Nevertheless, most of these reported approaches are based on analyzing the retrieval result set for one or two initial topics provided as query by a user, instead of being able to scale up to the whole set of literature database for the purpose of discovering real, novel and cross-silo biomedical hypotheses.
Furthermore, all the approaches are based on retrieval result set of one or two initial topics provided by a user, instead of being able to scale up to the whole set of topics within a literature database for the purpose of discovering real, novel and cross-silo biomedical hypotheses.
Existing approaches for discovering inclusion dependencies consist in producing the whole set of inclusion dependencies holding in a database, leaving the task of selecting the interesting ones to an expert user.
Although our analysis does not cover the whole set of ABC proteins present in the databases, it provides an insight into their astonishing diversity.
The complete UniProtKB/Swiss-Prot protein sequence database and the whole set of peptides predicted from the fully sequenced genomes of C. gigas (release 9) (Zhang et al. 2012) and P. fucata (v 1.0) (Takeuchi et al. 2012) were screened for the presence of the C-C-CC-C-C pattern with a custom Perl script, without any constraint about the spacing between cysteine residues.
The second reference service has as entry points the whole set of genes from the EMAGE, GXD, GENSAT and OMIM databases.
Then, we performed reciprocal BLASTX searches (Altschul et al. 1997) using the selected subset of A. vulgare genome sequences as queries to screen for homologous coding sequences in the whole set of nonredundant protein sequences of the National Center for Biotechnology Information (NCBI) database.
The whole set of microarray data were also deposited in the GEO database, accession number GSE44282.
For all the selected species, the database returned 119 orthologous protein families shared by the whole set of species.
Within this whole set of 105 RIs (29 + 75), we found 94 in RegulonDB and only 10 were missing in the database.
