In the second approach, ontologies have been used as basis for the development of mediators, i.e., software entities that encompasses a global knowledge (global database schema) and, at the same time, are able to provide mappings to the specific (local) schemas to be integrated (e.g., [ 33- 36]).
These do not include the mappings to species-specific ontologies, as we consider that mappings from multispecies ontologies to species-specific ontologies should not be treated as xrefs, but should be encoded separately in an association file, similar to the Gene Ontology Annotation mapping (Barrell et al., 2009).
To compare the "overlap" between the cross-species CAGE promoter mappings and the pig-specific CAGE mappings to the pig genome, features were considered to be in proximity if they were distant by at most 2 Kb.
We rejected general to specific mappings and accepted the reverse.
The main reasons for rejection were ambiguous terms and general to specific mappings.
The binary probe map (NCBI build 35) provided by Affymetrix with mappings to mm7 was used to associate probes with specific genomic locations.
Raw data from the Beer [ 40] study was processed using the same pipeline as the Bhattacharjee study, except that we used ProbeSet mappings to Entrez Gene IDs appropriate to the specific platform used in that study (hu6800hsentrezgcdf version 12.0.0).
Downloaded from GATExplorer [ 89- 91] GeneMapper (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php) includes the sets of unambiguous probes that map to each specific Ensemble Gene ID (ENSG ID).
As expected, a large portion of the genes show tissue specific expression in agreement with mappings to gene descriptions, Gene Ontology terms and KEGG pathways.
After these conjectures are verified, the successful mappings are stored as persistent mappings to constrain future analogies between the domains.
