The flexibility and extensibility to support interfacing with and capture of information from a majority of the existing file formats and databases.
The past years have shown an enormous advancement in sequencing and array-based technologies, producing supplementary or alternative views of the genome stored in various formats and databases.
Additionally, as knowledge bases are available in heterogeneous formats, we developed scripts to automatically index ontologies in open biomedical ontologies (OBO) and web ontology language (OWL) formats and databases in structured query language (SQL) format.
Among others, Cytoscape software platform for network analysis and visualization has been widely adopted by the biological community because of its ease of use, compatibility with and direct access to many network formats and databases, respectively, as well as straightforward extensibility through open-source plug-in development [ 4, 5, 20, 21].
On the other hand, IUGONET is a challenging approach because it handles a variety of observational projects and related components, for example, instrument, observatory, person, data itself, and so on, in single metadata format and database structure.
Our system also allows a user to submit their own sequence in specific file format and database will display its contents as an additional track.
Raw data were converted into MGF format and database searches were performed on a MASCOT server (MASCOT 2.2, MS/MS Ion Search) using fixed modification (none), variable modification carbamidomethyl (Cys), and methionine oxidation for each protein band sample (16 digested samples).
While open software for chemical format interconversion and database entry cross-linking have partially addressed database interoperability, computational resource integration is hindered by the great diversity of software interfaces, languages, access methods, and platforms, among others.
The DO annotation of the human genome is available in both tab-delimited format and relational database format, which allows them to be easily adapted for other applications.
