guided data-manipulation and content summary.
ZOOMA 2 is a search engine for automatic curation and a repository of annotation knowledge. It facilitates automated data annotation against a variety of ontologies by exploring context and previous annotation efforts as well as lexical matching.
ZOOMA 2 replaces ZOOMA, which was a command line only tool for generating ontology matches. For more information about the first version of ZOOMA, see http://zooma.sourceforge.net
Ontology Development Tools
Bubastis is an ontology change tool which is able to analyse two ontologies (typically two versions of the same ontology) to highlight logical changes which have occurred and to present these changes in more or less detail, as required.
efoimporter builds an OWL-format ontology module for the import of classes from one or more ontologies into another.
efovalidator validates the Experimental Factor Ontology (EFO). It reads EFO in OWL-format, validates the contents and writes a log file of validation errors.
URIGen is an online tool for managing the creation of URIs. It provides collaborative ontology development projects with a centralised server to manage their URI creation policy. There is a REST interface, a web client and a Protege 4.1 plugin for interacting with the URIGen server.
Semantic Web Tools
Lodestar is a Linked Data Browser and SPARQL endpoint. Lodestar is a Java based web app that can wrap any existing SPARQL endpoint to provide a set of additional SPARQL and Linked Data services.