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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.

SubmitData: Data Submission To Public Genomic Databases

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

Making information generated by the various genome projects available to the community is very important for the researcher submitting data and for the overall project to justify the expenses and resources. Public genome databases generally provide a protocol that defines the required data formats and details how they accept data, e.g., sequences, mapping information. These protocols have to strike a balance between ease of use for the user and operational considerations of the database provider, but are in most cases rather complex and subject to change to accommodate modifications in the database.

SubmitData is a user interface that formats data for submission to GSDB or GDB. The user interface serves data entry purposes, checking each field for data types, allowed ranges and controlled values, and gives the user feedback on any problems. Besides one-time submissions, templates can be created that can later be merged with TAB-delimited data files, e.g., as produced by common spreadsheet programs. Variables in the template are then replaced by values in defined columns of the input data file. Thus submitting large amounts of related data becomes as easy as selecting a format and supplying an input filename. This allows easy integration of data submission into the data generation process.

The interface is generated directly from the protocol specifications. A specific parser/compiler interprets the protocol definitions and creates internal objects that form the basis of the user interface. Thus a working user interface, i.e., static layout of buttons and fields, data validation, is automatically generated from the protocol definitions. Protocol modifications are propagated by simply regenerating the interface.

The program has been developed using ParcPlace VisualWorks and currently supports GSDB and GDB data submissions.

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