https://github.com/biopragmatics/obo-db-ingest -

• Add synonym files based on the biosynonyms format
• Add manifest for each resource, which also includes prefix maps
• Updates to OBO exports
• fully standardize prefix maps based on Bioregistry, preferring RDF URI prefixes when available

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest -

New Resources

• PharmGKB Disease
• PharmGKB Variant
• PharmGKB Drug
• PharmGKB Pathway
• PharmGKB Gene

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest - 2025-01-16

New Resources

• ChEMBL Compound
• ChEMBL Target
• NIH RePORTER

Full Changelog: https://github.com/biopragmatics/obo-db-ingest/compare/2025-01-14...2025-01-16

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest - 2025-01-14

Full Changelog: https://github.com/biopragmatics/obo-db-ingest/compare/2025-01-13...2025-01-14

New Resources

• Pathway Interaction Database (pid.pathway)
• NCBI Genetic Code (ncbi.gc)
• CIVIC Gene (civic.gid)
• Integrated Taxonomic Information System (itis)
• Cancer Dependency Map Cell Lines (depmap)
• ClinicalTrials.gov (clinicaltrials)

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest - 2025-01-13

Full Changelog: https://github.com/biopragmatics/obo-db-ingest/compare/2025-01-12...2025-01-13

New Resources

• OMIM Phenotypic Series (omim.ps)
• UMLS Semantic Type Ontology (sty)
• SIGNOR Complexes, Families, Phenotypes, and Experiments (signor)

Updates

• Add OFN outputs
• Improved metadata and idspace: definitions

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest -

New Resources

• NLM Publisher
• ICD10
• GeoNames Features
• ROR

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest - January 9, 2025 Release

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest - November 5th, 2024 Release

This is another rebuild, which includes all sorts of fixes for data going missing and getting messier. It also includes several improvements based on PyOBO's more aggressive identifier validation.

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/obo-db-ingest - March 14th, 2024 Build

- Python
Published by cthoyt about 2 years ago