The BioXSD/GTrack ecosystem is a family of interoperable data formats and supportive tools for basic bioinformatics data types; biomolecular sequences, features, alignments and references. This service provides a unified data model, suitable as exchange formats for web services, web applications and programmatic libraries. BioXSD aims to serve as a common, canonical tree-structured format (XML, JSON, YAML, binary) for the basic bioinformatics data. Specialized standard XML-schema formats such as for example SBML, MAGE-ML, GCDML, PDBML, PSI MI MIF, PhyloXML or NeXML are orthogonal efforts and should be used wherever applicable. BioXSD aims at filling the gap between these specialized XML formats.
BioXSD is a data model defining exchange formats for basic bioinformatics types of data: sequences, alignments, feature records with associated data and metadata. BioXSD aims to serve as a common, canonical tree-structured format (XML, JSON, YAML, binary) for the basic bioinformatics data. Specialised standard XML-schema formats such as for example SBML, MAGE-ML, GCDML, PDBML, PSI MI MIF, PhyloXML or NeXML are orthogonal efforts and should be used wherever applicable. BioXSD aims at filling the gap between these specialised XML formats.
A canonical data format does not mean “the only format”, but an exchange format that can be common to several tools (as one of multiple formats the tools are supporting). Tools can produce and consume BioXSD directly, or BioXSD can be used as an intermediate canonical format, rich enough to enable conversions among diverse formats. Using common exchange format enables smooth integration of compatible tools into analysis workflows.
BioXSD is a rich but not too complicated data model and exchange format, aiming to enable deployment of globally and smoothly interoperable bioinformatics tools on the World Wide Web of Services. BioXSD supports HTTP (“REST”) Web services and WS-I compliant SOAP Web services, and interoperates with ordinary HTTP (REST), SOAP, and XML libraries for common programming languages. No other infrastructure than standard HTTP and XML is necessary for using BioXSD-compatible Web services. In the near future, we would like to add smooth support for JSON, YAML, and eventually other data-serialisation languages, as alternatives to using BioXSD in XML.
BioXSD is a “blue-collar” initiative originating from the inside of the bioinformatics community, initiated among others by the EMBRACE project partners and the participants of the 1st DBCLS BioHackathon, in 2008.”
BioXSD/GTrack offers standardized data formats and models for bioinformatics data, enhancing interoperability and data exchange.
About this service
BioXSD/GTrack is a standardized ecosystem for bioinformatics data, providing data models and formats to promote interoperability and efficient data exchange. This ecosystem is maintained by ELIXIR Norway, offering comprehensive resources for bioinformaticians and software developers. BioXSD defines XML Schema for Bioinformatics, while GTrack provides a generic tabular format for genomic data. These standards ensure seamless integration and data management across various tools and platforms.
Why use this service: BioXSD/GTrack is essential for bioinformaticians, data analysts, and software developers who require standardized formats for bioinformatics data exchange. The ecosystem’s robust standards promote interoperability, ensuring efficient and accurate data sharing. By adopting BioXSD/GTrack, researchers can streamline their data management practices and enhance collaborative efforts. The comprehensive data models and tools provided by this ecosystem support a wide range of bioinformatics workflows.
How to get started: Researchers can integrate BioXSD/GTrack into their projects to standardize data formats and enhance interoperability. Visit BioXSD/GTrack to learn more about its features and start utilizing its tools.