luisff / nmrml

nmrML is an open mark-up language for NMR data.

nmrML is an open mark-up language for NMR data. It is currently under heavy development and is not yet ready for public use. The development of this standard is coordinated by Workpackage 2 of the COSMOS - COordination Of Standards In MetabOlomicS Project. COSMOS is a global effort to enable free and open sharing of metabolomics data. Coordinated by Dr Christoph Steinbeck of the EMBL-European Bioinformatics Institute, COSMOS brings together European data providers to set and promote community standards that will make it easier to disseminate metabolomics data through life science e-infrastructures. This Coordination Action has been financed with €2 million by the European Commission's Seventh Framework Programme. The nmrML data standard will be approved by the Metabolomics Standards Initiative and was derived from an earlier nmrML that was developed by the Metabolomics Innovation Centre (TMIC).

nmrML links

• Official Website
• nmrML on Google-Groups
• nmrML wiki
• nmrML at COSMOS
• News Feed

Development Partners & Contributions

The Metabolomics Innovation Centre

The Metabolomics Innovation Centre (TMIC) is a Canadian-funded core facility that has a unique combination of infrastructure and personnel to perform a wide range of cutting-edge metabolomic studies for clinical trials research, biomedical studies, bioproducts studies, nutrient profiling and environmental testing. The TMIC platform is led by Dr. David Wishart (University of Alberta), Dr. Christoph Borchers (University of Victoria) and Dr. Liang Li (University of Alberta). This group devivered the nmrML predecessor that is amended and extended in the COSMOS Project.

Leibniz-Institute of Plant Biochemistry

The Institute of Plant Biochemistry (IPB) is a non-university research centre of the Leibniz Association (www.wgl.de), It investigates in a multidisciplinary style structure and function of natural products from plants and fungi, analyse interactions of plants with pathogenic and symbiotic microorganisms and study molecular interactions as part of complex biological processes. At the IPB, plant metabolomics has been an important area of research for many years. The IPB leads the standards development workpackage within the COSMOS project.

The Metabolome Facility of Bordeaux Functional Genomics Centre

The Metabolome Facility of Bordeaux Functional Genomics Centre (MFB) is mostly dedicated to plant and plant-derived products metabolomics. MFB is implicated in the French Metabolomics and Fluxomics Network and is a partner of MetaboHUB project aiming at the development of a French Metabolome Infrastructure. MFB provides expertise and tools along the complete metabolomics pipeline. In collaboration with the Bioinformatics Facility of Bordeaux, it has developed MeRy-B database for NMR plant metabolome data. Recent dry-lab developments of MFB concern 1H-NMR spectra processing. MFB participates in the NMR group within the COSMOS project.

[...]

Versioning

The versioning follow the [Major].[Minor].[Build], the version number is tracked inthe VERSION file in the root of the nmrML directory. Versioning is tracked using the taggin feature of git. All previous versions can be viewed here.

Follow these intructions to create release a tagged version:

1. Commit changes in your working directory that you want in this release. It is a good idea to push these changes to GitHub before continuing. Make sure the changes you want in this release are merged with master.
2. Make sure the HISTORY.md file is updated with the changes in this release. Follow the format in the file.
3. Bump the version, rebuild the docs, tag the release and push the release to Github with one of the following commands:
   • For a major release: make release_major
   • For a minor release: make release_minor
   • For a build release: make release_build
4. Now you can push the release with: git push --tags

Directory Structure

• docs
  • SchemaDocumentation - The docs generated from the schema and ontology files
• examples
  • vendor - Useful example files from other software and data formats
  • nmrML - Example files for different use cases of nmrML
• lib - Scripts/code used for generating docs, etc.
• mappings - Files that map variable names in other formats to variable names in nmrML. Used by conversion software.
• ontologies - The ontology files describing the controlled vocabulary
• xml-schemata - The .xsd files describing the nmrML schema
• tools - Example software using nmrML