Themes and hacking projects

Data

Aims to identify key data resources across Europe and support the linkages between data and literature.

Text mining
  • C-SPARQL powered querying pipeline of bioRxiv publications
  • Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits

    • Interoperability

    Develops and encourages the adoption of standards to describe life science data.

    Structured metadata
  • Adding Bioschemas markup to data repositories and developing tools to find, consume and use it
  • Development or adaption of tools to apply bioschemas to Orphanet website and datasets output for the rare diseases community
  • From Biotea to Bioschemas: definition of profiles required to represent scholarly publications
  • Pathway effect prediction for protein targets
  • Putting structured data into individual entry pages in biological database
    • Identifiers
  • Support tools for rapid adoption of compact identifiers in the publishing process
  • Using blockchain in biomedical provenance, the identifiers use case.
    • Data distribution
  • Application of RDF-based models and tools for enhancing interoperable use of biomedical resources
  • Transfer of Research Assets between FAIRDOM SEEKs
  • Prototyping the new PSICQUIC 2.0
    • Data integration
  • OmicsPath: Finding Relevant omics datasets using pathway information
  • Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships
  • Development of a catalog of federated SPARQL queries in the field of Rare Diseases
  • ProtVista (protein annotation viewer) extension using Bioschemas data
    • Validation
  • Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases
  • JSON schema validation with ontologies

    • Tools

    Helps researchers find the best software tools to analyse their data.

    Containers
    Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)
    Tools discovery
    bio.tools & EDAM drop-in hackathon & discussions
    Visualisation
    Development of BioJS components
    Workflows
  • CWL support in Galaxy
  • Development of a GA4GH-compliant, language-agnostic workflow execution service
  • Enrichment and propagation of metagenomic experimental metadata
  • Import workflows into TeSS Concept Maps
  • Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

    • Training

    Helps scientists and developers find the training they need, and also provides that training.

    Training materials
  • Alternative episodes for the 4 Open Source Software (4OSS) lesson focused on different Open Source technologies: Github, Docker, Jupyter Notebook and so on
  • Assessing the FAIRness of Training Materials
  • Galaxy training material improvement and extension
    • © 2018 Elixir HUB
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