Researcher Edit me

Applies to

PhD candidates, research grant applicants, project managers, group leaders, PIs

Scenario

The funding organisation I am applying to requires a data management plan (DMP). I have little experience in writing a DMP, and I am not sure of the level of detail I am required to provide. I have limited access to data management experts within my institution. I am considering using the RDMkit for my data management needs. I also hope to find useful references to local training about data management requirements, data archives and DMP tools.

I know the types and the approximate amount of data I will generate, but I have not thought about how to share data with my collaborators and how to store data securely. Initially, my plan was to buy a powerful computer and portable hard drive, but I am now thinking that I need to use a national computing infrastructure. The field I work in has well defined data and curation standards, for example, capturing information (metadata) about how to collect and sample my data. However, I am not yet familiar with the importance of storing provenance data, such as tool and database versions used in analysis.

Focus

Write data management plans, also in the context of grant applications
Ensure compliance with institution policy, including legal and ethical aspects
Ensure proper data organisation and storage
Ensure secure sharing, reproducibility and preservation of data
Transmits the good practices in RDM to his group

Getting started

Check out the various steps of the RDM life cycle, in particular the planning stage
Identify and contact the data steward in your local organisation or your national contact in the ELIXIR network
Use local guidelines associated with the national or institutional DMP application and/or follow an introductory training
Start planning your project taking the DMP into account

More information

Related RDMkit pages in "Your tasks"

Compliance monitoring & measurement: measure compliance to data management regulations and standards.
Data analysis: how to make data analysis FAIR.
Data management plan: how to write a Data Management Plan (DMP).
Data organisation: best practices to name and organise research data.
Data publication: prepare data and find repositories for publication.
Data quality: ensure high quality research data.
Existing data: how to find and reuse existing data.
Documentation and metadata: how to document and describe your data.
Identifiers: how to use identifiers for research data.

Relevant tools and resources

Tool or resource	Description	Related pages	Registry
Argos	Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored.	Data management plan Data steward research
Arvados	With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.	Data steward infrastructure Data steward policy Data analysis
Atlas	Free, publicly available web-based, open-source software application developed by the OHDSI community to support the design and execution of observational analyses to generate real world evidence from patient level observational data.	Data steward research TransMed Assembly	bio.tools TeSS
Beacon	The Beacon protocol defines an open standard for genomics data discovery.	Data steward research Data steward infrastructure Human data	bio.tools TeSS
BIONDA	BIONDA is a free and open-access biomarker database, which employs various text mining methods to extract structured information on biomarkers from abstracts of scientific publications	Data storage Human data	bio.tools
BMRB	Biological Magnetic Resonance Data Bank	Intrinsically disordered proteins	bio.tools
Bulk Rename Utility	File renaming software for Windows	Data organisation Data steward research
Chipster	Chipster is a user-friendly analysis software for high-throughput data such as RNA-seq and single cell RNA-seq. It contains analysis tools and a large reference genome collection.	CSC - Finland Data analysis Data steward infrastructure	bio.tools TeSS
Choose a license	Choose an open source license	Licensing Data steward research Data steward policy	TeSS
Common Workflow Language (CWL)	An open standard for describing workflows that are build from command line tools	Data steward infrastructure Data steward policy Data analysis	FAIRsharing TeSS
COPO	Portal for scientists to broker more easily rich metadata alongside data to public repos.	Documentation and metadata Plant sciences	bio.tools FAIRsharing
Create a Codebook	Examples and tools to create a codebook by the Data Documentation Initiative (DDI)	Documentation and metadata Data steward research
Creative Commons License Chooser	It helps you choose the right Creative Commons license for your needs.	Licensing Data steward research Data steward policy
Crop Ontology	The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype.	Data steward research Data steward infrastructure Plant sciences	FAIRsharing TeSS
Data Curation Centre Metadata list	List of metadata standards	Documentation and metadata Data steward research
Data Use Ontology	DUO allows to semantically tag datasets with restriction about their usage.	Data steward research Human data	FAIRsharing TeSS
DATAVERSE	Open source research data respository software.	Data storage Data steward research Data steward infrastructure IFB - France	TeSS
dbGAP	The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans	Data publication Data steward infrastructure Human data	bio.tools FAIRsharing
DisGeNET	A discovery platform containing collections of genes and variants associated to human diseases.	Data analysis Human data	bio.tools
DisProt	A database of intrinsically disordered proteins	Intrinsically disordered proteins	bio.tools
DMP Canvas Generator	Questionnaire, which generates a pre-filled a DMP	Data management plan Data steward research
DMP OPIDoR	Online questionnaire for the development of data management plans - repository of DMPs	Data management plan Data steward research IFB - France
DMPlanner	Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans.	Data management plan Data steward research
DMPonline	A free tool to write, share and export a data management plan. Built-in data management plan templates for many major funders.	Data management plan Data steward research	TeSS
DMPTool	Build your Data Management Plan	Data management plan Data steward research
DMPTuuli	Data management planning tool (Finland)	Data management plan Data steward research CSC - Finland
Data Stewardship Wizard	Publicly available online tool for composing smart data management plans	Data management plan Data steward research Data steward infrastructure NeLS assembly TSD for sensitive data - Norway	bio.tools TeSS
e!DAL-PGP	Plant Genomics and Phenomics Research Data Repository	Plant sciences Plant Genomics Assembly Data steward research Data steward infrastructure	FAIRsharing
EasyDMP	DMP creation, versioning and sharing	Data management plan Data steward research
ECPGR	Hub for the identification of plant genetic resources in Europe	Plant sciences Data steward research
ELIXIR Deposition Databases for Biomolecular Data	List of discipline-specific deposition databases recommended by ELIXIR.	Data publication Data steward research Data steward infrastructure COVID-19 Data Portal NeLS assembly IFB - France CSC - Finland	FAIRsharing
EMBL-EBI Ontology Lookup Service	EMBL-EBI’s web portal for finding ontologies	Documentation and metadata Data steward research	TeSS
EMBL-EBI's data submission wizard	EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data.	Data publication Data steward research
EUDAT licence selector wizard	EUDAT's wizard for finding the right licence for your data or code.	Licensing Data steward research Data steward policy
EURISCO	European Search Catalogue for Plant Genetic Resources	Plant sciences Data steward research	bio.tools
Europe PMC	Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines.		bio.tools FAIRsharing TeSS
FAIDARE	FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI.	Data steward research Plant sciences IFB - France	bio.tools
FAIRDOMHub	Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. (public SEEK instance)	Data storage NeLS assembly Documentation and metadata Microbial biotechnology	FAIRsharing
fairsharing	A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.	Documentation and metadata Data publication Data steward policy Data steward research Microbial biotechnology Existing data	FAIRsharing TeSS
Galaxy	Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.	NeLS assembly Marine Metagenomics - Norway Data analysis Data steward infrastructure IFB - France	bio.tools TeSS
GENEID	Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms.	Data analysis	bio.tools
Harvard Medical School – ELN Comparison Grid	ELN Comparison Grid by Hardvard Medical School	Documentation and metadata Identifiers Data steward research
How to License Research Data - DCC	Guidelines about how to license research data from Digital Curation Centre	Licensing Data steward research Data steward policy
HumanMine	HumanMine integrates many types of human data and provides a powerful query engine, export for results, analysis for lists of data and FAIR access via web services.	Data organisation Data steward research Human data Data analysis	bio.tools TeSS
Linked Open Vocabularies (LOV)	Web portal for finding ontologies	Documentation and metadata Data steward research
LUMI	EuroHPC world-class supercomputer	Data analysis Data steward infrastructure CSC - Finland	bio.tools
MCPD	The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks.	Documentation and metadata Data steward infrastructure Data steward policy Plant sciences Plant sciences	FAIRsharing
MIADE	Minimum Information About Disorder Experiments (MIADE) standard	Documentation and metadata Data steward research Intrinsically disordered proteins
MIAPPE	Minimum Information About a Plant Phenotyping Experiment	Documentation and metadata Data steward research Plant sciences Plant Genomics Assembly	FAIRsharing TeSS
MIGS/MIMS	Minimum Information about a (Meta)Genome Sequence	Documentation and metadata Data steward research Marine metagenomics Microbial biotechnology	FAIRsharing
MIxS	Minimum Information about any (x) Sequence	Documentation and metadata Data steward research Marine metagenomics Plant Genomics Assembly	FAIRsharing TeSS
MobiDB	A database of protein disorder and mobility annotations	Intrinsically disordered proteins	bio.tools
MRI2DICOM	a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard	Data steward research XNAT-PIC
OHDSI	Multi-stakeholder, interdisciplinary collaborative to bring out the value of health data through large-scale analytics. All our solutions are open-source.	Data steward research Data analysis Data storage TransMed Assembly	bio.tools
Ontobee	A web portal to search and visualise ontologies	Documentation and metadata Data steward research
ONTOMATON	OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.	Data steward research Data steward infrastructure Documentation and metadata Identifiers
Open Definition Conformant Licenses	Licenses that are conformant with the principles laid out in the Open Definition.	Licensing Data steward research Data steward policy
OSF	OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration.	Data storage Data steward research
PAA	PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery.	Data analysis Human data	bio.tools
PCDDB	The Protein Circular Dichroism Data Bank	Intrinsically disordered proteins	bio.tools
PDB	The Protein Data Bank (PDB)	Intrinsically disordered proteins	bio.tools TeSS
PIA - Protein Inference Algorithms	PIA is a toolbox for mass spectrometrey based protein inference and identification analysis.	Data analysis	bio.tools
R Markdown	R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL.	Data analysis	TeSS
RD-Connect Genome Phenome Analysis Platform	The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research.	Human data	TeSS
RDA Standards	Directory of standard metadata, divided into different research areas	Documentation and metadata Data steward research
Renamer4Mac	File renaming software for Mac	Data organisation Data steward research
Repository Finder	Repository Finder can help you find an appropriate repository to deposit your research data. The tool is hosted by DataCite and queries the re3data registry of research data repositories.	Data publication Data steward research
Research Management Plan	Machine actionable DMPs.	Data management plan Data steward research	TeSS
Research Object Crate (RO-Crate)	RO-Crate is a lightweight approach to packaging research data with their metadata, using schema.org. An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations.	Documentation and metadata Data storage Data organisation Data steward research Microbial biotechnology	FAIRsharing
Rightfield	RightField is an open-source tool for adding ontology term selection to Excel spreadsheets	Documentation and metadata Data steward research Microbial biotechnology Identifiers	bio.tools
Rstudio	Rstudio notebooks allow to share code, documentation	Data analysis Data steward infrastructure	bio.tools TeSS
SASBDB	Small Angle Scattering Biological Data Bank	Intrinsically disordered proteins
Schemapedia	Web portal for finding ontologies	Documentation and metadata Data steward research
Scientific Data's Recommended Repositories	List of respositories recommended by Scientific Data, contains both discipline-specific and general repositories.	Data publication Data steward research Data steward infrastructure
semares	All-in-one platform for life science data management, semantic data integration, data analysis and visualization	Data steward research Documentation and metadata Data analysis Data steward infrastructure Data storage
SIFTS	Structure integration with function, taxonomy and sequence	Intrinsically disordered proteins
Talend	Talend is an open source data integration platform.	Data steward research TransMed Assembly
The Genomic Standards Consortium (GSC)	Minimum Information about any (x) Sequence	Documentation and metadata Data steward infrastructure Data steward policy Human data	FAIRsharing
The Open Biological and Biomedical Ontology (OBO) Foundry	Collaborative effort to develob interoperable ontologies for the biological sciences	Documentation and metadata Data steward research	FAIRsharing
tranSMART	Knowledge management and high-content analysis platform enabling analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research.	Data steward research Data analysis Data storage TransMed Assembly	bio.tools
UniProt	Comprehensive resource for protein sequence and annotation data	Documentation and metadata Intrinsically disordered proteins Microbial biotechnology	bio.tools FAIRsharing TeSS
University of Cambridge - Electronic Research Notebook Products	List of Electronic Research Notebook Products by University of Cambridge	Documentation and metadata Identifiers Data steward research
Wellcome Open Research - Data Guidelines	Wellcome Open Research requires that the source data underlying the results are made available as soon as an article is published. This page provides information about data you need to include, where your data can be stored, and how your data should be presented.	Data publication Data steward research
XNAT	Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data.	Data analysis TransMed Assembly XNAT-PIC
XNAT-PIC Pipelines	Analysing of single or multiple subjects within the same project in XNAT	Data steward research Data analysis XNAT-PIC
XNAT-PIC Uploader	Import tool for multimodal DICOM image datasets to XNAT	Data steward research XNAT-PIC