Recommendation

BioMed Central

This recommendation houses all the databases and standards mentioned in the submission checklist for the BioMed Central stable of journals. The checklist itself is listed as a policy document in this collection.

This record is maintained by: AmyeKenall

This recommendation is taken from the following policy:

BioMed Central - Minimum Standards of Reporting Checklist.

Record updated: Dec. 19, 2016, 5:42 p.m. by The FAIRsharing Team.

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45 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Addgene	Addgene	Database	Life Sciences	Bibliography Deoxyribonucleic acid Plasmid	All	None	FASTA GenBank Sequence Format RRID	Springer Nature - Nature Photonics - Availability of Data and materials Springer Nature - Nature Genetics - Availability of Data and materials Springer Nature - Nature Medicine - Availability of Data and materials Springer Nature - Nature Chemical Biology - Availability of Data and materials Springer Nature - Nature Cell Biology - Availability of Data and materials Plus 9 more...	Data Citation Implementation eTRIKS Standards Starter Pack
ArrayExpress	ArrayExpress	Database	Life Sciences	Chromatin immunoprecipitation - DNA microarray Chromatin immunoprecipitation - DNA sequencing DNA microarray Gene expression data Genotyping Plus 3 more...	All	BioSD Expression Atlas Bgee SMD DGVA Plus 6 more...	MAGE-TAB EFO MIAME/Env MINSEQE MIAME Plus 2 more...	UCL Child Open Health Research EMBO Recommended Databases and Data Standards HRB Open Research PLOS Recommended Repositories MNI Open Research Plus 47 more...	Data Citation Implementation DNA Microarray ELIXIR Core Data Resources and Deposition Databases Genetics & Genomics Next
caNanoLab	caNanoLab	Database	Biomedical Science	Nanotechnology Bioactivity Nanoparticle Structure	Homo sapiens Mus musculus	None	NPO	PLOS Recommended Repositories Elsevier Data Policy SciData Data Policy Cell Press - Cell Metabolism - Information for Authors GigaScience - Minimum Standards of Reporting Checklist Plus 9 more...	Data Citation Implementation
Coherent X-ray Imaging Data Bank	CXIDB	Database	Life Sciences	Molecular structure X-ray diffraction Imaging	All	None	CXI EDMI-Functional	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research HRB Open Research Plus 13 more...	Data Citation Implementation
Database of genomic structural VARiation	dbVar	Database	Biomedical Science Life Sciences	Genetic polymorphism Genome	All	DGVA ClinVar DGV BovineMine	VarioML	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Rockefeller University Press - Journal Of Cell Biology - Data Deposition Plus 34 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories Genetics & Genomics Next
Database of Genomic Variants Archive	DGVA	Database	Genomics Life Sciences	Genetic polymorphism Curated information Structure Sequence variant	All	ArrayExpress ENA EGA Ensembl dbVar Plus 1 more...	None	Springer Nature - Research Data Policies UCL Child Open Health Research HRB Open Research PLOS Recommended Repositories MNI Open Research Plus 24 more...	Data Citation Implementation Genetics & Genomics Next
Database of Genotypes and Phenotypes	dbGaP	Database	Biomedical Science Epigenetics Life Sciences	Gene expression data Genetic polymorphism Genotype Phenotype	Homo sapiens	ImmPort BioSample NSRR	SRA-XML VCF	Springer Nature Research Data Policy Type 4 IH Policy on sharing of model organisms for Biomedical Research Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards Plus 37 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories Genetics & Genomics Next
Database of Single Nucleotide Polymorphism	dbSNP	Database	Life Sciences	Genetic polymorphism Single nucleotide polymorphism Genome	Anas platyrhynchos Gallus gallus Glycine max Homo sapiens Oreochromis niloticus Plus 2 more...	PolymiRTS T1DBase EVA ClinVar mirDNMR Plus 3 more...	FASTA	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards PLOS Recommended Repositories Plus 35 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories National Child Development Study (UK) Genetics & Genomics Next
DNA Data Bank of Japan	DDBJ	Database	Data Submission, Annotation and Curation Life Sciences	Annotation DNA sequence data Amino acid sequence Genome Nucleotide Plus 1 more...	All	GenBank ENA NextDB JGA	NCBITAXON GenBank Sequence Format FASTA FASTQ Sequence and Sequence Quality Format INSDSeq Plus 1 more...	American Society for Clinical Investigation - Journal of Clinical Investigation - Information for Authors Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards Plus 48 more...	Data Citation Implementation
Dryad	Dryad	Database	None	Curated information Literature curation	All	None	Schema.org Common Metadata Elements for Cataloging Biomedical Datasets DOI	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Elsevier Data Policy Plus 27 more...	Data Citation Implementation BMJ - British Medical Journal
Electron Microscopy Data Bank	EMDB	Database	Biology Life Sciences	X-ray diffraction Electron density map Electron microscopy Microscopy Structure	All	CCD PDBe RCSB PDB EMPIAR	PDB PDBx/mmCIF	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards PLOS Recommended Repositories Plus 30 more...	Data Citation Implementation ELIXIR Core Data Resources and Deposition Databases
European Nucleotide Archive	ENA	Database	Bioinformatics Data Management Functional Genomics Genomics Life Sciences Plus 2 more...	Annotation Amino acid sequence Deoxyribonucleic acid Histone Nucleotide Plus 2 more...	All	GenBank BioSD DDBJ Europe PMC EGA Plus 5 more...	SRA-XML NCBITAXON MIASPPE FASTA FASTQ Sequence and Sequence Quality Format Plus 4 more...	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research EMBO Recommended Databases and Data Standards Plus 53 more...	Data Citation Implementation ELIXIR Core Data Resources and Deposition Databases Genetics & Genomics Next
European Variation Archive	EVA	Database	Biomedical Science Genetics Genomics Life Sciences	DNA structural variation Genetic polymorphism Genotype Sequencing	All	ENA EGA dbSNP UniProtKB ClinVar Plus 2 more...	SO HUGO	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research HRB Open Research Plus 25 more...	Data Citation Implementation ELIXIR Core Data Resources and Deposition Databases
Experimental data repository for KInetic MOdels of biological SYStems	KiMoSys	Database	Life Sciences Metabolomics	Enzyme Reaction data Metabolite	All	None	CellML SBML	PLOS Recommended Repositories SciData Data Policy GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Data Citation Implementation
FAIRsharing	FAIRsharing	Database	Agriculture Biomedical Science Earth Sciences Environmental Sciences Humanities Plus 2 more...	None	All	None	Schema.org BioDBCore Bioschemas SRAO DRAO Plus 2 more...	UCL Child Open Health Research EMBO Recommended Databases and Data Standards HRB Open Research PLOS Recommended Repositories MNI Open Research Plus 10 more...	ELIXIR UK node resources Genetics & Genomics Next
figshare	figshare	Database	Data visualization	Image	All	OSF	Schema.org DOI	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research HRB Open Research Plus 26 more...	Data Citation Implementation
GenBank	GenBank	Database	Life Sciences	DNA sequence data Nucleic acid sequence Disease Gene Genome	All	DDBJ GENI-ACT IRD ENA VirHostNet Plus 3 more...	SRA-XML NCBITAXON GenBank Sequence Format FASTA FASTQ Sequence and Sequence Quality Format Plus 4 more...	American Society for Clinical Investigation - Journal of Clinical Investigation - Information for Authors Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research Plus 58 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories Genetics & Genomics Next
Gene Expression Omnibus	GEO	Database	Life Sciences	DNA microarray Gene expression data Genome	All	Nematode.net Bgee SMD ImmPort BioSample Plus 7 more...	MINiML SOFT MIAME/Env MIAME	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research EMBO Recommended Databases and Data Standards Plus 56 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories DNA Microarray Genetics & Genomics Next
Giga Science Database	GigaDB	Database	Computational Biology Genetics Genomics Life Sciences Proteomics	Gene expression data Imaging Sequencing Software	All	None	ISA-Tab NCBITAXON Bioschemas	PLOS Recommended Repositories GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Data Citation Implementation
Global Biodiversity Information Facility	GBIF	Database	Biodiversity Bioinformatics Life Sciences	Taxonomic classification	All	Scratchpads Brazilian Flora 2020 REFLORA Atlas of Living Australia IPT - GBIF Australia Repository GBIF Spain IPT - GBIF Spain Repository Plus 25 more...	DwC TAPIR ABCD EML	PLOS Recommended Repositories SciData Data Policy Open Research Data and Data Management Plans - Information for ERC grantees by the ERC Scientific Council GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Data Citation Implementation Global Biodiversity Information Facility (GBIF) international open data infrastructure
HUGO Gene Nomenclature Committee	HGNC	Database	Life Sciences Ontology and Terminology	Gene name Gene	Homo sapiens	FlyBase STRING HPRD MGDD CRC Atlas Plus 5 more...	None	UCL Child Open Health Research HRB Open Research MNI Open Research AAS Policy Gates Open Research Data Guidelines Plus 4 more...	Data Citation Implementation Genetics & Genomics Next
IntAct molecular interaction database	IntAct	Database	Life Sciences Ontology and Terminology	Citation Experiment metadata Gene Ontology enrichment Gene name Protein domain Plus 5 more...	All	MINT Gene3D neXtProt APID Interactomes Reactome Plus 16 more...	CHEBI MIRO MITAB PSI-PAR XML PSI-MI XML Plus 5 more...	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards PLOS Recommended Repositories Plus 10 more...	Data Citation Implementation International Molecular Exchange Consortium (IMEx) ELIXIR Core Data Resources and Deposition Databases
International Neuroimaging Data-Sharing Initiative	INDI	Database	Biomedical Science Life Sciences	Diffusion tensor imaging Functional magnetic resonance imaging Neuroimaging Phenotype	Homo sapiens	NITRC ABIDE	MIfMRI	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Springer Nature Research Data Policy Type 2 (for life sciences) Plus 6 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories
MetaboLights	MTBLS	Database	Data Submission, Annotation and Curation Life Sciences Metabolomics	Biocuration Biological sample Chemical formula Chemical structure Mass spectrometry spectra Plus 9 more...	All	Rhea WikiPathways BRENDA OmicsDI	nmrCV CHEBI BTO ISA-Tab PSI-MS CV Plus 3 more...	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research EMBO Recommended Databases and Data Standards Plus 16 more...	Metabolomics Standards and Databases Data Citation Implementation H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project ELIXIR Core Data Resources and Deposition Databases Genetics & Genomics Next
MGnify	MGnify	Database	Biodiversity Biomedical Science Data Submission, Annotation and Curation Environmental Sciences Life Sciences Plus 3 more...	Annotation DNA sequence data Gene prediction Metagenome Sequence annotation Plus 5 more...	All Anopheles gambiae Arabidopsis thaliana Bos indicus Bos taurus Plus 6 more...	ENA	GO MIxS - MIGS/MIMS FASTA FASTQ Sequence and Sequence Quality Format MIxS	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research HRB Open Research Plus 13 more...	Data Citation Implementation ELIXIR Non-CDR and Non-Deposition Database
Minimum Information About a Microarray Experiment	MIAME	Standard	Life Sciences Transcriptomics	DNA microarray Gene expression data Deoxyribonucleic acid Genome Nucleic acid hybridization Plus 1 more...	All	BuG@Sbase ArrayExpress GermOnline GEO CEBS Plus 6 more...	MAGE-TAB ISA-Tab MINiML MIAME/Env MINSEQE Plus 5 more...	American Society for Clinical Investigation - Journal of Clinical Investigation - Information for Authors Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards Plus 32 more...	National Child Development Study (UK) DNA Microarray FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations
Minimum Information about a Molecular Interaction Experiment	MIMIx	Standard	Biochemistry Life Sciences Proteomics	Assay Chemical entity Deoxyribonucleic acid Interactome Lipid Plus 2 more...	Archaea Bacteria Eukaryota	IntAct MINT MatrixDB ProteoRed	PSI-MI CV MITAB PSI-MI XML MIAPAR MIAPE Plus 8 more...	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition Plus 6 more...	FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations HUPO Proteomics Standards Initiative Chemistry
miRBase Sequence Database	miRBase	Database	Life Sciences	Crowdsourcing RNA sequence Gene Micro RNA Ribonucleic acid	All	PolymiRTS miRNEST FlyMine GREENC MirGeneDB Plus 3 more...	EMBL sequence format FASTA	PLOS Recommended Repositories Cold Spring Harbor Lab Press - Genome Research GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist Cold Spring Harbor Laboratory Press - Genes and Development - Instructions Regarding Data Submission Plus 1 more...	Data Citation Implementation Open Science Prize
NCBI BioSample	BioSample	Database	Life Sciences	DNA structural variation Gene expression data Sequence Assay Cell line Plus 2 more...	All	GenBank GEO SRA dbGaP ENCODE Plus 1 more...	BioProject XML Schema FAANG metadata sample specification standard FAANG metadata experiment specification standard	UCL Child Open Health Research HRB Open Research MNI Open Research AAS Policy Springer Nature - Nature Photonics - Availability of Data and materials Plus 12 more...	Data Citation Implementation Genetics & Genomics Next
NeuroMorpho.Org	NeuroMorpho.Org	Database	Life Sciences	Cell morphology Neuron	Metazoa	None	None	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Elsevier Data Policy Plus 8 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories
NeuroVault	NeuroVault	Database	Biomedical Science Life Sciences Neurobiology	Functional magnetic resonance imaging Neuroimaging	Homo sapiens	None	NIDM	UCL Child Open Health Research HRB Open Research MNI Open Research AAS Policy Cell Press - Neuron - Information for Authors Plus 15 more...	Data Citation Implementation
Nucleic Acids Database	NDB	Database	Life Sciences	Nucleic acid sequence Deoxyribonucleic acid Ribonucleic acid	All	MINAS	RNAO PDB PDBx/mmCIF	EMBO Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Data Citation Implementation
OpenNeuro	OpenNeuro	Database	Biomedical Science Life Sciences Neurobiology	Cognition Imaging Magnetic resonance imaging	Homo sapiens	None	BIDS	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research HRB Open Research Plus 24 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories
Open Science Framework	OSF	Database	Life Sciences Psychology	Cancer Data storage Study design	All	figshare Mendeley Data DataverseNL	None	UCL Child Open Health Research HRB Open Research PLOS Recommended Repositories MNI Open Research AAS Policy Plus 8 more...	Data Citation Implementation Open Science Prize Genetics & Genomics Next
PANGAEA - Data Publisher for Earth and Environmental Science	PANGAEA	Database	Agriculture Atmospheric Science Biology Chemistry Chemistry Plus 9 more...	Marine environment	All	BacDive	DataCite Metadata Schema Micro B3 Schema.org DC DwC Plus 3 more...	UCL Child Open Health Research HRB Open Research PLOS Recommended Repositories MNI Open Research Elsevier Data Policy Plus 13 more...	Data Citation Implementation
PlasmID	PlasmID	Database	Biomedical Science Life Sciences	RNA interference Cloning plasmid Deoxyribonucleic acid Mutation analysis Plasmid	Homo sapiens Mus musculus	None	None	GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Data Citation Implementation
ProteomeXchange	ProteomeXchange	Database	Life Sciences Proteomics	None	All	PRIDE PeptideAtlas jPOSTrepo MassIVE	MIAPE PRIDE XML Format MIAPE-MS MIAPE-MSI	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Elsevier Data Policy Plus 10 more...	Data Citation Implementation
PRoteomics IDEntifications database	PRIDE	Database	Life Sciences Proteomics	Peptide identification Protein identification Curated information Peptide Protein	All	BioSD Ensembl ProteomeXchange jPOSTrepo OmicsDI Plus 2 more...	mzQuantML mzML HUPO-PSI TraML MIAPE OmicsDI XML format Plus 9 more...	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research EMBO Recommended Databases and Data Standards Plus 29 more...	Data Citation Implementation ELIXIR Core Data Resources and Deposition Databases Genetics & Genomics Next
PubChem	PubChem	Database	Life Sciences	Assay Protein Small molecule Structure	All	WikiPathways CTD Guide to Pharmacology ChemIDplus ChemSpider Plus 5 more...	GO MIARE NDFRT BAO HELM	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Springer Nature Research Data Policy Type 2 (for life sciences) Plus 18 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories Genetics & Genomics Next
Sequence Read Archive	SRA	Database	Life Sciences	DNA sequence data Sequence Sequence alignment Nucleic acid sequence alignment Allele Plus 2 more...	All	ImmPort BioSample HWG IPA BIP Plus 6 more...	SRA-XML MIxS - MIMARKS MINSEQE	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research HRB Open Research Plus 40 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories Wheat Data Interoperability Guidelines Genetics & Genomics Next
~~Springer Nature - Research Data Policies~~	N/A	Journal	Biomedical Science Environmental Sciences Life Sciences Medicine Preclinical and Clinical Studies	Journal article Publication	All	GenBank COD DDBJ IntAct GenomeRNAi Plus 32 more...	MIAME MIMIx	Springer Nature - Nature Photonics - Availability of Data and materials Springer Nature - Nature Genetics - Availability of Data and materials Springer Nature - Nature Structural & Molecular Biology - Availability of Data and materials Springer Nature - Nature Chemical Biology - Availability of Data and materials Springer Nature - Nature Cell Biology - Availability of Data and materials Springer Nature - Nature Nanotechology - Availability of Data and materials Springer Nature - Nature Biotechnology - Availability of Data and materials Springer Nature - Nature - Availability of Data and materials Springer Nature - Nature Methods - Availability of Data and Materials BioMed Central - Minimum Standards of Reporting Checklist Plus 5 more...	None
The Cambridge Structural Database	CSD	Database	Biochemistry Chemistry Life Sciences	Atomic coordinate Protein structure X-ray diffraction Structure	All	None	CIF	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 Elsevier Data Policy Springer Nature Research Data Policy Type 2 (for life sciences) Plus 21 more...	Data Citation Implementation Chemistry
TreeBase	TreeBase	Database	Life Sciences Phylogenetics Phylogenomics	Classification Taxonomic classification	All	None	MIAPA Newick tree Format CDAO NeXML	GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Data Citation Implementation
UniProt Knowledgebase	UniProtKB	Database	Functional Genomics Life Sciences	Annotation Biocuration Function analysis Gene expression data Gene functional annotation Plus 9 more...	All	DAMPD LegumeIP MitoMiner Pfam ProtoNet Plus 66 more...	ECO CHEBI NCBITAXON GO FASTA Plus 11 more...	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 UCL Child Open Health Research EMBO Recommended Databases and Data Standards Plus 44 more...	Data Citation Implementation Open Science Prize International Molecular Exchange Consortium (IMEx) ELIXIR Core Data Resources and Deposition Databases Genetics & Genomics Next
Worldwide Protein Data Bank	wwPDB	Database	Life Sciences	Protein structure Deoxyribonucleic acid Protein Ribonucleic acid Structure	All	ProtoNet ccPDB Nematode.net PoSSuM MetalPDB Plus 20 more...	PDB	Springer Nature Research Data Policy Type 4 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 EMBO Recommended Databases and Data Standards PLOS Recommended Repositories Plus 40 more...	Data Citation Implementation

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