In June 2020, X-omics organized the first online workshop series. Different aspects of challenges and solutions related to multi-omics data integration were addressed in four workshops.
The first workshop on “Data Standards and Multi-omics Integration” chaired by Jasmin Böhmer (UMC Utrecht, CMM) addressed standard data formats of -omics data.
The first invited speaker Juan Antonio Vizcaíno (EMBL-EBI, Hinxton, Cambridge) gave a comprehensive overview of established standards for proteomics, genomics, and transcriptomics data, including formats for raw, processed and archived data. He also gave an introduction to relevant standard initiatives such as the Proteomics Standards Initiative (PSI), and The Global Alliance for Genomics and Health (GA4GH). Finally, he shared his ideas on how new developments on standards for portable workflows, integrative data formats (e.g. for proteogenomics), and public databases for omics data and pathway related information can help integrate different types of omics data.
Standards for omics-data a personal view Juan Antonio Vizcaíno.pdf
The next speaker Joeri van der Velde (UMCG, Groningen) introduced the Dutch FAIR Genomes initiative, which develops a connected semantic model for metadata to promote optimal (re)use of Next Generation Sequencing (NGS) data in research and healthcare.
Introduction to FAIR data with the aid of RDF and ontologies Joeri van der Velde
Jasmin Böhmer (UMC Utrecht, CMM) addressed the requirements for the reuse of sensitive data. She explained how the implementation of Data Use Ontology (DUO) tags at the European Genome-phenome Archive (EGA) helps standardize data use conditions and querying available data, e.g. based on informed consent.
Jasmin K. Böhmer. (2020, June). X-omics workshop: data standards and multi-omics data integration - EGA DAC data standard (Version V2).
EGA data standard and Data Use Ontology (DUO) terms Jasmin Böhmer.pdf
The workshop was concluded by an interactive quiz and a Q&A session.
Key take-home messages
In the second workshop “Linked Data in Practice: An RDF-based Approach with SPARQLing-genomics” Jasmin Böhmer (UMC Utrecht, CMM) gave an introduction to linked data and FAIR data requirements. Roel Janssen (UMC Utrecht, CMM) gave a demo on how genomics data can be converted to the Resource Description Framework (RDF) and queried with the SPARQL Protocol And RDF Query Language. He showed how data can be harmonized by using ontological terms to capture metadata.
Jasmin K. Böhmer, & Roel Janssen. (2020, June). Linked data in practice: An RDF-based approach with SPARQLing Genomics (Version V4).
Linked data in practice an RDF based approach with SPARQLing Genomics Jasmin Böhmer Roel Janssen.pdf
Key take-home messages
During the third workshop “Showcases of Multi-omics Data Integration”, chaired by Jenny van Dongen (Vrije Universiteit Amsterdam), Ayşe Demirkan (University of Surrey) talked about “Stories of Two manuscripts”*. She shared insights on the challenges the research team encountered while integrating different types of -omics data (focusing, in particular, on genomic, transcriptomic, methylomic, and metabolomic data) from different sources. Ayşe explained which tools and strategies helped with these challenges.
 Liu, J., Carnero-Montoro, E., van Dongen, J. et al. An integrative cross-omics analysis of DNA methylation sites of glucose and insulin homeostasis. Nat Commun 10, 2581 (2019)
 Liu, J., Lahousse, L., Nivard, M.G. et al. Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug–metabolite atlas. Nat Med 26, 110–117 (2020).
Story of two manuscripts Ayse Demirkan.pdf
Key take-home messages
During the fourth workshop “Pitch Your Own Multi-omics Project”, chaired by Purva Kulkarni and Peter-Bram ’t Hoen (both Radboudumc, Nijmegen), three workshop participants- Arjan Hoogendijk (Sanquin), Tabea Riepe (Radboudumc, Nijmegen), Fiona A. Hagenbeek (Vrije Universiteit Amsterdam) were selected to give a brief pitch on their own multi-omics research project. Afterwards, we discussed these projects and the posed challenges in separate breakout sessions together with invited experts (Yang Li (Radboudumc, Nijmegen; Helmholtz Centre for Infection Research, Hannover), Peter Horvatovich (University of Groningen), Karlien Coene (Radboudumc, Nijmegen)) and other workshop participants.
We thank all the participants, the workshop organizing committee, the invited speakers and experts, and the X-omics project management team and look forward to future events.
Anna Niehues (workshop series coordinator) on behalf of the workshop series organizing committee (Jasmin Böhmer (UMC Utrecht, CMM), Jenny van Dongen (Vrije Universiteit Amsterdam), Victor Guryev (UMCG, Groningen), Yanick Paco Hagemeijer (University of Groningen), Peter-Bram ’t Hoen (Radboudumc, Nijmegen), Peter Horvatovich (University of Groningen), Purva Kulkarni (Radboudumc, Nijmegen), Anna Niehues (Radboudumc, Nijmegen), Gurnoor Singh (Radboudumc, Nijmegen))