Database management systems have been used to great advantage for industry usage scenarios. As science becomes increasingly dependent on carefully organized and curated data to inform and drive new discoveries, the need for database management systems has grown significantly. The long standing “20 questions” method was advocated in early studies of applying relational databases for science in order to elicit requirements for designing and developing information systems for scientific data. It has been observed, however, that database designs become outdated within months of usage leading to degradation in the quality of the database schema. In addition, there is limited evidence that scientists themselves have the tools and processes necessary to develop and maintain scientific databases without reliance on database administrators. Beyond learning to query databases, scientists need tools to create and evolve databases and guidance on how to apply those tools to develop information systems. In this paper, we present a simplified methodology for database evolution for scientists and a case study of database evolution by a scientist in the context of a research database for cell modeling. We include a detailed analysis of the activities and processes employed by the scientist during the schema evolution. Our results show that a scientist can successfully evolve a complex information system driven by new research requirements.

SUMMARY: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service. AVAILABILITY AND IMPLEMENTATION: RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org).

Abstract Summary: The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files. Availability: The current software translated XML schema file is located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd, and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/. PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML Contact: [email protected]

The Protein Data Bank (PDB) is a widely used biological database of macromolecular structures with a long history. This history is treated as lessons learned and is used to highlight what are believed to be the best practices important to developers of biological databases today. While the focus is on data quality, data representation and the information technology to support these data, the non-data and technology issues cannot be ignored. The role of the human factor in the form of users, collaborators, scientific society and ad hoc committees is also included.

UNLABELLED: TargetDB is a centralized target registration database that includes protein target data from the NIH structural genomics centers and a number of international sites. TargetDB, which is hosted by the Protein Data Bank (RCSB PDB), provides status information on target sequences and tracks their progress through the various stages of protein production and structure determination. A simple search form permits queries based on contributing site, target ID, protein name, sequence, status and other data. The progress of individual targets or entire structural genomics projects may be tracked over time, and target data from all contributing centers may also be downloaded in the XML format. AVAILABILITY: TargetDB is available at http://targetdb.pdb.org/

UNLABELLED: Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. AVAILABILITY: Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.