GCDML

Project Title Genomic Contextual Data Markup Language (GCDML)

Project Lead Renzo Kottmann

Team members See: http://wiki.gensc.org/index.php?title=GCDML

Elevator pitch The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that is a reference implementation of the “Minimum Information about any Sequence” (MIxS) specification in XML Schema.

Project Summary The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the “Minimum Information about any Genome Sequence” . GCDML is an XML Schema for generating MIxS compliant reports for data entry, exchange, and storage. When This sample-centric, strongly-typed schema provides a diverse set of descriptors for describing the exact origin and processing of a biological sample, from sampling to sequencing, and subsequent analysis. GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org).

Project Initiation Date The project was a follow up of the first XML for the Genomes Catalogue as discussed from the very first meeting. Then it grew into an own project.

What will this project aim to contribute to the GSC? An XML schema as a reference implementation of the MIxS specification.

Have you spoken about the project already within GSC? GCDML was formalized at GSC 5 and existed as an XML schema since the earliest efforts of the GSC to build the GSC Genome Catalogue. It is one of the GSC core projects.

Which existing projects, if any, does this one replace/complement/subsume/expand? GCDML is the first reference implementation of the MIxS specification.

How does this project fit into GSC’s mission statement? Helps implementation and adoption of MIxS and information exchange.

Will you start a GSC working group? Formed: http://wiki.gensc.org/index.php?title=GCDML

How do you wish to further engage the GSC ? GCDML is now primarily developed through the developer’s group.

Do you already have a website or do you wish to create a home page for the project in the GSC website? GSC website: http://wiki.gensc.org/index.php?title=GCDML

What other resources might you like from what the GSC can offer (mailing lists, etc)? All needed resources already well established.

What kind of timeline are you working to for building consensus, releasing a first version etc? The timeline is synced with MIxS timeline of development.

How is this work currently funded? Funded through PhD work of Renzo Kottmann and volunteer activities within GSC. Currently no funding.

What resources will be required for completion? Current version complete. Documentation missing. Need of 2-6 Pm (FTE) to create full documentation and next version release.

What are your current plans for publishing/promoting the project? No plans currently.

References or relevant websites:

GCDML Roadmap paper in SIGS:

[1] R. Kottmann et al., “A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML).,” Omics : a journal of integrative biology, vol. 12, no. 2, pp. 115-21, Jun. 2008.