Themes and hacking projects
Data
Aims to identify key data resources across Europe and support the linkages between data and literature.
Text mining
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C-SPARQL powered querying pipeline of bioRxiv publications
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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
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Adding Bioschemas markup to data repositories and developing tools to find, consume and use it
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Development or adaption of tools to apply bioschemas to Orphanet website and datasets output for the rare diseases
community
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From Biotea to Bioschemas: definition of profiles required to represent scholarly publications
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Pathway effect prediction for protein targets
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Putting structured data into individual entry pages in biological database
Identifiers
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Support tools for rapid adoption of compact identifiers in the publishing process
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Using blockchain in biomedical provenance, the identifiers use case.
Data distribution
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Application of RDF-based models and tools for enhancing interoperable use of biomedical resources
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Transfer of Research Assets between FAIRDOM SEEKs
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Prototyping the new PSICQUIC 2.0
Data integration
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OmicsPath: Finding Relevant omics datasets using pathway information
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Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships
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Development of a catalog of federated SPARQL queries in the field of Rare Diseases
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ProtVista (protein annotation viewer) extension using Bioschemas data
Validation
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Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases
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JSON schema validation with ontologies
Tools
Helps researchers find the best software tools to analyse their data.
Containers
Tools discovery
Visualisation
Workflows
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CWL support in Galaxy
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Development of a GA4GH-compliant, language-agnostic workflow execution service
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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
Interoperability
Develops and encourages the adoption of standards to describe life science data.
- 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
Tools discovery
Visualisation
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
- 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
Tools discovery
Visualisation
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
- 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
Tools discovery
Visualisation
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
Visualisation
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
- 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.