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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

Common problems

Relevant tools and resources

Skip tool table

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
Arvados With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources. IT support policy officer researcher data analysis
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
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 analysis researcher IT support
Choose a license Choose an open source license licensing researcher data manager policy officer
Common Workflow Language (CWL) An open standard for describing workflows that are build from command line tools IT support policy officer researcher data analysis
COPO Portal for scientists to broker more easily rich metadata alongside data to public repos. metadata researcher plants
Create a Codebook Examples and tools to create a codebook by the Data Documentation Initiative (DDI) metadata researcher data manager
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 Data management planning tool (Finland) DMP researcher data manager csc
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
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
FAIDARE FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. researcher data manager plants
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
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
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
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
Harvard Medical School – ELN Comparison Grid ELN Comparison Grid by Hardvard Medical School metadata identifiers researcher data manager
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
LUMI EuroHPC world-class supercomputer data analysis researcher IT support csc
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 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
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
MobiDB A database of protein disorder and mobility annotations IDP researcher
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 metadata identifiers
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
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
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
Rightfield RightField is an open-source tool for adding ontology term selection to Excel spreadsheets researcher metadata data manager micro biotech identifiers
Rstudio Rstudio notebooks allow to share code, documentation data analysis IT support researcher
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
semares All-in-one platform for life science data management, semantic data integration, data analysis and visualization researcher data manager metadata data analysis IT support storage
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
The Open Biological and Biomedical Ontology (OBO) Foundry Collaborative effort to develob interoperable ontologies for the biological sciences metadata data manager researcher
UniProt Comprehensive resource for protein sequence and annotation data metadata researcher IDP micro biotech
University of Cambridge - Electronic Research Notebook Products List of Electronic Research Notebook Products by University of Cambridge metadata identifiers researcher data manager
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
Contributors: Avatar of the contributor Alexander BotzkiAlexander Botzki Avatar of the contributor Alexia CardonaAlexia Cardona Avatar of the contributor Celia van GelderCelia van Gelder Avatar of the contributor Daniel WibbergDaniel Wibberg Avatar of the contributor Erik HjerdeErik Hjerde Avatar of the contributor Federico BianchiniFederico Bianchini Avatar of the contributor Graham HughesGraham Hughes Avatar of the contributor Gregoire RossierGregoire Rossier Avatar of the contributor Marko VidakMarko Vidak Avatar of the contributor Mijke JettenMijke Jetten Avatar of the contributor Minna AhokasMinna Ahokas Avatar of the contributor Munazah AndrabiMunazah Andrabi Avatar of the contributor Pedro FernandesPedro Fernandes Avatar of the contributor Pinar AlperPinar Alper Avatar of the contributor Priit AdlerPriit Adler Avatar of the contributor Robert AndrewsRobert Andrews Avatar of the contributor Siiri FuchsSiiri Fuchs Avatar of the contributor Victoria Dominguez D. AngelVictoria Dominguez D. Angel Avatar of the contributor Wolmar Nyberg ÅkerströmWolmar Nyberg Åkerström