Nuclear Magnetic Resonance Markup Language

Abbreviation: NMR-ML

General Information

nmrML is an open mark-up language for NMR raw and spectral data. It is has recently seen its first proper release, ready for public use. The development of this standard was previously coordinated by the COSMOS - COordination Of Standards In MetabOlomicS Project. It is now maintained within the PhenoMeNal Eu project tasked to disseminate metabolomics data through life science e-infrastructures. The nmrML data standard is approved by the Metabolomics Standards Initiative and was derived from an earlier nmrML that was developed by the Metabolomics Innovation Centre (TMIC). It follows design principles of its role model, the mzML data standard created by PSI for mass spectrometry.

Homepage http://nmrml.org

Countries that developed this resource Canada , France , Germany , Italy , Netherlands , United Kingdom

Created in 2015

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: NMR-ML; Nuclear Magnetic Resonance Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.es03fk; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Nov 18 2019 9:23 p.m.

This record is maintained by DanielSchober ORCID and salek ORCID

Record updated: March 15, 2018, 10:21 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'The FAIRsharing Team' at 10:21, 15 Mar 2018 (approved):

	'related_standards' has been modified:
		Before:
			bsg-s000069|Nuclear Magnetic Resonance Controlled Vocabulary
			bsg-s000175|Core Information for Metabolomics Reporting
		After:
			bsg-s000069|Nuclear Magnetic Resonance Controlled Vocabulary
			bsg-s000175|Core Information for Metabolomics Reporting
			bsg-s001143|Extensible Markup Language
		Added:
			bsg-s001143|Extensible Markup Language
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 13:01, 29 Jan 2018 (approved):

	'year' has been modified:
		Before: 2017
		After: 2015

Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 13:10, 24 Jan 2018 (approved):

	'related_standards' has been modified:
		Before:
			bsg-s000069|Nuclear Magnetic Resonance Controlled Vocabulary
		After:
			bsg-s000069|Nuclear Magnetic Resonance Controlled Vocabulary
			bsg-s000175|Core Information for Metabolomics Reporting
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			bsg-s000175|Core Information for Metabolomics Reporting
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Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 13:00, 24 Jan 2018 (approved):

	'related_databases' has been modified:
		Before:
			biodbcore-000168|MetaboLights
			biodbcore-000186|Golm Metabolome Database
			biodbcore-000552|The Human Metabolome Database
		After:
			biodbcore-000168|MetaboLights
			biodbcore-000186|Golm Metabolome Database
			biodbcore-000552|The Human Metabolome Database
			biodbcore-000584|Biological Magnetic Resonance Databank
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			biodbcore-000584|Biological Magnetic Resonance Databank
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Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'The FAIRsharing Team' at 12:48, 24 Jan 2018 (approved):

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			All|http://identifiers.org/taxonomy/1?resource=MIR:00100019
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			All|http://identifiers.org/taxonomy/1?resource=MIR:00100019
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Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 12:36, 24 Jan 2018 (approved):

	'organizations' has been modified:
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			European Union (EU)|Government body|Funds
			COSMOS European Union FP7|Government body|Maintains
			Proteomics Standard Initiative|Undefined|Maintains
			The Metabolomics Standards Initiative|Undefined|Maintains
			Metabolomics Standards Initiative (MSI)|Consortium|Undefined
		After:
			European Union (EU)|Government body|Funds
			COSMOS European Union FP7|Government body|Maintains
			Proteomics Standard Initiative|Undefined|Maintains
			The Metabolomics Standards Initiative|Undefined|Undefined
			Metabolomics Standards Initiative (MSI)|Consortium|Undefined
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			The Metabolomics Standards Initiative|Undefined|Undefined
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			The Metabolomics Standards Initiative|Undefined|Maintains

Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 12:19, 24 Jan 2018 (approved):

	'tools' has been modified:
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			Converter
			Validator
			nmrML2Isa
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			Converter
			Validator
			nmrML2Isa
			nmrProcFlow
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			nmrProcFlow
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Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 11:48, 24 Jan 2018 (approved):

	'description' has been modified:
		Before: 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).
		After: nmrML is an open mark-up language for NMR raw and spectral data. It is has recently seen its first proper release, ready for public use. The development of this standard was previously coordinated by the COSMOS - COordination Of Standards In MetabOlomicS Project. It is now maintained within the PhenoMeNal Eu project tasked to disseminate metabolomics data through life science e-infrastructures. The nmrML data standard is approved by the Metabolomics Standards Initiative and was derived from an earlier nmrML that was developed by the Metabolomics Innovation Centre (TMIC). It follows design principles of its role model, the mzML data standard created by PSI for mass spectrometry.

Edits to 'https://fairsharing.org/FAIRsharing.es03fk' by 'DanielSchober' at 13:00, 30 Mar 2017 (approved):

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In Collections

Metabolomics Standards and Databases

H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project

eTRIKS Standards Starter Pack

Chemistry

Support

General

forum	https://groups.google.com/forum/?hl=en#! ...
online documentation	https://github.com/nmrML/nmrML
online documentation	https://github.com/nmrML/nmrML/wiki
online documentation	http://nmrml.org/examples/
schema file	http://nmrml.org/schema
training	http://nmrml.org/tutorials/

Additional Information

Contact

Daniel Schober ORCID

Tools

Converter	http://nmrml.org/converter/
Validator	http://nmrml.org/validator/
nmrML2Isa	https://github.com/ISA-tools/nmrml2isa
nmrProcFlow	https://www.nmrprocflow.org/

Schemas

http://nmrml.org/schema

Name: nmrML
Version: 0.1.0

Download

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Other Web Services

A help page that list major nmrML compliant tools and webservices

http://nmrml.org/tools/

Publications

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data

Daniel Schober, * , † Daniel Jacob, ‡ Michael Wilson, § Joseph A. Cruz, § Ana Marcu, § Jason R. Grant, § Annick Moing, ‡ Catherine Deborde, ‡ Luis F. de Figueiredo, ∥ Kenneth Haug, ∥ Philippe Rocca-Serra, ⊥ John Easton, # Timothy M. D. Ebbels, ⊗ Jie Hao, ⊗ Christian Ludwig, $ Ulrich L. Gu ̈ nther, × Antonio Rosato, ○ Matthias S. Klein, ¶ Ian A. Lewis, ¶ Claudio Luchinat, ○ Andrew R. Jones, ∇ Arturas Grauslys, ∇ Martin Larralde, + Masashi Yokochi, ◆ Naohiro Kobayashi, ◆ Andrea Porzel, & Julian L. Gri ffi n, % Mark R. Viant, ■ David S. Wishart, § Christoph Steinbeck, ∥ Reza M. Salek, * , ∥ and Ste ff en Neumann
Anal. Chem. 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Core Information for Metabolomics Reporting

Terminology Artifacts

Nuclear Magnetic Resonance Controlled Vocabulary

Models and Formats

Extensible Markup Language

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (4)

MetaboLights
MetaboLights is a database is a collection of metabolite structures. This resource provides information on the compound origins,the biological roles, locations and concentrations, as well as experimental data from metabolic experiments. The tools and capabilities of this database is firmly routed in collaborative working worldwie with the metabolomics community such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.

The Human Metabolome Database
The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.

Biological Magnetic Resonance Databank
BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by DanielSchober ORCID and salek ORCID

Funds

European Union (EU) (Government body)

Maintains

COSMOS European Union FP7 (Government body)
Proteomics Standards Initiative (PSI) - Human Proteomics Organisation (HUPO) (Consortium)
Metabolomics Standards Initiative (MSI) (Consortium)

Grant Number(s)

654241 (European Union (EU))
EC312941 (European Union (EU))

Nuclear Magnetic Resonance Markup Language

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