v11.0.0rc1

What's Changed

• Make Class:MaterialProcessing, remove Class:BiosampleProcessing by @anastasiyaprymolenna in #1
• Change Class:OmicsProcessing to Class:DataGeneration by @turbomam in #2
• Updated type codes for MaterialProcessing and examples by @anastasiyaprymolenna in #6
• Added slot:analyte_category and Enum: AnalyteCategoryEnum by @turbomam in #4
• Make subclasses for DataGeneration by @aclum in #3
• Create Class ProtocolExecution by @anastasiyaprymolenna in #11
• deprecate Activity by @brynnz22 in #14
• add slots to LibraryPreparation by @mslarae13 in #8
• add slots to MaterialProcessing classes that were on omics processing by @mslarae13 in #7
• make WorkflowExecutionActivity a PlannedProcess by @brynnz22 in #18
• Add WorkflowChain class and valid data example by @mbthornton-lbl in #9
• remove phenol/chloroform extraction from ExtractionTargetEnum by @mslarae13 in #13
• Add slots and enumerations for MassSpectrometry, add FluidHandling and DirectInfusion classes needed differentiate mass spectrometry categories by @aclum in #12
• Update ChromatographicSeparationProcess by @anastasiyaprymolenna in #25
• remove Activity from class names by @brynnz22 in #24
• Replace relevant_protocols with protocol_link by @JamesTessmer in #21
• Created Class ChemicalConversionProcess by @JamesTessmer in #5
• refactor execution resource to enum by @mbthornton-lbl in #23
• Refactored enums and uses of to lower_snake by @JamesTessmer in #27
• Remove was_informed_by from WorkflowExecution and update data examples by @mbthornton-lbl in #30
• Update model to remove used slot by @mbthornton-lbl in #31
• Update has_output slot description by @mbthornton-lbl in #34
• create class Instrument by @aclum in #19
• Refactor has_calibration from WorkflowExecution by @corilo in #29
• remove slots from Biosample by @mslarae13 in #32
• updates to class Instrument by @aclum in #38
• Update DataObject model and example data by @mbthornton-lbl in #39
• mixs.yaml never autoregenrated by @turbomam in #41
• Delete contents of folders whose contents we want Git to ignore by @eecavanna in #35
• committing regenerateds by @turbomam in #43
• Add mass spectrum instrument models and vendors by @corilo in #44
• Add rules to ChromatographicSeparationProcess so has_calibration is required if chromatographic_category is gc by @brynnz22 in #46
• Created DissolvingProcess class in nmdc.yaml by @JamesTessmer in #40
• Merged 1564-make-classEnzyme into 1564-make-ClassEnzyme by @JamesTessmer in #48
• Updated ChemicalConversionProcess to accommodate Acidification by @JamesTessmer in #45
• Allowed enzymes to be used with ChemicalConversionProcess by @anastasiyaprymolenna in #37
• all class definitions require the nmdc:type slot and a class_uri by @turbomam in #10
• almost all examples have types and single faults by @turbomam in #49
• nmdc-schema misc. issue 1590 by @turbomam in #50
• Assign feature_category slot to FunctionalAnnotation and GenomeFeature classes by @turbomam in #51
• Test for reiterated inherited slots (and clean up related code) by @turbomam in #52
• Update WorkflowExecution model to remove multivalued: false slot_usage on part_of by @mbthornton-lbl in #54
• remove slots from Biosample & DataGeneration & update examples by @mslarae13 in #42
• Remove slots from Biosample if they are not about biosamples, and examples by @turbomam in #55
• Add external analysis project identifiers slots to WorkflowChain by @mbthornton-lbl in #47
• Restore omprc typecode for class DataGeneration by @aclum in #61
• Add description to execution_resource by @mbthornton-lbl in #63
• DataGeneration child/parent relationship by @brynnz22 in #53
• fix DataGeneration example file id error by @brynnz22 in #67
• add permissible values to InstrumentVendorEnum and InstrumentModelEnum for sequencing applications by @aclum in #70
• Resolve merge conflicts then merge upstream main into berkeley main by @eecavanna in #72
• add img_identifiers to WorkflowExecution subclasses by @aclum in #71
• Make class DataGeneration abstract by @aclum in #74
• Stage NMDC schema as local branch in preparation for merge by @turbomam in #75
• 1736 add associated_studies to biosample by @brynnz22 in #79
• Fix example validation issues before merging nmdc-schema/main into berkeley-schema-fy24/main by @turbomam in #73
• PR 53 and 79 migration for moving part_of studies to associated_studies` by @brynnz22 in #78
• remove AnalyticalSample class from schema by @brynnz22 in #77
• restore tsv by @brynnz22 in #82
• fixes to migrator by @brynnz22 in #85
• Pr10 type slot required migration by @brynnz22 in #66
• PR4 migration move omics_type to analyte_category and update values by @brynnz22 in #62
• add migrator for moving relevant_protocols to protocol_link PR21 by @brynnz22 in #76
• Add migration files for PR23 - execution_resource values update by @brynnz22 in #59
• Use CHMO mapping instead of AFO mapping by @anastasiyaprymolenna in #87
• DO NOT MERGE: Resolve merge conflicts by @eecavanna in #88
• Merge in latest nmdc-schema (v10.0.0+) by @turbomam in #89
• Added invalid example file to show compound appropriate/inappropriate values by @JamesTessmer in #68
• Update MassSpectrometry slots and enums by @brynnz22 in #90
• collection name change migrator and test all currently written migrators by @brynnz22 in #91
• Fix was_informed_by range in global definition vs. slot usage definition by @brynnz22 in #101
• updating saved output in in-repo-anaggregateds-report.ipynb so that it doesn't mention AnalyticalSample by @turbomam in #83
• Simplify modeling of chemical_conversion_process and update examples by @turbomam in #100
• Update Migrator for PR10 for other classes with inlined slots by @brynnz22 in #103
• 1580 add protein enzyme definitions and mappings by @brynnz22 in #102
• Add chemical_entity_set slot to schema with example by @turbomam in #105
• Add migrator for DataGeneration subclasses by @brynnz22 in #92
• add has_calibration back as a slot for WorkflowExecution subclasses by @brynnz22 in #107
• add permissible values for non-specific novaseq and hiseq to insturment enum by @brynnz22 in #108
• schema pattern linting by @turbomam in #111
• Use of any_of construct on slot ranges was not reflecting on class doc pages by @sujaypatil96 in #109
• build logs microbiomedata#1877 by @turbomam in #112
• experimental diagram image generation by @turbomam in #113
• remove inchi etc from Substance by @turbomam in #106
• Removal of Reaction class and the slots that it "owned" by @turbomam in #64
• 1882 simplify usage of Solution by DissolvingProcess by @turbomam in #114
• 1885 determine schema imports graph by @turbomam in #115
• MobilePhaseSegment instead of Solution for chromatography by @turbomam in #116
• fixed set arithmetic by @turbomam in #117
• Ensure that the schema modules compile independently by @turbomam in #118
• removed redundant range slot usages by @turbomam in #120
• remove-biosample-usage-gold-bs-ids-range by @turbomam in #121
• 2024-04-05-backmerge by @turbomam in #123
• Attempting an upstream merger by @sierra-moxon in #125
• set has_numeric_value.range to decimal, remove QuantityValue.slot_usage.has_numeric_value.range by @turbomam in #122
• Add additional values to StationaryPhaseEnum by @kheal in #128
• Update MetaboliteQuantification to MetaboliteIdentification by @brynnz22 in #129
• Move slots from DataGeneration to NucleotideSequencing by @bmeluch in #104
• Bump version of bioregistry by @kheal in #134
• Update SubstanceRoleEnum by @anastasiyaprymolenna in #135
• Add sampled_portion slot by @anastasiyaprymolenna in #132
• add activity_set to collection name change migrator by @brynnz22 in #138
• Add StorageProcess by @brynnz22 in #126
• add minimal InformationObject class by @turbomam in #142
• Edit slots and usages to accommodate multiple detection configurations for single MassSpectrometry instance by @kheal in #141
• Add Calibration class and associated slots and enums by @kheal in #133
• Add permissible values to FileTypeEnum and DataCategoryEnum to accomodate workflow configuration DataObjects by @brynnz22 in #140

New Contributors

• @anastasiyaprymolenna made their first contribution in #1
• @turbomam made their first contribution in #2
• @aclum made their first contribution in #3
• @brynnz22 made their first contribution in #14
• @mslarae13 made their first contribution in #8
• @mbthornton-lbl made their first contribution in #9
• @JamesTessmer made their first contribution in #21
• @corilo made their first contribution in #29
• @sujaypatil96 made their first contribution in #109
• @sierra-moxon made their first contribution in #125
• @kheal made their first contribution in #128
• @bmeluch made their first contribution in #104

Full Changelog: https://github.com/microbiomedata/berkeley-schema-fy24/commits/v11.0.0rc1