Data Management Tools
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People and History

Sponsors

An OPM Tutorial

OPM Data Management Tools

OPM Multidatabase Query System

Applications

Genome Databases

Database Directories and Schema Libraries

Electronic Notebooks for Scientific Experiments

OPM Web Schema Browsing and Query Interfaces

Publications

Presentations

OPM Data Management Tools Version 4

Release date: May 1997.

Platforms : Sun/SOlaris, SGI, Dec/Alpha

DBMSs : Sybase 10-11, Oracle7

OPM Data Management Tools for CORBA Compliant Environments.

Kosky, A., Szeto, E., Chen, I.A., Markowitz, V.M.,

Technical Report LBNL-38975, 1996.

OPM Database Schema Examples

Shotgun Sequencing Database

Chen, I.A., and Markowitz, V.M., Technical Report LBNL-35867 (revised), 1995.

GSDB 1.0 (released Aug 1996) Database

Viewed via a Java/Web Browser

Generated by A. Kosky with the OPM Retrofitting Tool.

GDB 6.0 Database

Genome DataBase (GDB 6.0 ), Johns Hopkins School of Medicine.

3DBase

Protein Data Bank(PDB), Brookhaven National Laboratory.

OPM Database Query Examples

OPM Query Examples

Expressed over Genome DataBase (GDB 6.0), Johns Hopkins School of Medicine.

OPM Based Web Query Interfaces

GDB Query Interfaces

Genome DataBase (GDB 6.0), Johns Hopkins School of Medicine.

Query Forms Constructed using the OPM Java Query Tool

for the Primary Database at the German Human Genome Project Resource Center.

OPM Java Query Tool

for the Primary Database at the German Human Genome Project Resource Center.

Exploring Heterogeneous Molecular Biology Databases in the Context of the Object-Protocol Model.

Markowitz, V.M., Chen, I.A., Kosky, A.,

Theoretical and Computational Genome Research, S. Suhai (ed.), Plenum, 1996.

OPM*QS: The Object-Protocol Model Multidatabase Query System.

Chen, I.A., Kosky, A., Markowitz, V.M., Szeto, E.

Documentation: Technical Report LBNL-38181, 1995.

Related Heterogeneous Database Management Systems.

Background papers and links to related heterogeneous molecular bilogy database systems.

Information Models for Biological Collection

A Database Directory for Molecular Biology Databases

Electronic Notebooks in the Context of the OPM Tools.

Markowitz, V.M., Chen, I.A., Kosky, A., Kuno, H., Szeto, E.

OPM Schema for the Spectro Microscopy Collaboratory at the Advanced Light Source (ALS) Beamline 7

Chen, I.A., Freitas, C.M.D., Kuno, H.A., Markowitz, V.M., Sachs, S.R.

See also Electronic Notebooks for Collaboratories

Exploring Heterogeneous Biological Databases: Tools and Applications

Chen, I.A., Kosky, A.S., Markowitz, V.M., and Szeto, E.

To appear in the proc. of the 6th International Conference on Extending Database Technology, EDBT'98, March 1998.

Constructing and Maintaining Scientific Database Views

Chen, I.A., Kosky, A.S., Markowitz, V.M., and Szeto, E.

In postscript format: 7MB. To appear in the proc. of the 9th Conference on Scientific and Statistical Database Management, August 1997.

Facilities for Exploring Molecular Biology Databases on the Web: A Comparative Study

Markowitz, V.M., Chen, I.A., Kosky, A.S., and Szeto, E.

In postscript format: 85KB. To appear in the proc. of the Pacific Symposium on Biocomputing, Hawaii, January 1997.

Version Management for Scientific Databases

Markowitz, V.M., Chen, I.A., Letovsky, S., Li, P., and Fasman, K.

In postscript format: 142KB. Proc. of the Int. Conference on Extending Database Technology (EDBT'96), 1996.

Modeling Scientific Experiments with an Object Data Model

Chen, I.A., and Markowitz, V.M.

In postscript format: 158KB. Proc. of the 11th Int. Conference on Data Engineering, 1995.

An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools

Chen, I.A., and Markowitz, V.M.

In postcript format: 654KB. Information Systems, Vol. 20, No. 5, 1995.

The Object-Protocol Model (Version 4)

Chen, I.A., and Markowitz, V.M.

Documentation: Technical Report LBNL-32738 (revised), 1996.

OPM Schema Translator (OPM Version 4)

Chen, I.A., and Markowitz, V.M.

Documentation: Technical Report LBNL-35582 (revised), 1996.

Mapping OPM Schemas into Relational Database Schemas and Procedures

Chen, I.A., and Markowitz, V.M.

Documentation: Technical Report LBNL-33048 (revised), 1996.

OPM Query Translator

Chen, I.A., Kosky, A., Markowitz, V.M., Szeto, E.

Documentation: Technical Report LBNL-38180, 1996.

Shotgun Sequencing Database

Chen, I.A., and Markowitz, V.M.

Documentation: Technical Report LBNL-35867 (revised), 1995.

OPM Data Management Tools for CORBA Compliant Environments,

Kosky, A., Szeto, E., Chen, I.A., Markowitz, V.M.,

Technical Report LBNL-38975, 1996.

Characterizing Heterogeneous Molecular Biology Database Systems,

Markowitz, V.M., and Ritter, O. Journal of Computational Biology, Vol 2, No 4, 1995.

Coping with Data Modeling Diversity, Markowitz, V.M.

Presented at the 2nd Meeting on Interconnection of Molecular Biology Databases, 1995,

OPM*QS: The Object-Protocol Model Multidatabase Query System

Chen, I.A., Kosky, A., Markowitz, V.M., Szeto, E.

Documentation: Technical Report LBNL-38181, 1995.

The 6th Int. Conference on Extending Database Technology, EDBT'98 (paper & demo), March 1998

Applied Bioinformatics Conference (invited talk), September 1997

9th International Genome Sequencing and Analysis Conference (talk), September 1997

The 9th Conference on Scientific and Statistical Database Management (paper & demo), August 1997

Bioinformatics and Genome Research Conference (invited talk), June 1997

Meeting on Genome Mapping and Sequencing (poster), Cold Spring Harbor, May 1997

Association of Systematics Collections (ASC) Annual Meeting (invited talk), April 1997

13th International Conference on Data Engineering (demo), April 1997

Pacific Symposium on Bioinformatics (paper), January 1997

Bioinformatics - Structure Conference (invited talk), Jerusalem, November 1996

Meeting on Interconnection of Molecular Biology Databases: Java and CORBA for Bioinformatics (presentation), 1996

Meeting on Genome Mapping and Sequencing (poster), Cold Spring Harbor, May 1996

International Sybase User Group Conference (invited talk), May 1996

International Conference on Extending Database Technology (EDBT'96), March 1996.

International Symposium on Theoretical and Computational Genome Research (invited talk), Heidelberg, Germany, March 1996

Workshop on Structuring Biological Information (invited talk), Heidelberg, Germany, March 1996

DOE Contractor-Grantee Meeting (poster), Santa Fe, January 1996

7th International Genome Sequencing and Analysis Conference (talk), 1995

Meeting on Interconnection of Molecular Biology Databases (paper, panel), 1995

Bioinformatics and Genome Research Conference (invited talk), June 1995

CODATA Meeting on Biomolecular Databases (invited talk), June 1995

Meeting on Genome Mapping and Sequencing (poster), Cold Spring Harbor, May 1995

Conference on the Human Genome Project: Commercial Implications (invited talk), March 1995

11th International Conference on Data Engineering (paper), March 1995

This work is supported by the

Victor M. Markowitz
VMMarkowitz@lbl.gov