Your role: Researcher
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
- Start planning your project taking the DMP into account
Related pages
-
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.
More information
Relevant tools and resources
Skip tool tableTool or resource | Description | Related pages | Registry |
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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 | Tool info Training |
Beacon | The Beacon protocol defines an open standard for genomics data discovery. | Data Steward: research Data Steward: infrastructure Human data | Tool info Training |
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 Proteomics | Tool info |
BMRB | Biological Magnetic Resonance Data Bank | Intrinsically disordered proteins | Tool info |
Bulk Rename Utility | File renaming software for Windows | Data organisation Data Steward: research | |
CEDAR | CEDAR is making data submission smarter and faster, so that scientific researchers and analysts can create and use better metadata. | Documentation and metadata Machine actionability Data Steward: research | Tool info Standards/Databases |
ChEMBL | Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties and abstracted bioactivities. | Data analysis Toxicology data | Tool info Standards/Databases Training |
Choose a license | Choose an open source license | Licensing Data Steward: research Data Steward: policy | |
Common Workflow Language (CWL) | An open standard for describing workflows that are build from command line tools | Data Steward: infrastructure Data analysis | Standards/Databases Training |
COPO | Portal for scientists to broker more easily rich metadata alongside data to public repos. | Documentation and metadata Plant sciences Machine actionability | Tool info Standards/Databases |
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 | Standards/Databases Training |
Data Curation Centre Metadata list | List of metadata standards | Documentation and metadata Data Steward: research | |
Data INRAE | Dataverse for life sciences and agronomic related data | Plant sciences Plant Genomics Data Steward: research | Standards/Databases |
Data Stewardship Wizard | Publicly available online tool for composing smart data management plans Different instances available | Data management plan Data Steward: research Data Steward: infrastructure NeLS TSD | Tool info Training |
Data Use Ontology | DUO allows to semantically tag datasets with restriction about their usage. | Data Steward: research Human data | Standards/Databases Training |
DATAVERSE | Open source research data respository software. Different instances available | Data storage Data Steward: research Data Steward: infrastructure IFB | Training |
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 | Tool info Standards/Databases Training |
DisGeNET | A discovery platform containing collections of genes and variants associated to human diseases. | Data analysis Human data Toxicology data | Tool info Standards/Databases |
DisProt | A database of intrinsically disordered proteins | Intrinsically disordered proteins | Tool info |
DMP Canvas Generator | Questionnaire, which generates a pre-filled a DMP | Data management plan Data Steward: research | |
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 | Training |
DMPRoadmap | DMP Roadmap is a Data Management Planning tool. Different instances available | Data management plan Data Steward: research | |
DMPTool | Build your Data Management Plan | Data management plan Data Steward: research | |
e!DAL-PGP | Plant Genomics and Phenomics Research Data Repository | Plant sciences Plant Genomics Data Steward: research Data Steward: infrastructure Data publication | Standards/Databases |
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 IFB CSC | Standards/Databases |
EMBL-EBI Ontology Lookup Service | EMBL-EBI’s web portal for finding ontologies | Documentation and metadata Data Steward: research | |
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 | Tool info |
Europe PMC | Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. | Tool info Standards/Databases Training | |
FAIDARE | FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. | Data Steward: research Plant sciences IFB | Tool info |
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 Documentation and metadata Microbial biotechnology Machine actionability | Standards/Databases |
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 | Standards/Databases Training |
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. Different instances available | NeLS Marine Metagenomics Data analysis Data Steward: infrastructure IFB | Tool info Training |
GENEID | Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms. | Data analysis | Tool info |
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 | Tool info Standards/Databases Training |
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 | Tool info |
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 | Standards/Databases Training |
MIGS/MIMS | Minimum Information about a (Meta)Genome Sequence | Documentation and metadata Data Steward: research Marine metagenomics Microbial biotechnology | Standards/Databases |
MIxS | Minimum Information about any (x) Sequence | Documentation and metadata Data Steward: research Marine metagenomics Plant Genomics | Standards/Databases Training |
MobiDB | A database of protein disorder and mobility annotations | Intrinsically disordered proteins | Tool info Standards/Databases |
MRI2DICOM | a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard | Data Steward: research XNAT-PIC | |
Multi-Crop Passport Descriptor (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 | Standards/Databases |
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 Toxicology data | Tool info |
Ontobee | A web portal to search and visualise ontologies | Documentation and metadata Data Steward: research | Standards/Databases |
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 | Training |
PAA | PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. | Data analysis Human data Proteomics | Tool info |
PCDDB | The Protein Circular Dichroism Data Bank | Intrinsically disordered proteins | Tool info |
PDB | The Protein Data Bank (PDB) | Intrinsically disordered proteins Structural Bioinformatics | Tool info Training |
PIA - Protein Inference Algorithms | PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. | Data analysis Proteomics | Tool info |
PLAZA | Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. | Plant sciences Plant Genomics | Standards/Databases Training |
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 | Training |
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 | Training |
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 | |
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 Machine actionability | Standards/Databases |
Rightfield | RightField is an open-source tool for adding ontology term selection to Excel spreadsheets | Documentation and metadata Data Steward: research Microbial biotechnology Identifiers Machine actionability | Tool info |
Rstudio | Rstudio notebooks allow to share code, documentation | Data analysis Data Steward: infrastructure | Tool info Training |
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 | |
The Genomic Standards Consortium (GSC) | Minimum Information about any (x) Sequence | Documentation and metadata Data Steward: infrastructure Data Steward: policy Human data | Standards/Databases |
The Open Biological and Biomedical Ontology (OBO) Foundry | Collaborative effort to develob interoperable ontologies for the biological sciences | Documentation and metadata Data Steward: research | Standards/Databases |
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 | Tool info |
TXG-MAPr | A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset. | Data analysis Toxicology data | Tool info |
UniProt | Comprehensive resource for protein sequence and annotation data | Documentation and metadata Intrinsically disordered proteins Microbial biotechnology Proteomics Structural Bioinformatics | Tool info Standards/Databases Training |
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 | |
WorkflowHub | WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. | Data publication Data Steward: research | Tool info Standards/Databases |
XNAT | Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. | Data analysis TransMed XNAT-PIC Bioimaging data | |
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 | |
Zooma | Find possible ontology mappings for free text terms in the ZOOMA repository. | Documentation and metadata Data Steward: research | Tool info Training |
National resources | |||
RDM Guide | RDM Guide describes Belgian data management guidelines, resources, tools and services available for researchers in Life Sciences. |
Data Steward: research | |
Galaxy Belgium | Galaxy Belgium is a Galaxy instance managed by the Belgian ELIXIR node, funded by the Flemish government, which utilizing infrastructure provided by the Flemish Supercomputer Center (VSC).
Galaxy
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Data analysis | |
ENA upload tool | The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). |
Data Steward: infrastructure Data Steward: research | |
DMPonline.be | This instance of DMPonline is provided by the DMPbelgium Consortium. We can help you write and maintain data management plans for your research.
DMPRoadmap
|
Data Steward: research Data management plan | |
PIPPA | PIPPA, the PSB Interface for Plant Phenotype Analysis, is the central web interface and database that provides the tools for the management of the plant imaging robots on the one hand, and the analysis of images and data on the other hand. |
Plant sciences Data Steward: research Data Steward: infrastructure | |
Belnet | Belnet is the privileged partner of higher education, research and administration for connectivity. We provide high-bandwidth internet access and related services for our specific target groups. |
Data Steward: research Data Steward: infrastructure Data transfer | |
e!DAL-PGP | Plant Genomics and Phenomics Research Data Repository |
Data storage Documentation and metadata Data Steward: research Data Steward: infrastructure Plant sciences Plant Genomics | |
GHGA | The German Human Genome-Phenome Archive |
Data storage Documentation and metadata Data Steward: research | |
FAIRDOM-SEEK | Data management platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. |
Data storage Documentation and metadata Data Steward: research Data Steward: infrastructure | |
PANGAEA | Data Publisher for Earth & Environmental Science |
Data storage Documentation and metadata Data Steward: research | |
PUBLISSO | Open access publishing platform for life sciences |
Data publication Data Steward: research | |
Galaxy Estonia | This is the Estonian instance of Galaxy, which is an open source, web-based platform for data intensive biomedical research.
Galaxy
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Data analysis | |
Red Española de Supercomputación | The Spanish Supercomputing Network’s mission is to offer the resources and services of supercomputing and data management necessary for the development of innovative and high-quality scientific and technological projects, through competitive calls based on the scientific excellence of the projects to be developed. |
Data Steward: research Data Steward: infrastructure | |
RedIRIS | Spanish academic and research network that provides advanced communication services to the scientific community and national universities. |
Data Steward: research Data Steward: infrastructure | |
Recolecta | The national aggregator of open access repositories. This platform brings together all the Spanish digital infrastructures in which open access research results are published and / or deposited. |
Data Steward: research Data Steward: infrastructure | |
Datos.gob.es | Open data portal of the spanish government. A meeting point for the various actors that make up the open data ecosystem. |
Data Steward: research Data Steward: infrastructure | |
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 Data Steward: infrastructure Data analysis | |
DMPTuuli | Data management planning tool (Finland)
DMPRoadmap
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CSC Data Steward: research Data management plan | |
Fairdata.fi | With the Fairdata Services you can store, share and publish your research data with easy-to-use web tools. |
CSC Data Steward: research Data storage Data publication Existing data | |
Federated EGA Finland | FEGA allows you to store and shaare sensitive data in Finland in a way that fulfils all the requirements of the General Data Protection Regulation (GDPR). |
CSC Data Steward: research Sensitive data Data publication Existing data Human data | |
Findata | The Health and Social Data Permit Authority. Findata offers services and enables secure and efficient utilisation of data materials containing health and social data. |
CSC Data Steward: research Sensitive data Existing data Human data | |
Fingenious | Finnish Biobank Cooperative (FINBB) connects researchers to Finnish biomedical research. Via Fingenious® services the researcher can connect to all Finnish public bio banks. |
CSC Data Steward: research Sensitive data Human data | |
Sensitive Data Services for Research | CSC Sensitive Data Services for Research are designed to support secure sensitive data management through web-user interfaces accessible from the user’s own computer |
CSC Data Steward: research Sensitive data Data analysis Data storage Data publication Human data | |
High performance computing | CSC Supercomputers Puhti, Mahti and LUMI performance ranges from medium scale simulations to one of the most competitive supercomputers in the world. |
CSC Data Steward: research Data analysis | |
Cloud computing | CSC offers a variety of cloud computing services: the Pouta IaaS services and the Rahti container cloud service. |
CSC Data Steward: research Data analysis | |
DMP OPIDoR | Online questionnaire for the development of data management plans - repository of DMPs
DMPRoadmap
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IFB Data Steward: research Data management plan | |
BioData.pt Service Hub | BioData.pt Service Hub includes several data management resources, tools and services available for researchers in Life Sciences. |
Data Steward: research Data analysis Data storage | |
BioData.pt Data Management Portal (DMPortal) | This instance of DataVerse is provided by the BioData.pt. We can help you write and maintain data management plans for your research.
DATAVERSE
|
Data Steward: research Data storage | |
BioData.pt Data Stewardship Wizard | Local instance of Data Stewardship Wizard. You can use this tool to create your own Data Management Plans.
Data Stewardship Wizard
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Data Steward: research Data management plan | |
Ready for BioData Management | Capacity building program in data management for the life sciences to empower researchers and institutions in managing their data more effectively and efficiently.
Data Stewardship Wizard
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Data management plan | |
DMPonline | DMPonline is a web-based tool that supports researchers to develop data management and sharing plans. It contains the latest funder templates and best practice guidelines to support users to create good quality DMPs.
DMPRoadmap
|
Data Steward: research Data management plan | |
COPO | COPO is an open source data brokering platform that helps researchers annotate their data with metadata conforming to repository standards, and supports submission of data to a number of these public repositories |
Data Steward: research Documentation and metadata |