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

AGR Curation Schema v1.0.0

What's Changed

• Antibody by @gildossantos in #8
• Antibody model by @gildossantos in #9
• add construct relation, ontology term by @sierra-moxon in #10
• First submission of geneInteraction.yaml to agr-curation-schema by @chris-grove in #11
• First submission of phentoypeAndDiseaseAnnotation.yaml to agr_curatio… by @chris-grove in #12
• Small fixes to orthology, gene descriptions, ontology term, etc. by @sierra-moxon in #14
• fix range on orthology by @sierra-moxon in #15
• ExpressionAnnotation, Image, miscellaneous tweaks by @gildossantos in #16
• Allele variant updates by @markquintontulloch in #18
• Removed fields that exist in the is_a class by @oblodgett in #24
• Updates to phenotypeAndDiseaseAnnotation.yaml by @chris-grove in #25
• Update phenotypeAndDiseaseAnnotation.yaml by @chris-grove in #27
• Added prefix stanza to the antibody schema yaml by @kevinschaper in #29
• SCRUM-248 Update to required fields by @markquintontulloch in #32
• Made "ECOTerm" range for "evidence_code" slot by @chris-grove in #33
• Disease subclasses by @sierra-moxon in #30
• Added ExperimentalConditionOntologyTerm class by @oblodgett in #34
• Gen java additions by @sierra-moxon in #36
• SCRUM-569 disease annotation updates by @markquintontulloch in #37
• Initial commit of schema for WB molecules by @markquintontulloch in #39
• Condition relation and supporting changes by @chris-grove in #40
• Update ExperimentalCondition slot_usage ranges by @chris-grove in #41
• Add 'AuditedObject' mixin to Molecule class by @chris-grove in #42
• added controlled vocabulary yaml by @sbello in #43
• Updated slot descriptions, added new slots and classes for phenotype … by @chris-grove in #44
• Initial use of inlining to create nested JSON schema by @markquintontulloch in #45
• Clean up to disease and phenotype annotation yaml by @chris-grove in #47
• PaperHandle class, paper_handle slot, other edits by @chris-grove in #48
• Made MA ontology term a type of anatomical term by @chris-grove in #49

New Contributors

• @sierra-moxon made their first contribution in #1
• @hsolbrig made their first contribution in #2
• @gildossantos made their first contribution in #8
• @chris-grove made their first contribution in #11
• @markquintontulloch made their first contribution in #18
• @oblodgett made their first contribution in #23
• @kevinschaper made their first contribution in #29
• @sbello made their first contribution in #43

Full Changelog: https://github.com/alliance-genome/agr_curation_schema/commits/v1.0.0