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About BioDOM
What is BioDOM?
BioDOM is a JAVA library to build XML files following the HOBIT format descriptions. Additionally, BioDOM provides functions to convert native non-XML output of various bioinformatic tools to XML formats that can be validated with the HOBIT XML schemas. It is freely available for download and may be included in your own programs under the conditions of the Apache Licence 2.0. You can also convert formats online by using the BioDOM WebService.
Current situation
Various bioinformatic tools use a great variety of different inhomogeneous formats for reading data and storing their results. While some formats, like FASTA or CLUSTAL, are common to several programs, others are utilized by only a single tool. Even worse, prevalent formats often lack consistence, e.g. there are many different "interpretations" of the FASTA format in use. This can probably be accredited to the fact, that the majority of formats are not well described - a formal definition is missing.
BioDOM formats are formally defined by XSDs (XML schemas, see HOBIT). The BioDOM package supplies converters, that can transform common native formats to these XML formats. With BioDOM it is easy to define a interface between different bioinformatic tools.
Note that BioDOM is a growing product. Currently it implements only the most common converters. Once need arises it can be extended by additional converters and more XML formats.
members
Bielefeld University, Bielefeld University Bioinformatics Service
University Würzburg, Institute of Bioinformatics
Georg-August University Göttingen, Department of Bioinformatics
former (non-active) members
collaborators
HOBIT
BioDOM validates the XML documents against XSD schemas developed and maintained by the HOBIT initiative. HOBIT is dedicated to form the core of a network linking bioinformatics centres together. It shall be understood as an initial organisational and technological platform for interconnection of bioinformatic activities. The aim of the network is to concatenate applications and resources in a uniform way so providing an efficient communication tier for bioinformatic resource access.
BioSchemas
BioDOM uses BioTypes. BioTypes is a type library hosted on BioSchemas and was initiated by Martin Szugat. It is developed in close cooperation with BioDOM.
