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
Common problems
- 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.
- Metadata management: find metadata standards and vocabularies.
Relevant tools and resources
Tool or resource | Description | Tags | Registry |
---|---|---|---|
Argos | Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored. | DMP researcher data manager | |
Beacon | The Beacon protocol defines an open standard for genomics data discovery. | researcher data manager IT support human data |
|
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 | storage researcher human data |
|
BMRB | Biological Magnetic Resonance Data Bank | IDP researcher |
|
Bulk Rename Utility | File renaming software for Windows | data organisation data manager researcher | |
Choose a license | Choose an open source license | licensing researcher data manager policy officer |
|
COPO | Portal for scientists to broker more easily rich metadata alongside data to public repos. | metadata researcher plants |
|
Creative Commons License Chooser | It helps you choose the right Creative Commons license for your needs. | licensing researcher data manager policy officer | |
Crop Ontology | The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype. | researcher data manager IT support plants |
|
Data Curation Centre Metadata list | List of metadata standards | metadata researcher data manager | |
Data Use Ontology | DUO allows to semantically tag datasets with restriction about their usage. | data manager researcher human data |
|
DATAVERSE | Open source research data respository software. | storage researcher data manager IT support |
|
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 researcher IT support human data |
|
DisGeNET | A discovery platform containing collections of genes and variants associated to human diseases. | data analysis human data researcher |
|
DisProt | A database of intrinsically disordered proteins | IDP researcher |
|
DMP Canvas Generator | Questionnaire, which generates a pre-filled a DMP | DMP researcher data manager | |
DMP OPIDoR | Online questionnaire for the development of data management plans - repository of DMPs | DMP researcher data manager | |
DMPlanner | Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans. | DMP researcher data manager | |
DMPonline | A free tool to write, share and export a data management plan. Built-in data management plan templates for many major funders. | DMP researcher data manager |
|
DMPonline Belgium | A free tool to write, share and export a data management plan. Instance aimed at Belgian researchers with built-in data management plan templates for the major funders. | DMP researcher data manager | |
DMPTool | Build your Data Management Plan | DMP researcher data manager | |
DMPTuuli Finland | Data management planning tool | DMP researcher data manager | |
DS-Wizard | Data Stewardship Wizard | DMP researcher data manager IT support nels |
|
e!DAL-PGP | Plant Genomics and Phenomics Research Data Repository | plants researcher data manager IT support |
|
EasyDMP | DMP creation, versioning and sharing | DMP researcher data manager | |
ECPGR | Hub for the identification of plant genetic resources in Europe | plants researcher data manager | |
ELIXIR Deposition Databases for Biomolecular Data | List of discipline-specific deposition databases recommended by ELIXIR. | data publication researcher data manager IT support |
|
EMBL-EBI Ontology Lookup Service | EMBL-EBI’s web portal for finding ontologies | metadata data manager researcher |
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EMBL-EBI's data submission wizard | EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. | data publication researcher data manager | |
EUDAT licence selector wizard | EUDAT's wizard for finding the right licence for your data or code. | licensing researcher data manager policy officer | |
EURISCO | European Search Catalogue for Plant Genetic Resources | plants researcher data manager |
|
Europe PMC | Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. | researcher |
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FAIDARE | FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. | researcher data manager plants |
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FAIRDOMHub | Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. (public SEEK instance) | storage researcher nels metadata micro biotech |
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fairsharing | A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. | metadata data publication policy officer data manager researcher micro biotech |
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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 data analysis researcher IT support |
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GENEID | Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms. | data analysis researcher |
|
How to License Research Data - DCC | Guidelines about how to license research data from Digital Curation Centre | licensing researcher data manager policy officer | |
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 manager researcher human data data analysis |
|
Linked Open Vocabularies (LOV) | Web portal for finding ontologies | metadata data manager researcher | |
MCPD | The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. | metadata researcher IT support policy officer plants |
|
MIADE | Minimum Information About Disorder Experiments (MIADE) standard | metadata researcher data manager IDP | |
MIAPPE | Minimum Information About a Plant Phenotyping Experiment | metadata researcher data manager plants |
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MIGS/MIMS | Minimum Information about a (Meta)Genome Sequence | metadata researcher data manager marine micro biotech |
|
MIxS | Minimum Information about any (x) Sequence | metadata researcher data manager marine |
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MobiDB | A database of protein disorder and mobility annotations | IDP researcher |
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Ontobee | A web portal to search and visualise ontologies | metadata data manager researcher | |
ONTOMATON | OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. | researcher data manager IT support | |
Open Definition Conformant Licenses | Licenses that are conformant with the principles laid out in the Open Definition. | licensing researcher data manager policy officer | |
OSF | OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. | storage researcher data manager | |
PAA | PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. | data analysis researcher human data |
|
PCDDB | The Protein Circular Dichroism Data Bank | IDP researcher |
|
PDB | The Protein Data Bank (PDB) | researcher IDP |
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PIA - Protein Inference Algorithms | PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. | data analysis researcher |
|
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 researcher |
|
RD-Connect Genome Phenome Analysis Platform | The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research. | researcher human data |
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RDA Standards | Directory of standard metadata, divided into different research areas | metadata researcher data manager | |
Renamer4Mac | File renaming software for Mac | data organisation data manager researcher | |
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 researcher data manager | |
Research Management Plan | Machine actionable DMPs. | DMP researcher data manager |
|
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. | metadata storage data organisation data manager researcher micro biotech |
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Rightfield | RightField is an open-source tool for adding ontology term selection to Excel spreadsheets | researcher metadata data manager micro biotech |
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Rstudio | Rstudio notebooks allow to share code, documentation | data analysis IT support researcher |
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SASBDB | Small Angle Scattering Biological Data Bank | IDP researcher | |
Schemapedia | Web portal for finding ontologies | metadata data manager researcher | |
Scientific Data's Recommended Repositories | List of respositories recommended by Scinetific Data, contains both discipline-specific and general repositories. | data publication researcher data manager IT support | |
SIFTS | Structure integration with function, taxonomy and sequence | researcher IDP | |
The Genomic Standards Consortium (GSC) | Minimum Information about any (x) Sequence | metadata researcher IT support policy officer human data |
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The Open Biological and Biomedical Ontology (OBO) Foundry | Collaborative effort to develob interoperable ontologies for the biological sciences | metadata data manager researcher |
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UniProt | Comprehensive resource for protein sequence and annotation data | metadata researcher IDP micro biotech |
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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 researcher data manager |