v0.6.0

What's Changed

• tutorial 2023 by @cmungall in #531
• Definitions should be enclosed in double quotes while updating via KGCL by @hrshdhgd in #520
• New feature: normalize CURIEs in association files at parse time by @cmungall in #534
• Update to latest class-resolver version by @pkalita-lbl in #536
• Adding more attributes to Synonymizer by @hrshdhgd in #537
• Add minimal AmiGOImplementation. Adding biolink source properties by @cmungall in #538
• RustSimImplementation by @hrshdhgd in #488
• Fixes for RustsimImplementation not completing search-based similarities by @caufieldjh in #540
• Added eutils/pubmed by @cmungall in #542
• Typo correction by @hrshdhgd in #543
• Fixing documentation issues. by @cmungall in #546
• Additional documentation and tests by @cmungall in #550
• Adding redundancy flags to enrichment model by @cmungall in #551
• Making rustsim a non-extra dependency. 552 by @cmungall in #553
• Windows wheel reference for PyWin32 (python version = 3.10) was absent in poetry.lock by @hrshdhgd in #555
• adding args to diff-associations by @cmungall in #547
• Adding co-associations (matrix) by @cmungall in #557
• docs and assoc diffs + requests cache by @cmungall in #560
• Leave keys unsorted when exporting yaml by @hrshdhgd in #559
• Slight addition to handle KGCL RemoveTextDefinition by @hrshdhgd in #558
• Replaced simple_mappings_by_curie to call sssom_mappings by @hrshdhgd in #563
• Adding property_type node to obograph schema. by @cmungall in #561
• demo notebook for g2d by @cmungall in #565
• Upgrade to KGCL 0.5.x series by @cmungall in #562
• rustsim => semsimian by @hrshdhgd in #567
• First pass at wrapper to Monarch API (alpha). by @cmungall in #568
• refactoring semsim implementation by @cmungall in #571
• Add benchmarking for semsimian by @caufieldjh in #570
• TextAnnotator: Reuse lexical index cache between calls. #573 by @cmungall in #574
• SqlImpl: rebuild the relationship index after a KGCL edge change is applied by @cmungall in #576
• Update to use semsimian 0.1.14 with better optimized semsim stuff by @justaddcoffee in #575
• Fix slug in benchmark target in Makefile (rustsim: -> semsimian) by @justaddcoffee in #577
• graph-traversal improvements. by @cmungall in #583
• Ensure kgx adapter works with sqlalchemy2 fixes #580 by @cmungall in #581
• modify lexmatch to utilize xrefs in both directions #585 by @cmungall in #586
• Update some dependencies to resolve conflicts by @glass-ships in #589
• minor semsim optimizations by @cmungall in #582
• Use prod api url for monarch_implementation by @kevinschaper in #591
• Add benchmark for Phenio HP vs MP by @caufieldjh in #578
• Implement all_by_all_pairwise_similarity in semsimian implementation by @justaddcoffee in #579
• Allow export of dot files and cx files from viz by @cmungall in #594
• Workaround for ontoportal prefix issue 592 by @cmungall in #593
• Applying thresholds to avoid expensive object production. by @cmungall in #595
• Semsimian handles thresholds for resnik and jaccard by @hrshdhgd in #597
• Make ensure_strict_prefixes default to False in lexmatch by @hrshdhgd in #601
• Improve descriptor processing for Gilda implementation by @cthoyt in #603
• Enable NER with Gilda by @cthoyt in #607
• Tools to analyze logical definitions by @cmungall in #610
• Fix broken link on README.md by @lubianat in #599
• Projecting anonymous type expressions to graph. Fixes #623 by @cmungall in #624
• Adding arbitrary properties to fill-table. Fixes #625 by @cmungall in #626
• Pinning pydantic to be <2 until we are sure the full stack works. See #628 Bumping semsimian to 0.1.20 by @cmungall in #630
• Making pydantic v1 vs v2 neutral by @cmungall in #632
• Adding more notebook examples of associations by @cmungall in #636
• Create Semsimian object with concerned predicates only. by @hrshdhgd in #631
• initial notebook example for omop by @cmungall in #640
• Output for semsimian's termset_pairwise_similarity formatted correctly by @hrshdhgd in #643
• New notebook that runs examples showcased in Mondo paper by @hrshdhgd in #584
• Allow diffs to be filtered by change type (kgcl) by @cmungall in #647
• First pass at interface for association search by @cmungall in #646
• Adding utilities for working with disjoint classes. by @cmungall in #650
• examples for working with disjoints by @cmungall in #651
• Adding validate-mappings command. by @cmungall in #652
• Adding llm as an extra, adding llm implementation for annotation by @cmungall in #658
• Additional documentation by @cmungall in #655
• Adding ability to retrieve axiom annotations on relationships (axiom annotations) by @cmungall in #656
• minor obographviz config change: new color disambiguating chebi by @cmungall in #657
• Fix for #662 - Update address for node normalizer endpoint by @caufieldjh in #663
• Use passthrough from curies v0.6.6 by @cthoyt in #669
• Added documentation on semsin, and additional command for handling IC by @cmungall in #673
• ChefBuildError fix by @hrshdhgd in #678
• Implemented entities_metadata_statements() for SQLImplementation() by @hrshdhgd in #679
• Include title and definition in vskit expand by @nicholsn in #677
• fixing image location by @cmungall in #667
• OAK dependency tuning by @hrshdhgd in #686
• Improve usage of SSSOM-py by @cthoyt in #666
• Fix broken md hyperlink by @yarikoptic in #672
• Update README.md by @azankl in #668
• VSKit Permissible Value Label Fix by @plbremer in #689
• VSKit - description newline replacement by @plbremer in #691
• Enhanced implementations for remote endpoints. by @cmungall in #682
• Expanded enrichment notebook by @cmungall in #692
• Update Validator Interface link in howto guide by @anitacaron in #694
• Add codespell support: config, action (to detect new) + get some typos fixed by @yarikoptic in #671
• Implementing search using translator endpoint. by @cmungall in #695
• d3viz writer by @cmungall in #700
• Adding a validate_mappings implementations for LLMImplementation by @cmungall in #705
• Add link to llm how-to by @cmungall in #709
• value_set_names is None rather than () by @hrshdhgd in #707
• llm exception handling by @cmungall in #711
• Autoadding current year to footer, fixes #710 by @cmungall in #712
• Adding pantherdb impl by @cmungall in #713
• Extending amigo and llm implementations by @cmungall in #714
• Create release notes markdown output for diff command by @hrshdhgd in #605
• OBO compliance suite (redux of #693) by @cmungall in #715
• Made semsimian an optional dependency by @hrshdhgd in #704
• Remove flake8 and replace it by ruff by @hrshdhgd in #716
• Update semsimian dependency version by @hrshdhgd in #717
• More efficient simple obo diffs by @cmungall in #719
• Handle RemoveTextDefinition by @hrshdhgd in #720
• Added mock tests by @hrshdhgd in #721
• Partial robot template implementation. by @cmungall in #722
• Adding additional statistics to coassociations by @cmungall in #726
• EdgeCreation object has about_edge == None by @hrshdhgd in #729
• synonymizer refactor2 by @cmungall in #728

New Contributors

• @kevinschaper made their first contribution in #591
• @lubianat made their first contribution in #599
• @nicholsn made their first contribution in #677
• @yarikoptic made their first contribution in #672
• @azankl made their first contribution in #668
• @plbremer made their first contribution in #689
• @anitacaron made their first contribution in #694

Full Changelog: v0.5.0...v0.6.0