DC-BASE databaseDatabases, factual
The experiments on human monocyte-derived DC are being annotated in DC-BASE, a unique DC-dedicated database integrated with data mining tools. The database uses a LIMS system based on the structure of Base2.9. The database currently contains 240 microarray experiments annotated accordingly to MIAME standards and thoroughly analyzed in order to pass severe quality control tests. A meeting will be organized for defining policies on data sharing within the DC-THERA community and beyond.
In order to populate DC-BASE with data obtained from the literature, we used the GEO Import Perl program to download the required experiments from the Gene Expression Omnibus (GEO) database, and to convert them into a spreadsheet based format called MAGE-TAB. MAGE-TAB data has then been imported into DC-BASE.
We have collaborated with the team lead by Andrea Splendiani for the definition of shared terminologies for the annotation of the microarray datasets. These terminologies are at the basis of semantic interoperability with other resources, and the DC-THERA Directory in particular. More specifically, a query to to the Directory will propagate to the DC-ATLAS microarray repository. The DC-THERA Directory will then present a summary of results found.
Access to DC-BASE is provided through the DC-THERA Directory.