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Project description

The BioSchemas project develops XML schemas for the exchange of biological data e.g. through SOAP-based web services. It is a collaborative and open project intended to increase the interoperability between bioinformatics applications. BioSchemas is part of the HOBIT project.

Read on here or choose one from the following sections:

[ Schemas ] [ Tools ] [ Members ] [ Contact ]

Schemas

Type libraries

Type libraries define common XML Schema types or so called Domain Specific Types (DST). They are the foundation for most of the building blocks and document formats.

• BioTypes: Common types for biological data
• HobitTypes

Building blocks

Building blocks are a reusable description of XML structures of a specific subdomain. Multiple building blocks can be mixed together to form a complex document format.

• AlignmentML
• CrossRefs: Cross references
• GOA: GO annotations
• RNAStructAlignmentML
• RNAStructML
• SequenceAnnotationML
• SequenceML

Document formats

Document formats define the format of a specific class of XML files.

• ProML: Description of proteins and protein sets
• ProThesaurus: Exchange of lists of protein synonyms and database identifiers

Tools

• Build Tools: Ant scripts and XSLT stylesheets to release a BioSchema.
• XmlStatistic: Tool to calculate some statistics for one or more XML documents, e.g. the ratio between the real data and the meta data.

Members

• Teaching and Research Unit of Bioinformatics of the Ludwig Maximilians-University, Munich
• BiBiServ (Bielefeld University Bioinformatics Server) of the University of Bielefeld

See here for a full list of all registered users. Read this if you like to contribute.

Publications

[1] XML schemas for common bioinformatic data types and their application in workflow systems, Philipp N Seibel , Jan Kruger , Sven Hartmeier , Knut Schwarzer , Kai Lowenthal , Henning Mersch , Thomas Dandekar and Robert Giegerich, BMC Bioinformatics 2006, 7:490, doi:10.1186/1471-2105-7-490

Contact

• User forums: To ask questions about the BioSchemas
• Developers' mailing list: To contact the BioSchemas developers
• Imprint: To contact the owner of the domain bioschemas.org

News:

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XmlStatistic 0.1 released

This is the first official release of XmlStatistic, a tiny tool for calculating some statistics over a collection of XML files, e.g. the meta-data/data-ratio. (0 comments)

BioSchemas.org online

The web site BioSchemas.org, dedicated to the collaborative development of open and extensible XML schemas for the exchange of biological data, is now online. (0 comments)

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