Toolbox

• Amsterdam UMC - locatie AMC
• Amsterdam UMC - locatie VUmc
• UMCG
• UMC Utrecht
• LUMC
• MUMC+
• Radboudumc
• Erasmus MC

• Clinical researchers that are working at UMCs are obliged to complete the ‘Basiscursus Regelgeving en Organisatie voor Klinisch onderzoekers (BROK®)’. After four years, a re-registration course should be followed. Every UMC organises a centre-specific BROK for its employees. This centre-specific BROK offers information on data management and local policies, facilities, and expertise.
• Many universities and UMCs organise specialised data management courses. See resources at your UMC above.
• You can visit the European training portal TeSS for international courses and training materials in the field of life sciences data (ELIXIR).
• More and more training programmes for project data stewards are becoming available. At the national level, the Netherlands Bioinformatics and Systems Biology research school (BioSB) and the Dutch Techcentre for Life Science (DTL) organise data management-related workshops and courses, such as Data Carpentry workshops, the bi-annual course on Managing and Integrating life science information, and Bring Your Own Data workshops (BYODs). They also provide links to internationally organised training, for instance within the framework of the ELIXIR Training Platform.
• The DTL Course Directory includes Dutch courses, trainings, and workshops in the field of data and technologies for the life sciences. DTL also offers an extensive overview of online trainings.
• Essentials 4 Data Support (organised by Research Data Netherlands) is an introductory course for those that wish to support researchers in storing, managing, archiving and sharing their research data.
• Datacarpentry develops and teaches workshops on the fundamental data skills needed to conduct research.
• Netherlands Bioinformatics and Systems Biology research school (BioSB)
• Expert Tour Guide on Data Management by CESSDA ERIC (the Consortium of European Social Science Data Archives European Infrastructure Consortium) aims to put social scientists at the heart of making their research data findable, understandable, sustainably accessible and reusable.
• The Coursera MOOC 'Research Data Management and Sharing' by the University of North Carolina at Chapel Hill and The University of Edinburgh (MANTRA course content incorporated) provides learners with an introduction to research data management and sharing.

International Data Collections:

• OpenAIRE offers a Data Provider Locator
• OpenDOAR is a global directory of Open Access repositories and their policies.
• DANS: EASY is an online archiving system for depositing and reusing research data. It contains datasets from the humanities, health sciences, social and behavioural sciences, oral history and spatial sciences. In addition, EASY offers access to the secure micro data of Statistics Netherlands (CBS).
• UvA/AUAS figshare: a system for safely storing, controlled sharing and publication of research data.
• Core Data Resources (ELIXIR-recommended repository)
• Deposition Databases for Biomolecular Data (ELIXIR-recommended repository)
• Orphadata: a comprehensive, high-quality and freely-accessible dataset related to rare diseases and orphan drugs, in a reusable format
• Decipher: Mapping the clinical genome
• Re3data: Registry of Research Data Repositories
• FAIRsharing: A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.

National Data Collections:

• Zorggegevens.nl
• DANS & DANS Data Portal
• 4TU-Datacentrum
• Patient registries in the Netherlands
• Patient registries and biobanks in Europe
• CTMM-TraIT catalogue
• Trusted digital repositories
• Dataportaal van de Nederlandse overheid

Biobanking:

• Eurobiobank
• BBMRI-NL Dutch biobanks catalogue and some background information about the catalogue
• Nederlandse en internationale catalogi voor biobanken (BBMRI-NL)
• Dutch National Tissuebank Portal (PALGA)
• PSI (Parelsnoer Instituut) (now integrated in Health-RI)
• Lifelines
• Durrer Center for cardiovascular research
• Netherlands Brain Bank

UMC Data Collections/Repositories:

Examples of data management plans (DMPs) can help you get a sense of issues that you should address. However, it is unlikely that you can reuse large parts of existing DMPs for your project because every project is unique. If you need help in writing a DMP, consider consulting an expert.

• Researchers in ZonMw funded projects can use the DMP template of their own institution, provided that it is acknowledged by ZonMw. 
• Project leaders of NWO funded projects have the option to use a DMP template from their own research institution, as long as that template has been approved by NWO. 
• The AMC has created a standard operational procedure (SOP) for research data management as well as a data management plan template.
• University Medical Centre Groningen has also created a DMP template UMCG
• Examples from the University of Cambridge can be found here (with information on, for example, data management and research data policies).
• ELIXIR has developed a Data Stewardship Wizard that converts a lengthy data management questionnaire into an effective flowchart, enhancing the quality of your DMP
• DMPonline helps you to create, review, and share data management plans that meet institutional and funder requirements. It is provided by the Digital Curation Centre (DCC).
• The LCRDM has created an overview of RDM practices and knowledge at Dutch research institutions
• DTL has created an overview of RDM tools and online trainings
• GO FAIR has compiled an RDM Starter Kit that lists resources designed to help researchers organise their data and make it findable, accessible, interoperable and reusable

GDPR webinars and trainings:

• Quero Systems & Proserve Information Day: Biobank conform GDPR
• BBMRI-ERIC Webinar: The GDPR and Health Research
• ELIXIR webinar: Requirements in data protection law and the upcoming GDPR implementation.

GDPR compliancy:

• BBMRI-NL: data protection impact assessments app  

A terminology is a standardised list of terms that are used in a particular domain.

General information:

• Registratie aan de Bron (NFU) for registration of care data
• Nictiz Standaarden-overzicht en Referentielijsten (both in Dutch)

Phenotype (clinical) data:

• SNOMED CT (also see Nictiz SNOMED CT (in Dutch))
• LOINC (also see NICTIZ Standaarden (in Dutch))
• ICD10 (also see NICTIZ Standaarden (in Dutch))
• Clinical Data Acquisition Standard Harmonisation (CDASH) by CDISC (a global, nonprofit charitable organization that develops data standards to streamline clinical research and enable connections to healthcare). (This is not (yet) widely adopted for investigator-driven trials.)

Genomics:

• Online Mendelian Inheritance in Man (OMIM)
• NCBI Sequence Identifiers (GI and Version)

Proteomics:

• mzML for Mass Spectrometry Data
• mzQuantML for peptide and protein quantification data
• mzIdentML for peptide and protein identification data

Metabolomics:

• MSI

Imaging:

• DICOM (also see NICTIZ Standaarden (in Dutch))

Multichannel biological and physical signals:       

• EDF+ for EEG, PSG, ECG, EMG, and Evoked Potential

Rare diseases:

• Human Phenotype Ontology (HPO) ID

Neurological Disorders and Stroke:

• National Institute of Neurological Disorders and Stroke (NINDS): Common Data Elements. This is not (yet) widely adopted for investigator-driven trials.

• DataverseNL offers online storage, sharing and registration of research data, during the research period and up to the prescribed term of ten years after its completion.
• BBMRI-NL has developed a data protection impact assessments app to assist researchers in showing they are GDPR compliant.

Repository finders:

• OpenDOAR is a global directory of Open Access repositories and their policies.
• Re3data is a registry of research data repositories

General repositories:

• DANS: Electronic Archiving System (EASY) is an online archiving system for depositing and reusing research data. It contains datasets from the humanities, health sciences, social and behavioural sciences, oral history and spatial sciences. In addition, EASY offers access to the secure micro data of Statistics Netherlands (CBS).
• Figshare: a system for safely storing, controlled sharing and publication of research data.
• 4TU.ResearchData
• Data Archive (SURF)
• FAIRsharing
• Mendeley
• DRYAD

Repositories for genetic data:

• Database of Genotypes and Phenotypes (dbGaP)
• European Genome-phenome Archive (EGA)
• NCBI Gene Expression Omnibus (GEO)
• ArrayExpress
• European Nucleotide Archive (ENA)
• Sequence Read Archive (SRA)

Repositories for biomedical data:

• Core Data Resources  (ELIXIR-recommended repository)
• Deposition Databases for Biomolecular Data (ELIXIR-recommended repository for biological and biomedical data)
• National Center for Biotechnology Information (NCBI (NIH))

Repositories at UMCs and Universities:

This is listed in the UMC resources at the Toolbox section

Data sharing:

• Data Sharing Checklist (Radboudumc)
• Figshare: a system for safely storing, controlled sharing and publication of research data.
• Contracts: examples of Data Transfer Agreements templates:
  • RIVM – Data Transfer Agreement template
  • BioMedbridges - Data Transfer Agreement template

Persistent Identifiers:

• Github/ZENODO: DOI
• Mendeley: DOI
• SURFSara: Handle
• DataCite: DOI
• Koninklijke Bibliotheek: National Bibliographic Number (NBN) (or URN)
• Netherlands Biodiversity Data Services: PURL
• EZID: Archival Resource Key (Ark)

PID Resolvers (retrieval of publication or data):

• DOI Resolver
• Handle resolver
• Nationale Resolver (NBN)
• Ark resolver

• UU: overview costs of data management - overview of possible costs per research phase and research activity
• UK Data Service: overview costs of data management and an acivity-based tool (version 2015)
• LCRDM: Research Data Management: Storage and Beyond, including a guide to research data management and costs