H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project

PhenoMeNal (Phenome and Metabolome aNalysis) aims to build a comprehensive and standardised e-infrastructure that will support the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications. PhenoMeNal will provide services enabling computation and analysis to improve the understanding of the causes and mechanisms underlying health, healthy ageing and diseases. As part of this development, PhenoMenal has commissioned a survey to assess to landscape of format specification, vocabularies and nomenclatures as well as policies in the clinical and technical area to gauge coverage and diffusion/acceptance of such resources. The Biosharing collection represents an overview of the resources considered so far.

This record is maintained by: proccaserra ORCID

Record added: Aug. 16, 2016, 12:18 p.m..
Record updated: Aug. 20, 2016, 3:41 p.m. by The FAIRsharing Team.

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Taxonomic range

Homo sapiens

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29 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Biological Expression Language	BEL	Standard	Biology	None	All	NDEx	None	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
CDISC Clinical Data Acquisition Standards Harmonization	CDISC CDASH	Standard	Biomedical Science Preclinical and Clinical Studies	Report Data acquisition	Homo sapiens	MDM	CDISC SDTM CDISC ADaM CDISC SEND CDISC ODM CDISC Define-XML Plus 8 more...	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack CDISC
CDISC Controlled Terminology	CDISC CT	Standard	Biomedical Science Preclinical and Clinical Studies	None	Homo sapiens	ImmPort	CDISC SDTM CDISC ADaM CDISC CDASH CDISC SEND CDISC ODM Plus 8 more...	None	CDISC H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
CDISC Study Data Tabulation Model	CDISC SDTM	Standard	Biomedical Science Preclinical and Clinical Studies	Report Device	Homo sapiens	NIDA CSDR	CDISC ADaM CDISC CDASH CDISC SEND CDISC ODM CDISC Define-XML Plus 8 more...	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack CDISC
Common Workflow Language	CWL	Standard	Bioinformatics Natural Sciences	Workflow	All	None	EDAM	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
Core Information for Metabolomics Reporting	CIMR	Standard	Life Sciences Metabolomics	Centrally registered identifier Chemical entity Metabolite	All	Plantmetabolomics.org MTBLS	nmrCV NMR-ML ISA-Tab	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations Chemistry
Fast Healthcare Interoperability Resources	FHIR	Standard	Biomedical Science Medicine Preclinical and Clinical Studies	Electronic health record	Homo sapiens	MDM	SNOMEDCT NCIt RxNORM LOINC	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
Health Level Seven Reference Implementation Model	HL7	Standard	Biomedical Science Medicine	None	Homo sapiens	GUDID MDM	DICOM LOINC	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
Human Phenotype Ontology	HP	Standard	Biomedical Science Genetics Preclinical and Clinical Studies	Disease Phenotype	Homo sapiens	GWASdb MGI Orphanet GWAS Central ClinVar Plus 5 more...	PFO PXF Semantic reference model for making rare disease resources linkable ORDO	None	OBO Foundry Cell Migration Standardisation Organisation H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack
HUPO PSI Mass Spectrometry Controlled Vocabulary	PSI-MS CV	Standard	Life Sciences Proteomics	Mass spectrometry assay Protein	All	MTBLS GMD jPOSTrepo OBO	mzQuantML mzIdentML PSI GelML	None	OBO Foundry H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack FAIRDOM Community Standards HUPO Proteomics Standards Initiative
imaging mz Markup Language	imzML	Standard	Life Sciences	Image Imaging Mass spectrometry assay Tissue	All	None	PSI SpML XML MIAPE-MSI MIAPE mzML	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
International Classification of Diseases Version 10	ICD-10	Standard	Biomedical Science	Diagnosis Disease	Homo sapiens	DistiLD Orphanet Progenetix arrayMap EudraCT Plus 1 more...	ICECI ImmDis ICD-10-PCS ROO ICD-10-CM Plus 1 more...	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack
Investigation Study Assay Tabular	ISA-Tab	Standard	Functional Genomics Life Sciences	Biological sample DNA microarray Experiment metadata Gene expression data Report Plus 3 more...	All	SCDE MTBLS GMD GigaDB SCC Plus 7 more...	OBI CIMR MINSEQE MIAME MIQE Plus 5 more...	EMBO Recommended Databases and Data Standards GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project bioCADDIE eTRIKS Standards Starter Pack FAIRDOM Community Standards Plus 1 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 ChemSpider ExplorEnz SwissLipids MNXref Plus 1 more...	AnIML	Cell Press - Trends In Biochemical Sciences - Instructions for Authors	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Chemistry
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 Chemistry
Logical Observation Identifier Names and Codes	LOINC	Standard	Biomedical Science Life Sciences Preclinical and Clinical Studies	Genetic polymorphism Assay Diagnosis Genetic disorder Phenotype	Homo sapiens	None	Apollo XSD UCUM DICOM HL7 CDISC LAB Plus 1 more...	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack
MetaboLights	MTBLS	Database	Life Sciences Metabolomics	Mass spectrometry spectra Lipid Metabolite Nuclear Magnetic Resonance (NMR) spectroscopy Publication	All	Rhea WikiPathways BRENDA OmicsDI	CHEBI BTO PSI-MS CV nmrCV ISA-Tab Plus 3 more...	GigaScience - Minimum Standards of Reporting Checklist EMBO Recommended Databases and Data Standards Gates Open Research Data Guidelines BioMed Central - Minimum Standards of Reporting Checklist F1000Research Data Policy Plus 16 more...	Metabolomics Standards and Databases Data Citation Implementation H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project ELIXIR node contributed resources
Metabolomics Workbench	MW	Database	Life Sciences Metabolomics	None	All	OmicsDI	OmicsDI XML format mwTab	PLOS Recommended Repositories	Metabolomics Standards and Databases Open Science Prize H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
mz5	mz5	Standard	Life Sciences Ontology and Terminology	Mass spectrometry assay	All	None	HDF5 mzML	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
mz Markup Language	mzML	Standard	Life Sciences	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	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack FAIRDOM Community Standards HUPO Proteomics Standards Initiative
NCI Thesaurus	NCIt	Standard	Biomedical Science Preclinical and Clinical Studies Translational Medicine	Cancer Disease	Homo sapiens	neXtProt PID arrayMap OBO	ROO FHIR CSEO	None	OBO Foundry H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack
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	CIMR NMR-ML	None	Metabolomics Standards and Databases OBO Foundry H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Chemistry
Nuclear Magnetic Resonance Markup Language	NMR-ML	Standard	Life Sciences Metabolomics	Chemical structure Omics data analysis Chemical entity Metabolite Nuclear Magnetic Resonance (NMR) spectroscopy	None	MTBLS GMD HMDB BMRB	nmrCV CIMR XML	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 Sciences	Molecular structure Molecular entity	All	BitterDB Nematode.net CCD enviPath SwissLipids Plus 3 more...	None	None	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
Standard Preanalytical Code	SPREC	Standard	Biomedical Science	Biobank Biological sample Biological sample annotation Quality control	Homo sapiens	None	None	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
Systematized Nomenclature of Medicine-Clinical Terms	SNOMEDCT	Standard	Biomedical Science Medicine Preclinical and Clinical Studies	None	Homo sapiens	HPA Orphanet ClinVar MEP LINCS Project Tycho	Apollo XSD Read v2 CTV3 FHIR Project Tycho Pre-compiled Data Format Plus 1 more...	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack
Systems Biology Markup Language	SBML	Standard	Life Sciences Systems biology	Mathematical model Enzymatic reaction Molecular entity pathway Network model	All	MetaCrop 2.0 IPAVS BRENDA BioModels Reactome Plus 10 more...	CellML SED-ML SBGN MIRIAM OFSMR Plus 3 more...	EMBO Recommended Databases and Data Standards	Computational Modeling (COMBINE) Computational Modeling H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards The NormSys Registry for Modeling Standards
The Human Metabolome Database	HMDB	Database	Biochemistry Life Sciences Metabolomics Molecular biology	Chemical entity Metabolite Small molecule	Homo sapiens	WikiPathways YMDB SMPDB MNXref Wikidata Plus 1 more...	CHEBI nmrCV NMR-ML GO FASTA	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project Chemistry
The Unified Code for Units of Measure	UCUM	Standard	None	Measurement Unit	All	None	LOINC	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project

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