Introduction to the Workshop
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Mapping

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Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Object-Protocol Model Tools: Overview and Applications

Victor M. Markowitz, I-Min A. Chen, and Ernest Szeto
Data Management Research and Development Group, Information and Computing Sciences Division, Lawrence Berkeley Laboratory, Berkeley, California 94720

Genomic applications require facilities for keeping track and manipulating data. Data need to be described, presented, browsed and queried in a way that scientists can understand. Commercial database management systems (DBMSs) provide data management facilities, but do not provide capabilities for describing, browsing, and querying data in terms familiar to scientists. Thus, both relational and object-oriented databases can hardly be comprehended by scientists and entail tedious, error-prone, and time-consuming database development and maintenance. Consequently, there is a need for data management tools that would allow scientists interact efficiently with both relational and object-oriented DBMSs using clear and concise constructs and operations.

We have developed data management tools that facilitate the development of genomic databases and that allow scientists to define, query, and browse genomic databases in terms of application-specific objects and protocols. These tools are based on a data model called the Object-Protocol Model (OPM) developed by us [1]. OPM provides constructs for directly modeling objects and protocols (laboratory experiments) specific to genomic database applications, for specifying protocols in terms of alternative and sequences of component protocol steps, and for specifying different database views. Furthermore, OPM supports modeling inter-database references that allow developing multidatabase systems and provides object versioning constructs that allow keeping track of the history of objects in a genomic database.

The suite of OPM data management tools currently target relational DBMSs, and include a reverse engineering tool for determining the OPM description of existing relational genomic databases, a graphical editor for specifying the structure of genomic databases, a translator that maps OPM specifications into DBMS specifications, a graphical browsing and data entry interface for browsing and updating genomic databases. The OPM tools provide version management and support for database replication. In future, we plan to port the OPM tools to an object-oriented or object-relational DBMS.

OPM and the OPM data management tools have been used for developing a prototype database for the large scale sequencing project in Dr. Lee Hood's laboratory at University of Washington, Seattle, and are currently used for developing version 6 of Genome Data Base (GDB) at Johns Hopkins School of Medicine, Baltimore.

OPM and OPM data management tools are overviewed in [2]. This overview, other OPM papers, OPM documents, and the OPM tools are available via World Wide Web using URL: ftp://gizmo.lbl.gov/pub/DM TOOLS/OPM/opm.html.

This work was funded by the Human Genome Program of the Office of Health and Environmental Research, U.S. Department of Energy under Contract DE-AC03-76SF00098.

[1] Chen, I.A., and Markowitz, V.M., Modeling Scientific Applications with an Object Data Model, to appear in Proceedings of the 11th International Conference on Data Engineering, 1995.
[2] Chen, I-Min, and Markowitz, V.M., An Overview of the Object Protocol Model (OPM) and OPM Data Management Tools, TR LBL-33706, Lawrence Berkeley Laboratory, 1994.