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Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

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.

Data Management for the Molecular Cytogenetic Resource

Jenny E. Marstaller and Manfred D. Zorn
Software Technologies and Applications Group, Information and Computing Sciences Division, Lawrence Berkeley Laboratory, Berkeley CA 94720

The LBL/UCSF Resource for Molecular Cytogenetics has been created to facilitate the application of molecular cytogenetics in clinical and biological studies. Work is being pursued in three areas: Development and application of improved hybridization technology, selection of probes optimized for use in fluorescence in situ hybridization (FISH) and development of digital imaging microscopy. All of these areas entail creation and manipulation of large images and other laboratory data. Our group is focussed to provide data management support for all the activities in the Resource.

To facilitate the free data exchange between researchers at UCSF and LBL which are a few miles apart we developed a Mosaic interface to access and modify information using the World Wide Web. The data are located on a central database. The Mosaic client allows to formulate retrieval and edit operations that are sent to the database. Results are filtered through a Perl script which generates HTML documents with Hypertext links that are sent back to the Mosaic client. We plan to make data from the Resource available using a similar mechanism that is open to outside access.

Probe information and mapping data from the Resource will be submitted to the public databases, i.e., GDB. In a collaboration with GDB we are developing a data submission tool (see separate abstract by Manfred Zorn) to facilitate the distribution of our research results.

In order to handle large amounts of images we are developing an image annotation database. The images themselves are automatically transferred to the LBL Mass Storage System. The annotation will be reformatted and loaded into a relational database to allow efficient query processing.

We will present an overview and the current status of our work.

This work was supported by the Director, Office of Energy Research, Office of Health and Environmental Reseach, Human Genome Program, of the US Department of Energy under Contract No. DE-AC03-76SF00098.