AGR Curation Schema v1.3.1

What's Changed

• SCRUM-2119 Require DQMs to submit LinkML schema version with ingest files by @markquintontulloch in #159

Full Changelog: v1.3.0...v1.3.1

AGR Curation Schema v1.3.0

What's Changed

• SCRUM-2000 Add date_last_loaded slot to BulkLoadFile by @markquintontulloch in #158
• Slot annotation by @sierra-moxon in #152
• Add children, parents, ancestors, and descendants to OntologyTerm by @chris-grove in #146

Note: Significant restructuring of the Allele class model using the SlotAnnotation approach. New OntologyTerm modeling to accommodate closure calculations (and storage).

Full Changelog: v1.2.4...v1.3.0

AGR Curation Schema v1.2.4

What's Changed

• SCRUM-1925 Synchronise with curation DB by @markquintontulloch in #156
• Correct range for condition_chemical by @markquintontulloch in #157

Full Changelog: v1.2.3...v1.2.4

AGR Curation Schema v1.2.3

What's Changed

• revert identifier:true removal from curie slot to fix submission tests by @sierra-moxon in #154
• Add-test-data-for-asserted-inferred-gene-allele-and-condition_free_text by @chris-grove in #155

Full Changelog: v1.2.2...v1.2.3

AGR Curation Schema v1.2.2

What's Changed

• Added curie to DiseaseAnnotation and test examples by @chris-grove in #145
• retire EntityStatement, use Note object and related_notes slot instead by @gildossantos in #141
• SCRUM-1855: represent a range of identifiers by @abecerra in #153

Full Changelog: v1.2.1...v1.2.2

v1.2.1

What's Changed

• biologicalEntitySet updated with draft WB fields by @MagdalenaZZ in #144
• SCRUM-1840 load ATP into persistent store by @cmpich in #149

New Contributors

• @MagdalenaZZ made their first contribution in #144

Full Changelog: v1.2.0...v1.2.1

AGR Curation Schema v1.2.0

What's Changed

• merging 'main' updates into xprn_update branch by @edwong57 in #84
• SCRUM-1142 tweaks by @gildossantos in #98
• update reference to conform to literature database by @dougli1sqrd in #97
• Changes to modelling of source and curated consequences by @markquintontulloch in #96
• SCRUM-1321 Replace disease annotation enums with VocabularyTerms by @markquintontulloch in #99
• Rename bulkload.yml to bulkload.yaml by @chris-grove in #92
• SCRUM-1329 model paper handle for experimental conditions by @cmpich in #100
• Update sgd_disease_test.json by @edwong57 in #103
• SCRUM-1246: Suggested changes for discussion by @gildossantos in #106
• fixing dependencies and regenerating artifacts by @sierra-moxon in #107
• minor tweaks by @gildossantos in #108
• Add permissible note types by @chris-grove in #104
• add variant descriptions from Jennifer Smith by @sierra-moxon in #101
• Variant and associated class updates by @markquintontulloch in #105
• variant_locations -> variant_genome_location, variant_polypeptide_location, variant_transcript_location by @sierra-moxon in #102
• adding sqlddlgen to makefile for development by @sierra-moxon in #111
• add aliases by @gildossantos in #109
• encode variant rule by @sierra-moxon in #113
• Add valid and invalid variant object tests by @sierra-moxon in #114
• Add MIT LICENSE file by @chris-grove in #116
• add test data for allelevariantassociation by @sierra-moxon in #115
• Scrum 1421 by @azurebrd in #110
• SCRUM-1246 - LinkML for MOD association table by @gildossantos in #112
• add rule for variant association by @sierra-moxon in #117
• add construct, sqtr from json-schema as a starting point for construct, sqtr classes by @sierra-moxon in #119
• Adding test data for AGM, SqTR, Allele by @sierra-moxon in #120
• Make auto-documentation work with new docgen instead of markdowngen by @sierra-moxon in #121
• Adding Xenopus anatomy and stage ontology term classes by @chris-grove in #122
• ignore python directory to reduce noise in build process by @sierra-moxon in #123
• SCRUM-1232 Add Xenopus ontology terms XBED, XSMO, XPO by @markquintontulloch in #124
• repo maintenance, swap out pipenv for poetry, streamline actions by @sierra-moxon in #125
• Make AuditedObject base class by @chris-grove in #126
• Update AuditedObject, update GenomicLocation by @chris-grove in #127
• SCRUM-1509 CurationReport model for BIRT reports by @markquintontulloch in #128
• add mermaid, clean up fixable warnings in the build by @sierra-moxon in #130
• SCRUM-1532 updating / adding / removing fields as appropriate to conf… by @azurebrd in #131
• SCRUM-1080 Add user_settings slot to LoggedInPerson by @markquintontulloch in #133
• Changes to gene descriptions by @chris-grove in #134
• Gene yaml by @gildossantos in #135
• Clean up AuditedObject mixin references by @chris-grove in #136
• Change 'modified_by' to 'updated_by' by @chris-grove in #140
• Gene set suggestions 2 by @sierra-moxon in #139
• Add asserted_gene and asserted_allele slots by @chris-grove in #142
• Xprn update by @sierra-moxon in #143

New Contributors

• @dougli1sqrd made their first contribution in #97
• @cmpich made their first contribution in #100
• @azurebrd made their first contribution in #110

Full Changelog: v1.1.2...v1.2.0

v1.1.2

What's Changed

• Add rules examples by @sierra-moxon in #89
• Allele and allele association updates by @markquintontulloch in #87
• Update sgd_disease_test.json by @edwong57 in #91
• Allele association updates by @markquintontulloch in #90
• Remove 'inferred_gene' entry by @chris-grove in #93
• Add note_type permissible values to Note by @chris-grove in #94
• regenerate artifacts by @sierra-moxon in #95

Full Changelog: v1.1.1...v1.1.2

1.1.1

What's Changed

• documentation clean up by @sierra-moxon in #75
• Add WB disease annotation test file and Person class update by @markquintontulloch in #77
• modify mkdocs and github action to fix documenation, clean out old documentation by @sierra-moxon in #78
• Fix docs by @sierra-moxon in #79
• docs by @sierra-moxon in #80
• Fb disease test by @gildossantos in #81
• Add "related_notes" slot to "Antibody" class and delete the "AntibodyStatement" class. by @gildossantos in #82
• SCRUM-1185 person, data provider, experimental conditions updates by @chris-grove in #83
• Added Bulk Load File History by @oblodgett in #86
• Variant updates by @markquintontulloch in #85
• Minor disease annotation updates by @markquintontulloch in #88

Full Changelog: v1.1.0...v1.1.1

1.1.0

What's Changed

• SCRUM-963 Add letter code abbreviations of ECO terms by @markquintontulloch in #51
• SCRUM-879 vocabulary changes by @markquintontulloch in #54
• Fix typo by @markquintontulloch in #55
• SCRUM-1004 Add gene_type slot linking Gene to SOTerm by @markquintontulloch in #57
• SCRUM-1037 Replace curie with unique_id on DiseaseAnnotation by @markquintontulloch in #58
• Remove identifier flag by @markquintontulloch in #59
• SCRUM-1037 More curie to unique_id changes by @markquintontulloch in #60
• Proposed solution to conditionChemical issue by @markquintontulloch in #65
• SCRUM-1068 Instantiate NCBITaxonTerm and update references by @markquintontulloch in #63
• Added bulkload model by @oblodgett in #64
• SCRUM-1079: adding slots to Person by @abecerra in #66
• SCRUM-1079: fixes for middle_name by @abecerra in #67
• Grove Person changes 1-29-2022 by @chris-grove in #69
• Validate json schema + sets by @sierra-moxon in #62
• add more test files by @sierra-moxon in #70
• add gene tests by @sierra-moxon in #71
• change 'reference' slot to 'single_reference' by @chris-grove in #68
• SCRUM-1185: Add "Note" object. by @gildossantos in #74
• Introduces higher level "Expression Experiment" that groups "ExpressionAnnotation" objects by @gildossantos @edwong57 @sierra-moxon in #52
• Remove 'paper_handle' from ExperimentalCondition by @chris-grove @sierra-moxon in #72

New Contributors

• @abecerra made their first contribution in #66

Full Changelog: v1.0.0...v1.1.0