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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"

Relevant tools and resources

Skip tool table
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