This software can be used for populating Research Data Australia (RDA) with collection descriptions of Australian-related biomolecular data held in the European Bioinformatics Institute (EBI) databanks. This project is ANDS-funded through the DIISR Education Infrastructure Fund.
The tool was released as open source software in June, 2011. The current
version can be downloaded from the SourceForge download
The European Bioinformatics Institute provides international access to data in molecular bioscience generated by researchers worldwide, including Australia. In its present state, Australian specific data is difficult to isolate within the EBI databases, particularly for the non-domain user. This software allows for Australian data to be discoverable in the form of collections of nucleotide and protein sequences. These collections can be defined as Australian data of two types: a) data submitted from Australian-based researchers; b) data associated with sets (and subsets thereof) of Australian species.
RDA - Research Data Australia, is a mesh of searchable web pages describing Australian research data collections. This software generates collections of Australian data from the EBI that can be discoverable through the RDA.
The EBI-RDA linkage system is comprised of two main parts:
1. Data extractor: this system is a standalone Java Program (executable jar) that pulls query items from a local data store (MySQL database) and queries them (using web services) against the Uniprot and ENA databases made available by EBI.
2. Landing page: a website to allow visual display of the data. This was developed used JSP/Servlets and displays the relevant data that is stored in the MySQL database.
Intsructions for how to install and use this software can be found on the documentation page