We have made several improvements to the annotation system after the BGSAC annotation project and publication of the bovine genome (Fig 2), including support for direct writebacks from Apollo to the intermediate Chado database, database auditing and support for installing and launching Apollo using Java Webstart.
This architecture adds an intermediate layer (database) to the well-known client and server layers, that isolates the client part from the industrial process, allowing to incorporate the required data management and neural network processing tasks.
All scripts to create and configure the intermediate local database are included in the software package.
Periodically, a BGD curator used XORT to load the Chado-XML files into the intermediate Chado database for pre-reviewed annotations.
Large results such as those generated by these kinds of experiments are extremely resource-demanding to view through the MASCOT web interface, so an intermediate relational database (MySQL) was created, the MASCOT Large Results Viewer (MLRV), in which the peptide, protein, modification and search hit information could be stored in a readily queryable manner.
The similarity measure described here was thus applied to the three domains of the Gene Ontology, The Human Phenotype Ontology, Uberpheno, Uberon and The Pathway Ontology, with IC of each term, and pairwise similarities between all terms within each ontology stored in an intermediate MySQL database.
The framework includes a user-supplied design database, intermediate representations for pipeline organization and custom instruction set architecture, and a reconfigurable simulator and performance analysis tool.
A primary drawback of the FP-growth based algorithms is to require the large size of main memory for saving the original database and intermediate projected databases.
We have now modified the system to allow direct write-back of annotations to the intermediate (pre-review) Chado database.
