Documentation

Manuals

Find here user manuals of broadly used MOLGENIS applications:

• MOLGENIS Data Platform manual
• MOLGENIS Catalogue
• MOLGENIS Armadillo DataSHIELD manual
• MOLGENIS Variant Interpretation Pipeline manual

The full list of applications can be found at the MOLGENIS Github.

Publications

Publications by MOLGENIS community members:

Sample and data catalogues:

• Swertz et al (2022) Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies. Yearb Med Inform
• Holub et al (2016) BBMRI-ERIC Directory: 515 Biobanks with Over 60 Million Biological Samples. Biopreservation and Biobanking
• Roxana Merino-Martinez et al (2016) Toward Global Biobank Integration by Implementation of the Minimum Information About BIobank Data Sharing (MIABIS 2.0 Core). Biopreservation and Biobanking

FAIRification:

• Van der Velde et al (2022) FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. Sci Data
• Wilkinson et al (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data
• Lancaster et al (2015) Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts. Human Mutation

Harmonisation:

• Pang et al (2017) BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. Bioinformatics
• Pang et al (2016) MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks. Bioinformatics
• Pang et al (2015) BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. Journal of the Medical Informatics Association
• Pang et al (2015,)SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data. Database(Oxford)

Large research projects and studies:

• Van der Velde et al (2018) MOLGENIS Research: Advanced bioinformatics data software for non-bioinformaticians. Bioinformatics
• Li et al (2016) A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell
• Netea et al (2016) Understanding human immune function using the resources from the Human Functional Genomics Project. Nature Medicine
• Snoek et al (2013) WormQTL–public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Research

Patient and mutation registries:

• Van den Akker et al (2011) The international dystrophic epidermolysis bullosa patient registry: an online database of dystrophic epidermolysis bullosa patients and their COL7A1 mutations. Human Mutation
• Lazarinne et al (2015) The ARVD/C genetic variants database: 2014 update. Human Mutation
• Van der Velde et al (2013) An overview and online registry of microvillus inclusion disease patients and their MYO5B mutations. Human Mutation
• Janssen et al (2012) Mutation update on the CHD7 gene involved in CHARGE syndrome. Human Mutation

Rare disease genome knowledge systems:

• Van der Velde (2017) GAVIN: Gene-Aware Variant INterpretation for medical sequencing. Genome Biology
• Van Gijn et al (2018) New workflow for classification of genetic variants’ pathogenicity applied to hereditary recurrent fevers by the International Study Group for Systemic Autoinflammatory Diseases (INSAID).Journal of Medical Genetics
• Engwerda et al (2018) The phenotypic spectrum of proximal 6q deletions based on a large cohort derived from social media and literature reports. European Journal of Human Genetics
• Sikkema-Raddatz et al (2016) NIPTRIC: an online tool for clinical interpretation of non-invasive prenatal testing (NIPT) results. Science reports

Genotype processing:

• Kanterakis et al (2015) Molgenis-impute: imputation pipeline in a box. BMC Research Notes
• Deelen et al (2015) Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels. Genome Medicine
• Johanson et al (2016) CoNVaDING: Single Exon Variation Detection in Targeted NGS Data. Human Mutation
• Deelen et al (2014) Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Research Notes