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Related Experiment Video

Updated: Jul 19, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

XML schemas for common bioinformatic data types and their application in workflow systems.

Philipp N Seibel¹, Jan Krüger, Sven Hartmeier

¹Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany. philipp.seibel@biozentrum.uni-wuerzburg.de <philipp.seibel@biozentrum.uni-wuerzburg.de>

BMC Bioinformatics

|November 8, 2006

Summary

Bioinformatic software tools require common data formats for workflow integration. The Helmholtz Open BioInformatics Technology network (HOBIT) developed XML schemas and a Java library (BioDOM) to enable seamless tool interoperability.

Related Experiment Videos

Last Updated: Jul 19, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

Bioinformatics
Computational Biology
Software Engineering

Background:

Bioinformatic tools often use diverse, heterogeneous data formats, hindering workflow integration.
Combining single-task software into complex applications necessitates standardized data exchange.
Lack of common formats impedes the creation of seamless bioinformatic workflows.

Purpose of the Study:

To address the need for common data formats in bioinformatics.
To develop standardized descriptions for essential bioinformatics data types.
To facilitate the interoperability of diverse bioinformatic software tools.

Main Methods:

The Helmholtz Open BioInformatics Technology network (HOBIT) identified key bioinformatics data types.
Developed XML schemas for sequence, sequence alignment, RNA secondary structure, and RNA secondary structure alignment.
Integrated these XML schemas into a Java library named BioDOM.

Main Results:

Created a set of XML schemas for fundamental bioinformatics data formats.
The BioDOM library provides a Java implementation for these XML formats.
The formats are program-independent, promoting seamless data exchange between tools.
XML schemas and BioDOM library are publicly available online.

Conclusions:

The HOBIT XML schemas and BioDOM library simplify the integration of XML support into bioinformatic tools.
Enables seamless interoperability of bioinformatic tools within workflow scenarios.
Facilitates the development of complex, integrated bioinformatic applications.