Related Issues (20)
- Update `extract_study` command to search Legacy IDs
- workarround: generate RDF joining element labels to id-based IRIs
- Check referential integrity of Napa squad's MongoDB database via SPARQL in Fuseki
- Add `associated_studies` onto Biosample and make part_of not required for Biosample
- Developer documentation and `Dockerfile` contradict one another HOT 3
- try robot extract -> gra.fo in berkeley schema (for proteolytic cleavage)
- capture ideas about proteolytic cleavage from 2024-01-29 OBI call
- provide documentation for SPARQL referential integrity checks in Fuseki in Docker
- make sure nmdc-schema documentation is getting published
- Poetry conflicts between host's Poetry .venv and Docker container's .venv HOT 4
- rewrite slash-containing MS/MS file type permissible value
- Improve logging for database tools: extract-study. Warn for missing Data Objects
- remove `Reaction` and repurpose `has_part` (with domain and range Any?) in nmdc-schema as well as berkeley-schema-fy24
- NMDC Capture of Alternate and Related Identifiers HOT 2
- `local/mongo_as_nmdc_database_rdf_safe.yaml` target in `berkeley-schema-fy24`'s `main` fails to run migration HOT 3
- restore `assets/TermsUpdated_organicmatterextraction/TermsUpdated_organicmatterextraction.tsv` in `berkeley-schema-fy24` HOT 1
- log when RDF data artifacts are generated
- still some slots we need to move from DataGeneration to NucleotideSequencing
- migrator for berkeley schema slot has_calibration
- (NEW) Add `reduced_profile` enum to `mass_spectrum_collection_mode`, update `profile` to `full_profile`
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