NMR-ML Work Group

This WP2 subgroup will deliver the NMR related exchange formats and terminological artifacts needed to describe, exchange and query both the metabolomics data generated via nuclear magnetic resonance spectroscopy and the contextual information such as ‘experimental metadata’ ( e.g., provenance of study materials, technology and measurement types, sample-to-data relationships).

We will develop and maintain an XML-based exchange format for 1D and 2D NMR raw and spectral data together with processed information (identification, quantification), building on experience from standards development within the Proteomics Standards Initiative (PSI). We will create an XML Schema Definition (XSD) and an accompanying Controlled Vocabulary (an OWL file). For NMR spectroscopy, we will develop the missing open standard NMR Markup Language (nmrML) for capturing and disseminating Nuclear Magnetic Resonance spectroscopy data in metabolomics. This is urgently needed as long-term archival format if metabolomic databases are to capture all the formats of metabolomic data, as well as supporting developments in cheminformatics and structural biology.

We will ensure that nmrML is widely accepted and used. We are hence involving all major global players, i.e. commercial NMR software vendors like Bruker and open source tool developers, in the development process. These interested parties are invited both to workshops as well as to regular stakeholder meetings. We expect the nmrML standard to be easily put to work as a)  we also provide parsers able to convert vendor specific nmr formats to nmrML and b) make sure our standard is also supported by open source tools such as Batman and rNMR. Together, we hope these efforts will ensure a wide and fast community adoption.

We will review, maintain and, where needed, extend reporting requirements and terminological artefacts developed by Metabolomics Standards Initiative (MSI). We need to represent quantification options in MS and NMR, and the semantics of data matrices used to summarize experimental results, key information which often is only available in PDF tables associated to manuscripts. As research in biomedical and life sciences is increasingly moving towards multi-omics studies, metabolomics must not be an island. The ‘Investigation/Study/Assay’ ISA-Tab format was developed to represent experimental metadata independently from the assay technology used. We will use ISA-Tab to standardize metabolomics reporting requirements and terminologies through customized configurations. Finally, we will explore semantic web standards that facilitate linked open data (LOD) throughout the biomedical and life science realms, and demonstrate their use for metabolomics data. While the technical standards already exist, we will need to develop the “inventory” of terms and concepts required to express facts about metabolomics, capturing the data to characterize studies and digital objects in metabolomics to facilitate the data flow in biomedical e-infrastructures.


Resource:

nmrML google user group - to Join click here if we want to attract a critical mass.

  1. Meeting notes will be collected on the Googledoc.
  2. Result of the discussion will be shared via email list.
  3. nmrML results related to COMSO WP and deliverable will be kept at http://cosmos-fp7.eu/nmrML
  1. Including COSMOS contribution and information
  1. Development of the nmrML will be captured in

https://github.com/nmrML/nmrML/wiki

  1. Raw files
  2. Parsers and convertor
  3. tools developed
  1. NMR exchange format and link to other resource kept at http://www.metabolomicscentre.ca/exchangeformats 
  1. A central point, linking to other resources
  1. nmrML google user group will be used for distribution for the result to the community and interested parties. NMR google user group at:

https://groups.google.com/forum/#!forum/nmrml

Agenda and past meetings

  • nmrML Hackaton IPB-Halle (October 2013)
  • nmrML Hackathon in EBML-EBI Cambridge (April 2013)
  • nmrML meeting in Florence (December 2012)