This section provides an overview of the status of various EMO-BON components and features.
Infrastructure Status¶
Production¶
| Component | Status | URL |
|---|---|---|
| Main Website | ✅ Live | https:// |
| Observatory Crates | ✅ Live | Various |
| Governance Data | ✅ Live | https:// |
| Observatory Profile | ✅ Live | https:// |
In Development¶
| Component | Status | Expected |
|---|---|---|
| Analysis Results Profile | 🚧 In Progress | TBD |
| Sequencing Crate | 🚧 Planned | TBD |
| Sequencing Profile | 🚧 Planned | TBD |
| Triple Store / SPARQL Endpoint | 🚧 In Development | TBD |
| UDAL Query Service | 🚧 Planned | TBD |
GitHub Actions Status¶
Operational¶
| Action | Repository | Status |
|---|---|---|
| repo-constructor-action | Link | ✅ Operational |
| logsheet-downloader-action | Link | ✅ Operational |
| data-quality-control-action | Link | ✅ Operational |
| rocrate-sembench-setup | Link | ✅ Operational |
In Development¶
| Action | Repository | Status |
|---|---|---|
| semantify | Link | 🚧 Partial |
| rocrate-validate | TBD | 🚧 Planned |
| rocrate-to-pages | TBD | 🚧 Planned |
Data Products¶
Available¶
✅ Observatory Crates with logsheet data
✅ RDF triples for samples and sampling events
✅ Observatory profile specifications
✅ Some analysis results (cluster-01)
Planned¶
🚧 Complete sequencing metadata
🚧 Systematic analysis results for all samples
🚧 Integrated knowledge graph
🚧 Public SPARQL endpoint
Features¶
Implemented¶
| Feature | Description | Status |
|---|---|---|
| Logsheet Ingestion | Automated download from Google Sheets | ✅ Live |
| Data Quality Control | Validation and repair of logsheet data | ✅ Live |
| RO-Crate Generation | Creation of observatory crates | ✅ Live |
| GitHub Pages Publishing | Automated website deployment | ✅ Live |
| Large File Support (DVC) | Version control for large files | ✅ Live |
In Progress¶
| Feature | Description | Status |
|---|---|---|
| RDF Generation | Complete semantic uplifting pipeline | 🚧 Partial |
| SHACL Validation | Validation of RDF triples | 🚧 In Development |
| LDES Feeds | Linked Data Event Streams | 🚧 Planned |
| Triple Store | Central knowledge graph | 🚧 In Development |
Documentation¶
Complete¶
✅ This handbook (migrated to MyST)
✅ Repository READMEs
✅ Action documentation
Needs Update¶
🚧 Installation guides
🚧 Tutorial materials
🚧 API documentation
Integration Points¶
Active¶
| System | Type | Status |
|---|---|---|
| Google Sheets | Data Source | ✅ Connected |
| GitHub | Repository & CI/CD | ✅ Operational |
| ENA | Sequence Archive | ✅ Submitting |
| S3 | Large File Storage | ✅ Operational |
Planned¶
| System | Type | Status |
|---|---|---|
| FAIR EASE IDDAS | Catalogue | 🚧 Planned |
| EurOBIS | Biodiversity Portal | 🚧 Planned |
| Blue Cloud | Data Platform | 🚧 Planned |
Known Issues and Limitations¶
Current Limitations¶
SPARQL Endpoint: Not yet publicly available
Sequencing Logistics Crate: Structure not finalized
Analysis Results: Not complete for all observatories
URI Dereferenceability: Some URIs not yet dereferenceable
Planned Improvements¶
Automation: More automated workflows
Validation: Enhanced data validation
Performance: Optimization of processing
Documentation: More examples and tutorials
Release Schedule¶
Recent Releases¶
v1.0.0 (2024-Q1): Initial observatory crate workflow
v1.1.0 (2024-Q2): Data quality control improvements
v1.2.0 (2024-Q3): Enhanced RDF generation
Upcoming¶
v2.0.0 (TBD): Complete semantic uplifting pipeline
v2.1.0 (TBD): SPARQL endpoint launch
v3.0.0 (TBD): Analysis results integration
Contact for Status Updates¶
For questions about component status or roadmap:
Email: opsci@vliz.be
GitHub Issues: Use repository issue tracker
Documentation: Check this handbook for updates
Legend¶
✅ Live/Operational: Fully functional in production
🚧 In Development: Being actively developed
🚧 Planned: On roadmap but not yet started
❌ Deprecated: No longer supported
⚠️ Issues Known: Operational but with known limitations