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Metabolomics Standards and Databases

The Metabolomics Standards and Databases collection in FAIRsharing lists the standards and databases relevant to the metabolomics field, as identified in the article "Data standards can boost metabolomics research, and if there is a will, there is a way", Metabolomics, January 2016, 12:14.

This record is maintained by: agbeltran ORCID

Record updated: April 27, 2020, 2:01 p.m. by The FAIRsharing Team.

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Edits to 'https://fairsharing.org/bsg-c000006' by 'The FAIRsharing Team' at 15:20, 01 Aug 2016 (approved):

	'home_url' has been modified:
		Before: http://dx.doi.org/10.1007/s11306-015-0879-3
		After: http://dx.doi.org/10.1007/s11306-015-0879-3 Taxonomy list has changed:  Previous values: New values:  All|http://identifiers.org/taxonomy/1?resource=MIR:00100019

Edits to 'https://fairsharing.org/bsg-c000006' by 'The FAIRsharing Team' at 13:44, 07 Jul 2017 (approved):

	'description' has been modified:
		Before: The Metabolomics Standards and Databases collection in FAIRsharing lists the standards and databases relevant to the metabolomics field, as identified in the article "Data standards can boost metabolomics research, and if there is a will, there is a way", Metabolomics, January 2016, 12:14.
		After: The Metabolomics Standards and Databases collection in FAIRsharing lists the standards and databases relevant to the metabolomics field, as identified in the article "Data standards can boost metabolomics research, and if there is a will, there is a way", Metabolomics, January 2016, 12:14.

Edits to 'https://fairsharing.org/bsg-c000006' by 'The FAIRsharing Team' at 14:00, 27 Apr 2020 (approved):

	'standards' has been modified:
		Before:
			Nuclear Magnetic Resonance Controlled Vocabulary
			Investigation Study Assay Tabular
			mz Markup Language
			Core Information for Metabolomics Reporting
			imaging mz Markup Language
			mz5
			Nuclear Magnetic Resonance Markup Language
			Joint Committee on Atomic and Molecular Physical data - working group on Data eXchange
			mzXML
			mzData
			IUPAC International Chemical Identifier
			Simplified Molecular Input Line Entry Specification Format
			eXtensible Experiment Markup Language
		After:
			Nuclear Magnetic Resonance Controlled Vocabulary
			Investigation Study Assay Tabular
			mz Markup Language
			Core Information for Metabolomics Reporting
			imaging mz Markup Language
			mz5
			Nuclear Magnetic Resonance Markup Language
			Joint Committee on Atomic and Molecular Physical data - working group on Data eXchange
			mzXML
			mzData
			IUPAC International Chemical Identifier
			Simplified Molecular Input Line Entry Specification Format
			eXtensible Experiment Markup Language
			Analytical Data Interchange Protocol for Chromatographic Data
		Added:
			Analytical Data Interchange Protocol for Chromatographic Data
		Removed:

Publications

Data standards can boost metabolomics research, and if there is a will, there is a way.

Rocca-Serra P,Salek RM,Arita M,Correa E,Dayalan S,Gonzalez-Beltran A,Ebbels T,Goodacre R,Hastings J,Haug K,Koulman A,Nikolski M,Oresic M,Sansone SA,Schober D,Smith J,Steinbeck C,Viant MR,Neumann S
Metabolomics 2015

View Paper (PubMed) View Publication

16 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Analytical Data Interchange Protocol for Chromatographic Data	ANDI-MS	Standard	Data Management Life Science	Chromatography Data model Mass spectrometry assay	All	None	netCDF AnIML	None	Metabolomics Standards and Databases
Core Information for Metabolomics Reporting	CIMR	Standard	Life Science Metabolomics	Centrally registered identifier Chemical entity Metabolite	All	Plantmetabolomics.org MTBLS	ISA-Tab NMR-ML nmrCV	EMBO Recommended Databases and Data Standards	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations Chemistry Plus 1 more...
~~eXtensible Experiment Markup Language~~	~~XEML~~	Standard	Life Science	Protocol Study design	All	GMD	XML XEO	None	Metabolomics Standards and Databases
imaging mz Markup Language	imzML	Standard	Life Science	Image Imaging Mass spectrometry assay Tissue	All	None	PSI SpML MIAPE-MSI mzML XML MIAPE	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
Investigation Study Assay Tabular	ISA-Tab	Standard	Functional Genomics Life Science	Biological sample DNA microarray Experimental measurement Gene expression data Report Plus 7 more...	All	SCDE MTBLS GMD CEBS GigaDB Plus 11 more...	CL OBI ECO BTO RNAO Plus 21 more...	EMBO Recommended Databases and Data Standards Advanced Genetics BioMed Central - Minimum Standards of Reporting Checklist GigaScience - Minimum Standards of Reporting Checklist	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards bioCADDIE eTRIKS Standards Starter Pack Plus 8 more...
IUPAC International Chemical Identifier	InChI	Standard	Cheminformatics Chemistry Knowledge and Information Systems	Chemical structure Molecular structure Centrally registered identifier Chemical descriptor Chemical entity Plus 1 more...	Not applicable	CCD Guide to Pharmacology ChemSpider ExplorEnz SwissLipids Plus 5 more...	FAIR chemical structure template AnIML	Cell Press - Trends In Biochemical Sciences - Instructions for Authors	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Chemistry ISO/CD 20691 Collection - DRAFT
Joint Committee on Atomic and Molecular Physical data - working group on Data eXchange	JCAMP-DX	Standard	Chemistry	Mass spectrometry spectra Infared spectroscopy Spectroscopy	All	ChemSpider	AnIML	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Semantic Assets for Materials Science Chemistry
MetaboLights	MTBLS	Database	Data Submission, Annotation and Curation Metabolomics Structural Biology	Biocuration Biological sample Chemical formula Chemical structure Mass spectrometry spectra Plus 9 more...	All	Rhea WikiPathways BRENDA OmicsDI DES-TOMATO Plus 1 more...	nmrCV ISA-Tab ChEBI PSI-MS CV BTO Plus 3 more...	MNI Open Research UCL Child Open Health Research PLOS Recommended Repositories Springer Nature Research Data Policy Type 1 Springer Nature - Research Data Policies Plus 18 more...	Metabolomics Standards and Databases Data Citation Implementation H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project EOSC-Life ELIXIR Core Data Resources and Deposition Databases Plus 2 more...
Metabolomics Workbench	MW	Database	Metabolomics	Metabolite Protocol	All	DataMed OmicsDI	mwTab RefMet OmicsDI XML format	PLOS Recommended Repositories EMBO Recommended Databases and Data Standards	NIH-supported data repositories Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Open Science Prize
mz5	mz5	Standard	Life Science Ontology and Terminology	Mass spectrometry assay	All	None	mzML HDF5	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
~~mzData~~	~~mzData~~	Standard	Life Science Proteomics	Mass spectrometry spectra	Not applicable	None	mzML	None	ISO/CD 20691 Collection - DRAFT Metabolomics Standards and Databases HUPO Proteomics Standards Initiative
mz Markup Language	mzML	Standard	Life Science	Mass spectrometry spectra Centrally registered identifier Mass spectrometry assay Protein	All	MOPED MitoZoa PRIDE PeptideAtlas World-2DPAGE Plus 2 more...	mzQuantML PSI SpML imzML MIAPE mz5 Plus 7 more...	EMBO Recommended Databases and Data Standards Advanced Genetics	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards eTRIKS Standards Starter Pack HUPO Proteomics Standards Initiative Plus 2 more...
~~mzXML~~	~~mzXML~~	Standard	Life Science Proteomics	Mass spectrometry spectra	Not applicable	MassIVE	mzML	None	Metabolomics Standards and Databases
Nuclear Magnetic Resonance Controlled Vocabulary	nmrCV	Standard	Chemistry Metabolomics	Chemical structure Molecular structure Assay Chemical screen Metabolite Plus 1 more...	None	MTBLS HMDB BMRB OBO	NMR-ML CIMR	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Chemistry
Nuclear Magnetic Resonance Markup Language	NMR-ML	Standard	Life Science Metabolomics	Chemical structure Omics data analysis Chemical entity Metabolite Nuclear Magnetic Resonance (NMR) spectroscopy	None	MTBLS GMD HMDB BMRB	nmrCV XML CIMR	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack Chemistry
Simplified Molecular Input Line Entry Specification Format	SMILES	Standard	Chemistry Life Science	Molecular structure Molecular entity	All	BitterDB COD Nematode.net CCD Guide to Pharmacology Plus 9 more...	FAIR chemical structure template BpForms Grammar BcForms Grammar	None	Toxicology Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project ISO/CD 20691 Collection - DRAFT

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