C04853: Johns Hopkins University PROTEIN-DB2 Database SystemNovelty:
The current invention is a relational database for proteomic experiments.
Value Proposition:
Proteomic data collection follows complex workflow, ranging from gel electrophoresis to mass spectrometry to liquid chromatography or a combination thereof. In addition, amplification of low-abundance proteins is difficult due to their level of expression and undesirable post-translational modifications that can occur outside their normal environment. Therefore, it is vital to keep track of all experimental conditions in proteomic data collection to ensure that the data collected truly represents the protein(s) of interest. While most laboratory information management systems (LIMS) already handle the tracking of experimental conditions, they do not have the ability to store primary data and the subsequent analyses of that data. This platform alleviates this burden, providing a mechanism for collaborators to share primary experimental data and store their respective analyses of the data. Advantages include:
• Supports international standards in proteomics data
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• Data may be loaded from multiple sources, analyzed with commercial off-the-shelf software tools
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• Portable to many platforms
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Technical Details:
Johns Hopkins researchers have developed a relational database derived from the Protein Standards Initiative Object Model (PSI-OM). Within this database, users have the ability to store information related to a single experiment and compare data from multiple experiments. Information stored by the system includes primary n-dimensional gel image and mass spectrometry (MS) data on a file server, along with commercial off-the-shelf analysis of the n-dimensional gel images, and MS in the database itself. In addition, the database has the capability of storing commercial off-the-shelf protein identification. While users can associate primary data with an experiment, they also have the ability to link primary data to one another, to follow the path to identifying a particular protein of interest, from n-dimensional gels to MS to protein identification. While the IBM DB2/UDB Relational Database Management System (RDBMS) is the platform used to instantiate the database, the table creation scripts, as well as the SQL commands within the web interfaces and source code, are all in SQL92 format. Therefore the database itself is portable to other RDBMSs, either open-source (i.e. mySQL, PostgreSQL, etc.) or commercial (i.e. Oracle, Microsoft SQL Server, etc,).
Looking for Partners:
To develop and commercialize the technology as a database for protein data collection and analysis.
Stage of Development:
Available for public use since 2004.
Data Availability:
Under CDA/NDA
Publications/Associated Cases:
Not available at this time.
