The chromosomal distribution of mouse OR genes, obtained from the Trask Laboratory mouse OR gene database (http://www.fhere.org/science/labs/trask/OR/), is shown in Table S1.
This case study explored the usefulness of argumentation in helping biologists work around conflicting information presented by an online biological database, in this case a developmental mouse gene expression database called EMAGE.
These include the EBI Alternative Splicing and Transcripts Diversity database (ASTD, v1.1) (http://www.ebi.ac.uk/astd/main.html) and Mouse Gene Index database (v4.0) developed by National Institute of Aging (http://lgsun.grc.nia.nih.gov/geneindex4/index.html) [17], [18].
The mouse gene expression database developed by Mouse Genome Informatics (MGI) is a community resource for gene expression information from the laboratory mouse (12).
Future work will extend this to include data from a complementary developmental mouse gene expression database, GXD (Ringwald et al., 2001).
This is not the only work needed, in particular an effort must be made to extend the system so that it can create arguments based on the data held in another developmental mouse gene expression database, GXD.
The GUDMAP ontology is currently being incorporated into the existing EMAP ontology, which is used by other resources such as the mouse Gene Expression Database (GXD) (Smith et al., 2007) and EMAGE (Richardson et al., 2010).
This case study created a prototype using a third-party argumentation engine from ASPIC, Argumentation Services Platform with Integrated Components (www.argumentation.org), to generate arguments for the data held in the EMAGE developmental mouse gene expression database (Davidson et al., 1997).
More specifically, it looks closely at a gene expression case study, creating an appropriate representation of the underlying data and series of rules that are used by a third-party argumentation engine to reason over the query results provided by the mouse gene expression database EMAGE.
The mouse gene in the database includes a 3' exon encoding 60 amino acids.
