Semantic Mapping Reasoner and Assembler (SeMRA)

What's Changed

Note: this release includes a few changes that are backwards incompatible with the versions of the raw mappings database that are included in the SeMRA pre-print. New data files will be uploaded soon.

• Improvements to full mapping database build by @cthoyt in https://github.com/biopragmatics/semra/pull/22
• Update cruft by @cthoyt in https://github.com/biopragmatics/semra/pull/26
• Add workflow for updating literal mappings by @cthoyt in https://github.com/biopragmatics/semra/pull/24
• Replace Creator model with named reference by @cthoyt in https://github.com/biopragmatics/semra/pull/23
• Fix deprecated pydantic components by @cthoyt in https://github.com/biopragmatics/semra/pull/28
• Rewrite PyOBO mapping import by @cthoyt in https://github.com/biopragmatics/semra/pull/27
• Update Intact urls by @kkaris in https://github.com/biopragmatics/semra/pull/30
• Incorporate PyOBO xref sources directly by @cthoyt in https://github.com/biopragmatics/semra/pull/31
• Update storage of subsets by @cthoyt in https://github.com/biopragmatics/semra/pull/32
• Improve typing with overloads by @cthoyt in https://github.com/biopragmatics/semra/pull/35
• Improve landscape CLI by @cthoyt in https://github.com/biopragmatics/semra/pull/34
• Update cruft by @cthoyt in https://github.com/biopragmatics/semra/pull/37
• Refactor I/O functions by @cthoyt in https://github.com/biopragmatics/semra/pull/38
• Add --build-docker flag to landscape by @cthoyt in https://github.com/biopragmatics/semra/pull/39
• Standardize references in SeMRA sources by @cthoyt in https://github.com/biopragmatics/semra/pull/36
• Refactor and landscape re-analysis by @cthoyt in https://github.com/biopragmatics/semra/pull/40
• Update type checking for class-resolver by @cthoyt in https://github.com/biopragmatics/semra/pull/47
• Add pandas-based prioritization function by @cthoyt in https://github.com/biopragmatics/semra/pull/48
• Refactor raw database build by @cthoyt in https://github.com/biopragmatics/semra/pull/44
• Add strict type checking by @cthoyt in https://github.com/biopragmatics/semra/pull/50
• Improve CURIE generation for evidences by @cthoyt in https://github.com/biopragmatics/semra/pull/49
• Reorganize I/O functions by @cthoyt in https://github.com/biopragmatics/semra/pull/51
• Improve Neo4j output by @cthoyt in https://github.com/biopragmatics/semra/pull/45
• Hide landscape functions by @cthoyt in https://github.com/biopragmatics/semra/pull/53
• Add JSONL I/O by @cthoyt in https://github.com/biopragmatics/semra/pull/54
• Refactor inference and graph code by @cthoyt in https://github.com/biopragmatics/semra/pull/56
• Add testing for graph I/O by @cthoyt in https://github.com/biopragmatics/semra/pull/57
• Refactor mutation inference implementation and improve docs by @cthoyt in https://github.com/biopragmatics/semra/pull/58
• Additional documentation improvements by @cthoyt in https://github.com/biopragmatics/semra/pull/59
• Fully stream database build by @cthoyt in https://github.com/biopragmatics/semra/pull/62
• Remove UUIDs from evidences by @cthoyt in https://github.com/biopragmatics/semra/pull/63
• Update mapping set field documentation by @cthoyt in https://github.com/biopragmatics/semra/pull/64
• Update SSSOM implementation and example in README by @cthoyt in https://github.com/biopragmatics/semra/pull/61
• Add PURL to mapping set to align with SSSOM's mapping_set_id by @cthoyt in https://github.com/biopragmatics/semra/pull/65
• Rename fields in mapping by @cthoyt in https://github.com/biopragmatics/semra/pull/66
• Reorganize triple data models by @cthoyt in https://github.com/biopragmatics/semra/pull/68
• Reuse triples objects from curies by @cthoyt in https://github.com/biopragmatics/semra/pull/69

Full Changelog: https://github.com/biopragmatics/semra/compare/v0.0.9...v0.1.0