diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
index 673f39311..aa699123a 100644
--- a/RELEASE-NOTES.md
+++ b/RELEASE-NOTES.md
@@ -2,6 +2,41 @@
  
 https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
 
+## v0.35.0
+* New features
+   * Load FBcv into the persistent store (SCRUM-2190)
+   * Implement Gene Type field/column for Genes data table (SCRUM-3983)
+   * Turn off auxiliary clean up for associated entities (e.g. clean up of disease annotations based on a gene load) - public site Indexer work	(SCRUM-4150)
+   * SQTR Gene Associations import into Persistent store (SCRUM-4185, SCRUM-4187, SCRUM-4188)
+   * HTPdataset loaded into persistent store (SCRUM-4192,SCRUM-4303, SCRUM-4341)
+   * Make obsolete disease annotations hidden by default for all MOD default settings	(SCRUM-4277)
+   * HTPdataset ZFIN Fms files having wrong naming of property	(SCRUM-4328)
+   * Clean up erroneous DOTerms (SCRUM-4337)
+   * Importing expression annotations into the persistent store - Load ExpressionPattern, TemporalContext, and AnatomicalSite (SCRUM-3952)
+   * Implement programmatic, regular purging of exception message history for all exceptions older than 2 weeks (SCRUM-4377)
+   * HTPdatasetSample import P1 - Creating entities and migration file (SCRUM-4426)
+   * Reenable downloading of all exception messages for a given data load (SCRUM-4452)
+   * P1: Expression Atlas Import: Load accession data files from Ensembl, etc... (SCRUM-4118)
+   * GFF Loading (Load assembly, transcripts, exons, and CDSs without positional information; Load positional information for Transcripts, Exons, and CDSs; Load associations between Genes, Transcripts, Exons, and CDSs) (SCRUM-4174, SCRUM-4175, SCRUM-4176)
+   * Associate Expression Annotations with Go Slim Terms	(SCRUM-4300)
+   * Implement caching of references for DQM loads	(SCRUM-4336)
+   * Accommodate BIOGRID-ORCS loader data type: to establish 3rd part link out to BIOGRID from gene page phenotypes section P1 - create DTO, load via migration, and loading infrastructure (SCRUM-4440)
+   * Investigate: Accommodate BIOGRID-ORCS loader data type: to establish 3rd part link out to BIOGRID from gene page phenotypes section (SCRUM-4471)
+   * Load VariantGenomicLocationAssociation from FMS submissions and generate HGVSg identifiers	(SCRUM-4499)
+   * Test effect of removing AuditedObject fields on disease annotation indexing speed	(SCRUM-4520)
+   * Java model changes for disease genetic modifier changes to split based on modifier type	(SCRUM-4523)
+   * Curation UI changes to Disease Annotations table to split out Genetic Modifiers into 3 separate fields for each of Gene, Allele and AGM modifier types	(SCRUM-4524)
+* Fixes and maintenance
+   * Edit cancelation button getting squeezed out of frame on alpha data tables (SCRUM-4236)
+   * Constructs data table on alpha-curation throwing 500 error and not loading	(SCRUM-4259)
+   * Fix SQTR Gene Association Integration Tests (SCRUM-4299)
+   * Curl timing out when uploading to persistent store (SCRUM-3683)
+   * Annotations and interactions not indexed on alpha-curation (despite attempts to reindex) (SCRUM-4254)
+   * Loads not showing in the Data Loads page "Data Processing Info Table" widget (SCRUM-4428)
+   * New "Running Time" showing negative time counting down	(SCRUM-4429)
+   * Molecule table columns expand automatically when sorting	(SCRUM-4531)
+
+
 ## v0.34.0
 * New features
   * Paralogy annotations loaded into persistent store (SCRUM-4086, SCRUM-4088, SCRUM-4089, SCRUM-4090)
diff --git a/src/main/cliapp/src/components/EntityCountsComponent.js b/src/main/cliapp/src/components/EntityCountsComponent.js
index 7cd9ad915..857410235 100644
--- a/src/main/cliapp/src/components/EntityCountsComponent.js
+++ b/src/main/cliapp/src/components/EntityCountsComponent.js
@@ -28,6 +28,8 @@ export const EntityCountsComponent = () => {
 					_tableData[type].push({
 						name: CLASSES[key].name,
 						link: CLASSES[key].link,
+						type: CLASSES[key].type,
+						isIndexed: CLASSES[key].isIndexed,
 						dbCount: res.entity[key]['dbCount'],
 						esCount: res.entity[key]['esCount'],
 					});
@@ -42,13 +44,15 @@ export const EntityCountsComponent = () => {
 	}, []);
 
 	const nameHyperlinkTemplate = (rowData) => {
+		if (!rowData.link) {
+			return rowData.name;
+		}
 		return <a href={rowData.link}>{rowData.name}</a>;
 	};
 
-	const ROW_HIGHLIGHT_IGNORE = ['Disease Annotations', 'Literature References', 'Bulk Loads / Failed Loads'];
-
 	const getRowClass = (rowData) => {
-		if (ROW_HIGHLIGHT_IGNORE.includes(rowData.name)) return;
+		console.log(rowData);
+		if (!rowData.isIndexed) return;
 
 		if (rowData?.dbCount !== rowData.esCount) {
 			return 'bg-gray-500 text-white';
@@ -58,7 +62,7 @@ export const EntityCountsComponent = () => {
 	return (
 		<>
 			<div className="grid nested dashboard">
-				<div className="col-4">
+				<div className="col-3">
 					<DataTable
 						header="Entities"
 						value={tableData.entity}
@@ -79,7 +83,7 @@ export const EntityCountsComponent = () => {
 						/>
 					</DataTable>
 				</div>
-				<div className="col-4">
+				<div className="col-3">
 					<DataTable
 						header="Ontologies"
 						value={tableData.ontology}
@@ -100,7 +104,23 @@ export const EntityCountsComponent = () => {
 						/>
 					</DataTable>
 				</div>
-				<div className="col-4">
+				<div className="col-3">
+					<DataTable
+						header="Associations"
+						value={tableData.association}
+						sortField="name"
+						sortOrder={1}
+						rowClassName={(rowData) => getRowClass(rowData)}
+					>
+						<Column field="name" header="Association Type" body={nameHyperlinkTemplate} />
+						<Column
+							field="dbCount"
+							header="Database Association Count"
+							body={(rowData) => <NumberTemplate number={rowData.dbCount} />}
+						/>
+					</DataTable>
+				</div>
+				<div className="col-3">
 					<DataTable
 						header="System"
 						value={tableData.system}
diff --git a/src/main/cliapp/src/components/Templates/dialog/ListDialogTemplate.js b/src/main/cliapp/src/components/Templates/dialog/ListDialogTemplate.js
index 13da123e8..3dd8c92ad 100644
--- a/src/main/cliapp/src/components/Templates/dialog/ListDialogTemplate.js
+++ b/src/main/cliapp/src/components/Templates/dialog/ListDialogTemplate.js
@@ -9,7 +9,7 @@ export const ListDialogTemplate = ({ entities, handleOpen, getTextField, underli
 
 	const listTemplate = (item) => (
 		<div
-			className={`overflow-hidden text-overflow-ellipsis ${underline ? 'underline' : ''}`}
+			className={`overflow-hidden text-left text-overflow-ellipsis ${underline ? 'underline' : ''}`}
 			dangerouslySetInnerHTML={{ __html: item }}
 		/>
 	);
diff --git a/src/main/cliapp/src/constants/Classes.js b/src/main/cliapp/src/constants/Classes.js
index 278e71e7e..0ec2de27d 100644
--- a/src/main/cliapp/src/constants/Classes.js
+++ b/src/main/cliapp/src/constants/Classes.js
@@ -1,73 +1,278 @@
 export const CLASSES = Object.freeze({
-	Gene: { name: 'Genes', link: '/#/genes', type: 'entity' },
-	Allele: { name: 'Alleles', link: '/#/alleles', type: 'entity' },
-	AffectedGenomicModel: { name: 'Affected Genomic Models', link: '/#/agms', type: 'entity' },
-	Variant: { name: 'Variants', link: '/#/variants', type: 'entity' },
-	DiseaseAnnotation: { name: 'Disease Annotations', link: '/#/diseaseAnnotations', type: 'entity' },
-	AGMDiseaseAnnotation: { name: 'AGM Disease Annotations', link: '/#/diseaseAnnotations', type: 'entity' },
-	AlleleDiseaseAnnotation: { name: 'Allele Disease Annotations', link: '/#/diseaseAnnotations', type: 'entity' },
-	GeneDiseaseAnnotation: { name: 'Gene Disease Annotations', link: '/#/diseaseAnnotations', type: 'entity' },
-	PhenotypeAnnotation: { name: 'Phenotype Annotations', link: '/#/phenotypeAnnotations', type: 'entity' },
-	AGMPhenotypeAnnotation: { name: 'AGM Phenotype Annotations', link: '/#/phenotypeAnnotations', type: 'entity' },
-	AllelePhenotypeAnnotation: { name: 'Allele Phenotype Annotations', link: '/#/phenotypeAnnotations', type: 'entity' },
-	GeneGeneticInteraction: { name: 'Gene Genetic Interactions', link: '/#/geneGeneticInteractions', type: 'entity' },
+	Gene: { name: 'Genes', link: '/#/genes', type: 'entity', hasTable: true, isIndexed: true },
+	Allele: { name: 'Alleles', link: '/#/alleles', type: 'entity', hasTable: true, isIndexed: true },
+	AffectedGenomicModel: {
+		name: 'Affected Genomic Models',
+		link: '/#/agms',
+		type: 'entity',
+		hasTable: true,
+		isIndexed: true,
+	},
+	Variant: { name: 'Variants', link: '/#/variants', type: 'entity', hasTable: true, isIndexed: true },
+	DiseaseAnnotation: {
+		name: 'Disease Annotations',
+		link: '/#/diseaseAnnotations',
+		type: 'entity',
+		hasTable: true,
+		isIndexed: false,
+	},
+	AGMDiseaseAnnotation: {
+		name: 'AGM Disease Annotations',
+		link: '/#/diseaseAnnotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	AlleleDiseaseAnnotation: {
+		name: 'Allele Disease Annotations',
+		link: '/#/diseaseAnnotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	GeneDiseaseAnnotation: {
+		name: 'Gene Disease Annotations',
+		link: '/#/diseaseAnnotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	PhenotypeAnnotation: {
+		name: 'Phenotype Annotations',
+		link: '/#/phenotypeAnnotations',
+		type: 'entity',
+		hasTable: true,
+		isIndexed: false,
+	},
+	AGMPhenotypeAnnotation: {
+		name: 'AGM Phenotype Annotations',
+		link: '/#/phenotypeAnnotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	AllelePhenotypeAnnotation: {
+		name: 'Allele Phenotype Annotations',
+		link: '/#/phenotypeAnnotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	GenePhenotypeAnnotation: {
+		name: 'Gene Phenotype Annotations',
+		link: '/#/phenotypeAnnotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	GeneGeneticInteraction: {
+		name: 'Gene Genetic Interactions',
+		link: '/#/geneGeneticInteractions',
+		type: 'entity',
+		hasTable: true,
+		isIndexed: true,
+	},
 	GeneMolecularInteraction: {
 		name: 'Gene Molecular Interactions',
 		link: '/#/geneMolecularInteractions',
 		type: 'entity',
+		hasTable: true,
+		isIndexed: true,
+	},
+	ExperimentalCondition: {
+		name: 'Experimental Conditions',
+		link: '/#/experimentalConditions',
+		type: 'entity',
+		hasTable: true,
+		isIndexed: true,
 	},
-	GenePhenotypeAnnotation: { name: 'Gene Phenotype Annotations', link: '/#/phenotypeAnnotations', type: 'entity' },
-	ExperimentalCondition: { name: 'Experimental Conditions', link: '/#/experimentalConditions', type: 'entity' },
-	ConditionRelation: { name: 'Condition Relations', link: '/#/conditionRelations', type: 'entity' },
-	Construct: { name: 'Constructs', link: '/#/constructs', type: 'entity' },
-	Molecule: { name: 'Molecules', link: '/#/molecules', type: 'entity' },
-	Reference: { name: 'Literature References', link: '/#/references', type: 'entity' },
-	Specie: { name: 'Species', link: '/#/species', type: 'entity' },
+	ConditionRelation: {
+		name: 'Condition Relations',
+		link: '/#/conditionRelations',
+		type: 'entity',
+		hasTable: true,
+		isIndexed: true,
+	},
+	Construct: { name: 'Constructs', link: '/#/constructs', type: 'entity', hasTable: true, isIndexed: true },
+	Molecule: { name: 'Molecules', link: '/#/molecules', type: 'entity', hasTable: true, isIndexed: true },
+	Reference: { name: 'Literature References', link: '/#/references', type: 'entity', hasTable: true, isIndexed: false },
+	SequenceTargetingReagent: {
+		name: 'Sequence Targeting Reagents',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	Species: { name: 'Species', link: '/#/species', type: 'entity', hasTable: true, isIndexed: true },
+	Transcript: { name: 'Transcripts', type: 'entity', hasTable: false, isIndexed: false },
+	Exon: { name: 'Exons', type: 'entity', hasTable: false, isIndexed: false },
+	CodingSequence: {
+		name: 'Coding Sequences',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: false,
+	},
+	AssemblyComponent: {
+		name: 'Assembly Components',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: false,
+	},
+	GenomeAssembly: {
+		name: 'Genome Assemblies',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	GeneExpressionAnnotation: {
+		name: 'Gene Expression Annotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: true,
+	},
+	PredictedVariantConsequence: {
+		name: 'Predicted Variant Consequences',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: false,
+	},
+	HTPExpressionDatasetAnnotation: {
+		name: 'HTP Expression Dataset Annotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: false,
+	},
+	HTPExpressionDatasetSampleAnnotation: {
+		name: 'HTP Expression Dataset Sample Annotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: false,
+	},
+	GeneOntologyAnnotation: {
+		name: 'Gene Ontology Annotations',
+		type: 'entity',
+		hasTable: false,
+		isIndexed: false,
+	},
+	GeneToGeneParalogy: { name: 'Paralogy', type: 'entity', hasTable: false, isIndexed: false },
+	GeneToGeneOrthology: { name: 'Orthology', type: 'entity', hasTable: false, isIndexed: false },
+
+	DOTerm: { name: 'DO', link: '/#/ontology/do', type: 'ontology', hasTable: true, isIndexed: true },
+	CHEBITerm: { name: 'CHEBI', link: '/#/ontology/chebi', type: 'ontology', hasTable: true, isIndexed: true },
+	XSMOTerm: { name: 'XSMO', link: '/#/ontology/xsmo', type: 'ontology', hasTable: true, isIndexed: true },
+	ECOTerm: { name: 'ECO', link: '/#/ontology/eco', type: 'ontology', hasTable: true, isIndexed: true },
+	SOTerm: { name: 'SO', link: '/#/ontology/so', type: 'ontology', hasTable: true, isIndexed: true },
+	GOTerm: { name: 'GO', link: '/#/ontology/go', type: 'ontology', hasTable: true, isIndexed: true },
+	MATerm: { name: 'MA', link: '/#/ontology/ma', type: 'ontology', hasTable: true, isIndexed: true },
+	ZFATerm: { name: 'ZFA', link: '/#/ontology/zfa', type: 'ontology', hasTable: true, isIndexed: true },
+	MPTerm: { name: 'MP', link: '/#/ontology/mp', type: 'ontology', hasTable: true, isIndexed: true },
+	DAOTerm: { name: 'DAO', link: '/#/ontology/dao', type: 'ontology', hasTable: true, isIndexed: true },
+	EMAPATerm: { name: 'EMAPA', link: '/#/ontology/emapa', type: 'ontology', hasTable: true, isIndexed: true },
+	WBBTTerm: { name: 'WBBT', link: '/#/ontology/wbbt', type: 'ontology', hasTable: true, isIndexed: true },
+	XBATerm: { name: 'XBA', link: '/#/ontology/xba', type: 'ontology', hasTable: true, isIndexed: true },
+	XBSTerm: { name: 'XBS', link: '/#/ontology/xbs', type: 'ontology', hasTable: true, isIndexed: true },
+	XCOTerm: { name: 'XCO', link: '/#/ontology/xco', type: 'ontology', hasTable: true, isIndexed: true },
+	ROTerm: { name: 'RO', link: '/#/ontology/ro', type: 'ontology', hasTable: true, isIndexed: true },
+	ZECOTerm: { name: 'ZECO', link: '/#/ontology/zeco', type: 'ontology', hasTable: true, isIndexed: true },
+	NCBITaxonTerm: {
+		name: 'NCBITaxon',
+		link: '/#/ontology/ncbitaxon',
+		type: 'ontology',
+		hasTable: true,
+		isIndexed: true,
+	},
+	WBLSTerm: { name: 'WBLS', link: '/#/ontology/wbls', type: 'ontology', hasTable: true, isIndexed: true },
+	FBDVTerm: { name: 'FBDV', link: '/#/ontology/fbdv', type: 'ontology', hasTable: true, isIndexed: true },
+	MMUSDVTerm: { name: 'MMUSDV', link: '/#/ontology/mmusdv', type: 'ontology', hasTable: true, isIndexed: true },
+	ZFSTerm: { name: 'ZFS', link: '/#/ontology/zfs', type: 'ontology', hasTable: true, isIndexed: true },
+	XPOTerm: { name: 'XPO', link: '/#/ontology/xpo', type: 'ontology', hasTable: true, isIndexed: true },
+	ATPTerm: { name: 'ATP', link: '/#/ontology/atp', type: 'ontology', hasTable: true, isIndexed: true },
+	VTTerm: { name: 'VT', link: '/#/ontology/vt', type: 'ontology', hasTable: true, isIndexed: true },
+	XBEDTerm: { name: 'XBED', link: '/#/ontology/xbed', type: 'ontology', hasTable: true, isIndexed: true },
+	OBITerm: { name: 'OBI', link: '/#/ontology/obi', type: 'ontology', hasTable: true, isIndexed: true },
+	WBPhenotypeTerm: { name: 'WBPheno', link: '/#/ontology/wbpheno', type: 'ontology', hasTable: true, isIndexed: true },
+	PATOTerm: { name: 'PATO', link: '/#/ontology/pato', type: 'ontology', hasTable: true, isIndexed: true },
+	HPTerm: { name: 'HP', link: '/#/ontology/hp', type: 'ontology', hasTable: true, isIndexed: true },
+	FBCVTerm: { name: 'FBCV', link: '/#/ontology/fbcv', type: 'ontology', hasTable: true, isIndexed: true },
+	MMOTerm: { name: 'MMO', link: '/#/ontology/mmo', type: 'ontology', hasTable: true, isIndexed: true },
+	APOTerm: { name: 'APO', link: '/#/ontology/apo', type: 'ontology', hasTable: true, isIndexed: true },
+	MITerm: { name: 'MI', link: '/#/ontology/mi', type: 'ontology', hasTable: true, isIndexed: true },
+	MPATHTerm: { name: 'MPATH', link: '/#/ontology/mpath', type: 'ontology', hasTable: true, isIndexed: true },
+	MODTerm: { name: 'MOD', link: '/#/ontology/mod', type: 'ontology', hasTable: true, isIndexed: true },
+	UBERONTerm: { name: 'UBERON', link: '/#/ontology/uberon', type: 'ontology', hasTable: true, isIndexed: true },
+	RSTerm: { name: 'RS', link: '/#/ontology/rs', type: 'ontology', hasTable: true, isIndexed: true },
+	PWTerm: { name: 'PW', link: '/#/ontology/pw', type: 'ontology', hasTable: true, isIndexed: true },
+	CLTerm: { name: 'CL', link: '/#/ontology/cl', type: 'ontology', hasTable: true, isIndexed: true },
+	CMOTerm: { name: 'CMO', link: '/#/ontology/cmo', type: 'ontology', hasTable: true, isIndexed: true },
+	BSPOTerm: { name: 'BSPO', link: '/#/ontology/bspo', type: 'ontology', hasTable: true, isIndexed: true },
+	GENOTerm: { name: 'GENO', link: '/#/ontology/geno', type: 'ontology', hasTable: true, isIndexed: true },
 
-	DOTerm: { name: 'DO', link: '/#/ontology/do', type: 'ontology' },
-	CHEBITerm: { name: 'CHEBI', link: '/#/ontology/chebi', type: 'ontology' },
-	XSMOTerm: { name: 'XSMO', link: '/#/ontology/xsmo', type: 'ontology' },
-	ECOTerm: { name: 'ECO', link: '/#/ontology/eco', type: 'ontology' },
-	SOTerm: { name: 'SO', link: '/#/ontology/so', type: 'ontology' },
-	GOTerm: { name: 'GO', link: '/#/ontology/go', type: 'ontology' },
-	MATerm: { name: 'MA', link: '/#/ontology/ma', type: 'ontology' },
-	ZFATerm: { name: 'ZFA', link: '/#/ontology/zfa', type: 'ontology' },
-	MPTerm: { name: 'MP', link: '/#/ontology/mp', type: 'ontology' },
-	DAOTerm: { name: 'DAO', link: '/#/ontology/dao', type: 'ontology' },
-	EMAPATerm: { name: 'EMAPA', link: '/#/ontology/emapa', type: 'ontology' },
-	WBBTTerm: { name: 'WBBT', link: '/#/ontology/wbbt', type: 'ontology' },
-	XBATerm: { name: 'XBA', link: '/#/ontology/xba', type: 'ontology' },
-	XBSTerm: { name: 'XBS', link: '/#/ontology/xbs', type: 'ontology' },
-	XCOTerm: { name: 'XCO', link: '/#/ontology/xco', type: 'ontology' },
-	ROTerm: { name: 'RO', link: '/#/ontology/ro', type: 'ontology' },
-	ZECOTerm: { name: 'ZECO', link: '/#/ontology/zeco', type: 'ontology' },
-	NCBITaxonTerm: { name: 'NCBITaxon', link: '/#/ontology/ncbitaxon', type: 'ontology' },
-	WBLSTerm: { name: 'WBLS', link: '/#/ontology/wbls', type: 'ontology' },
-	FBDVTerm: { name: 'FBDV', link: '/#/ontology/fbdv', type: 'ontology' },
-	MMUSDVTerm: { name: 'MMUSDV', link: '/#/ontology/mmusdv', type: 'ontology' },
-	ZFSTerm: { name: 'ZFS', link: '/#/ontology/zfs', type: 'ontology' },
-	XPOTerm: { name: 'XPO', link: '/#/ontology/xpo', type: 'ontology' },
-	ATPTerm: { name: 'ATP', link: '/#/ontology/atp', type: 'ontology' },
-	VTTerm: { name: 'VT', link: '/#/ontology/vt', type: 'ontology' },
-	XBEDTerm: { name: 'XBED', link: '/#/ontology/xbed', type: 'ontology' },
-	OBITerm: { name: 'OBI', link: '/#/ontology/obi', type: 'ontology' },
-	WBPhenotypeTerm: { name: 'WBPheno', link: '/#/ontology/wbpheno', type: 'ontology' },
-	PATOTerm: { name: 'PATO', link: '/#/ontology/pato', type: 'ontology' },
-	HPTerm: { name: 'HP', link: '/#/ontology/hp', type: 'ontology' },
-	FBCVTerm: { name: 'FBCV', link: '/#/ontology/fbcv', type: 'ontology' },
-	MMOTerm: { name: 'MMO', link: '/#/ontology/mmo', type: 'ontology' },
-	APOTerm: { name: 'APO', link: '/#/ontology/apo', type: 'ontology' },
-	MITerm: { name: 'MI', link: '/#/ontology/mi', type: 'ontology' },
-	MPATHTerm: { name: 'MPATH', link: '/#/ontology/mpath', type: 'ontology' },
-	MODTerm: { name: 'MOD', link: '/#/ontology/mod', type: 'ontology' },
-	UBERONTerm: { name: 'UBERON', link: '/#/ontology/uberon', type: 'ontology' },
-	RSTerm: { name: 'RS', link: '/#/ontology/rs', type: 'ontology' },
-	PWTerm: { name: 'PW', link: '/#/ontology/pw', type: 'ontology' },
-	CLTerm: { name: 'CL', link: '/#/ontology/cl', type: 'ontology' },
-	CMOTerm: { name: 'CMO', link: '/#/ontology/cmo', type: 'ontology' },
-	BSPOTerm: { name: 'BSPO', link: '/#/ontology/bspo', type: 'ontology' },
-	GENOTerm: { name: 'GENO', link: '/#/ontology/geno', type: 'ontology' },
+	CurationReport: { name: 'Curation Reports', link: '/#/reports', type: 'system', hasTable: true, isIndexed: false },
+	BulkLoad: {
+		name: 'Bulk Loads / Failed Loads',
+		link: '/#/dataloads',
+		type: 'system',
+		hasTable: true,
+		isIndexed: false,
+	},
 
-	CurationReport: { name: 'Curation Reports', link: '/#/reports', type: 'system' },
-	BulkLoad: { name: 'Bulk Loads / Failed Loads', link: '/#/dataloads', type: 'system' },
+	AlleleGeneAssociation: {
+		name: 'Allele Gene Associations',
+		type: 'association',
+		hasTable: false,
+	},
+	AlleleVariantAssociation: {
+		name: 'Allele Variant Associations',
+		type: 'association',
+		hasTable: false,
+	},
+	CodingSequenceGenomicLocationAssociation: {
+		name: 'CDS Genomic Locations',
+		type: 'association',
+		hasTable: false,
+	},
+	ExonGenomicLocationAssociation: {
+		name: 'Exon Genomic Locations',
+		type: 'association',
+		hasTable: false,
+	},
+	GeneGenomicLocationAssociation: {
+		name: 'Gene Genomic Locations',
+		type: 'association',
+		hasTable: false,
+	},
+	TranscriptGenomicLocationAssociation: {
+		name: 'Transcript Genomic Locations',
+		type: 'association',
+		hasTable: false,
+	},
+	VariantGenomicLocationAssociation: {
+		name: 'Variant Genomic Locations',
+		type: 'association',
+		hasTable: false,
+	},
+	ConstructGenomicEntityAssociation: {
+		name: 'Construct Genomic Entity Associations',
+		type: 'association',
+		hasTable: false,
+	},
+	SequenceTargetingReagentGeneAssociation: {
+		name: 'SQTR Gene Associations',
+		type: 'association',
+		hasTable: false,
+	},
+	TranscriptCodingSequenceAssociation: {
+		name: 'Transcript CDS Associations',
+		type: 'association',
+		hasTable: false,
+	},
+	TranscriptExonAssociation: {
+		name: 'Transcript Exon Associations',
+		type: 'association',
+		hasTable: false,
+	},
+	TranscriptGeneAssociation: {
+		name: 'Transcript Gene Associations',
+		type: 'association',
+		hasTable: false,
+	},
 });
diff --git a/src/main/cliapp/src/containers/controlledVocabularyPage/ControlledVocabularyTable.js b/src/main/cliapp/src/containers/controlledVocabularyPage/ControlledVocabularyTable.js
index 383b1177b..6cba730c7 100644
--- a/src/main/cliapp/src/containers/controlledVocabularyPage/ControlledVocabularyTable.js
+++ b/src/main/cliapp/src/containers/controlledVocabularyPage/ControlledVocabularyTable.js
@@ -233,6 +233,37 @@ export const ControlledVocabularyTable = () => {
 			editor: (props) => definitionEditorTemplate(props),
 			body: (rowData) => <StringTemplate string={rowData.definition} />,
 		},
+		{
+			field: 'updatedBy.uniqueId',
+			header: 'Updated By',
+			sortable: true,
+			body: (rowData) => <StringTemplate string={rowData.updatedBy?.uniqueId} />,
+			filterConfig: FILTER_CONFIGS.updatedByFilterConfig,
+		},
+		{
+			field: 'dateUpdated',
+			header: 'Date Updated',
+			sortable: true,
+			filter: true,
+			body: (rowData) => <StringTemplate string={rowData.dateUpdated} />,
+			filterConfig: FILTER_CONFIGS.dateUpdatedFilterConfig,
+		},
+		{
+			field: 'createdBy.uniqueId',
+			header: 'Created By',
+			sortable: true,
+			filter: true,
+			body: (rowData) => <StringTemplate string={rowData.createdBy?.uniqueId} />,
+			filterConfig: FILTER_CONFIGS.createdByFilterConfig,
+		},
+		{
+			field: 'dateCreated',
+			header: 'Date Created',
+			sortable: true,
+			filter: true,
+			body: (rowData) => <StringTemplate string={rowData.dateCreated} />,
+			filterConfig: FILTER_CONFIGS.dataCreatedFilterConfig,
+		},
 		{
 			field: 'obsolete',
 			header: 'Obsolete',
diff --git a/src/main/cliapp/src/containers/dashboardPage/Dashboard.js b/src/main/cliapp/src/containers/dashboardPage/Dashboard.js
index 873d75db9..856dda775 100644
--- a/src/main/cliapp/src/containers/dashboardPage/Dashboard.js
+++ b/src/main/cliapp/src/containers/dashboardPage/Dashboard.js
@@ -9,22 +9,13 @@ export const Dashboard = () => {
 
 	useEffect(() => {
 		let _tableData = {};
-		const excludedEntities = [
-			'AGMDiseaseAnnotation',
-			'AlleleDiseaseAnnotation',
-			'GeneDiseaseAnnotation',
-			'AGMPhenotypeAnnotation',
-			'AllelePhenotypeAnnotation',
-			'GenePhenotypeAnnotation',
-		];
-
 		for (const key in CLASSES) {
 			const { type } = CLASSES[key];
 
 			if (!_tableData[type]) {
 				_tableData[type] = [];
 			}
-			if (!excludedEntities.includes(key)) {
+			if (CLASSES[key].hasTable) {
 				_tableData[type].push({
 					name: CLASSES[key].name,
 					link: CLASSES[key].link,
@@ -35,6 +26,9 @@ export const Dashboard = () => {
 	}, []);
 
 	const nameHyperlinkTemplate = (rowData) => {
+		if (!rowData.link) {
+			return rowData.name;
+		}
 		return <a href={rowData.link}>{rowData.name}</a>;
 	};
 
diff --git a/src/main/cliapp/src/containers/dataLoadsPage/DataLoadsComponent.js b/src/main/cliapp/src/containers/dataLoadsPage/DataLoadsComponent.js
index 936baa078..9095911eb 100644
--- a/src/main/cliapp/src/containers/dataLoadsPage/DataLoadsComponent.js
+++ b/src/main/cliapp/src/containers/dataLoadsPage/DataLoadsComponent.js
@@ -22,6 +22,8 @@ import { SiteContext } from '../layout/SiteContext';
 import { LoadingOverlay } from '../../components/LoadingOverlay';
 import moment from 'moment-timezone';
 import { NumberTemplate } from '../../components/Templates/NumberTemplate';
+import { StickyHeader } from '../../components/StickyHeader';
+import { Splitter, SplitterPanel } from 'primereact/splitter';
 
 export const DataLoadsComponent = () => {
 	const { authState } = useOktaAuth();
@@ -599,8 +601,8 @@ export const DataLoadsComponent = () => {
 		let filesWithoutDates = [];
 		files.forEach((file) => {
 			if (file.bulkloadStatus === 'FINISHED' || file.bulkloadStatus === 'STOPPED' || file.bulkloadStatus === 'FAILED') {
-				if (file.dateLastLoaded) {
-					lastLoadedDates.set(file.dateLastLoaded, file);
+				if (file.loadStarted) {
+					lastLoadedDates.set(file.loadStarted, file);
 				} else {
 					filesWithoutDates.push(file);
 				}
@@ -708,7 +710,9 @@ export const DataLoadsComponent = () => {
 	};
 
 	const exemptTypes = (loadType) => {
-		return loadType === 'GFF_EXON' || loadType === 'GFF_TRANSCRIPT' || loadType === 'GFF_CDS';
+		return (
+			loadType === 'GFF_EXON' || loadType === 'GFF_TRANSCRIPT' || loadType === 'GFF_CDS' || loadType === 'GFF_GENE'
+		);
 	};
 
 	const fileWithinSchemaRange = (fileVersion, loadType) => {
@@ -850,20 +854,26 @@ export const DataLoadsComponent = () => {
 		<>
 			<Toast ref={toast}></Toast>
 			<LoadingOverlay isLoading={isLoading} />
+			<StickyHeader>
+				<Splitter className="bg-primary-reverse border-none lg:h-5rem" gutterSize={0}>
+					<SplitterPanel size={1} className="flex justify-content-start py-3">
+						<Button
+							label="New Group"
+							icon="pi pi-plus"
+							className="p-button-success mr-2"
+							onClick={handleNewBulkLoadGroupOpen}
+						/>
+						<Button
+							label="New Bulk Load"
+							icon="pi pi-plus"
+							className="p-button-success mr-2"
+							onClick={handleNewBulkLoadOpen}
+						/>
+						<Button label="Refresh Data" icon="pi pi-plus" className="p-button-success mr-2" onClick={refresh} />
+					</SplitterPanel>
+				</Splitter>
+			</StickyHeader>
 			<div className="card">
-				<Button
-					label="New Group"
-					icon="pi pi-plus"
-					className="p-button-success mr-2"
-					onClick={handleNewBulkLoadGroupOpen}
-				/>
-				<Button
-					label="New Bulk Load"
-					icon="pi pi-plus"
-					className="p-button-success mr-2"
-					onClick={handleNewBulkLoadOpen}
-				/>
-				<Button label="Refresh Data" icon="pi pi-plus" className="p-button-success mr-2" onClick={refresh} />
 				<Messages ref={errorMessage} />
 				{errorLoads.length > 0 && (
 					<div>
diff --git a/src/main/cliapp/src/containers/layout/SiteLayout.js b/src/main/cliapp/src/containers/layout/SiteLayout.js
index 7c8838a6b..2bce1553c 100644
--- a/src/main/cliapp/src/containers/layout/SiteLayout.js
+++ b/src/main/cliapp/src/containers/layout/SiteLayout.js
@@ -375,7 +375,7 @@ export const SiteLayout = (props) => {
 						{
 							label: 'Search index UI (cerebro)',
 							icon: 'pi pi-fw pi-home',
-							url: `http://cerebro.alliancegenome.org:9000/#!/overview?host=https://${siteContext?.apiVersion?.esHost}`,
+							url: `http://cerebro.alliancegenome.org:9000/#!/overview?host=http://${siteContext?.apiVersion?.esHost}`,
 							target: '_blank',
 						},
 						{
@@ -384,6 +384,12 @@ export const SiteLayout = (props) => {
 							url: `http://logs.alliancegenome.org:5601/app/logtrail#/?q=*&h=agr.curation.${siteContext?.apiVersion?.env}.api.server&t=Now&i=logstash*&_g=()`,
 							target: '_blank',
 						},
+						{
+							label: 'MaTI Swagger UI',
+							icon: 'pi pi-fw pi-home',
+							url: siteContext?.apiVersion?.matiHost + '/q/swagger-ui/',
+							target: '_blank',
+						},
 						{ label: 'Site Health', icon: 'pi pi-fw pi-plus', to: '/healthpage' },
 					],
 				},
diff --git a/src/main/cliapp/src/service/DataLoadService.js b/src/main/cliapp/src/service/DataLoadService.js
index dc60d520d..d150ad6d6 100644
--- a/src/main/cliapp/src/service/DataLoadService.js
+++ b/src/main/cliapp/src/service/DataLoadService.js
@@ -81,10 +81,11 @@ export class DataLoadService extends BaseAuthService {
 	getBackendBulkLoadTypes(loadType) {
 		const bulkLoadTypes = {
 			BulkFMSLoad: [
+				'BIOGRID-ORCS',
 				'GFF', // This needs to be removed at some point
-
-				'GFF_EXON',
 				'GFF_CDS',
+				'GFF_EXON',
+				'GFF_GENE',
 				'GFF_TRANSCRIPT',
 				'HTPDATASET',
 				'HTPDATASAMPLE',
@@ -95,8 +96,9 @@ export class DataLoadService extends BaseAuthService {
 				'PHENOTYPE',
 				'PARALOGY',
 				'SEQUENCE_TARGETING_REAGENT',
-				// 'VARIATION',
-				'BIOGRID-ORCS',
+				'VARIATION',
+				'VEPGENE',
+				'VEPTRANSCRIPT',
 			],
 			BulkURLLoad: [
 				'ONTOLOGY',
@@ -106,6 +108,7 @@ export class DataLoadService extends BaseAuthService {
 				'DISEASE_ANNOTATION',
 				'RESOURCE_DESCRIPTOR',
 				'EXPRESSION_ATLAS',
+				'GAF',
 			],
 			BulkManualLoad: [
 				'FULL_INGEST',
diff --git a/src/main/java/org/alliancegenome/curation_api/constants/EntityFieldConstants.java b/src/main/java/org/alliancegenome/curation_api/constants/EntityFieldConstants.java
index 7eb0a89cd..557a17593 100644
--- a/src/main/java/org/alliancegenome/curation_api/constants/EntityFieldConstants.java
+++ b/src/main/java/org/alliancegenome/curation_api/constants/EntityFieldConstants.java
@@ -11,44 +11,52 @@ private EntityFieldConstants() {
 	public static final String SOURCE_ORGANIZATION = "sourceOrganization.abbreviation";
 	public static final String DATA_PROVIDER = "dataProvider." + SOURCE_ORGANIZATION;
 	public static final String SECONDARY_DATA_PROVIDER = "secondaryDataProvider." + SOURCE_ORGANIZATION;
-	
+
 	public static final String DA_SUBJECT = "diseaseAnnotationSubject";
 	public static final String EA_SUBJECT = "expressionAnnotationSubject";
 	public static final String PA_SUBJECT = "phenotypeAnnotationSubject";
+	public static final String EXP_EXPERIMENT_SUBJECT = "entityAssayed";
 	public static final String ALLELE_ASSOCIATION_SUBJECT = "alleleAssociationSubject";
 	public static final String CODING_SEQUENCE_ASSOCIATION_SUBJECT = "codingSequenceAssociationSubject";
 	public static final String CONSTRUCT_ASSOCIATION_SUBJECT = "constructAssociationSubject";
 	public static final String EXON_ASSOCIATION_SUBJECT = "exonAssociationSubject";
+	public static final String GENE_ASSOCIATION_SUBJECT = "geneAssociationSubject";
 	public static final String VARIANT_ASSOCIATION_SUBJECT = "variantAssociationSubject";
 	public static final String SQTR_ASSOCIATION_SUBJECT = "sequenceTargetingReagentAssociationSubject";
 	public static final String TRANSCRIPT_ASSOCIATION_SUBJECT = "transcriptAssociationSubject";
-	
+
+
 	public static final String DA_SUBJECT_TAXON = DA_SUBJECT + "." + TAXON;
 	public static final String EA_SUBJECT_TAXON = EA_SUBJECT + "." + TAXON;
 	public static final String PA_SUBJECT_TAXON = PA_SUBJECT + "." + TAXON;
-	
+	public static final String EXP_EXPERIMENT_TAXON = EXP_EXPERIMENT_SUBJECT + "." + TAXON;
+
 	public static final String ALLELE_ASSOCIATION_SUBJECT_DATA_PROVIDER = ALLELE_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
 	public static final String CODING_SEQUENCE_ASSOCIATION_SUBJECT_DATA_PROVIDER = CODING_SEQUENCE_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
 	public static final String CONSTRUCT_ASSOCIATION_SUBJECT_DATA_PROVIDER = CONSTRUCT_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
 	public static final String EXON_ASSOCIATION_SUBJECT_DATA_PROVIDER = EXON_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+	public static final String GENE_ASSOCIATION_SUBJECT_DATA_PROVIDER = GENE_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
 	public static final String VARIANT_ASSOCIATION_SUBJECT_DATA_PROVIDER = VARIANT_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
 	public static final String SQTR_ASSOCIATION_SUBJECT_DATA_PROVIDER = SQTR_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
 	public static final String TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER = TRANSCRIPT_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
-	
+
 	public static final String CODING_SEQUENCE_ASSOCIATION_SUBJECT_TAXON = CODING_SEQUENCE_ASSOCIATION_SUBJECT + "." + TAXON;
 	public static final String EXON_ASSOCIATION_SUBJECT_TAXON = EXON_ASSOCIATION_SUBJECT + "." + TAXON;
+	public static final String GENE_ASSOCIATION_SUBJECT_TAXON = GENE_ASSOCIATION_SUBJECT + "." + TAXON;
 	public static final String TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON = TRANSCRIPT_ASSOCIATION_SUBJECT + "." + TAXON;
 	public static final String VARIANT_ASSOCIATION_SUBJECT_TAXON = VARIANT_ASSOCIATION_SUBJECT + "." + TAXON;
-	
+
 	public static final String GENOMIC_LOCATION_ASSOCIATION_OBJECT = "GenomicLocationAssociationObject";
 	public static final String CODING_SEQUENCE_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "codingSequence" + GENOMIC_LOCATION_ASSOCIATION_OBJECT;
 	public static final String EXON_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "exon" + GENOMIC_LOCATION_ASSOCIATION_OBJECT;
+	public static final String GENE_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "gene" + GENOMIC_LOCATION_ASSOCIATION_OBJECT;
 	public static final String TRANSCRIPT_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "transcript" + GENOMIC_LOCATION_ASSOCIATION_OBJECT;
 	public static final String VARIANT_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "variant" + GENOMIC_LOCATION_ASSOCIATION_OBJECT;
 	public static final String CODING_SEQUENCE_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "codingSequence" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
 	public static final String EXON_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "exon" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
 	public static final String TRANSCRIPT_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "transcript" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
-	
+	public static final String GENE_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "gene" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
+
 	public static final String SUBJECT_GENE_DATA_PROVIDER = "subjectGene." + DATA_PROVIDER;
 	public static final String SUBJECT_GENE_TAXON = "subjectGene." + TAXON;
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/constants/Gff3Constants.java b/src/main/java/org/alliancegenome/curation_api/constants/Gff3Constants.java
index 9ecf6976c..06acbcd48 100644
--- a/src/main/java/org/alliancegenome/curation_api/constants/Gff3Constants.java
+++ b/src/main/java/org/alliancegenome/curation_api/constants/Gff3Constants.java
@@ -8,11 +8,16 @@ private Gff3Constants() {
 		throw new UnsupportedOperationException("This is a utility class and cannot be instantiated");
 	}
 	
+	public static final List<String> GENE_TYPES = List.of(
+		"gene", "pseudogene", "lincRNA_gene", "lncRNA_gene", "ncRNA_gene", "rRNA_gene",
+		"snRNA_gene", "snoRNA_gene", "tRNA_gene", "telomerase_RNA_gene", "transposable_element_gene"
+	);
+	
 	public static final List<String> TRANSCRIPT_TYPES = List.of(
 		"mRNA", "ncRNA", "piRNA", "lincRNA", "miRNA", "pre_miRNA", "snoRNA", "lncRNA",
 		"tRNA", "snRNA", "rRNA", "antisense_RNA", "C_gene_segment", "V_gene_segment",
 		"pseudogene_attribute", "pseudogenic_transcript", "lnc_RNA", "nc_primary_transcript",
-		"circular_ncRNA"
+		"circular_ncRNA", "transcript"
 	);
 	
 	public static final List<String> STRANDS = List.of("+", "-");
diff --git a/src/main/java/org/alliancegenome/curation_api/constants/LinkMLSchemaConstants.java b/src/main/java/org/alliancegenome/curation_api/constants/LinkMLSchemaConstants.java
index 4c54350c0..92cb9891d 100644
--- a/src/main/java/org/alliancegenome/curation_api/constants/LinkMLSchemaConstants.java
+++ b/src/main/java/org/alliancegenome/curation_api/constants/LinkMLSchemaConstants.java
@@ -5,7 +5,7 @@ public class LinkMLSchemaConstants {
 	private LinkMLSchemaConstants() {
 		// Hidden from view, as it is a utility class
 	}
-	public static final String LATEST_RELEASE = "2.8.0";
+	public static final String LATEST_RELEASE = "2.8.1";
 	public static final String MIN_ONTOLOGY_RELEASE = "1.2.4";
 	public static final String MAX_ONTOLOGY_RELEASE = LATEST_RELEASE;
 
diff --git a/src/main/java/org/alliancegenome/curation_api/constants/ValidationConstants.java b/src/main/java/org/alliancegenome/curation_api/constants/ValidationConstants.java
index 0e879c431..2ca7244d2 100644
--- a/src/main/java/org/alliancegenome/curation_api/constants/ValidationConstants.java
+++ b/src/main/java/org/alliancegenome/curation_api/constants/ValidationConstants.java
@@ -15,5 +15,6 @@ private ValidationConstants() {
 	public static final String DUPLICATE_MESSAGE = "Duplicate entries found";
 	public static final String DUPLICATE_RELATION_PREFIX = "Entries found with same relation field - ";
 	public static final String UNRECOGNIZED_MESSAGE = "Unrecognized entry"; // To be used instead of INVALID_MESSAGE when entry to be skipped instead of failed
+	public static final String AMBIGUOUS_MESSAGE = "Could not be unambiguously resolved";
 	
 }
\ No newline at end of file
diff --git a/src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java b/src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java
index db0a0d007..d7a3f03b8 100644
--- a/src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java
+++ b/src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java
@@ -84,7 +84,14 @@ private VocabularyConstants() {
 	public static final String ANATOMICAL_SUBSTRUCTURE_QUALIFIER = "anatomical_subtructure_qualifier";
 	public static final String CELLULAR_COMPONENT_QUALIFIER = "cellular_component_qualifier";
 
-	public static final String HTP_DATASET_CATEGORY_TAGS = "data_set_category_tags";
+	public static final String HTP_DATASET_CATEGORY_TAGS_VOCABULARY = "data_set_category_tags";
 	public static final String HTP_DATASET_NOTE_TYPE_VOCABULARY_TERM_SET = "htp_expression_dataset_note_type";
 	public static final String HTP_DATASET_SAMPLE_NOTE_TYPE_VOCABULARY_TERM_SET = "htp_expression_dataset_sample_note_type";
+	
+	public static final String VEP_IMPACT_VOCABULARY = "vep_impact";
+	public static final String VEP_CONSEQUENCE_VOCABULARY = "vep_consequence";
+	public static final String SIFT_PREDICTION_VOCABULARY = "sift_prediction";
+	public static final String POLYPHEN_PREDICTION_VOCABULARY = "polyphen_prediction";
+
+	public static final String HTP_DATASET_SAMPLE_SEQUENCE_FORMAT_VOCABULARY = "htp_data_sample_sequencing_format";
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/APIVersionInfoController.java b/src/main/java/org/alliancegenome/curation_api/controllers/APIVersionInfoController.java
index 3f2d12494..2a5f88b1f 100644
--- a/src/main/java/org/alliancegenome/curation_api/controllers/APIVersionInfoController.java
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/APIVersionInfoController.java
@@ -1,10 +1,7 @@
 package org.alliancegenome.curation_api.controllers;
 
-import static org.reflections.scanners.Scanners.TypesAnnotated;
-
-import java.util.Set;
-import java.util.TreeMap;
-
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.interfaces.APIVersionInterface;
 import org.alliancegenome.curation_api.model.output.APIVersionInfo;
@@ -12,8 +9,10 @@
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import org.reflections.Reflections;
 
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
+import java.util.Set;
+import java.util.TreeMap;
+
+import static org.reflections.scanners.Scanners.TypesAnnotated;
 
 @RequestScoped
 public class APIVersionInfoController implements APIVersionInterface {
@@ -33,6 +32,9 @@ public class APIVersionInfoController implements APIVersionInterface {
 	@ConfigProperty(name = "NET")
 	String env;
 
+	@ConfigProperty(name = "mati.url")
+	String matiURL;
+
 	@Override
 	public APIVersionInfo get() {
 
@@ -59,9 +61,14 @@ public APIVersionInfo get() {
 		info.setName(name);
 		info.setAgrCurationSchemaVersions(linkMLClassVersions);
 		info.setSubmittedClassSchemaVersions(submittedClassVersions);
-		info.setEsHost(esHost);
+		String[] array = esHost.split(",");
+		if (array.length > 0) {
+			info.setEsHost(array[0]);
+		} else {
+			info.setEsHost(esHost);
+		}
+		info.setMatiHost(matiURL);
 		info.setEnv(env);
 		return info;
 	}
-
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/crud/BiogridOrcCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/crud/BiogridOrcCrudController.java
new file mode 100644
index 000000000..c7011821c
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/crud/BiogridOrcCrudController.java
@@ -0,0 +1,35 @@
+package org.alliancegenome.curation_api.controllers.crud;
+
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
+import org.alliancegenome.curation_api.dao.CrossReferenceDAO;
+import org.alliancegenome.curation_api.interfaces.crud.BiogridOrcCrudInterface;
+import org.alliancegenome.curation_api.jobs.executors.BiogridOrcExecutor;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.BiogridOrcIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.services.CrossReferenceService;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class BiogridOrcCrudController extends BaseEntityCrudController<CrossReferenceService, CrossReference, CrossReferenceDAO> implements BiogridOrcCrudInterface {
+
+	@Inject
+	CrossReferenceService crossReferenceService;
+
+	@Inject
+	BiogridOrcExecutor biogridOrcExecutor;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setService(crossReferenceService);
+	}
+
+	@Override
+	public APIResponse updateBiogridOrc(String dataProvider, BiogridOrcIngestFmsDTO biogridOrcData) {
+		return biogridOrcExecutor.runLoadApi(dataProvider, biogridOrcData.getData());
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionAnnotationCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionAnnotationCrudController.java
index c86c11831..42322337b 100644
--- a/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionAnnotationCrudController.java
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionAnnotationCrudController.java
@@ -32,7 +32,7 @@ public ObjectResponse<GeneExpressionAnnotation> getByIdentifier(String identifie
 	}
 
 	public APIResponse updateExpressionAnnotations(String dataProvider, List<GeneExpressionFmsDTO> annotations) {
-		return geneExpressionExecutor.runLoadApi(geneExpressionAnnotationService, dataProvider, annotations);
+		APIResponse response = geneExpressionExecutor.runLoadAPI(geneExpressionAnnotationService, dataProvider, annotations);
+		return response;
 	}
 }
-
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionExperimentCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionExperimentCrudController.java
new file mode 100644
index 000000000..b44393683
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneExpressionExperimentCrudController.java
@@ -0,0 +1,34 @@
+package org.alliancegenome.curation_api.controllers.crud;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
+import org.alliancegenome.curation_api.dao.GeneExpressionExperimentDAO;
+import org.alliancegenome.curation_api.interfaces.crud.GeneExpressionExperimentCrudInterface;
+import org.alliancegenome.curation_api.jobs.executors.GeneExpressionExecutor;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.services.GeneExpressionExperimentService;
+
+
+@RequestScoped
+public class GeneExpressionExperimentCrudController extends BaseEntityCrudController<GeneExpressionExperimentService, GeneExpressionExperiment, GeneExpressionExperimentDAO> implements GeneExpressionExperimentCrudInterface {
+
+	@Inject
+	GeneExpressionExperimentService geneExpressionExperimentService;
+	@Inject
+	GeneExpressionExecutor geneExpressionExecutor;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setService(geneExpressionExperimentService);
+	}
+
+	public ObjectResponse<GeneExpressionExperiment> getByIdentifier(String identifierString) {
+		return geneExpressionExperimentService.getByIdentifier(identifierString);
+	}
+
+}
+
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/crud/HTPExpressionDatasetSampleAnnotationCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/crud/HTPExpressionDatasetSampleAnnotationCrudController.java
new file mode 100644
index 000000000..a75bdefba
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/crud/HTPExpressionDatasetSampleAnnotationCrudController.java
@@ -0,0 +1,35 @@
+package org.alliancegenome.curation_api.controllers.crud;
+
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
+import org.alliancegenome.curation_api.dao.HTPExpressionDatasetSampleAnnotationDAO;
+import org.alliancegenome.curation_api.interfaces.crud.HTPExpressionDatasetSampleAnnotationCrudInterface;
+import org.alliancegenome.curation_api.jobs.executors.HTPExpressionDatasetSampleAnnotationExecutor;
+import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetSampleAnnotation;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetSampleAnnotationIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.services.HTPExpressionDatasetSampleAnnotationService;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class HTPExpressionDatasetSampleAnnotationCrudController extends BaseEntityCrudController<HTPExpressionDatasetSampleAnnotationService, HTPExpressionDatasetSampleAnnotation, HTPExpressionDatasetSampleAnnotationDAO> implements HTPExpressionDatasetSampleAnnotationCrudInterface {
+
+	@Inject
+	HTPExpressionDatasetSampleAnnotationService htpExpressionDatasetSampleAnnotationService;
+	@Inject
+	HTPExpressionDatasetSampleAnnotationExecutor htpExpressionDatasetSampleAnnotationExecutor;
+
+	@Override
+	@PostConstruct
+	public void init() {
+		setService(htpExpressionDatasetSampleAnnotationService);
+	}
+
+	@Override
+	public APIResponse updateHTPExpressionDatasetSampleAnnotation(String dataProvider, HTPExpressionDatasetSampleAnnotationIngestFmsDTO htpDatasetSampleData) {
+		return htpExpressionDatasetSampleAnnotationExecutor.runLoadApi(htpExpressionDatasetSampleAnnotationService, dataProvider, htpDatasetSampleData.getData());
+	}
+	
+}
\ No newline at end of file
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/crud/PredictedVariantConsequenceCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/crud/PredictedVariantConsequenceCrudController.java
new file mode 100644
index 000000000..1a709cce6
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/crud/PredictedVariantConsequenceCrudController.java
@@ -0,0 +1,40 @@
+package org.alliancegenome.curation_api.controllers.crud;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
+import org.alliancegenome.curation_api.dao.PredictedVariantConsequenceDAO;
+import org.alliancegenome.curation_api.interfaces.crud.PredictedVariantConsequenceCrudInterface;
+import org.alliancegenome.curation_api.jobs.executors.VepGeneExecutor;
+import org.alliancegenome.curation_api.jobs.executors.VepTranscriptExecutor;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.services.PredictedVariantConsequenceService;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class PredictedVariantConsequenceCrudController extends BaseEntityCrudController<PredictedVariantConsequenceService, PredictedVariantConsequence, PredictedVariantConsequenceDAO>
+	implements PredictedVariantConsequenceCrudInterface {
+
+	@Inject PredictedVariantConsequenceService predictedVariantConsequenceService;
+	@Inject VepTranscriptExecutor vepTranscriptExecutor;
+	@Inject VepGeneExecutor vepGeneExecutor;
+	
+	@Override
+	@PostConstruct
+	protected void init() {
+		setService(predictedVariantConsequenceService);
+	}
+
+	public APIResponse updateTranscriptLevelConsequences(String dataProvider, List<VepTxtDTO> consequenceData) {
+		return vepTranscriptExecutor.runLoadApi(predictedVariantConsequenceService, dataProvider, consequenceData);
+	}
+
+	public APIResponse updateGeneLevelConsequences(String dataProvider, List<VepTxtDTO> consequenceData) {
+		return vepGeneExecutor.runLoadApi(dataProvider, consequenceData);
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/crud/geneAssociations/GeneGenomicLocationAssociationCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/crud/geneAssociations/GeneGenomicLocationAssociationCrudController.java
new file mode 100644
index 000000000..92c175e7f
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/controllers/crud/geneAssociations/GeneGenomicLocationAssociationCrudController.java
@@ -0,0 +1,36 @@
+package org.alliancegenome.curation_api.controllers.crud.geneAssociations;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
+import org.alliancegenome.curation_api.dao.associations.geneAssociations.GeneGenomicLocationAssociationDAO;
+import org.alliancegenome.curation_api.interfaces.crud.geneAssociations.GeneGenomicLocationAssociationCrudInterface;
+import org.alliancegenome.curation_api.jobs.executors.gff.Gff3GeneExecutor;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.Gff3DTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.response.LoadHistoryResponce;
+import org.alliancegenome.curation_api.services.associations.geneAssociations.GeneGenomicLocationAssociationService;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class GeneGenomicLocationAssociationCrudController extends BaseEntityCrudController<GeneGenomicLocationAssociationService, GeneGenomicLocationAssociation, GeneGenomicLocationAssociationDAO> implements GeneGenomicLocationAssociationCrudInterface {
+
+	@Inject GeneGenomicLocationAssociationService geneGenomicLocationService;
+
+	@Inject Gff3GeneExecutor gff3GeneExecutor;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setService(geneGenomicLocationService);
+	}
+
+	public APIResponse updateGeneLocations(String dataProvider, String assembly, List<Gff3DTO> gffData) {
+		LoadHistoryResponce resp = (LoadHistoryResponce) gff3GeneExecutor.runLoadApi(dataProvider, assembly, gffData);
+		return new LoadHistoryResponce(resp.getHistory());
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/AnatomicalSiteDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/AnatomicalSiteDAO.java
new file mode 100644
index 000000000..1147a7532
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/dao/AnatomicalSiteDAO.java
@@ -0,0 +1,13 @@
+package org.alliancegenome.curation_api.dao;
+
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.AnatomicalSite;
+
+import jakarta.enterprise.context.ApplicationScoped;
+
+@ApplicationScoped
+public class AnatomicalSiteDAO extends BaseSQLDAO<AnatomicalSite> {
+	protected AnatomicalSiteDAO() {
+		super(AnatomicalSite.class);
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/CrossReferenceDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/CrossReferenceDAO.java
index 162d95391..5908c9952 100644
--- a/src/main/java/org/alliancegenome/curation_api/dao/CrossReferenceDAO.java
+++ b/src/main/java/org/alliancegenome/curation_api/dao/CrossReferenceDAO.java
@@ -5,10 +5,13 @@
 import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
 import org.alliancegenome.curation_api.model.entities.CrossReference;
 import org.alliancegenome.curation_api.model.entities.ResourceDescriptorPage;
+import org.alliancegenome.curation_api.model.input.Pagination;
+import org.alliancegenome.curation_api.response.SearchResponse;
 
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 @ApplicationScoped
 public class CrossReferenceDAO extends BaseSQLDAO<CrossReference> {
@@ -32,6 +35,31 @@ public Map<String, Long> getGenesWithCrossRefs(ResourceDescriptorPage page) {
 		return ensemblGeneMap;
 	}
 
+	public Map<String, Long> getGenesWithCrossRefs(Set<String> referencedCuries) {
+		String sql = """
+			select gc.genomicentity_id, cr.referencedcurie from genomicentity_crossreference as gc, crossreference as cr
+				where gc.crossreferences_id = cr.id AND cr.referencedCurie IN (:referencedCuries)
+			""";
+		Query query = entityManager.createNativeQuery(sql);
+		query.setParameter("referencedCuries", referencedCuries);
+		List<Object[]> objects = query.getResultList();
+		Map<String, Long> idCurieMap = new HashMap<>();
+		objects.forEach(object -> {
+			idCurieMap.put((String) object[1], (Long) object[0]);
+		});
+		return idCurieMap;
+
+	}
+
+	public List<CrossReference> getAllCrossRefsByPage(ResourceDescriptorPage page) {
+		HashMap<String, Object> params = new HashMap<>();
+		params.put("resourceDescriptorPage.name", page.getName());
+		Pagination pagination = new Pagination();
+		pagination.setLimit(10_000_000);
+		SearchResponse<CrossReference> crossReferenceResponse = findByParams(pagination, params);
+		return crossReferenceResponse.getResults();
+	}
+
 	public Integer persistAccessionGeneAssociated(Long crossReferenceID, Long geneID) {
 		String sql = """
 			insert into genomicentity_crossreference (crossreferences_id,genomicentity_id)
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/GeneExpressionExperimentDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/GeneExpressionExperimentDAO.java
new file mode 100644
index 000000000..ab3b8604a
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/dao/GeneExpressionExperimentDAO.java
@@ -0,0 +1,13 @@
+package org.alliancegenome.curation_api.dao;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+
+@ApplicationScoped
+public class GeneExpressionExperimentDAO extends BaseSQLDAO<GeneExpressionExperiment> {
+
+	protected GeneExpressionExperimentDAO() {
+		super(GeneExpressionExperiment.class);
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/GeneOntologyAnnotationDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/GeneOntologyAnnotationDAO.java
new file mode 100644
index 000000000..455352f1b
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/dao/GeneOntologyAnnotationDAO.java
@@ -0,0 +1,59 @@
+package org.alliancegenome.curation_api.dao;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.persistence.Query;
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.GeneOntologyAnnotation;
+import org.alliancegenome.curation_api.model.entities.Organization;
+import org.alliancegenome.curation_api.model.ingest.dto.GeneOntologyAnnotationDTO;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@ApplicationScoped
+public class GeneOntologyAnnotationDAO extends BaseSQLDAO<GeneOntologyAnnotation> {
+
+	protected GeneOntologyAnnotationDAO() {
+		super(GeneOntologyAnnotation.class);
+	}
+
+	public GeneOntologyAnnotation persistGeneGoAssociation(GeneOntologyAnnotation gaf) {
+		String sql = """
+			insert into GeneOntologyAnnotation (id, singlegene_id,goterm_id)
+			VALUES (nextval('GeneOntologyAnnotation_SEQ'), :geneID, :goID)
+						""";
+		Query query = entityManager.createNativeQuery(sql);
+		query.setParameter("goID", gaf.getGoTerm().getId());
+		query.setParameter("geneID", gaf.getSingleGene().getId());
+		query.executeUpdate();
+
+		sql = "select currval('GeneOntologyAnnotation_SEQ')";
+		Object object = entityManager.createNativeQuery(sql).getSingleResult();
+		gaf.setId((Long) object);
+		return gaf;
+	}
+
+	public Map<Long, GeneOntologyAnnotationDTO> getAllGafIdsPerProvider(Organization sourceOrganization) {
+		Query query = entityManager.createNativeQuery("""
+			select gga.id, be.modentityid, ot.curie
+			from GeneOntologyAnnotation as gga , BiologicalEntity as be, ontologyterm as ot,
+			species as spec
+			where gga.singlegene_id = be.id
+			and be.taxon_id = spec.taxon_id
+			and spec.displayname = :speciesName
+			and gga.goterm_id = ot.id
+			""");
+		query.setParameter("speciesName", sourceOrganization.getAbbreviation());
+		List<Object[]> result = query.getResultList();
+		Map<Long, GeneOntologyAnnotationDTO> map = new HashMap<>();
+		result.forEach(object -> {
+			GeneOntologyAnnotationDTO dto = new GeneOntologyAnnotationDTO();
+			dto.setGeneIdentifier((String) object[1]);
+			dto.setGoTermCurie((String) object[2]);
+			map.put((Long) object[0], dto);
+		});
+		return map;
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/HTPExpressionDatasetSampleAnnotationDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/HTPExpressionDatasetSampleAnnotationDAO.java
new file mode 100644
index 000000000..910d492f8
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/dao/HTPExpressionDatasetSampleAnnotationDAO.java
@@ -0,0 +1,14 @@
+package org.alliancegenome.curation_api.dao;
+
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetSampleAnnotation;
+
+import jakarta.enterprise.context.ApplicationScoped;
+
+@ApplicationScoped
+public class HTPExpressionDatasetSampleAnnotationDAO extends BaseSQLDAO<HTPExpressionDatasetSampleAnnotation> {
+	
+	protected HTPExpressionDatasetSampleAnnotationDAO() {
+		super(HTPExpressionDatasetSampleAnnotation.class);
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/PredictedVariantConsequenceDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/PredictedVariantConsequenceDAO.java
new file mode 100644
index 000000000..e602925cf
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/dao/PredictedVariantConsequenceDAO.java
@@ -0,0 +1,15 @@
+package org.alliancegenome.curation_api.dao;
+
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+
+import jakarta.enterprise.context.ApplicationScoped;
+
+@ApplicationScoped
+public class PredictedVariantConsequenceDAO extends BaseSQLDAO<PredictedVariantConsequence> {
+
+	protected PredictedVariantConsequenceDAO() {
+		super(PredictedVariantConsequence.class);
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/ReferenceDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/ReferenceDAO.java
index 3edde99bb..994971505 100644
--- a/src/main/java/org/alliancegenome/curation_api/dao/ReferenceDAO.java
+++ b/src/main/java/org/alliancegenome/curation_api/dao/ReferenceDAO.java
@@ -1,11 +1,13 @@
 package org.alliancegenome.curation_api.dao;
 
-import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
-import org.alliancegenome.curation_api.model.entities.Reference;
-
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.persistence.Query;
 import jakarta.transaction.Transactional;
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.Reference;
+
+import java.util.*;
+import java.util.stream.Collectors;
 
 @ApplicationScoped
 public class ReferenceDAO extends BaseSQLDAO<Reference> {
@@ -35,4 +37,55 @@ protected void deleteReferenceForeignKey(String table, String column, String ori
 		jpqlQuery.executeUpdate();
 	}
 
+	public HashMap<String, Reference> getReferenceMap() {
+		HashMap<String, Reference> referenceIdMap = new HashMap<>();
+		Query q = entityManager.createNativeQuery("""
+					SELECT ref.id, cr.referencedcurie
+					FROM Reference as ref, reference_crossreference as assoc, Crossreference as cr
+					where assoc.reference_id = ref.id
+					and assoc.crossreferences_id = cr.id
+			""");
+		List<Object[]> ids = q.getResultList();
+		Set<Long> refIDs = ids.stream().map(object -> (Long) object[0]).collect(Collectors.toSet());
+		Map<Long, List<Object[]>> idMap = ids.stream().collect(Collectors.groupingBy(o -> (Long) o[0]));
+		List<Reference> refs = new ArrayList<>();
+		refIDs.forEach(id -> {
+			Reference reference = entityManager.getReference(Reference.class, id);
+			// populate cross references
+			reference.getCrossReferences().size();
+			refs.add(reference);
+			referenceIdMap.put(String.valueOf(id), reference);
+			if (idMap.get(id) != null) {
+				idMap.get(id).forEach(objects -> {
+					referenceIdMap.put((String) objects[1], reference);
+				});
+			}
+		});
+		return referenceIdMap;
+	}
+
+	public HashMap<String, Reference> getShallowReferenceMap() {
+		HashMap<String, Reference> referenceIdMap = new HashMap<>();
+		Query q = entityManager.createNativeQuery("""
+					SELECT ref.id, cr.referencedcurie
+					FROM Reference as ref, reference_crossreference as assoc, Crossreference as cr
+					where assoc.reference_id = ref.id
+					and assoc.crossreferences_id = cr.id
+			""");
+		List<Object[]> ids = q.getResultList();
+		Set<Long> refIDs = ids.stream().map(object -> (Long) object[0]).collect(Collectors.toSet());
+		Map<Long, List<Object[]>> idMap = ids.stream().collect(Collectors.groupingBy(o -> (Long) o[0]));
+		List<Reference> refs = new ArrayList<>();
+		refIDs.forEach(id -> {
+			Reference reference = getShallowEntity(Reference.class, id);
+			refs.add(reference);
+			referenceIdMap.put(String.valueOf(id), reference);
+			if (idMap.get(id) != null) {
+				idMap.get(id).forEach(objects -> {
+					referenceIdMap.put((String) objects[1], reference);
+				});
+			}
+		});
+		return referenceIdMap;
+	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/associations/geneAssociations/GeneGenomicLocationAssociationDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/associations/geneAssociations/GeneGenomicLocationAssociationDAO.java
new file mode 100644
index 000000000..53c731649
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/dao/associations/geneAssociations/GeneGenomicLocationAssociationDAO.java
@@ -0,0 +1,15 @@
+package org.alliancegenome.curation_api.dao.associations.geneAssociations;
+
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
+
+import jakarta.enterprise.context.ApplicationScoped;
+
+@ApplicationScoped
+public class GeneGenomicLocationAssociationDAO extends BaseSQLDAO<GeneGenomicLocationAssociation> {
+
+	protected GeneGenomicLocationAssociationDAO() {
+		super(GeneGenomicLocationAssociation.class);
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/ontology/GoTermDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/ontology/GoTermDAO.java
index 2dc7e19ec..9b8d9ab98 100644
--- a/src/main/java/org/alliancegenome/curation_api/dao/ontology/GoTermDAO.java
+++ b/src/main/java/org/alliancegenome/curation_api/dao/ontology/GoTermDAO.java
@@ -1,9 +1,13 @@
 package org.alliancegenome.curation_api.dao.ontology;
 
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.persistence.Query;
 import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
 import org.alliancegenome.curation_api.model.entities.ontology.GOTerm;
 
-import jakarta.enterprise.context.ApplicationScoped;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 @ApplicationScoped
 public class GoTermDAO extends BaseSQLDAO<GOTerm> {
@@ -12,4 +16,19 @@ protected GoTermDAO() {
 		super(GOTerm.class);
 	}
 
+	public Map<String, Long> getAllGOIds() {
+		String sql = """
+						select id, curie
+						from ontologyterm
+						where ontologytermtype = :type
+			""";
+		Query query = entityManager.createNativeQuery(sql);
+		query.setParameter("type", "GOTerm");
+		List<Object[]> objects = query.getResultList();
+		Map<String, Long> ensemblGeneMap = new HashMap<>();
+		objects.forEach(object -> {
+			ensemblGeneMap.put((String) object[1], (Long) object[0]);
+		});
+		return ensemblGeneMap;
+	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/enums/BackendBulkLoadType.java b/src/main/java/org/alliancegenome/curation_api/enums/BackendBulkLoadType.java
index 11b17cb8a..76d49d794 100644
--- a/src/main/java/org/alliancegenome/curation_api/enums/BackendBulkLoadType.java
+++ b/src/main/java/org/alliancegenome/curation_api/enums/BackendBulkLoadType.java
@@ -19,6 +19,8 @@ public enum BackendBulkLoadType {
 	CONSTRUCT_ASSOCIATION("json"),
 	VARIANT("json"),
 	VARIATION("json"), // FMS variants as opposed to direct submission for VARIANT
+	VEPTRANSCRIPT("tsv"),
+	VEPGENE("tsv"),
 
 	// GFF all from the same file but split out
 	GFF("gff"), // For Database entries
@@ -26,9 +28,11 @@ public enum BackendBulkLoadType {
 	GFF_EXON("gff"),
 	GFF_CDS("gff"),
 	GFF_TRANSCRIPT("gff"),
+	GFF_GENE("gff"),
 	
 	INTERACTION_MOL("tsv"),
 	EXPRESSION_ATLAS("tsv"),
+	GAF("tsv"),
 	INTERACTION_GEN("tsv"),
 	BIOGRID_ORCS("tsv"),
 	PARALOGY("json"),
diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/crud/BiogridOrcCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/BiogridOrcCrudInterface.java
new file mode 100644
index 000000000..52c5ed605
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/BiogridOrcCrudInterface.java
@@ -0,0 +1,26 @@
+package org.alliancegenome.curation_api.interfaces.crud;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.MediaType;
+import org.alliancegenome.curation_api.interfaces.base.crud.BaseCreateControllerInterface;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.BiogridOrcIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+
+@Path("/biogrid-orc")
+@Tag(name = "CRUD - Biogrid Orc")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface BiogridOrcCrudInterface extends BaseCreateControllerInterface<CrossReference> {
+
+
+	@POST
+	@Path("/bulk/{dataProvider}/biogridfile")
+	@JsonView(View.FieldsAndLists.class)
+	APIResponse updateBiogridOrc(@PathParam("dataProvider") String dataProvider, BiogridOrcIngestFmsDTO biogridOrcData);
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/crud/GeneExpressionExperimentCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/GeneExpressionExperimentCrudInterface.java
new file mode 100644
index 000000000..4e868b9ed
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/GeneExpressionExperimentCrudInterface.java
@@ -0,0 +1,22 @@
+package org.alliancegenome.curation_api.interfaces.crud;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.MediaType;
+import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+
+@Path("/gene-expression-experiment")
+@Tag(name = "CRUD - Gene Expression Experiments")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface GeneExpressionExperimentCrudInterface extends BaseIdCrudInterface<GeneExpressionExperiment> {
+	@GET
+	@Path("/findBy/{identifier}")
+	@JsonView(View.FieldsAndLists.class)
+	ObjectResponse<GeneExpressionExperiment> getByIdentifier(@PathParam("identifier") String identifier);
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/crud/GeneOntologyAnnotationCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/GeneOntologyAnnotationCrudInterface.java
new file mode 100644
index 000000000..53d81e7e4
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/GeneOntologyAnnotationCrudInterface.java
@@ -0,0 +1,17 @@
+package org.alliancegenome.curation_api.interfaces.crud;
+
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+import org.alliancegenome.curation_api.interfaces.base.crud.BaseCreateControllerInterface;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+@Path("/gaf")
+@Tag(name = "CRUD - GAF")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface GeneOntologyAnnotationCrudInterface extends BaseCreateControllerInterface<CrossReference> {
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/crud/HTPExpressionDatasetSampleAnnotationCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/HTPExpressionDatasetSampleAnnotationCrudInterface.java
new file mode 100644
index 000000000..1b4187ec1
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/HTPExpressionDatasetSampleAnnotationCrudInterface.java
@@ -0,0 +1,29 @@
+package org.alliancegenome.curation_api.interfaces.crud;
+
+import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface;
+import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetSampleAnnotation;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetSampleAnnotationIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+import com.fasterxml.jackson.annotation.JsonView;
+
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+
+@Path("/htpexpressiondatasetsampleannotation")
+@Tag(name = "CRUD - HTP Expression Dataset Sample Annotation")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface HTPExpressionDatasetSampleAnnotationCrudInterface extends BaseIdCrudInterface<HTPExpressionDatasetSampleAnnotation> {
+	
+	@POST
+	@Path("/bulk/{dataProvider}/htpexpressiondatasetsampleannotationfile")
+	@JsonView(View.FieldsAndLists.class)
+	APIResponse updateHTPExpressionDatasetSampleAnnotation(@PathParam("dataProvider") String dataProvider, HTPExpressionDatasetSampleAnnotationIngestFmsDTO htpDatasetSampleData);
+}
\ No newline at end of file
diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/crud/PredictedVariantConsequenceCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/PredictedVariantConsequenceCrudInterface.java
new file mode 100644
index 000000000..25139fde7
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/PredictedVariantConsequenceCrudInterface.java
@@ -0,0 +1,37 @@
+package org.alliancegenome.curation_api.interfaces.crud;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+import com.fasterxml.jackson.annotation.JsonView;
+
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+
+@Path("predictedvariantconsequence")
+@Tag(name = "CRUD - Predicted Variant Consequence")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface PredictedVariantConsequenceCrudInterface extends BaseIdCrudInterface<PredictedVariantConsequence> {
+
+	@POST
+	@Path("/bulk/{dataProvider}/transcriptConsequenceFile")
+	@JsonView(View.FieldsAndLists.class)
+	APIResponse updateTranscriptLevelConsequences(@PathParam("dataProvider") String dataProvider, List<VepTxtDTO> consequenceData);
+	
+	@POST
+	@Path("/bulk/{dataProvider}/geneConsequenceFile")
+	@JsonView(View.FieldsAndLists.class)
+	APIResponse updateGeneLevelConsequences(@PathParam("dataProvider") String dataProvider, List<VepTxtDTO> consequenceData);
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/crud/geneAssociations/GeneGenomicLocationAssociationCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/geneAssociations/GeneGenomicLocationAssociationCrudInterface.java
new file mode 100644
index 000000000..6b8a65d5e
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/interfaces/crud/geneAssociations/GeneGenomicLocationAssociationCrudInterface.java
@@ -0,0 +1,32 @@
+package org.alliancegenome.curation_api.interfaces.crud.geneAssociations;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.Gff3DTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+import com.fasterxml.jackson.annotation.JsonView;
+
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+
+@Path("/genegenomiclocation")
+@Tag(name = "CRUD - GeneGenomicLocationAssociation")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface GeneGenomicLocationAssociationCrudInterface extends BaseIdCrudInterface<GeneGenomicLocationAssociation> {
+
+	@POST
+	@Path("/bulk/{dataProvider}_{assemblyName}/geneLocations")
+	@JsonView(View.FieldsAndLists.class)
+	APIResponse updateGeneLocations(@PathParam("dataProvider") String dataProvider, @PathParam("assemblyName") String assemblyName, List<Gff3DTO> gff3Data);
+	
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/AgmDiseaseAnnotationExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/AgmDiseaseAnnotationExecutor.java
index 3e3cf0656..de4318c49 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/AgmDiseaseAnnotationExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/AgmDiseaseAnnotationExecutor.java
@@ -51,12 +51,10 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) {
 		bulkLoadFileHistory.getBulkLoadFile().setRecordCount(annotations.size() + bulkLoadFileHistory.getBulkLoadFile().getRecordCount());
 		bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile());
 
-		bulkLoadFileHistory.setCount(annotations.size());
-		updateHistory(bulkLoadFileHistory);
-		
-		boolean success = runLoad(agmDiseaseAnnotationService, bulkLoadFileHistory, dataProvider, annotations, annotationIdsLoaded);
+		String countType = "AGM Disease Annotations";
+		boolean success = runLoad(agmDiseaseAnnotationService, bulkLoadFileHistory, dataProvider, annotations, annotationIdsLoaded, countType);
 		if (success && cleanUp) {
-			runCleanup(diseaseAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, "AGM disease annotation");
+			runCleanup(diseaseAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, countType);
 		}
 		bulkLoadFileHistory.finishLoad();
 		updateHistory(bulkLoadFileHistory);
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/AlleleDiseaseAnnotationExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/AlleleDiseaseAnnotationExecutor.java
index 324f1e17e..eb3c6bc5a 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/AlleleDiseaseAnnotationExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/AlleleDiseaseAnnotationExecutor.java
@@ -50,14 +50,11 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) {
 
 		bulkLoadFileHistory.getBulkLoadFile().setRecordCount(annotations.size() + bulkLoadFileHistory.getBulkLoadFile().getRecordCount());
 		bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile());
-
-		bulkLoadFileHistory.setCount(annotations.size());
-		
-		updateHistory(bulkLoadFileHistory);
 		
-		boolean success = runLoad(alleleDiseaseAnnotationService, bulkLoadFileHistory, dataProvider, annotations, annotationIdsLoaded);
+		String countType = "Allele Disease Annotations";
+		boolean success = runLoad(alleleDiseaseAnnotationService, bulkLoadFileHistory, dataProvider, annotations, annotationIdsLoaded, countType);
 		if (success && cleanUp) {
-			runCleanup(diseaseAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, "allele disease annotation");
+			runCleanup(diseaseAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, countType);
 		}
 		bulkLoadFileHistory.finishLoad();
 		updateHistory(bulkLoadFileHistory);
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/BiogridOrcExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/BiogridOrcExecutor.java
index b90f3f015..f47f472bd 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/BiogridOrcExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/BiogridOrcExecutor.java
@@ -1,17 +1,30 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
 import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.zip.GZIPInputStream;
 
-import org.alliancegenome.curation_api.exceptions.ObjectUpdateException.ObjectUpdateExceptionData;
+import org.alliancegenome.curation_api.dao.CrossReferenceDAO;
+import org.alliancegenome.curation_api.dao.GeneDAO;
+import org.alliancegenome.curation_api.dao.ResourceDescriptorPageDAO;
 import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.entities.Organization;
+import org.alliancegenome.curation_api.model.entities.ResourceDescriptorPage;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
 import org.alliancegenome.curation_api.model.ingest.dto.fms.BiogridOrcFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.response.LoadHistoryResponce;
+import org.alliancegenome.curation_api.services.CrossReferenceService;
+import org.alliancegenome.curation_api.services.DataProviderService;
+import org.alliancegenome.curation_api.services.OrganizationService;
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
@@ -23,16 +36,44 @@
 import com.fasterxml.jackson.dataformat.csv.CsvSchema;
 
 import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 
 @ApplicationScoped
 public class BiogridOrcExecutor extends LoadFileExecutor {
 
+	@Inject
+	ResourceDescriptorPageDAO resourceDescriptorPageDAO;
+
+	@Inject
+	GeneDAO geneDAO;
+
+	@Inject
+	CrossReferenceDAO crossRefDAO;
+
+	@Inject
+	CrossReferenceService crossReferenceService;
+
+	@Inject
+	OrganizationService organizationService;
+
+	@Inject
+	DataProviderService dataProviderService;
+
 	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 		try (TarArchiveInputStream tarInputStream = new TarArchiveInputStream(
-			new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())))) {
+				new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())))) {
 			TarArchiveEntry tarEntry;
 
-			Set<String> biogridIds = new HashSet<>();
+			List<BiogridOrcFmsDTO> biogridData = new ArrayList<>();
+			String name = bulkLoadFileHistory.getBulkLoad().getName();
+			String dataProviderName = name.substring(0, name.indexOf(" "));
+
+			Organization organization = organizationService.getByAbbr(dataProviderName).getEntity();
+
+			HashMap<String, Object> rdpParams = new HashMap<>();
+			rdpParams.put("name", "biogrid/orcs");
+			ResourceDescriptorPage resourceDescriptorPage = resourceDescriptorPageDAO.findByParams(rdpParams)
+					.getSingleResult();
 
 			while ((tarEntry = tarInputStream.getNextEntry()) != null) {
 
@@ -53,40 +94,53 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 						.with(biogridOrcFmsSchema)
 						.readValues(tarInputStream.readAllBytes());
 
-				List<BiogridOrcFmsDTO> biogridData = it.readAll();
-				runLoad(bulkLoadFileHistory, biogridData, biogridIds);
+				biogridData.addAll(it.readAll());
 
 			}
+			runLoad(bulkLoadFileHistory, biogridData, resourceDescriptorPage, organization, dataProviderService);
+
 		} catch (Exception e) {
 			failLoad(bulkLoadFileHistory, e);
 			e.printStackTrace();
 		}
 	}
 
-	private boolean runLoad(BulkLoadFileHistory history, List<BiogridOrcFmsDTO> biogridList, Set<String> biogridIds) {
+	private boolean runLoad(BulkLoadFileHistory history, List<BiogridOrcFmsDTO> biogridList,
+			ResourceDescriptorPage resourceDescriptorPage, Organization organization,
+			DataProviderService dataProviderService) {
 		ProcessDisplayHelper ph = new ProcessDisplayHelper();
 		ph.addDisplayHandler(loadProcessDisplayService);
 		if (CollectionUtils.isNotEmpty(biogridList)) {
-			String loadMessage = biogridList.get(0).getClass().getSimpleName() + " update";
-			ph.startProcess(loadMessage, biogridList.size());
+			try {
+				String loadMessage = "BioGrid update";
+				Set<String> referencedCuries = populateEntrezIdsFromFiles(biogridList, history);
+				ph.startProcess(loadMessage, referencedCuries.size());
+				updateHistory(history);
 
-			updateHistory(history);
-			for (BiogridOrcFmsDTO biogridOrcFmsDTO : biogridList) {
-				try {
-					if (biogridOrcFmsDTO.getIdentifierType().equals("ENTREZ_GENE")) {
-						String identifier = "NCBI_Gene:" + biogridOrcFmsDTO.getIdentifierId();
-						biogridIds.add(identifier);
+				Map<String, Long> genomicEntityCrossRefMap = crossReferenceService
+						.getGenomicEntityCrossRefMap(referencedCuries);
+
+				for (String referencedCurie : referencedCuries) {
+
+					CrossReference newCrossRef = new CrossReference();
+					newCrossRef.setReferencedCurie(referencedCurie);
+					newCrossRef.setDisplayName("BioGRID CRISPR Screen Cell Line Phenotypes");
+					newCrossRef.setResourceDescriptorPage(resourceDescriptorPage);
+
+					CrossReference entity = crossReferenceService
+							.insertBioGridOrcCrossReference(newCrossRef, genomicEntityCrossRefMap.get(referencedCurie))
+							.getEntity();
+
+					if (entity != null) {
 						history.incrementCompleted();
 					} else {
 						history.incrementSkipped();
-
 					}
-				} catch (Exception e) {
-					e.printStackTrace();
-					history.incrementFailed();
-					addException(history,
-							new ObjectUpdateExceptionData(biogridOrcFmsDTO, e.getMessage(), e.getStackTrace()));
+
 				}
+			} catch (Exception e) {
+				e.printStackTrace();
+				history.incrementFailed();
 				ph.progressProcess();
 			}
 			updateHistory(history);
@@ -96,4 +150,42 @@ private boolean runLoad(BulkLoadFileHistory history, List<BiogridOrcFmsDTO> biog
 
 		return true;
 	}
+
+	public APIResponse runLoadApi(String dataProviderName, List<BiogridOrcFmsDTO> biogridDTOs) {
+		Organization organization = organizationService.getByAbbr(dataProviderName).getEntity();
+
+		HashMap<String, Object> rdpParams = new HashMap<>();
+		rdpParams.put("name", "biogrid/orcs");
+		ResourceDescriptorPage resourceDescriptorPage = resourceDescriptorPageDAO.findByParams(rdpParams)
+				.getSingleResult();
+
+		BulkLoadFileHistory history = new BulkLoadFileHistory(biogridDTOs.size());
+		history = bulkLoadFileHistoryDAO.persist(history);
+		runLoad(history, biogridDTOs, resourceDescriptorPage, organization, dataProviderService);
+		history.finishLoad();
+
+		return new LoadHistoryResponce(history);
+	}
+
+	private Set<String> populateEntrezIdsFromFiles(List<BiogridOrcFmsDTO> biogridList, BulkLoadFileHistory history) {
+		Set<String> biogridIds = new HashSet<>();
+
+		for (BiogridOrcFmsDTO biogridOrcFmsDTO : biogridList) {
+			try {
+				if (!biogridOrcFmsDTO.getIdentifierType().equals("ENTREZ_GENE")) {
+					history.incrementSkipped();
+					continue;
+				}
+
+				String identifier = "NCBI_Gene:" + biogridOrcFmsDTO.getIdentifierId();
+				biogridIds.add(identifier);
+
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		}
+
+		return biogridIds;
+
+	}
 }
\ No newline at end of file
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/BulkLoadJobExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/BulkLoadJobExecutor.java
index 9fe7ab0b3..fe45f99d5 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/BulkLoadJobExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/BulkLoadJobExecutor.java
@@ -21,6 +21,7 @@
 import org.alliancegenome.curation_api.jobs.executors.associations.constructAssociations.ConstructGenomicEntityAssociationExecutor;
 import org.alliancegenome.curation_api.jobs.executors.gff.Gff3CDSExecutor;
 import org.alliancegenome.curation_api.jobs.executors.gff.Gff3ExonExecutor;
+import org.alliancegenome.curation_api.jobs.executors.gff.Gff3GeneExecutor;
 import org.alliancegenome.curation_api.jobs.executors.gff.Gff3TranscriptExecutor;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
 
@@ -55,12 +56,19 @@ public class BulkLoadJobExecutor {
 	@Inject GeneExpressionExecutor geneExpressionExecutor;
 	@Inject SequenceTargetingReagentExecutor sqtrExecutor;
 	@Inject VariantFmsExecutor variantFmsExecutor;
+	@Inject HTPExpressionDatasetAnnotationExecutor htpExpressionDatasetAnnotationExecutor;
+	@Inject HTPExpressionDatasetSampleAnnotationExecutor htpExpressionDatasetSampleAnnotationExecutor;
+
 	@Inject Gff3ExonExecutor gff3ExonExecutor;
 	@Inject Gff3CDSExecutor gff3CDSExecutor;
+	@Inject Gff3GeneExecutor gff3GeneExecutor;
 	@Inject Gff3TranscriptExecutor gff3TranscriptExecutor;
+	@Inject VepTranscriptExecutor vepTranscriptExecutor;
+	@Inject VepGeneExecutor vepGeneExecutor;
 	
-	@Inject HTPExpressionDatasetAnnotationExecutor htpExpressionDatasetAnnotationExecutor;
 	@Inject ExpressionAtlasExecutor expressionAtlasExecutor;
+	@Inject
+	GeneOntologyAnnotationExecutor gafExecutor;
 
 	@Inject BiogridOrcExecutor biogridOrcExecutor;
 
@@ -132,12 +140,22 @@ public void process(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) th
 			gff3CDSExecutor.execLoad(bulkLoadFileHistory);
 		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.GFF_TRANSCRIPT) {
 			gff3TranscriptExecutor.execLoad(bulkLoadFileHistory);
+		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.GFF_GENE) {
+			gff3GeneExecutor.execLoad(bulkLoadFileHistory);
 		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.HTPDATASET) {
 			htpExpressionDatasetAnnotationExecutor.execLoad(bulkLoadFileHistory);
 		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.EXPRESSION_ATLAS) {
 			expressionAtlasExecutor.execLoad(bulkLoadFileHistory);
 		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.BIOGRID_ORCS) {
 			biogridOrcExecutor.execLoad(bulkLoadFileHistory);
+		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.VEPTRANSCRIPT) {
+			vepTranscriptExecutor.execLoad(bulkLoadFileHistory);
+		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.VEPGENE) {
+			vepGeneExecutor.execLoad(bulkLoadFileHistory);
+		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.HTPDATASAMPLE) {
+			htpExpressionDatasetSampleAnnotationExecutor.execLoad(bulkLoadFileHistory);
+		} else if (bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() == BackendBulkLoadType.GAF) {
+			gafExecutor.execLoad(bulkLoadFileHistory);
 		} else {
 			log.info("Load: " + bulkLoadFileHistory.getBulkLoad().getName() + " for type " + bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() + " not implemented");
 			throw new Exception("Load: " + bulkLoadFileHistory.getBulkLoad().getName() + " for type " + bulkLoadFileHistory.getBulkLoad().getBackendBulkLoadType() + " not implemented");
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/ExpressionAtlasExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/ExpressionAtlasExecutor.java
index b8bbb4e25..d5e36f8e9 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/ExpressionAtlasExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/ExpressionAtlasExecutor.java
@@ -1,10 +1,13 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
-import com.fasterxml.jackson.dataformat.xml.XmlMapper;
-import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
-import lombok.extern.jbosslog.JBossLog;
+import static org.alliancegenome.curation_api.services.DataProviderService.RESOURCE_DESCRIPTOR_PREFIX;
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+
 import org.alliancegenome.curation_api.model.entities.CrossReference;
 import org.alliancegenome.curation_api.model.entities.DataProvider;
 import org.alliancegenome.curation_api.model.entities.Organization;
@@ -17,15 +20,12 @@
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
 import org.jetbrains.annotations.NotNull;
 
-import java.io.IOException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
+import com.fasterxml.jackson.dataformat.xml.XmlMapper;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
 
-import static org.alliancegenome.curation_api.services.DataProviderService.RESOURCE_DESCRIPTOR_PREFIX;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 
-@JBossLog
 @ApplicationScoped
 public class ExpressionAtlasExecutor extends LoadFileExecutor {
 
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneDiseaseAnnotationExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneDiseaseAnnotationExecutor.java
index 07a68d88e..2e0c8c5a1 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneDiseaseAnnotationExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneDiseaseAnnotationExecutor.java
@@ -51,12 +51,10 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) {
 		bulkLoadFileHistory.getBulkLoadFile().setRecordCount(annotations.size() + bulkLoadFileHistory.getBulkLoadFile().getRecordCount());
 		bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile());
 
-		bulkLoadFileHistory.setCount(annotations.size());
-		updateHistory(bulkLoadFileHistory);
-
-		boolean success = runLoad(geneDiseaseAnnotationService, bulkLoadFileHistory, dataProvider, annotations, annotationIdsLoaded);
+		String countType = "Gene Disease Annotations";
+		boolean success = runLoad(geneDiseaseAnnotationService, bulkLoadFileHistory, dataProvider, annotations, annotationIdsLoaded, countType);
 		if (success && cleanUp) {
-			runCleanup(diseaseAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, "gene disease annotation");
+			runCleanup(diseaseAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, countType);
 		}
 		bulkLoadFileHistory.finishLoad();
 		updateHistory(bulkLoadFileHistory);
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneExpressionExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneExpressionExecutor.java
index a3898eca6..57150355b 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneExpressionExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneExpressionExecutor.java
@@ -1,26 +1,37 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.model.entities.GeneExpressionAnnotation;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.GeneExpressionFmsDTO;
 import org.alliancegenome.curation_api.model.ingest.dto.fms.GeneExpressionIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.response.LoadHistoryResponce;
 import org.alliancegenome.curation_api.services.GeneExpressionAnnotationService;
+import org.alliancegenome.curation_api.services.GeneExpressionExperimentService;
+import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
 import org.apache.commons.lang3.StringUtils;
 
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.zip.GZIPInputStream;
 
 @ApplicationScoped
 public class GeneExpressionExecutor extends LoadFileExecutor {
-	@Inject
-	GeneExpressionAnnotationService geneExpressionAnnotationService;
+	@Inject GeneExpressionAnnotationService geneExpressionAnnotationService;
+	@Inject GeneExpressionExperimentService geneExpressionExperimentService;
+	static final String ANNOTATIONS = "Annotations";
+	static final String EXPERIMENTS = "Experiments";
+
 
 	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 		try {
@@ -37,23 +48,69 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 			}
 			bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile());
 
-			bulkLoadFileHistory.setCount(geneExpressionIngestFmsDTO.getData().size());
-			updateHistory(bulkLoadFileHistory);
-			
 			List<Long> annotationIdsLoaded = new ArrayList<>();
 			List<Long> annotationIdsBefore = geneExpressionAnnotationService.getAnnotationIdsByDataProvider(dataProvider);
 
-			boolean success = runLoad(geneExpressionAnnotationService, bulkLoadFileHistory, dataProvider, geneExpressionIngestFmsDTO.getData(), annotationIdsLoaded);
+			List<Long> experimentIdsLoaded = new ArrayList<>();
+			List<Long> experimentIdsBefore = geneExpressionExperimentService.getExperimentIdsByDataProvider(dataProvider);
+
+			boolean success = runLoad(geneExpressionAnnotationService, bulkLoadFileHistory, dataProvider, geneExpressionIngestFmsDTO.getData(), annotationIdsLoaded, ANNOTATIONS);
+
 			if (success) {
-				runCleanup(geneExpressionAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, "gene expression annotation");
+				runCleanup(geneExpressionAnnotationService, bulkLoadFileHistory, dataProvider.name(), annotationIdsBefore, annotationIdsLoaded, ANNOTATIONS);
+				loadExperiments(bulkLoadFileHistory, dataProvider, experimentIdsLoaded);
+				runCleanup(geneExpressionExperimentService, bulkLoadFileHistory, dataProvider.name(), experimentIdsBefore, experimentIdsLoaded, EXPERIMENTS);
 			}
 
 			bulkLoadFileHistory.finishLoad();
 			updateHistory(bulkLoadFileHistory);
 			updateExceptions(bulkLoadFileHistory);
+
 		} catch (Exception e) {
 			failLoad(bulkLoadFileHistory, e);
 			e.printStackTrace();
 		}
 	}
+
+	public APIResponse runLoadAPI(GeneExpressionAnnotationService service, String dataProviderName, List<GeneExpressionFmsDTO> objectList) {
+		List<Long> idsLoaded = new ArrayList<>();
+		BulkLoadFileHistory history = new BulkLoadFileHistory(objectList.size());
+		history = bulkLoadFileHistoryDAO.persist(history);
+		BackendBulkDataProvider dataProvider = null;
+		if (dataProviderName != null) {
+			dataProvider = BackendBulkDataProvider.valueOf(dataProviderName);
+		}
+		boolean success = runLoad(service, history, dataProvider, objectList, idsLoaded, true, ANNOTATIONS);
+		if (success) {
+			loadExperiments(history, dataProvider, new ArrayList<>());
+		}
+		history.finishLoad();
+		return new LoadHistoryResponce(history);
+	}
+
+	private void loadExperiments(BulkLoadFileHistory history, BackendBulkDataProvider dataProvider, List<Long> experimentIdsLoaded) {
+		ProcessDisplayHelper ph = new ProcessDisplayHelper();
+		Map<String, Set<String>> experiments = geneExpressionAnnotationService.getExperiments();
+		ph.startProcess("Saving gene expression experiments: ", experiments.size());
+		history.setCount(EXPERIMENTS, geneExpressionAnnotationService.getExperiments().size());
+		for (String experimentId: experiments.keySet()) {
+			try {
+				GeneExpressionExperiment experiment = geneExpressionExperimentService.upsert(experimentId, experiments.get(experimentId), dataProvider);
+				if (experiment != null) {
+					experimentIdsLoaded.add(experiment.getId());
+					history.incrementCompleted(EXPERIMENTS);
+				}
+			} catch (ObjectUpdateException e) {
+				history.incrementFailed(EXPERIMENTS);
+				addException(history, e.getData());
+			} catch (Exception e) {
+				e.printStackTrace();
+				history.incrementFailed(EXPERIMENTS);
+				addException(history, new ObjectUpdateException.ObjectUpdateExceptionData(experimentId, e.getMessage(), e.getStackTrace()));
+			}
+			ph.progressProcess();
+		}
+		updateHistory(history);
+		ph.finishProcess();
+	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneGeneticInteractionExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneGeneticInteractionExecutor.java
index 74e9c0259..4d6a5084e 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneGeneticInteractionExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneGeneticInteractionExecutor.java
@@ -1,10 +1,11 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
+import com.fasterxml.jackson.databind.MappingIterator;
+import com.fasterxml.jackson.dataformat.csv.CsvMapper;
+import com.fasterxml.jackson.dataformat.csv.CsvParser;
+import com.fasterxml.jackson.dataformat.csv.CsvSchema;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.dao.GeneGeneticInteractionDAO;
 import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
@@ -12,13 +13,10 @@
 import org.alliancegenome.curation_api.services.GeneGeneticInteractionService;
 import org.alliancegenome.curation_api.services.GeneInteractionService;
 
-import com.fasterxml.jackson.databind.MappingIterator;
-import com.fasterxml.jackson.dataformat.csv.CsvMapper;
-import com.fasterxml.jackson.dataformat.csv.CsvParser;
-import com.fasterxml.jackson.dataformat.csv.CsvSchema;
-
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 @ApplicationScoped
 public class GeneGeneticInteractionExecutor extends LoadFileExecutor {
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneMolecularInteractionExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneMolecularInteractionExecutor.java
index 482ee00be..1714fd19d 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneMolecularInteractionExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneMolecularInteractionExecutor.java
@@ -1,10 +1,11 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
+import com.fasterxml.jackson.databind.MappingIterator;
+import com.fasterxml.jackson.dataformat.csv.CsvMapper;
+import com.fasterxml.jackson.dataformat.csv.CsvParser;
+import com.fasterxml.jackson.dataformat.csv.CsvSchema;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.dao.GeneMolecularInteractionDAO;
 import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
@@ -12,13 +13,10 @@
 import org.alliancegenome.curation_api.services.GeneInteractionService;
 import org.alliancegenome.curation_api.services.GeneMolecularInteractionService;
 
-import com.fasterxml.jackson.databind.MappingIterator;
-import com.fasterxml.jackson.dataformat.csv.CsvMapper;
-import com.fasterxml.jackson.dataformat.csv.CsvParser;
-import com.fasterxml.jackson.dataformat.csv.CsvSchema;
-
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 @ApplicationScoped
 public class GeneMolecularInteractionExecutor extends LoadFileExecutor {
@@ -37,10 +35,10 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 
 			List<Long> interactionIdsLoaded = new ArrayList<>();
 			List<Long> interactionIdsBefore = geneMolecularInteractionDAO.findAllIds().getResults();
-			
+
 			bulkLoadFileHistory.setCount(interactionData.size());
 			updateHistory(bulkLoadFileHistory);
-			
+
 			boolean success = runLoad(geneMolecularInteractionService, bulkLoadFileHistory, null, interactionData, interactionIdsLoaded, false);
 			if (success) {
 				runCleanup(geneInteractionService, bulkLoadFileHistory, "COMBINED", interactionIdsBefore, interactionIdsLoaded, "gene molecular interaction");
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneOntologyAnnotationExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneOntologyAnnotationExecutor.java
new file mode 100644
index 000000000..9df7d1b29
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneOntologyAnnotationExecutor.java
@@ -0,0 +1,115 @@
+package org.alliancegenome.curation_api.jobs.executors;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+import lombok.extern.jbosslog.JBossLog;
+import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
+import org.alliancegenome.curation_api.model.entities.GeneOntologyAnnotation;
+import org.alliancegenome.curation_api.model.entities.Organization;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
+import org.alliancegenome.curation_api.model.ingest.dto.GeneOntologyAnnotationDTO;
+import org.alliancegenome.curation_api.services.GeneOntologyAnnotationService;
+import org.alliancegenome.curation_api.services.OrganizationService;
+import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
+import org.apache.commons.lang3.StringUtils;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+import java.util.zip.GZIPInputStream;
+
+@JBossLog
+@ApplicationScoped
+public class GeneOntologyAnnotationExecutor extends LoadFileExecutor {
+
+	@Inject
+	GeneOntologyAnnotationService service;
+	@Inject
+	OrganizationService organizationService;
+
+	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException {
+
+		String abbr = ((BulkFMSLoad) bulkLoadFileHistory.getBulkLoad()).getFmsDataSubType();
+		Organization organization = organizationService.getByAbbr(abbr).getEntity();
+
+		// curie, List<GO curie>
+		Map<String, List<String>> uiMap = new HashMap<>();
+		GZIPInputStream stream = new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath()));
+		try (BufferedReader br = new BufferedReader(new InputStreamReader(stream))) {
+			Stream<String> lines = br.lines();
+
+			// Process each line
+			lines.filter(s -> !s.startsWith("!") && StringUtils.isNotEmpty(s)).forEach(s -> {
+				String[] token = s.split("\t");
+				String orgID = token[0];
+				String modID = token[1];
+				String goID = token[4];
+				if (abbr.equalsIgnoreCase(orgID) || orgID.equalsIgnoreCase("Xenbase") || abbr.equals("HUMAN") && orgID.equals("RGD")) {
+					List<String> goIDs = uiMap.computeIfAbsent(modID, list -> new ArrayList<>());
+					goIDs.add(goID);
+				}
+			});
+
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		String name = bulkLoadFileHistory.getBulkLoad().getName();
+
+		Map<Long, GeneOntologyAnnotationDTO> gafMap = service.getGafMap(organization);
+		List<Long> gafIdsBefore = new ArrayList<>(gafMap.keySet().stream().toList());
+		gafIdsBefore.removeIf(Objects::isNull);
+
+		List<Long> geneGoIdsLoaded = new ArrayList<>();
+		ProcessDisplayHelper ph = new ProcessDisplayHelper();
+		ph.addDisplayHandler(loadProcessDisplayService);
+		Set<GeneOntologyAnnotationDTO> dtos = uiMap.entrySet()
+			.stream()
+			.map(entry -> entry.getValue().stream().map(goID -> {
+				GeneOntologyAnnotationDTO dto = new GeneOntologyAnnotationDTO();
+				String prefix = abbr;
+				if (abbr.equalsIgnoreCase("XB")) {
+					prefix = "Xenbase";
+				}
+				if (abbr.equalsIgnoreCase("HUMAN")) {
+					prefix = null;
+				}
+				String geneIdentifier = prefix != null ? prefix + ":" + entry.getKey() : entry.getKey();
+				dto.setGeneIdentifier(geneIdentifier);
+				dto.setGoTermCurie(goID);
+				return dto;
+			}).toList()).flatMap(Collection::stream).collect(Collectors.toSet());
+
+		ph.startProcess(name, dtos.size());
+		for (GeneOntologyAnnotationDTO modID : dtos) {
+			Long geneID = service.getGeneID(modID, abbr);
+			if (geneID != null) {
+				GeneOntologyAnnotation newGaf = service.insert(modID, abbr).getEntity();
+				if (newGaf != null) {
+					geneGoIdsLoaded.add(newGaf.getId());
+					bulkLoadFileHistory.incrementCompleted();
+				} else {
+					bulkLoadFileHistory.incrementSkipped();
+				}
+			} else {
+				addException(bulkLoadFileHistory, new ObjectUpdateException.ObjectUpdateExceptionData(modID, "Could not find gene " + modID.getGeneIdentifier(), null));
+				bulkLoadFileHistory.incrementFailed();
+			}
+			ph.progressProcess();
+		}
+		bulkLoadFileHistory.setTotalCount(dtos.size());
+		runCleanup(service, bulkLoadFileHistory, abbr, gafIdsBefore, geneGoIdsLoaded, "GAF Load");
+		ph.finishProcess();
+		updateHistory(bulkLoadFileHistory);
+
+		bulkLoadFileHistory.finishLoad();
+		updateHistory(bulkLoadFileHistory);
+		updateExceptions(bulkLoadFileHistory);
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/HTPExpressionDatasetSampleAnnotationExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/HTPExpressionDatasetSampleAnnotationExecutor.java
new file mode 100644
index 000000000..f2c12bf3d
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/HTPExpressionDatasetSampleAnnotationExecutor.java
@@ -0,0 +1,68 @@
+package org.alliancegenome.curation_api.jobs.executors;
+
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+import org.alliancegenome.curation_api.dao.ExternalDataBaseEntityDAO;
+import org.alliancegenome.curation_api.dao.HTPExpressionDatasetSampleAnnotationDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetSampleAnnotation;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetSampleAnnotationIngestFmsDTO;
+import org.alliancegenome.curation_api.services.ExternalDataBaseEntityService;
+import org.alliancegenome.curation_api.services.HTPExpressionDatasetSampleAnnotationService;
+import org.apache.commons.lang3.StringUtils;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+
+@ApplicationScoped
+public class HTPExpressionDatasetSampleAnnotationExecutor extends LoadFileExecutor {
+
+	@Inject ExternalDataBaseEntityService externalDataBaseEntityService;
+	@Inject ExternalDataBaseEntityDAO externalDataBaseEntityDAO;
+	@Inject HTPExpressionDatasetSampleAnnotationService htpExpressionDatasetSampleAnnotationService;
+	@Inject HTPExpressionDatasetSampleAnnotationDAO htpExpressionDatasetSampleAnnotationDAO;
+
+	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
+		try {
+			BulkFMSLoad fms = (BulkFMSLoad) bulkLoadFileHistory.getBulkLoad();
+
+			HTPExpressionDatasetSampleAnnotationIngestFmsDTO htpExpressionDatasetSampleData = mapper.readValue(new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())), HTPExpressionDatasetSampleAnnotationIngestFmsDTO.class);
+			bulkLoadFileHistory.getBulkLoadFile().setRecordCount(htpExpressionDatasetSampleData.getData().size());
+
+			AGRCurationSchemaVersion version = HTPExpressionDatasetSampleAnnotation.class.getAnnotation(AGRCurationSchemaVersion.class);
+			bulkLoadFileHistory.getBulkLoadFile().setLinkMLSchemaVersion(version.max());
+			if (htpExpressionDatasetSampleData.getMetaData() != null && StringUtils.isNotBlank(htpExpressionDatasetSampleData.getMetaData().getRelease())) {
+			bulkLoadFileHistory.getBulkLoadFile().setAllianceMemberReleaseVersion(htpExpressionDatasetSampleData.getMetaData().getRelease());
+			}
+
+			BackendBulkDataProvider dataProvider = BackendBulkDataProvider.valueOf(fms.getFmsDataSubType());
+			List<Long> htpAnnotationsIdsLoaded = new ArrayList<>();
+			List<Long> previousIds = htpExpressionDatasetSampleAnnotationService.getAnnotationIdsByDataProvider(dataProvider.name());
+			
+			bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile());
+
+			bulkLoadFileHistory.setCount((long) htpExpressionDatasetSampleData.getData().size());
+			updateHistory(bulkLoadFileHistory);
+			
+			boolean success = runLoad(htpExpressionDatasetSampleAnnotationService, bulkLoadFileHistory, dataProvider, htpExpressionDatasetSampleData.getData(), htpAnnotationsIdsLoaded);
+			
+			if (success) {
+				runCleanup(htpExpressionDatasetSampleAnnotationService, bulkLoadFileHistory, dataProvider.name(), previousIds, htpAnnotationsIdsLoaded, fms.getFmsDataType());
+			}
+			bulkLoadFileHistory.finishLoad();
+
+			updateHistory(bulkLoadFileHistory);
+			updateExceptions(bulkLoadFileHistory);
+
+		} catch (Exception e) {
+			failLoad(bulkLoadFileHistory, e);
+			e.printStackTrace();
+		}
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/LoadFileExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/LoadFileExecutor.java
index d7b6b8b52..ef1034f1d 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/LoadFileExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/LoadFileExecutor.java
@@ -1,14 +1,8 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.stream.Collectors;
-import java.util.zip.GZIPInputStream;
-
+import com.fasterxml.jackson.databind.ObjectMapper;
+import io.quarkus.logging.Log;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.dao.loads.BulkLoadFileDAO;
 import org.alliancegenome.curation_api.dao.loads.BulkLoadFileExceptionDAO;
 import org.alliancegenome.curation_api.dao.loads.BulkLoadFileHistoryDAO;
@@ -35,10 +29,10 @@
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.StringUtils;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import io.quarkus.logging.Log;
-import jakarta.inject.Inject;
+import java.io.FileInputStream;
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.zip.GZIPInputStream;
 
 public class LoadFileExecutor {
 
@@ -124,9 +118,9 @@ protected IngestDTO readIngestFile(BulkLoadFileHistory bulkLoadFileHistory, Clas
 			if (StringUtils.isNotBlank(ingestDto.getAllianceMemberReleaseVersion())) {
 				bulkLoadFileHistory.getBulkLoadFile().setAllianceMemberReleaseVersion(ingestDto.getAllianceMemberReleaseVersion());
 			}
-			
+
 			bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile());
-			
+
 			if (!checkSchemaVersion(bulkLoadFileHistory, dtoClass)) {
 				return null;
 			}
@@ -190,16 +184,24 @@ public <E extends AuditedObject, T extends BaseDTO> APIResponse runLoadApi(BaseU
 		if (dataProviderName != null) {
 			dataProvider = BackendBulkDataProvider.valueOf(dataProviderName);
 		}
-		runLoad(service, history, dataProvider, objectList, idsLoaded, true);
+		runLoad(service, history, dataProvider, objectList, idsLoaded, true, "Records");
 		history.finishLoad();
 		return new LoadHistoryResponce(history);
 	}
-	
+
 	protected <E extends AuditedObject, T extends BaseDTO> boolean runLoad(BaseUpsertServiceInterface<E, T> service, BulkLoadFileHistory history, BackendBulkDataProvider dataProvider, List<T> objectList, List<Long> idsAdded) {
-		return runLoad(service, history, dataProvider, objectList, idsAdded, true);
+		return runLoad(service, history, dataProvider, objectList, idsAdded, true, "Records");
 	}
 
 	protected <E extends AuditedObject, T extends BaseDTO> boolean runLoad(BaseUpsertServiceInterface<E, T> service, BulkLoadFileHistory history, BackendBulkDataProvider dataProvider, List<T> objectList, List<Long> idsAdded, Boolean terminateFailing) {
+		return runLoad(service, history, dataProvider, objectList, idsAdded, terminateFailing, "Records");
+	}
+
+	protected <E extends AuditedObject, T extends BaseDTO> boolean runLoad(BaseUpsertServiceInterface<E, T> service, BulkLoadFileHistory history, BackendBulkDataProvider dataProvider, List<T> objectList, List<Long> idsAdded, String countType) {
+		return runLoad(service, history, dataProvider, objectList, idsAdded, true, countType);
+	}
+
+	protected <E extends AuditedObject, T extends BaseDTO> boolean runLoad(BaseUpsertServiceInterface<E, T> service, BulkLoadFileHistory history, BackendBulkDataProvider dataProvider, List<T> objectList, List<Long> idsAdded, Boolean terminateFailing, String countType) {
 		ProcessDisplayHelper ph = new ProcessDisplayHelper();
 		ph.addDisplayHandler(loadProcessDisplayService);
 		if (CollectionUtils.isNotEmpty(objectList)) {
@@ -208,28 +210,28 @@ protected <E extends AuditedObject, T extends BaseDTO> boolean runLoad(BaseUpser
 				loadMessage = loadMessage + " for " + dataProvider.name();
 			}
 			ph.startProcess(loadMessage, objectList.size());
-			
+
+			history.setCount(countType, objectList.size());
 			updateHistory(history);
 			for (T dtoObject : objectList) {
 				try {
 					E dbObject = service.upsert(dtoObject, dataProvider);
-					history.incrementCompleted();
+					history.incrementCompleted(countType);
 					if (idsAdded != null) {
 						idsAdded.add(dbObject.getId());
 					}
 				} catch (ObjectUpdateException e) {
-					// e.printStackTrace();
-					history.incrementFailed();
+					history.incrementFailed(countType);
 					addException(history, e.getData());
 				} catch (KnownIssueValidationException e) {
 					Log.debug(e.getMessage());
-					history.incrementSkipped();
+					history.incrementSkipped(countType);
 				} catch (Exception e) {
-					// e.printStackTrace();
-					history.incrementFailed();
+					e.printStackTrace();
+					history.incrementFailed(countType);
 					addException(history, new ObjectUpdateExceptionData(dtoObject, e.getMessage(), e.getStackTrace()));
 				}
-				if (terminateFailing && history.getErrorRate() > 0.25) {
+				if (terminateFailing && history.getErrorRate(countType) > 0.25) {
 					Log.error("Failure Rate > 25% aborting load");
 					updateHistory(history);
 					updateExceptions(history);
@@ -260,12 +262,12 @@ protected <E extends AuditedObject, T extends BaseDTO> boolean runLoad(BaseUpser
 		Log.debug("runLoad: Remove: " + dataProviderName + " " + idsToRemove.size());
 
 		String countType = loadTypeString + " Deleted";
-		
+
 		long existingDeletes = history.getCount(countType).getTotal() == null ? 0 : history.getCount(countType).getTotal();
 		history.setCount(countType, idsToRemove.size() + existingDeletes);
 
 		String loadDescription = dataProviderName + " " + loadTypeString + " bulk load (" + history.getBulkLoadFile().getMd5Sum() + ")";
-		
+
 		ProcessDisplayHelper ph = new ProcessDisplayHelper(10000);
 		ph.startProcess("Deletion/deprecation of: " + dataProviderName + " " + loadTypeString, idsToRemove.size());
 		//updateHistory(history);
@@ -303,7 +305,7 @@ protected void failLoad(BulkLoadFileHistory bulkLoadFileHistory, Exception e) {
 		slackNotifier.slackalert(bulkLoadFileHistory);
 		updateHistory(bulkLoadFileHistory);
 	}
-	
+
 	protected void failLoadAboveErrorRateCutoff(BulkLoadFileHistory bulkLoadFileHistory) {
 		bulkLoadFileHistory.setBulkloadStatus(JobStatus.FAILED);
 		bulkLoadFileHistory.setErrorMessage("Failure rate exceeded cutoff");
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/ParalogyExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/ParalogyExecutor.java
index a4f5ff276..113871b64 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/ParalogyExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/ParalogyExecutor.java
@@ -1,10 +1,8 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
+import io.quarkus.logging.Log;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.dao.GeneToGeneParalogyDAO;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
@@ -15,9 +13,10 @@
 import org.alliancegenome.curation_api.services.GeneToGeneParalogyService;
 import org.apache.commons.lang3.StringUtils;
 
-import io.quarkus.logging.Log;
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 @ApplicationScoped
 public class ParalogyExecutor extends LoadFileExecutor {
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/VepGeneExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/VepGeneExecutor.java
new file mode 100644
index 000000000..ac4659bc3
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/VepGeneExecutor.java
@@ -0,0 +1,169 @@
+package org.alliancegenome.curation_api.jobs.executors;
+
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+import java.util.zip.GZIPInputStream;
+
+import org.alliancegenome.curation_api.dao.PredictedVariantConsequenceDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.KnownIssueValidationException;
+import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
+import org.alliancegenome.curation_api.exceptions.ObjectUpdateException.ObjectUpdateExceptionData;
+import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.response.LoadHistoryResponce;
+import org.alliancegenome.curation_api.services.PredictedVariantConsequenceService;
+import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.ListUtils;
+
+import com.fasterxml.jackson.databind.MappingIterator;
+import com.fasterxml.jackson.dataformat.csv.CsvMapper;
+import com.fasterxml.jackson.dataformat.csv.CsvParser;
+import com.fasterxml.jackson.dataformat.csv.CsvSchema;
+
+import io.quarkus.logging.Log;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+
+@ApplicationScoped
+public class VepGeneExecutor extends LoadFileExecutor {
+
+	@Inject PredictedVariantConsequenceDAO predictedVariantConsequenceDAO;
+	@Inject PredictedVariantConsequenceService predictedVariantConsequenceService;
+
+	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
+		try {
+
+			CsvSchema vepTxtSchema = CsvSchemaBuilder.vepTxtSchema();
+			CsvMapper csvMapper = new CsvMapper();
+			MappingIterator<VepTxtDTO> it = csvMapper.enable(CsvParser.Feature.INSERT_NULLS_FOR_MISSING_COLUMNS).readerFor(VepTxtDTO.class).with(vepTxtSchema).readValues(new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())));
+			List<VepTxtDTO> vepData = it.readAll();
+			
+
+			BulkFMSLoad fmsLoad = (BulkFMSLoad) bulkLoadFileHistory.getBulkLoad();
+			BackendBulkDataProvider dataProvider = BackendBulkDataProvider.valueOf(fmsLoad.getFmsDataSubType());
+
+			List<Long> consequenceIdsLoaded = new ArrayList<>();
+			List<Long> consequenceIdsBefore = predictedVariantConsequenceService.getGeneLevelIdsByDataProvider(dataProvider);
+			
+			bulkLoadFileHistory.setCount(vepData.size());
+			updateHistory(bulkLoadFileHistory);
+			
+			boolean success = runLoad(bulkLoadFileHistory, dataProvider, vepData, consequenceIdsLoaded);
+			if (success) {
+				runCleanup(predictedVariantConsequenceService, bulkLoadFileHistory, dataProvider.name(), consequenceIdsBefore, consequenceIdsLoaded, "gene-level predicted variant consequences");
+			}
+			bulkLoadFileHistory.finishLoad();
+			updateHistory(bulkLoadFileHistory);
+			updateExceptions(bulkLoadFileHistory);
+
+		} catch (Exception e) {
+			failLoad(bulkLoadFileHistory, e);
+			e.printStackTrace();
+		}
+	}
+	
+	protected boolean runLoad(BulkLoadFileHistory history, BackendBulkDataProvider dataProvider, List<VepTxtDTO> objectList, List<Long> idsUpdated) {
+		ProcessDisplayHelper ph = new ProcessDisplayHelper();
+		ph.addDisplayHandler(loadProcessDisplayService);
+		if (CollectionUtils.isNotEmpty(objectList)) {
+			String loadMessage = objectList.get(0).getClass().getSimpleName() + " update";
+			if (dataProvider != null) {
+				loadMessage = loadMessage + " for " + dataProvider.name();
+			}
+			ph.startProcess(loadMessage, objectList.size());
+			
+			updateHistory(history);
+			for (VepTxtDTO dtoObject : objectList) {
+				try {
+					Long idUpdated = predictedVariantConsequenceService.updateGeneLevelConsequence(dtoObject);
+					history.incrementCompleted();
+					if (idsUpdated != null) {
+						idsUpdated.add(idUpdated);
+					}
+				} catch (ObjectUpdateException e) {
+					history.incrementFailed();
+					addException(history, e.getData());
+				} catch (KnownIssueValidationException e) {
+					Log.debug(e.getMessage());
+					history.incrementSkipped();
+				} catch (Exception e) {
+					e.printStackTrace();
+					history.incrementFailed();
+					addException(history, new ObjectUpdateExceptionData(dtoObject, e.getMessage(), e.getStackTrace()));
+				}
+				if (history.getErrorRate() > 0.25) {
+					Log.error("Failure Rate > 25% aborting load");
+					updateHistory(history);
+					updateExceptions(history);
+					failLoadAboveErrorRateCutoff(history);
+					return false;
+				}
+				ph.progressProcess();
+			}
+			updateHistory(history);
+			updateExceptions(history);
+			ph.finishProcess();
+		}
+		return true;
+	}
+	
+	protected void runCleanup(BulkLoadFileHistory history, String dataProviderName, List<Long> annotationIdsBefore, List<Long> annotationIdsAfter, String loadTypeString, Boolean deprecate) {
+		Log.debug("runLoad: After: " + dataProviderName + " " + annotationIdsAfter.size());
+
+		List<Long> distinctAfter = annotationIdsAfter.stream().distinct().collect(Collectors.toList());
+		Log.debug("runLoad: Distinct: " + dataProviderName + " " + distinctAfter.size());
+
+		List<Long> idsToReset = ListUtils.subtract(annotationIdsBefore, distinctAfter);
+		Log.debug("runLoad: Reset: " + dataProviderName + " " + idsToReset.size());
+
+		String countType = loadTypeString + " reset";
+		
+		long existingResets = history.getCount(countType).getTotal() == null ? 0 : history.getCount(countType).getTotal();
+		history.setCount(countType, idsToReset.size() + existingResets);
+
+		String loadDescription = dataProviderName + " " + loadTypeString + " bulk load (" + history.getBulkLoadFile().getMd5Sum() + ")";
+		
+		ProcessDisplayHelper ph = new ProcessDisplayHelper(10000);
+		ph.startProcess("Deletion/deprecation of: " + dataProviderName + " " + loadTypeString, idsToReset.size());
+		
+		for (Long id : idsToReset) {
+			try {
+				predictedVariantConsequenceService.resetGeneLevelConsequence(id, loadDescription);
+				history.incrementCompleted(countType);
+			} catch (Exception e) {
+				history.incrementFailed(countType);
+				addException(history, new ObjectUpdateExceptionData("{ \"id\": " + id + "}", e.getMessage(), e.getStackTrace()));
+			}
+			if (history.getErrorRate(countType) > 0.25) {
+				Log.error(countType + " failure rate > 25% aborting load");
+				failLoadAboveErrorRateCutoff(history);
+				break;
+			}
+			ph.progressProcess();
+		}
+		updateHistory(history);
+		updateExceptions(history);
+		ph.finishProcess();
+	}
+
+	public APIResponse runLoadApi(String dataProviderName, List<VepTxtDTO> consequenceData) {
+		List<Long> idsLoaded = new ArrayList<>();
+		BulkLoadFileHistory history = new BulkLoadFileHistory(consequenceData.size());
+		history = bulkLoadFileHistoryDAO.persist(history);
+		BackendBulkDataProvider dataProvider = null;
+		if (dataProviderName != null) {
+			dataProvider = BackendBulkDataProvider.valueOf(dataProviderName);
+		}
+		runLoad(history, dataProvider, consequenceData, idsLoaded);
+		history.finishLoad();
+		return new LoadHistoryResponce(history);
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/VepTranscriptExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/VepTranscriptExecutor.java
new file mode 100644
index 000000000..dfa877ad4
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/VepTranscriptExecutor.java
@@ -0,0 +1,62 @@
+package org.alliancegenome.curation_api.jobs.executors;
+
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+import org.alliancegenome.curation_api.dao.PredictedVariantConsequenceDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.services.PredictedVariantConsequenceService;
+
+import com.fasterxml.jackson.databind.MappingIterator;
+import com.fasterxml.jackson.dataformat.csv.CsvMapper;
+import com.fasterxml.jackson.dataformat.csv.CsvParser;
+import com.fasterxml.jackson.dataformat.csv.CsvSchema;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+
+@ApplicationScoped
+public class VepTranscriptExecutor extends LoadFileExecutor {
+
+	@Inject PredictedVariantConsequenceDAO predictedVariantConsequenceDAO;
+	@Inject PredictedVariantConsequenceService predictedVariantConsequenceService;
+
+	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
+		try {
+
+			CsvSchema vepTxtSchema = CsvSchemaBuilder.vepTxtSchema();
+			CsvMapper csvMapper = new CsvMapper();
+			MappingIterator<VepTxtDTO> it = csvMapper.enable(CsvParser.Feature.INSERT_NULLS_FOR_MISSING_COLUMNS).readerFor(VepTxtDTO.class).with(vepTxtSchema).readValues(new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())));
+			List<VepTxtDTO> vepData = it.readAll();
+			
+
+			BulkFMSLoad fmsLoad = (BulkFMSLoad) bulkLoadFileHistory.getBulkLoad();
+			BackendBulkDataProvider dataProvider = BackendBulkDataProvider.valueOf(fmsLoad.getFmsDataSubType());
+
+			List<Long> consequenceIdsLoaded = new ArrayList<>();
+			List<Long> consequenceIdsBefore = predictedVariantConsequenceService.getIdsByDataProvider(dataProvider);
+			
+			bulkLoadFileHistory.setCount(vepData.size());
+			updateHistory(bulkLoadFileHistory);
+			
+			boolean success = runLoad(predictedVariantConsequenceService, bulkLoadFileHistory, dataProvider, vepData, consequenceIdsLoaded);
+			if (success) {
+				runCleanup(predictedVariantConsequenceService, bulkLoadFileHistory, dataProvider.name(), consequenceIdsBefore, consequenceIdsLoaded, "predicted variant consequences");
+			}
+			bulkLoadFileHistory.finishLoad();
+			updateHistory(bulkLoadFileHistory);
+			updateExceptions(bulkLoadFileHistory);
+
+		} catch (Exception e) {
+			failLoad(bulkLoadFileHistory, e);
+			e.printStackTrace();
+		}
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/associations/constructAssociations/ConstructGenomicEntityAssociationExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/associations/constructAssociations/ConstructGenomicEntityAssociationExecutor.java
index 5e94cadaf..3e0ee50e9 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/executors/associations/constructAssociations/ConstructGenomicEntityAssociationExecutor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/associations/constructAssociations/ConstructGenomicEntityAssociationExecutor.java
@@ -53,8 +53,8 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) {
 		bulkLoadFileHistory.setCount(associations.size());
 		updateHistory(bulkLoadFileHistory);
 
-		runLoad(constructGenomicEntityAssociationService, bulkLoadFileHistory, dataProvider, associations, associationIdsLoaded);
-		if (cleanUp) {
+		boolean success = runLoad(constructGenomicEntityAssociationService, bulkLoadFileHistory, dataProvider, associations, associationIdsLoaded);
+		if (cleanUp && success) {
 			runCleanup(constructGenomicEntityAssociationService, bulkLoadFileHistory, dataProvider.name(), associationIdsBefore, associationIdsLoaded, "construct genomic entity association");
 		}
 		bulkLoadFileHistory.finishLoad();
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/executors/gff/Gff3GeneExecutor.java b/src/main/java/org/alliancegenome/curation_api/jobs/executors/gff/Gff3GeneExecutor.java
new file mode 100644
index 000000000..f4834db0f
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/executors/gff/Gff3GeneExecutor.java
@@ -0,0 +1,135 @@
+package org.alliancegenome.curation_api.jobs.executors.gff;
+
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.zip.GZIPInputStream;
+
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.KnownIssueValidationException;
+import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
+import org.alliancegenome.curation_api.exceptions.ObjectUpdateException.ObjectUpdateExceptionData;
+import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.Gff3DTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.response.LoadHistoryResponce;
+import org.alliancegenome.curation_api.services.associations.geneAssociations.GeneGenomicLocationAssociationService;
+import org.alliancegenome.curation_api.services.helpers.gff3.Gff3AttributesHelper;
+import org.alliancegenome.curation_api.services.validation.dto.Gff3DtoValidator;
+import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+
+import com.fasterxml.jackson.databind.MappingIterator;
+import com.fasterxml.jackson.dataformat.csv.CsvMapper;
+import com.fasterxml.jackson.dataformat.csv.CsvParser;
+import com.fasterxml.jackson.dataformat.csv.CsvSchema;
+
+import io.quarkus.logging.Log;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+
+@ApplicationScoped
+public class Gff3GeneExecutor extends Gff3Executor {
+
+	@Inject GeneGenomicLocationAssociationService geneLocationService;
+	@Inject Gff3DtoValidator gff3DtoValidator;
+	
+	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
+		try {
+
+			CsvSchema gff3Schema = CsvSchemaBuilder.gff3Schema();
+			CsvMapper csvMapper = new CsvMapper();
+			MappingIterator<Gff3DTO> it = csvMapper.enable(CsvParser.Feature.INSERT_NULLS_FOR_MISSING_COLUMNS).readerFor(Gff3DTO.class).with(gff3Schema).readValues(new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())));
+			List<Gff3DTO> gffData = it.readAll();
+			List<String> gffHeaderData = new ArrayList<>();
+			for (Gff3DTO gffLine : gffData) {
+				if (gffLine.getSeqId().startsWith("#")) {
+					gffHeaderData.add(gffLine.getSeqId());
+				} else {
+					break;
+				}
+			}
+			gffData.subList(0, gffHeaderData.size()).clear();
+			
+			BulkFMSLoad fmsLoad = (BulkFMSLoad) bulkLoadFileHistory.getBulkLoad();
+			BackendBulkDataProvider dataProvider = BackendBulkDataProvider.valueOf(fmsLoad.getFmsDataSubType());
+
+			List<ImmutablePair<Gff3DTO, Map<String, String>>> preProcessedGeneGffData = Gff3AttributesHelper.getGeneGffData(gffData, dataProvider);
+			
+			gffData.clear();
+			
+			List<Long> locationIdsAdded = new ArrayList<>();
+			String assemblyId = loadGenomeAssemblyFromGFF(gffHeaderData);
+			
+			boolean success = runLoad(bulkLoadFileHistory, gffHeaderData, preProcessedGeneGffData, locationIdsAdded, dataProvider, assemblyId);
+
+			if (success) {
+				runCleanup(geneLocationService, bulkLoadFileHistory, dataProvider.name(), geneLocationService.getIdsByDataProvider(dataProvider), locationIdsAdded, "GFF gene genomic location association");
+			}
+			bulkLoadFileHistory.finishLoad();
+			updateHistory(bulkLoadFileHistory);
+			updateExceptions(bulkLoadFileHistory);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+	
+	private boolean runLoad(
+		BulkLoadFileHistory history,
+		List<String> gffHeaderData,
+		List<ImmutablePair<Gff3DTO, Map<String, String>>> gffData,
+		List<Long> locationIdsAdded,
+		BackendBulkDataProvider dataProvider,
+		String assemblyId) {
+	
+		ProcessDisplayHelper ph = new ProcessDisplayHelper();
+		ph.addDisplayHandler(loadProcessDisplayService);
+		ph.startProcess("GFF Gene update for " + dataProvider.name(), gffData.size());
+
+		String countType = "Locations";
+		history.setCount(countType, gffData.size());
+		updateHistory(history);
+
+		for (ImmutablePair<Gff3DTO, Map<String, String>> gff3EntryPair : gffData) {
+			if (assemblyId != null) {
+				countType = "Locations";
+				try {
+					gff3Service.loadGeneLocationAssociations(gff3EntryPair, locationIdsAdded, dataProvider, assemblyId);
+					history.incrementCompleted(countType);
+				} catch (ObjectUpdateException e) {
+					history.incrementFailed(countType);
+					addException(history, e.getData());
+				} catch (KnownIssueValidationException e) {
+					Log.debug(e.getMessage());
+					history.incrementSkipped(countType);
+				} catch (Exception e) {
+					e.printStackTrace();
+					history.incrementFailed(countType);
+					addException(history, new ObjectUpdateExceptionData(gff3EntryPair.getKey(), e.getMessage(), e.getStackTrace()));
+				}
+			}
+			ph.progressProcess();
+		}
+		updateHistory(history);
+		ph.finishProcess();
+		return true;
+	}
+	
+	public APIResponse runLoadApi(String dataProviderName, String assemblyName, List<Gff3DTO> gffData) {
+		List<Long> idsAdded = new ArrayList<>();
+		BackendBulkDataProvider dataProvider = BackendBulkDataProvider.valueOf(dataProviderName);
+		List<ImmutablePair<Gff3DTO, Map<String, String>>> preProcessedGeneGffData = Gff3AttributesHelper.getGeneGffData(gffData, dataProvider);
+		BulkLoadFileHistory history = new BulkLoadFileHistory();
+		history = bulkLoadFileHistoryDAO.persist(history);
+		runLoad(history, null, preProcessedGeneGffData, idsAdded, dataProvider, assemblyName);
+		history.finishLoad();
+		
+		return new LoadHistoryResponce(history);
+	}
+
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/processors/BulkLoadProcessor.java b/src/main/java/org/alliancegenome/curation_api/jobs/processors/BulkLoadProcessor.java
index 86c18ec11..e61b1a910 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/processors/BulkLoadProcessor.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/processors/BulkLoadProcessor.java
@@ -131,6 +131,12 @@ protected void processFilePath(BulkLoad bulkLoad, String localFilePath, Boolean
 				bulkLoadFile.setBulkloadCleanUp(BulkLoadCleanUp.YES);
 			}
 			bulkLoadFileDAO.persist(bulkLoadFile);
+			history.setBulkLoad(bulkLoad);
+			history.setBulkLoadFile(bulkLoadFile);
+			bulkLoadFileHistoryDAO.persist(history);
+
+			Log.info("Firing Pending Bulk File History Event: " + history.getId());
+			pendingFileJobEvents.fireAsync(new PendingLoadJobEvent(history.getId()));
 		} else if (load.getBulkloadStatus().isForced()) {
 			bulkLoadFile = bulkLoadFiles.getResults().get(0);
 			if (history.getBulkloadStatus().isNotRunning()) {
@@ -142,25 +148,26 @@ protected void processFilePath(BulkLoad bulkLoad, String localFilePath, Boolean
 				Log.info("Cleaning up downloaded file: " + localFilePath);
 				new File(localFilePath).delete();
 			}
+			if (cleanUp) {
+				bulkLoadFile.setBulkloadCleanUp(BulkLoadCleanUp.YES);
+			}
+			bulkLoadFileDAO.merge(bulkLoadFile);
+			history.setBulkLoad(bulkLoad);
+			history.setBulkLoadFile(bulkLoadFile);
+			bulkLoadFileHistoryDAO.persist(history);
+
+			Log.info("Firing Pending Bulk File History Event: " + history.getId());
+			pendingFileJobEvents.fireAsync(new PendingLoadJobEvent(history.getId()));
 		} else {
 			Log.info("Bulk File already exists not creating it");
 			bulkLoadFile = bulkLoadFiles.getResults().get(0);
 			Log.info("Cleaning up downloaded file: " + localFilePath);
 			new File(localFilePath).delete();
 			bulkLoadFile.setLocalFilePath(null);
+			bulkLoadFileDAO.merge(bulkLoadFile);
+			Log.info("File already exists not running load");
 		}
-		
-		history.setBulkLoad(bulkLoad);
-		history.setBulkLoadFile(bulkLoadFile);
-		bulkLoadFileHistoryDAO.persist(history);
 
-		if (cleanUp) {
-			bulkLoadFile.setBulkloadCleanUp(BulkLoadCleanUp.YES);
-		}
-		bulkLoadFileDAO.merge(bulkLoadFile);
-		bulkLoadDAO.merge(load);
-		Log.info("Firing Pending Bulk File History Event: " + history.getId());
-		pendingFileJobEvents.fireAsync(new PendingLoadJobEvent(history.getId()));
 	}
 
 	protected void startLoad(BulkLoad load) {
diff --git a/src/main/java/org/alliancegenome/curation_api/jobs/util/CsvSchemaBuilder.java b/src/main/java/org/alliancegenome/curation_api/jobs/util/CsvSchemaBuilder.java
index 28c4bfca0..8320586b8 100644
--- a/src/main/java/org/alliancegenome/curation_api/jobs/util/CsvSchemaBuilder.java
+++ b/src/main/java/org/alliancegenome/curation_api/jobs/util/CsvSchemaBuilder.java
@@ -105,4 +105,30 @@ public static CsvSchema gff3Schema() {
 		
 		return schema;
 	}
+	
+	public static CsvSchema vepTxtSchema() {
+		CsvSchema schema = CsvSchema.builder()
+				.setColumnSeparator('\t')
+				.setArrayElementSeparator(";")
+				.setAllowComments(true)
+				.setNullValue("-")
+				.disableQuoteChar()
+				.addColumn("uploadedVariation")
+				.addColumn("location")
+				.addColumn("allele")
+				.addColumn("gene")
+				.addColumn("feature")
+				.addColumn("featureType")
+				.addColumn("consequence")
+				.addColumn("cdnaPosition")
+				.addColumn("cdsPosition")
+				.addColumn("proteinPosition")
+				.addColumn("aminoAcids")
+				.addColumn("codons")
+				.addColumn("existingVariation")
+				.addColumn("extra")
+				.build();
+		
+		return schema;
+	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java
index bf2b61b71..c9611c9a3 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java
@@ -4,6 +4,7 @@
 
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
@@ -26,7 +27,7 @@
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(exclude = { "agmDiseaseAnnotations" }, callSuper = true)
+@ToString(exclude = { "agmDiseaseAnnotations", "constructGenomicEntityAssociations" }, callSuper = true)
 @Schema(name = "AffectedGenomicModel", description = "POJO that represents the AGM")
 @AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class }, partial = true)
 public class AffectedGenomicModel extends GenomicEntity {
@@ -43,4 +44,15 @@ public class AffectedGenomicModel extends GenomicEntity {
 	@ManyToOne
 	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
 	private VocabularyTerm subtype;
+
+	@IndexedEmbedded(includePaths = {
+		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
+		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
+		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
+		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
+	})
+	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
+
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java
index d5d9a1bbc..18bd7a5e1 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java
@@ -2,11 +2,13 @@
 
 import java.util.List;
 
+import jakarta.persistence.*;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.model.bridges.BooleanAndNullValueBridge;
 import org.alliancegenome.curation_api.model.entities.associations.alleleAssociations.AlleleGeneAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.alleleAssociations.AlleleVariantAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.alleleSlotAnnotations.AlleleDatabaseStatusSlotAnnotation;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.alleleSlotAnnotations.AlleleFullNameSlotAnnotation;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.alleleSlotAnnotations.AlleleFunctionalImpactSlotAnnotation;
@@ -34,15 +36,6 @@
 import com.fasterxml.jackson.annotation.JsonManagedReference;
 import com.fasterxml.jackson.annotation.JsonView;
 
-import jakarta.persistence.CascadeType;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.ManyToMany;
-import jakarta.persistence.ManyToOne;
-import jakarta.persistence.OneToMany;
-import jakarta.persistence.OneToOne;
-import jakarta.persistence.Table;
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 import lombok.ToString;
@@ -55,7 +48,7 @@
 	exclude = {
 		"alleleGeneAssociations", "alleleVariantAssociations", "alleleDiseaseAnnotations", "alleleMutationTypes", "alleleSymbol", "alleleFullName", "alleleSynonyms",
 		"alleleSecondaryIds", "alleleInheritanceModes", "alleleFunctionalImpacts", "alleleGermlineTransmissionStatus", "alleleDatabaseStatus",
-		"alleleNomenclatureEvents"
+		"alleleNomenclatureEvents", "constructGenomicEntityAssociations"
 	},
 	callSuper = true
 )
@@ -212,4 +205,15 @@ public class Allele extends GenomicEntity {
 		@Index(name = "allele_note_relatednotes_index", columnList = "relatedNotes_id")})
 	private List<Note> relatedNotes;
 
+
+	@IndexedEmbedded(includePaths = {
+		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
+		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
+		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
+		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
+	})
+	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
+
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/BioSampleAge.java b/src/main/java/org/alliancegenome/curation_api/model/entities/BioSampleAge.java
index d359e8e83..ff37f7e7e 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/BioSampleAge.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/BioSampleAge.java
@@ -34,7 +34,7 @@ public class BioSampleAge extends AuditedObject {
 
 	@IndexedEmbedded(includePaths = {"age", "age_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
-	@ManyToOne
+	@ManyToOne(cascade = CascadeType.ALL)
 	@JsonView({ View.FieldsOnly.class })
 	private TemporalContext stage;
 
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java
index 96b84b062..d295c7e0d 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java
@@ -1,13 +1,20 @@
 package org.alliancegenome.curation_api.model.entities;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonSubTypes;
+import com.fasterxml.jackson.annotation.JsonSubTypes.Type;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.persistence.*;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.model.bridges.BooleanValueBridge;
 import org.alliancegenome.curation_api.model.entities.ontology.DOTerm;
 import org.alliancegenome.curation_api.model.entities.ontology.ECOTerm;
 import org.alliancegenome.curation_api.view.View;
+import org.apache.commons.collections4.CollectionUtils;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.hibernate.search.engine.backend.types.Aggregable;
 import org.hibernate.search.engine.backend.types.Searchable;
@@ -19,25 +26,9 @@
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonSubTypes;
-import com.fasterxml.jackson.annotation.JsonSubTypes.Type;
-import com.fasterxml.jackson.annotation.JsonTypeInfo;
-import com.fasterxml.jackson.annotation.JsonView;
-
-import jakarta.persistence.Column;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.Inheritance;
-import jakarta.persistence.InheritanceType;
-import jakarta.persistence.JoinColumn;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.ManyToMany;
-import jakarta.persistence.ManyToOne;
-import jakarta.persistence.Table;
-import jakarta.persistence.Transient;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
 
 @Inheritance(strategy = InheritanceType.JOINED)
 @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
@@ -49,7 +40,7 @@
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { Annotation.class })
+@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {Annotation.class})
 @Schema(name = "Disease_Annotation", description = "Annotation class representing a disease annotation")
 @Table(indexes = {
 	@Index(name = "DiseaseAnnotation_internal_index", columnList = "internal"),
@@ -73,29 +64,29 @@
 public abstract class DiseaseAnnotation extends Annotation {
 
 	@IndexedEmbedded(includePaths = {"curie", "name", "secondaryIdentifiers", "synonyms.name", "namespace",
-			"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "namespace_keyword" })
+		"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "namespace_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	private DOTerm diseaseAnnotationObject;
 
 	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer", valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
 	@KeywordField(name = "negated_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	@Column(columnDefinition = "boolean default false", nullable = false)
 	private Boolean negated = false;
 
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	private VocabularyTerm relation;
 
 	@IndexedEmbedded(includePaths = {"curie", "name", "secondaryIdentifiers", "synonyms.name", "abbreviation",
-			"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "abbreviation_keyword" })
+		"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "abbreviation_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToMany
-	@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
+	@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
 	@JoinTable(
 		joinColumns = @JoinColumn(name = "diseaseannotation_id"),
 		inverseJoinColumns = @JoinColumn(name = "evidencecodes_id"),
@@ -107,16 +98,16 @@ public abstract class DiseaseAnnotation extends Annotation {
 	private List<ECOTerm> evidenceCodes;
 
 	@IndexedEmbedded(includePaths = {
-			"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
-			"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
-			"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
-			"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
-			"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
-			"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
+		"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
+		"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
+		"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
+		"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
+		"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
+		"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
 	})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToMany
-	@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
+	@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
 	@JoinTable(
 		joinColumns = @JoinColumn(name = "diseaseannotation_id"),
 		inverseJoinColumns = @JoinColumn(name = "with_id"),
@@ -130,13 +121,13 @@ public abstract class DiseaseAnnotation extends Annotation {
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	private VocabularyTerm annotationType;
 
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToMany
-	@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
+	@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
 	@JoinTable(
 		joinColumns = @JoinColumn(name = "diseaseannotation_id"),
 		inverseJoinColumns = @JoinColumn(name = "diseasequalifiers_id"),
@@ -150,27 +141,27 @@ public abstract class DiseaseAnnotation extends Annotation {
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	private VocabularyTerm geneticSex;
 
 	@IndexedEmbedded(includePaths = {"sourceOrganization.abbreviation", "sourceOrganization.fullName", "sourceOrganization.shortName", "crossReference.displayName", "crossReference.referencedCurie",
-			"sourceOrganization.abbreviation_keyword", "sourceOrganization.fullName_keyword", "sourceOrganization.shortName_keyword", "crossReference.displayName_keyword", "crossReference.referencedCurie_keyword"})
+		"sourceOrganization.abbreviation_keyword", "sourceOrganization.fullName_keyword", "sourceOrganization.shortName_keyword", "crossReference.displayName_keyword", "crossReference.referencedCurie_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	private DataProvider secondaryDataProvider;
 
 	@IndexedEmbedded(includePaths = {
-			"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
-			"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
-			"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
-			"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
-			"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
-			"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
+		"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
+		"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
+		"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
+		"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
+		"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
+		"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
 	})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToMany
-	@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
+	@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
 	@JoinTable(
 		name = "diseaseannotation_modifiergene",
 		joinColumns = @JoinColumn(name = "diseaseannotation_id"),
@@ -183,15 +174,15 @@ public abstract class DiseaseAnnotation extends Annotation {
 	private List<Gene> diseaseGeneticModifierGenes;
 
 	@IndexedEmbedded(includePaths = {
-			"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
-			"alleleSymbol.formatText", "alleleSymbol.displayText", "alleleSymbol.formatText_keyword", "alleleSymbol.displayText_keyword",
-			"alleleFullName.formatText", "alleleFullName.displayText", "alleleFullName.formatText_keyword", "alleleFullName.displayText_keyword",
-			"alleleSynonyms.formatText", "alleleSynonyms.displayText", "alleleSynonyms.formatText_keyword", "alleleSynonyms.displayText_keyword",
-			"alleleSecondaryIds.secondaryId", "alleleSecondaryIds.secondaryId_keyword"
+		"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
+		"alleleSymbol.formatText", "alleleSymbol.displayText", "alleleSymbol.formatText_keyword", "alleleSymbol.displayText_keyword",
+		"alleleFullName.formatText", "alleleFullName.displayText", "alleleFullName.formatText_keyword", "alleleFullName.displayText_keyword",
+		"alleleSynonyms.formatText", "alleleSynonyms.displayText", "alleleSynonyms.formatText_keyword", "alleleSynonyms.displayText_keyword",
+		"alleleSecondaryIds.secondaryId", "alleleSecondaryIds.secondaryId_keyword"
 	})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToMany
-	@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
+	@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
 	@JoinTable(
 		name = "diseaseannotation_modifierallele",
 		joinColumns = @JoinColumn(name = "diseaseannotation_id"),
@@ -206,7 +197,7 @@ public abstract class DiseaseAnnotation extends Annotation {
 	@IndexedEmbedded(includePaths = {"name", "name_keyword", "curie", "curie_keyword", "modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToMany
-	@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
+	@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
 	@JoinTable(
 		name = "diseaseannotation_modifieragm",
 		joinColumns = @JoinColumn(name = "diseaseannotation_id"),
@@ -218,10 +209,24 @@ public abstract class DiseaseAnnotation extends Annotation {
 	)
 	private List<AffectedGenomicModel> diseaseGeneticModifierAgms;
 
+	public List<BiologicalEntity> getDiseaseGeneticModifiers() {
+		List<BiologicalEntity> geneticModifiers = new ArrayList<>();
+		if (CollectionUtils.isNotEmpty(getDiseaseGeneticModifierAlleles())) {
+			geneticModifiers.addAll(getDiseaseGeneticModifierAlleles().stream().filter(Objects::nonNull).toList());
+		}
+		if (CollectionUtils.isNotEmpty(getDiseaseGeneticModifierGenes())) {
+			geneticModifiers.addAll(getDiseaseGeneticModifierGenes().stream().filter(Objects::nonNull).toList());
+		}
+		if (CollectionUtils.isNotEmpty(getDiseaseGeneticModifierAgms())) {
+			geneticModifiers.addAll(getDiseaseGeneticModifierAgms().stream().filter(Objects::nonNull).toList());
+		}
+		return geneticModifiers;
+	}
+
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class, View.ForPublic.class})
 	private VocabularyTerm diseaseGeneticModifierRelation;
 
 	@Transient
@@ -232,7 +237,7 @@ public abstract class DiseaseAnnotation extends Annotation {
 
 	@Transient
 	public abstract String getSubjectSpeciesName();
-	
+
 	@Transient
 	public abstract String getSubjectIdentifier();
 
@@ -246,4 +251,21 @@ public String getDataProviderString() {
 		}
 		return builder.toString();
 	}
+
+	@Transient
+	public String getFullRelationString() {
+		if (relation == null) {
+			return null;
+		}
+		if (!negated) {
+			return relation.getName();
+		}
+
+		if (relation.getName().equals("is_model_of")) {
+			return "does_not_model";
+		}
+		return relation.getName().replaceFirst("_", "_not_");
+	}
+
+
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionExperiment.java b/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionExperiment.java
new file mode 100644
index 000000000..9ee6bbd92
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionExperiment.java
@@ -0,0 +1,66 @@
+package org.alliancegenome.curation_api.model.entities;
+
+import com.fasterxml.jackson.annotation.JsonSubTypes;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.persistence.*;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.base.SubmittedObject;
+import org.alliancegenome.curation_api.model.entities.ontology.MMOTerm;
+import org.alliancegenome.curation_api.view.View;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.*;
+
+import java.util.List;
+import java.util.Set;
+
+@MappedSuperclass
+@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
+@JsonSubTypes({ @JsonSubTypes.Type(value = GeneExpressionExperiment.class, name = "GeneExpressionExperiment") })
+@Indexed
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = false)
+@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { SubmittedObject.class }, partial = true)
+public abstract class ExpressionExperiment extends SubmittedObject {
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "uniqueId_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@Column(length = 3500)
+	@JsonView({ View.FieldsOnly.class })
+	@EqualsAndHashCode.Include
+	private String uniqueId;
+
+	@IndexedEmbedded(includePaths = {"geneSymbol.displayText", "geneSymbol.formatText", "geneSymbol.displayText_keyword", "geneSymbol.formatText_keyword", "curie", "curie_keyword", "taxon.curie", "taxon.name", "taxon.curie_keyword", "taxon.name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class })
+	private Gene entityAssayed;
+
+	@IndexedEmbedded(includePaths = {"curie", "primaryCrossReferenceCurie", "crossReferences.referencedCurie", "curie_keyword", "primaryCrossReferenceCurie_keyword", "crossReferences.referencedCurie_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	private Reference singleReference;
+
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class})
+	private MMOTerm expressionAssayUsed;
+
+	@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({View.FieldsAndLists.class})
+	private Set<GeneExpressionAnnotation> expressionAnnotations;
+
+	@Transient private Allele specimenGenomicModel;
+	@Transient private List<Reagent> detectionReagents;
+	@Transient private List<Allele> specimenAlleles;
+	@Transient private List<Note> relatedNotes;
+	@Transient private List<ConditionRelation> conditionRelations;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java
index a2ed18954..c84a39d07 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java
@@ -5,6 +5,8 @@
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.model.entities.associations.alleleAssociations.AlleleGeneAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.sequenceTargetingReagentAssociations.SequenceTargetingReagentGeneAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptGeneAssociation;
 import org.alliancegenome.curation_api.model.entities.ontology.SOTerm;
@@ -38,7 +40,8 @@
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(exclude = { "geneDiseaseAnnotations", "geneGeneAssociations", "geneSymbol", "geneFullName", "geneSystematicName", "geneSynonyms", "geneSecondaryIds", "alleleGeneAssociations", "sequenceTargetingReagentGeneAssociations", "transcriptGeneAssociations" }, callSuper = true)
+@ToString(exclude = { "geneDiseaseAnnotations", "geneGeneAssociations", "geneSymbol", "geneFullName", "geneSystematicName", "geneSynonyms", "geneSecondaryIds",
+		"geneGenomicLocationAssociations", "alleleGeneAssociations", "sequenceTargetingReagentGeneAssociations", "transcriptGeneAssociations", "constructGenomicEntityAssociations" }, callSuper = true)
 @Schema(name = "Gene", description = "POJO that represents the Gene")
 @AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class }, partial = true)
 @Table(indexes = { @Index(name = "gene_genetype_index", columnList = "geneType_id") })
@@ -105,4 +108,28 @@ public class Gene extends GenomicEntity {
 	@OneToMany(mappedBy = "transcriptGeneAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
 	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
 	private List<TranscriptGeneAssociation> transcriptGeneAssociations;
+	
+	@IndexedEmbedded(
+		includePaths = {
+			"geneGenomicLocationAssociationObject.curie", "geneGenomicLocationAssociationObject.curie_keyword",
+			"geneGenomicLocationAssociationObject.modEntityId", "geneGenomicLocationAssociationObject.modEntityId_keyword",
+			"geneGenomicLocationAssociationObject.modInternalId", "geneGenomicLocationAssociationObject.modInternalId_keyword",
+			"start", "end"
+		}
+	)
+	@OneToMany(mappedBy = "geneAssociationSubject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<GeneGenomicLocationAssociation> geneGenomicLocationAssociations;
+
+
+	@IndexedEmbedded(includePaths = {
+		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
+		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
+		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
+		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
+	})
+	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
+
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/GeneExpressionExperiment.java b/src/main/java/org/alliancegenome/curation_api/model/entities/GeneExpressionExperiment.java
new file mode 100644
index 000000000..d9d587f5f
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/GeneExpressionExperiment.java
@@ -0,0 +1,32 @@
+package org.alliancegenome.curation_api.model.entities;
+
+import jakarta.persistence.Entity;
+import jakarta.persistence.Index;
+import jakarta.persistence.Table;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
+
+@Indexed
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = false)
+@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { ExpressionExperiment.class }, partial = true)
+@Table(indexes = {
+	@Index(name = "geneexpressionexperiment_uniqueid_index", columnList = "uniqueid"),
+	@Index(name = "geneexpressionexperiment_curie_index", columnList = "curie"),
+	@Index(name = "geneexpressionexperiment_modentityid_index", columnList = "modinternalid"),
+	@Index(name = "geneexpressionexperiment_modinternalid_index", columnList = "modinternalid"),
+	@Index(name = "geneexpressionexperiment_singlereference_index", columnList = "singlereference_id"),
+	@Index(name = "geneexpressionexperiment_entityassayedused_index", columnList = "entityassayed_id"),
+	@Index(name = "geneexpressionexperiment_expressionassayused_index", columnList = "expressionassayused_id"),
+	@Index(name = "geneexpressionexperiment_dataprovider_index", columnList = "dataprovider_id"),
+	@Index(name = "geneexpressionexperiment_internal_index", columnList = "internal"),
+	@Index(name = "geneexpressionexperiment_obsolete_index", columnList = "obsolete"),
+	@Index(name = "geneexpressionexperiment_createdby_index", columnList = "createdby_id"),
+	@Index(name = "geneexpressionexperiment_updatedby_index", columnList = "updatedby_id")
+})
+public class GeneExpressionExperiment extends ExpressionExperiment {
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/GeneOntologyAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/GeneOntologyAnnotation.java
new file mode 100644
index 000000000..2751d1bbd
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/GeneOntologyAnnotation.java
@@ -0,0 +1,27 @@
+package org.alliancegenome.curation_api.model.entities;
+
+import com.fasterxml.jackson.annotation.JsonTypeName;
+import jakarta.persistence.Entity;
+import jakarta.persistence.ManyToOne;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.base.AuditedObject;
+import org.alliancegenome.curation_api.model.entities.ontology.GOTerm;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
+
+@Entity
+@Data
+@EqualsAndHashCode
+@Schema(name = "Gene_Disease_Annotation", description = "Annotation class representing a gene disease annotation")
+@JsonTypeName("GeneOntologyAnnotation")
+@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE)
+public class GeneOntologyAnnotation extends AuditedObject {
+
+	@ManyToOne
+	private GOTerm goTerm;
+	@ManyToOne
+	private Gene singleGene;
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java b/src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java
index 3bc9a17c8..1ff242104 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java
@@ -1,31 +1,24 @@
 package org.alliancegenome.curation_api.model.entities;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.persistence.*;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
-import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.view.View;
 import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
 
-import com.fasterxml.jackson.annotation.JsonView;
-
-import jakarta.persistence.CascadeType;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.OneToMany;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-import lombok.ToString;
+import java.util.List;
 
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(exclude = { "constructGenomicEntityAssociations" }, callSuper = true)
-@AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { BiologicalEntity.class })
+@ToString(callSuper = true)
+@AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {BiologicalEntity.class})
 public class GenomicEntity extends BiologicalEntity {
 
 	@IndexedEmbedded(includePaths = {"referencedCurie", "displayName", "resourceDescriptorPage.name", "referencedCurie_keyword", "displayName_keyword", "resourceDescriptorPage.name_keyword"})
@@ -37,18 +30,8 @@ public class GenomicEntity extends BiologicalEntity {
 		@Index(columnList = "crossreferences_id", name = "genomicentity_crossreference_crossreferences_index")
 	})
 	@EqualsAndHashCode.Include
-	@JsonView({ View.FieldsAndLists.class, View.AlleleView.class, View.GeneView.class, View.AffectedGenomicModelView.class, View.VariantView.class })
+	@JsonView({View.FieldsAndLists.class, View.AlleleView.class, View.GeneView.class, View.AffectedGenomicModelView.class, View.VariantView.class})
 	private List<CrossReference> crossReferences;
-	
 
-	@IndexedEmbedded(includePaths = {
-		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
-		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
-		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
-		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
-	})
-	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
-	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
 
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/HTPExpressionDatasetSampleAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/HTPExpressionDatasetSampleAnnotation.java
index 4941d6d84..49cab988a 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/HTPExpressionDatasetSampleAnnotation.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/HTPExpressionDatasetSampleAnnotation.java
@@ -115,7 +115,7 @@ public class HTPExpressionDatasetSampleAnnotation extends AuditedObject {
 	private VocabularyTerm sequencingFormat;
 
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
-	@ManyToMany
+	@ManyToMany(cascade = CascadeType.ALL)
 	@JoinTable(indexes = {
 		@Index(name = "htpdatasample_anatomicalsite_htpdatasample_index", columnList = "htpexpressiondatasetsampleannotation_id"),
 		@Index(name = "htpdatasample_anatomicalsite_samplelocations_index", columnList = "htpexpressionsamplelocations_id")
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/PredictedVariantConsequence.java b/src/main/java/org/alliancegenome/curation_api/model/entities/PredictedVariantConsequence.java
new file mode 100644
index 000000000..7920ede56
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/PredictedVariantConsequence.java
@@ -0,0 +1,170 @@
+package org.alliancegenome.curation_api.model.entities;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.bridges.BooleanValueBridge;
+import org.alliancegenome.curation_api.model.entities.associations.variantAssociations.CuratedVariantGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.entities.base.AuditedObject;
+import org.alliancegenome.curation_api.model.entities.ontology.SOTerm;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Projectable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.ValueBridgeRef;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.GenericField;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
+
+import com.fasterxml.jackson.annotation.JsonBackReference;
+import com.fasterxml.jackson.annotation.JsonView;
+
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
+
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
+@ToString(callSuper = true)
+@AGRCurationSchemaVersion(min = "2.7.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { AuditedObject.class })
+@Schema(name = "PredictedVariantConsequence", description = "POJO representing VEP predicted variant consequence results")
+@Table(indexes = {
+	@Index(name = "predictedvariantconsequence_varianttranscript_index", columnList = "varianttranscript_id"),
+	@Index(name = "predictedvariantconsequence_vepimpact_index", columnList = "vepimpact_id"),
+	@Index(name = "predictedvariantconsequence_polyphenprediction_index", columnList = "polyphenprediction_id"),
+	@Index(name = "predictedvariantconsequence_siftprediction_index", columnList = "siftprediction_id"),
+	@Index(name = "predictedvariantconsequence_createdby_index", columnList = "createdby_id"),
+	@Index(name = "predictedvariantconsequence_updatedby_index", columnList = "updatedby_id"),
+	@Index(name = "predictedvariantconsequence_hgvsproteinnomenclature_index", columnList = "hgvsProteinNomenclature"),
+	@Index(name = "predictedvariantconsequence_hgvscodingnomenclature_index", columnList = "hgvsCodingNomenclature"),
+	@Index(name = "predictedvariantconsequence_variantgenomiclocation_index", columnList = "variantGenomicLocation_id")
+})
+public class PredictedVariantConsequence extends AuditedObject {
+
+	@ManyToOne
+	@JsonBackReference
+	private CuratedVariantGenomicLocationAssociation variantGenomicLocation;
+	
+	@IndexedEmbedded(includePaths = {"name", "name_keyword", "curie", "curie_keyword", "modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({ View.FieldsOnly.class })
+	private Transcript variantTranscript;
+	
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({ View.FieldsOnly.class })
+	private VocabularyTerm vepImpact;
+	
+	@IndexedEmbedded(includePaths = {"curie", "name", "secondaryIdentifiers", "synonyms.name", "namespace",
+			"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "namespace_keyword" })
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToMany
+	@JoinTable(indexes = {
+		@Index(name = "predictedvariantconsequence_ontologyterm_pvc_index", columnList = "predictedvariantconsequence_id"),
+		@Index(name = "predictedvariantconsequence_ontologyterm_vc_index", columnList = "vepconsequences_id")
+	})
+	@JsonView({ View.FieldsAndLists.class, View.VariantView.class })
+	private List<SOTerm> vepConsequences;
+	
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({ View.FieldsOnly.class })
+	private VocabularyTerm polyphenPrediction;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Float polyphenScore;
+	
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({ View.FieldsOnly.class })
+	private VocabularyTerm siftPrediction;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Float siftScore;
+	
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "aminoAcidReference_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "TEXT")
+	private String aminoAcidReference;
+	
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "aminoAcidVariant_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "TEXT")
+	private String aminoAcidVariant;
+	
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "codonReference_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "TEXT")
+	private String codonReference;
+	
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "codonVariant_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "TEXT")
+	private String codonVariant;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Integer calculatedCdnaStart;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Integer calculatedCdnaEnd;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Integer calculatedCdsStart;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Integer calculatedCdsEnd;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Integer calculatedProteinStart;
+	
+	@GenericField(projectable = Projectable.YES, sortable = Sortable.YES)
+	@JsonView({ View.FieldsOnly.class })
+	private Integer calculatedProteinEnd;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "hgvsProteinNomenclature_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "TEXT")
+	private String hgvsProteinNomenclature;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "hgvsCodingNomenclature_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "TEXT")
+	private String hgvsCodingNomenclature;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer", valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
+	@KeywordField(name = "geneLevelConsequence_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
+	@JsonView({ View.FieldsOnly.class })
+	@Column(columnDefinition = "boolean default false", nullable = false)
+	private Boolean geneLevelConsequence = false;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Transcript.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Transcript.java
index 46254b04e..0617af6f8 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/Transcript.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/Transcript.java
@@ -11,9 +11,14 @@
 import org.alliancegenome.curation_api.model.entities.ontology.SOTerm;
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
 import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
 
 import com.fasterxml.jackson.annotation.JsonView;
 
@@ -33,12 +38,18 @@
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
 @ToString(exclude = { "transcriptGenomicLocationAssociations", "transcriptGeneAssociations", "transcriptCodingSequenceAssociations", "transcriptExonAssociations" }, callSuper = true)
 @Schema(name = "Transcript", description = "POJO that represents the Transcript")
-@AGRCurationSchemaVersion(min = "2.4.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class })
+@AGRCurationSchemaVersion(min = "2.8.1", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class })
 @Table(indexes = {
+	@Index(name = "transcript_transcriptId_index", columnList = "transcriptId"),
 	@Index(name = "transcript_transcriptType_index", columnList = "transcriptType_id")
 })
 public class Transcript extends GenomicEntity {
 
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "transcriptId_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	private String transcriptId;
+	
 	@JsonView({ View.FieldsOnly.class })
 	private String name;
 
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/associations/constructAssociations/ConstructGenomicEntityAssociation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/associations/constructAssociations/ConstructGenomicEntityAssociation.java
index b848b3b0c..67b208014 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/associations/constructAssociations/ConstructGenomicEntityAssociation.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/associations/constructAssociations/ConstructGenomicEntityAssociation.java
@@ -1,14 +1,14 @@
 package org.alliancegenome.curation_api.model.entities.associations.constructAssociations;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.persistence.*;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
-import org.alliancegenome.curation_api.model.entities.Construct;
-import org.alliancegenome.curation_api.model.entities.EvidenceAssociation;
-import org.alliancegenome.curation_api.model.entities.GenomicEntity;
-import org.alliancegenome.curation_api.model.entities.Note;
-import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
+import org.alliancegenome.curation_api.model.entities.*;
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.hibernate.annotations.Fetch;
@@ -17,26 +17,13 @@
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonView;
-
-import jakarta.persistence.CascadeType;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.JoinColumn;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.ManyToOne;
-import jakarta.persistence.OneToMany;
-import jakarta.persistence.Table;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-import lombok.ToString;
+import java.util.List;
 
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
 @ToString(callSuper = true)
-@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { EvidenceAssociation.class })
+@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {EvidenceAssociation.class})
 @Schema(name = "ConstructGenomicEntityAssociation", description = "POJO representing an association between a construct and a genomic entity")
 
 @Table(indexes = {
@@ -57,24 +44,25 @@ public class ConstructGenomicEntityAssociation extends EvidenceAssociation {
 		"curie_keyword", "constructSymbol.displayText_keyword", "constructSymbol.formatText_keyword",
 		"constructFullName.displayText_keyword", "constructFullName.formatText_keyword", "modEntityId_keyword", "modInternalId_keyword"})
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class })
+	@JsonView({View.FieldsOnly.class})
 	@JsonIgnoreProperties("constructGenomicEntityAssociations")
 	@Fetch(FetchMode.JOIN)
 	private Construct constructAssociationSubject;
-	
+
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class })
+	@JsonView({View.FieldsOnly.class})
 	private VocabularyTerm relation;
-	
+
 	@IndexedEmbedded(includeDepth = 1)
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class })
+	@JsonView({View.FieldsOnly.class})
 	@JsonIgnoreProperties({
 		"alleleGeneAssociations", "constructGenomicEntityAssociations", "sequenceTargetingReagentGeneAssociations",
-		"transcriptGenomicLocationAssociations", "exonGenomicLocationAssociations", "codingSequenceGenomicLocationAssociations"
+		"transcriptGenomicLocationAssociations", "exonGenomicLocationAssociations", "codingSequenceGenomicLocationAssociations",
+		"transcriptGeneAssociations", "geneGenomicLocationAssociations", "transcriptExonAssociations", "transcriptCodingSequenceAssociations"
 	})
 	private GenomicEntity constructGenomicEntityAssociationObject;
 
@@ -84,7 +72,7 @@ public class ConstructGenomicEntityAssociation extends EvidenceAssociation {
 	})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({ View.FieldsAndLists.class, View.ConstructView.class })
+	@JsonView({View.FieldsAndLists.class, View.ConstructView.class})
 	@JoinTable(
 		joinColumns = @JoinColumn(name = "constructgenomicentityassociation_id"),
 		inverseJoinColumns = @JoinColumn(name = "relatedNotes_id"),
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/associations/geneAssociations/GeneGenomicLocationAssociation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/associations/geneAssociations/GeneGenomicLocationAssociation.java
new file mode 100644
index 000000000..c829b5059
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/associations/geneAssociations/GeneGenomicLocationAssociation.java
@@ -0,0 +1,82 @@
+package org.alliancegenome.curation_api.model.entities.associations.geneAssociations;
+
+import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.AssemblyComponent;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.model.entities.LocationAssociation;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonView;
+
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Index;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
+
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
+@ToString(callSuper = true)
+@AGRCurationSchemaVersion(min = "2.4.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { LocationAssociation.class })
+@Schema(name = "GeneGenomicLocationAssociation", description = "POJO representing an association between a gene and a genomic location")
+
+@Table(indexes = {
+	@Index(name = "geneGenomicLocationAssociation_internal_index", columnList = "internal"),
+	@Index(name = "geneGenomicLocationAssociation_obsolete_index", columnList = "obsolete"),
+	@Index(name = "geneGenomicLocationAssociation_strand_index", columnList = "strand"),
+	@Index(name = "geneGenomicLocationAssociation_createdBy_index", columnList = "createdBy_id"),
+	@Index(name = "geneGenomicLocationAssociation_updatedBy_index", columnList = "updatedBy_id"),
+	@Index(name = "geneGenomicLocationAssociation_relation_index", columnList = "relation_id"),
+	@Index(name = "geneGenomicLocationAssociation_subject_index", columnList = "geneassociationsubject_id"),
+	@Index(name = "geneGenomicLocationAssociation_object_index", columnList = "genegenomiclocationassociationobject_id")
+})
+
+public class GeneGenomicLocationAssociation extends LocationAssociation {
+
+	@IndexedEmbedded(includePaths = {"curie", "geneSymbol.displayText", "geneSymbol.formatText", "geneFullName.displayText", "geneFullName.formatText",
+			"curie_keyword", "geneSymbol.displayText_keyword", "geneSymbol.formatText_keyword", "geneFullName.displayText_keyword", "geneFullName.formatText_keyword",
+			"modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonIgnoreProperties({
+		"geneGenomicLocationAssociations",
+		"sequenceTargetingReagentGeneAssociations",
+		"transcriptGeneAssociations",
+		"alleleGeneAssociations"
+	})
+	@JsonView({ View.FieldsOnly.class })
+	private Gene geneAssociationSubject;
+
+	@IndexedEmbedded(includePaths = {
+		"curie", "curie_keyword", "modEntityId", "modEntityId_keyword",
+		"modInternalId", "modInternalId_keyword", "name", "name_keyword"
+	})
+	@ManyToOne
+	@JsonView({ View.FieldsOnly.class })
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@Fetch(FetchMode.JOIN)
+	private AssemblyComponent geneGenomicLocationAssociationObject;
+	
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "strand_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({ View.FieldsOnly.class })
+	@Column(length = 1)
+	private String strand;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/associations/variantAssociations/CuratedVariantGenomicLocationAssociation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/associations/variantAssociations/CuratedVariantGenomicLocationAssociation.java
index 82508a178..f62005b21 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/entities/associations/variantAssociations/CuratedVariantGenomicLocationAssociation.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/entities/associations/variantAssociations/CuratedVariantGenomicLocationAssociation.java
@@ -1,11 +1,22 @@
 package org.alliancegenome.curation_api.model.entities.associations.variantAssociations;
 
+import java.util.List;
+
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+import org.alliancegenome.curation_api.view.View;
+import org.alliancegenome.curation_api.view.View.VariantView;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
+
+import com.fasterxml.jackson.annotation.JsonManagedReference;
+import com.fasterxml.jackson.annotation.JsonView;
 
+import jakarta.persistence.CascadeType;
 import jakarta.persistence.Entity;
 import jakarta.persistence.Index;
+import jakarta.persistence.OneToMany;
 import jakarta.persistence.Table;
 import lombok.Data;
 import lombok.EqualsAndHashCode;
@@ -14,7 +25,7 @@
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(callSuper = true)
+@ToString(exclude = "predictedVariantConsequences", callSuper = true)
 @AGRCurationSchemaVersion(min = "2.4.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { VariantGenomicLocationAssociation.class })
 @Schema(name = "CuratedVariantGenomicLocationAssociation", description = "POJO representing an association between a variant and a curated genomic location")
 
@@ -35,5 +46,19 @@
 )
 
 public class CuratedVariantGenomicLocationAssociation extends VariantGenomicLocationAssociation {
-
+	
+	@IndexedEmbedded(
+		includePaths = {
+			"variantTranscript.name", "variantTranscript.modEntityId",
+			"variantTranscript.modInternalId", "variantTranscript.curie",
+			"vepConsequence.name", "variantTranscript.name_keyword",
+			"variantTranscript.modEntityId_keyword", "variantTranscript.modInternalId_keyword",
+			"variantTranscript.curie_keyword", "vepConsequence.name_keyword",
+			"variantTranscript.transcriptId", "variantTranscript.transcriptId_keyword"
+		}
+	)
+	@OneToMany(mappedBy = "variantGenomicLocation", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonManagedReference
+	@JsonView({ View.FieldsAndLists.class, VariantView.class })
+	private List<PredictedVariantConsequence> predictedVariantConsequences;
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/GeneOntologyAnnotationDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/GeneOntologyAnnotationDTO.java
new file mode 100644
index 000000000..56c21d54d
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/GeneOntologyAnnotationDTO.java
@@ -0,0 +1,19 @@
+package org.alliancegenome.curation_api.model.ingest.dto;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
+import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.Annotation;
+
+@Data
+@EqualsAndHashCode(callSuper = false)
+@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {Annotation.class})
+public class GeneOntologyAnnotationDTO {
+
+	private String geneIdentifier;
+
+	private String goTermCurie;
+
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BioSampleAgeFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BioSampleAgeFmsDTO.java
new file mode 100644
index 000000000..c2e54bb03
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BioSampleAgeFmsDTO.java
@@ -0,0 +1,13 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class BioSampleAgeFmsDTO extends BaseDTO {
+	private WhenExpressedFmsDTO stage;
+	private String age;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BioSampleGenomicInformationFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BioSampleGenomicInformationFmsDTO.java
new file mode 100644
index 000000000..47e6e4f51
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BioSampleGenomicInformationFmsDTO.java
@@ -0,0 +1,13 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class BioSampleGenomicInformationFmsDTO extends BaseDTO {
+	private String biosampleId;
+	private String idType;
+	private String bioSampleText;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcFmsDTO.java
index 6742ac634..10ef0c806 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcFmsDTO.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcFmsDTO.java
@@ -1,8 +1,5 @@
 package org.alliancegenome.curation_api.model.ingest.dto.fms;
 
-import java.util.List;
-
-import org.alliancegenome.curation_api.model.ingest.dto.CrossReferenceDTO;
 import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
 
 import lombok.Data;
@@ -25,5 +22,4 @@ public class BiogridOrcFmsDTO extends BaseDTO {
 	private Double score5;
 	private String hit;
 	private String source;
-	private List<CrossReferenceDTO> crossReferenceDtos;
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcIngestFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcIngestFmsDTO.java
new file mode 100644
index 000000000..45b40347d
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcIngestFmsDTO.java
@@ -0,0 +1,16 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class BiogridOrcIngestFmsDTO extends BaseDTO {
+
+	private MetaDataFmsDTO metaData;
+	private List<BiogridOrcFmsDTO> data;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/GeneExpressionFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/GeneExpressionFmsDTO.java
index 73e5da75f..07ed8a065 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/GeneExpressionFmsDTO.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/GeneExpressionFmsDTO.java
@@ -13,7 +13,7 @@ public class GeneExpressionFmsDTO extends BaseDTO {
 	private String assay;
 	private String dateAssigned;
 	private PublicationFmsDTO evidence;
-	private WhenExpressedDTO whenExpressed;
-	private WhereExpressedDTO whereExpressed;
+	private WhenExpressedFmsDTO whenExpressed;
+	private WhereExpressedFmsDTO whereExpressed;
 
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTO.java
new file mode 100644
index 000000000..9fe958615
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTO.java
@@ -0,0 +1,29 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class HTPExpressionDatasetSampleAnnotationFmsDTO extends BaseDTO {
+	private HTPIdFmsDTO sampleId;
+	private String sampleTitle;
+	private String sampleType;
+	private BioSampleAgeFmsDTO sampleAge;
+	private List<WhereExpressedFmsDTO> sampleLocations;
+	private String abundance;
+	private BioSampleGenomicInformationFmsDTO genomicInformation;
+	private String taxonId;
+	private String sex;
+	private String assayType;
+	private String sequencingFormat;
+	private List<String> assemblyVersions;
+	private String notes;
+	private List<String> datasetIds;
+	private MicroarraySampleDetailsFmsDTO microarraySampleDetails;
+	private String dateAssigned;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/HTPExpressionDatasetSampleAnnotationIngestFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/HTPExpressionDatasetSampleAnnotationIngestFmsDTO.java
new file mode 100644
index 000000000..b72b7927c
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/HTPExpressionDatasetSampleAnnotationIngestFmsDTO.java
@@ -0,0 +1,15 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class HTPExpressionDatasetSampleAnnotationIngestFmsDTO extends BaseDTO {
+	private MetaDataFmsDTO metaData;
+	private List<HTPExpressionDatasetSampleAnnotationFmsDTO> data;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/MicroarraySampleDetailsFmsDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/MicroarraySampleDetailsFmsDTO.java
new file mode 100644
index 000000000..29219fb0e
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/MicroarraySampleDetailsFmsDTO.java
@@ -0,0 +1,13 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class MicroarraySampleDetailsFmsDTO extends BaseDTO {
+	private String channelId;
+	private Integer channelNum;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/VepTxtDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/VepTxtDTO.java
new file mode 100644
index 000000000..a25fe8eac
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/VepTxtDTO.java
@@ -0,0 +1,29 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class VepTxtDTO extends BaseDTO {
+
+	private String uploadedVariation;
+	private String location;
+	private String allele;
+	private String gene;
+	private String feature;
+	private String featureType;
+	private String consequence;
+	private String cdnaPosition;
+	private String cdsPosition;
+	private String proteinPosition;
+	private String aminoAcids;
+	private String codons;
+	private String existingVariation;
+	private List<String> extra;
+	
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhenExpressedDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhenExpressedFmsDTO.java
similarity index 86%
rename from src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhenExpressedDTO.java
rename to src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhenExpressedFmsDTO.java
index 341945676..e5e7fc37f 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhenExpressedDTO.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhenExpressedFmsDTO.java
@@ -6,7 +6,7 @@
 
 @Data
 @EqualsAndHashCode(callSuper = true)
-public class WhenExpressedDTO extends BaseDTO {
+public class WhenExpressedFmsDTO extends BaseDTO {
 	private String stageTermId;
 	private String stageName;
 	private UberonSlimTermDTO stageUberonSlimTerm;
diff --git a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhereExpressedDTO.java b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhereExpressedFmsDTO.java
similarity index 93%
rename from src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhereExpressedDTO.java
rename to src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhereExpressedFmsDTO.java
index 92268423a..90c19fdc3 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhereExpressedDTO.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/WhereExpressedFmsDTO.java
@@ -9,7 +9,7 @@
 
 @Data
 @EqualsAndHashCode(callSuper = true)
-public class WhereExpressedDTO extends BaseDTO {
+public class WhereExpressedFmsDTO extends BaseDTO {
 	private String whereExpressedStatement;
 	private String cellularComponentTermId;
 	private String cellularComponentQualifierTermId;
diff --git a/src/main/java/org/alliancegenome/curation_api/model/output/APIVersionInfo.java b/src/main/java/org/alliancegenome/curation_api/model/output/APIVersionInfo.java
index f2c342205..aa3d241d3 100644
--- a/src/main/java/org/alliancegenome/curation_api/model/output/APIVersionInfo.java
+++ b/src/main/java/org/alliancegenome/curation_api/model/output/APIVersionInfo.java
@@ -1,12 +1,10 @@
 package org.alliancegenome.curation_api.model.output;
 
-import java.util.TreeMap;
-
-import org.alliancegenome.curation_api.view.View;
-
 import com.fasterxml.jackson.annotation.JsonView;
-
 import lombok.Data;
+import org.alliancegenome.curation_api.view.View;
+
+import java.util.TreeMap;
 
 @Data
 public class APIVersionInfo {
@@ -23,5 +21,6 @@ public class APIVersionInfo {
 	private String esHost;
 	@JsonView(View.FieldsOnly.class)
 	private String env;
-
+	@JsonView(View.FieldsOnly.class)
+	private String matiHost;
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/services/CodingSequenceService.java b/src/main/java/org/alliancegenome/curation_api/services/CodingSequenceService.java
index badc7798b..62fcfdcd3 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/CodingSequenceService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/CodingSequenceService.java
@@ -34,7 +34,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> ids = codingSequenceDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java b/src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java
index eff5ba8d7..670bddd20 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java
@@ -8,6 +8,7 @@
 import org.alliancegenome.curation_api.model.entities.CrossReference;
 import org.alliancegenome.curation_api.model.entities.ResourceDescriptorPage;
 import org.alliancegenome.curation_api.model.ingest.dto.fms.CrossReferenceFmsDTO;
+import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -16,9 +17,12 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
 
 @RequestScoped
 public class CrossReferenceService extends BaseEntityCrudService<CrossReference, CrossReferenceDAO> {
+	HashMap<String, CrossReference> crossReferenceCache = new HashMap<>();
 
 	@Inject
 	CrossReferenceDAO crossReferenceDAO;
@@ -109,4 +113,40 @@ public String getCrossReferenceUniqueId(CrossReference xref) {
 	public Map<String, Long> getGenomicEntityCrossRefMap(ResourceDescriptorPage page) {
 		return crossReferenceDAO.getGenesWithCrossRefs(page);
 	}
+
+	public Map<String, Long> getGenomicEntityCrossRefMap(Set<String> referencedCuries) {
+		return crossReferenceDAO.getGenesWithCrossRefs(referencedCuries);
+	}
+
+	@Transactional
+	public ObjectResponse<CrossReference> insertBioGridOrcCrossReference(CrossReference crossReference, Long geneticEntityId) {
+		String referencedCurie = crossReference.getReferencedCurie();
+		
+		CrossReference dbEntity = getCrossReference(referencedCurie, crossReference.getResourceDescriptorPage());
+		
+		// we only create new records, no updates
+		if (dbEntity == null) {
+			crossReferenceDAO.persist(crossReference);
+			crossReferenceDAO.persistAccessionGeneAssociated(crossReference.getId(), geneticEntityId);
+			return new ObjectResponse<>(crossReference);
+		}
+		return new ObjectResponse<>(dbEntity);
+	}
+
+	private CrossReference getCrossReference(String crossReferenceCurie, ResourceDescriptorPage page) {
+		if (crossReferenceCache.size() > 0) {
+			return crossReferenceCache.get(crossReferenceCurie);
+		}
+		populateCrossReferenceCache(page);
+		return crossReferenceCache.get(crossReferenceCurie);
+	}
+
+	private void populateCrossReferenceCache(ResourceDescriptorPage page) {
+		List<CrossReference> allCrossRefs = crossReferenceDAO.getAllCrossRefsByPage(page);
+		allCrossRefs.stream()
+			.filter(crossRef -> Objects.equals(crossRef.getResourceDescriptorPage().getId(), page.getId()))
+			.forEach(crossRef -> {
+				crossReferenceCache.put(crossRef.getReferencedCurie(), crossRef);
+			});
+	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/services/ExonService.java b/src/main/java/org/alliancegenome/curation_api/services/ExonService.java
index d5cbfddda..09710dfb4 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/ExonService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/ExonService.java
@@ -32,7 +32,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> ids = exonDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionAnnotationService.java b/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionAnnotationService.java
index 1ffe515ac..2d1229ed8 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionAnnotationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionAnnotationService.java
@@ -4,6 +4,7 @@
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
 import jakarta.transaction.Transactional;
+import lombok.Getter;
 import org.alliancegenome.curation_api.constants.EntityFieldConstants;
 import org.alliancegenome.curation_api.dao.GeneExpressionAnnotationDAO;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
@@ -18,17 +19,21 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 @RequestScoped
 public class GeneExpressionAnnotationService extends BaseAnnotationCrudService<GeneExpressionAnnotation, GeneExpressionAnnotationDAO> implements BaseUpsertServiceInterface<GeneExpressionAnnotation, GeneExpressionFmsDTO> {
 
 	@Inject GeneExpressionAnnotationDAO geneExpressionAnnotationDAO;
 	@Inject GeneExpressionAnnotationFmsDTOValidator geneExpressionAnnotationFmsDTOValidator;
+	@Getter
+	private Map<String, Set<String>> experiments;
 
 	@Override
 	@PostConstruct
 	protected void init() {
 		setSQLDao(geneExpressionAnnotationDAO);
+		experiments = new HashMap<>();
 	}
 
 	public List<Long> getAnnotationIdsByDataProvider(BackendBulkDataProvider dataProvider) {
@@ -44,7 +49,7 @@ public List<Long> getAnnotationIdsByDataProvider(BackendBulkDataProvider dataPro
 	@Transactional
 	@Override
 	public GeneExpressionAnnotation upsert(GeneExpressionFmsDTO geneExpressionFmsDTO, BackendBulkDataProvider dataProvider) throws ValidationException {
-		GeneExpressionAnnotation geneExpressionAnnotation = geneExpressionAnnotationFmsDTOValidator.validateAnnotation(geneExpressionFmsDTO, dataProvider);
+		GeneExpressionAnnotation geneExpressionAnnotation = geneExpressionAnnotationFmsDTOValidator.validateAnnotation(geneExpressionFmsDTO, dataProvider, experiments);
 		return geneExpressionAnnotationDAO.persist(geneExpressionAnnotation);
 	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionExperimentService.java b/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionExperimentService.java
new file mode 100644
index 000000000..4d1a8514f
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/GeneExpressionExperimentService.java
@@ -0,0 +1,83 @@
+package org.alliancegenome.curation_api.services;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+import lombok.extern.jbosslog.JBossLog;
+import org.alliancegenome.curation_api.constants.EntityFieldConstants;
+import org.alliancegenome.curation_api.dao.GeneExpressionAnnotationDAO;
+import org.alliancegenome.curation_api.dao.GeneExpressionExperimentDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionAnnotation;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
+import org.alliancegenome.curation_api.services.ontology.MmoTermService;
+import org.apache.commons.lang.StringUtils;
+
+import java.util.*;
+
+@JBossLog
+@RequestScoped
+public class GeneExpressionExperimentService extends BaseEntityCrudService<GeneExpressionExperiment, GeneExpressionExperimentDAO> {
+
+	@Inject GeneExpressionExperimentDAO geneExpressionExperimentDAO;
+	@Inject GeneExpressionAnnotationDAO geneExpressionAnnotationDAO;
+	@Inject GeneService geneService;
+	@Inject MmoTermService mmoTermService;
+	@Inject ReferenceService referenceService;
+	@Inject DataProviderService dataProviderService;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setSQLDao(geneExpressionExperimentDAO);
+	}
+
+	public List<Long> getExperimentIdsByDataProvider(BackendBulkDataProvider dataProvider) {
+		Map<String, Object> params = new HashMap<>();
+		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
+			params.put(EntityFieldConstants.EXP_EXPERIMENT_TAXON, dataProvider.canonicalTaxonCurie);
+		}
+		return geneExpressionExperimentDAO.findIdsByParams(params);
+	}
+
+	@Transactional
+	public GeneExpressionExperiment upsert(String experimentId, Set<String> geneExpressionAnnotationIds, BackendBulkDataProvider dataProvider) throws ValidationException {
+		GeneExpressionExperiment geneExpressionExperiment;
+		Set<GeneExpressionAnnotation> annotations;
+
+		//	example of experimentId: Xenbase:XB-GENE-972235|AGRKB:101000000874667|MMO:0000658
+		String[] definingFields = experimentId.split("\\|", 3);
+		String geneId = definingFields[0];
+		String referenceId = definingFields[1];
+		String assayId = definingFields[2];
+		SearchResponse<GeneExpressionExperiment> response = geneExpressionExperimentDAO.findByField("uniqueId", experimentId);
+		if (response != null && response.getSingleResult() != null) {
+			geneExpressionExperiment = response.getSingleResult();
+		} else {
+			geneExpressionExperiment = new GeneExpressionExperiment();
+			geneExpressionExperiment.setUniqueId(experimentId);
+		}
+		geneExpressionExperiment.setDataProvider(dataProviderService.getDefaultDataProvider(dataProvider.sourceOrganization));
+		geneExpressionExperiment.setEntityAssayed(geneService.findByIdentifierString(geneId));
+		geneExpressionExperiment.setSingleReference(referenceService.getByCurie(referenceId).getEntity());
+		geneExpressionExperiment.setExpressionAssayUsed(mmoTermService.findByCurie(assayId));
+		geneExpressionExperiment.setInternal(false);
+		geneExpressionExperiment.setObsolete(false);
+
+		annotations = geneExpressionExperiment.getExpressionAnnotations();
+		if (annotations == null) {
+			annotations = new HashSet<>();
+		}
+		for (String geneExpressionAnnotationId: geneExpressionAnnotationIds) {
+			annotations.add(geneExpressionAnnotationDAO.findByField("uniqueId", geneExpressionAnnotationId).getSingleResult());
+		}
+		geneExpressionExperiment.setExpressionAnnotations(annotations);
+
+		return geneExpressionExperimentDAO.persist(geneExpressionExperiment);
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/GeneOntologyAnnotationService.java b/src/main/java/org/alliancegenome/curation_api/services/GeneOntologyAnnotationService.java
new file mode 100644
index 000000000..2c7575e7f
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/GeneOntologyAnnotationService.java
@@ -0,0 +1,148 @@
+package org.alliancegenome.curation_api.services;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+import org.alliancegenome.curation_api.auth.AuthenticatedUser;
+import org.alliancegenome.curation_api.dao.GeneDAO;
+import org.alliancegenome.curation_api.dao.GeneOntologyAnnotationDAO;
+import org.alliancegenome.curation_api.dao.SpeciesDAO;
+import org.alliancegenome.curation_api.dao.ontology.GoTermDAO;
+import org.alliancegenome.curation_api.model.entities.*;
+import org.alliancegenome.curation_api.model.entities.ontology.GOTerm;
+import org.alliancegenome.curation_api.model.ingest.dto.GeneOntologyAnnotationDTO;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
+import org.alliancegenome.curation_api.services.validation.DataProviderValidator;
+import org.apache.commons.collections.CollectionUtils;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@RequestScoped
+public class GeneOntologyAnnotationService extends BaseEntityCrudService<GeneOntologyAnnotation, GeneOntologyAnnotationDAO> {
+
+	private List<Species> species;
+	public static final String RESOURCE_DESCRIPTOR_PREFIX = "ENSEMBL";
+	public static final String RESOURCE_DESCRIPTOR_PAGE_NAME = "default";
+	// <crossReference.referencedCurie, DataProvider>
+	Map<String, Long> accessionGeneMap = new HashMap<>();
+	Map<String, Long> goTermMap = new HashMap<>();
+	HashMap<String, DataProvider> dataProviderMap = new HashMap<>();
+	private Map<Long, GeneOntologyAnnotationDTO> gafMap = new HashMap<>();
+
+
+	@Inject
+	@AuthenticatedUser
+	protected Person authenticatedPerson;
+	@Inject
+	GeneOntologyAnnotationDAO gafDAO;
+	@Inject
+	GeneDAO geneDAO;
+	@Inject
+	SpeciesDAO speciesDAO;
+	@Inject
+	GoTermDAO goTermDAO;
+	@Inject
+	DataProviderValidator dataProviderValidator;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setSQLDao(gafDAO);
+	}
+
+	@Transactional
+	public ObjectResponse<GeneOntologyAnnotation> insert(GeneOntologyAnnotationDTO uiEntity, String orgAbbreviation) {
+		// if record exists skip over it
+		if (gafMap.values().stream().anyMatch(gafDTO -> gafDTO.equals(uiEntity))) {
+			for (Map.Entry<Long, GeneOntologyAnnotationDTO> entry : gafMap.entrySet()) {
+				if (entry.getValue().equals(uiEntity)) {
+					GeneOntologyAnnotation gaf = new GeneOntologyAnnotation();
+					gaf.setId(entry.getKey());
+					ObjectResponse<GeneOntologyAnnotation> objectObjectResponse = new ObjectResponse<>();
+					objectObjectResponse.setEntity(gaf);
+					return objectObjectResponse;
+				}
+			}
+		}
+		// convert curies into IDs
+
+		Long geneID = getGeneID(uiEntity, orgAbbreviation);
+		GeneOntologyAnnotation gaf = new GeneOntologyAnnotation();
+		Gene gene = new Gene();
+		gene.setId(geneID);
+		gaf.setSingleGene(gene);
+		Long goID = getGOID(uiEntity);
+		GOTerm term = new GOTerm();
+		term.setId(goID);
+		gaf.setGoTerm(term);
+		GeneOntologyAnnotation gafNew = gafDAO.persistGeneGoAssociation(gaf);
+		addNewRecordToMap(gafNew, uiEntity);
+		return new ObjectResponse<>(gafNew);
+	}
+
+	private void addNewRecordToMap(GeneOntologyAnnotation gafNew, GeneOntologyAnnotationDTO uiEntity) {
+		GeneOntologyAnnotationDTO dto = new GeneOntologyAnnotationDTO();
+		dto.setGeneIdentifier(uiEntity.getGeneIdentifier());
+		dto.setGoTermCurie(uiEntity.getGoTermCurie());
+		gafMap.put(gafNew.getId(), dto);
+	}
+
+	public Long getGeneID(GeneOntologyAnnotationDTO uiEntity, String orgAbbreviation) {
+		if (accessionGeneMap.isEmpty()) {
+			List<Species> speciesList = getSpecies(orgAbbreviation);
+			speciesList.forEach(species -> accessionGeneMap.putAll(geneDAO.getAllGeneIdsPerSpecies(species)));
+		}
+		Long geneID = accessionGeneMap.get(uiEntity.getGeneIdentifier());
+		return geneID;
+	}
+
+	private Long getGOID(GeneOntologyAnnotationDTO uiEntity) {
+		if (goTermMap.isEmpty()) {
+			goTermMap = goTermDAO.getAllGOIds();
+		}
+		Long goID = goTermMap.get(uiEntity.getGoTermCurie());
+		return goID;
+	}
+
+	private List<Species> getSpecies(String orgAbbreviation) {
+		if (CollectionUtils.isNotEmpty(species)) {
+			return species;
+		}
+		if (orgAbbreviation.equalsIgnoreCase("XB")) {
+			species = new ArrayList<>();
+			species.add(getSingleSpecies("XBXL"));
+			species.add(getSingleSpecies("XBXT"));
+		} else {
+			species = List.of(getSingleSpecies(orgAbbreviation));
+		}
+		return species;
+	}
+
+	private Species getSingleSpecies(String orgAbbreviation) {
+		return speciesDAO.findByField("displayName", orgAbbreviation).getSingleResult();
+	}
+
+	public ObjectResponse<DataProvider> validate(DataProvider uiEntity) {
+		return dataProviderValidator.validateDataProvider(uiEntity, null, true);
+	}
+
+
+	public Map<Long, GeneOntologyAnnotationDTO> getGafMap(Organization organization) {
+		if (gafMap.size() > 0) {
+			return gafMap;
+		}
+		gafMap = gafDAO.getAllGafIdsPerProvider(organization);
+		return gafMap;
+	}
+
+	@Transactional
+	public GeneOntologyAnnotation deprecateOrDelete(Long id, Boolean throwApiError, String requestSource, Boolean deprecate) {
+		return gafDAO.remove(id);
+	}
+
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/Gff3Service.java b/src/main/java/org/alliancegenome/curation_api/services/Gff3Service.java
index 4b41cfec2..53992dc80 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/Gff3Service.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/Gff3Service.java
@@ -11,13 +11,16 @@
 import org.alliancegenome.curation_api.dao.GenomeAssemblyDAO;
 import org.alliancegenome.curation_api.dao.TranscriptDAO;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
-import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.exceptions.KnownIssueValidationException;
 import org.alliancegenome.curation_api.exceptions.ObjectValidationException;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
 import org.alliancegenome.curation_api.model.entities.CodingSequence;
 import org.alliancegenome.curation_api.model.entities.Exon;
+import org.alliancegenome.curation_api.model.entities.Gene;
 import org.alliancegenome.curation_api.model.entities.Transcript;
 import org.alliancegenome.curation_api.model.entities.associations.codingSequenceAssociations.CodingSequenceGenomicLocationAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.exonAssociations.ExonGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptCodingSequenceAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptExonAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptGeneAssociation;
@@ -26,6 +29,7 @@
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.associations.codingSequenceAssociations.CodingSequenceGenomicLocationAssociationService;
 import org.alliancegenome.curation_api.services.associations.exonAssociations.ExonGenomicLocationAssociationService;
+import org.alliancegenome.curation_api.services.associations.geneAssociations.GeneGenomicLocationAssociationService;
 import org.alliancegenome.curation_api.services.associations.transcriptAssociations.TranscriptCodingSequenceAssociationService;
 import org.alliancegenome.curation_api.services.associations.transcriptAssociations.TranscriptExonAssociationService;
 import org.alliancegenome.curation_api.services.associations.transcriptAssociations.TranscriptGeneAssociationService;
@@ -51,12 +55,14 @@ public class Gff3Service {
 	@Inject ExonGenomicLocationAssociationService exonLocationService;
 	@Inject CodingSequenceGenomicLocationAssociationService cdsLocationService;
 	@Inject TranscriptGenomicLocationAssociationService transcriptLocationService;
+	@Inject GeneGenomicLocationAssociationService geneLocationService;
 	@Inject TranscriptGeneAssociationService transcriptGeneService;
 	@Inject TranscriptCodingSequenceAssociationService transcriptCdsService;
 	@Inject TranscriptExonAssociationService transcriptExonService;
 	@Inject DataProviderService dataProviderService;
 	@Inject NcbiTaxonTermService ncbiTaxonTermService;
 	@Inject Gff3DtoValidator gff3DtoValidator;
+	@Inject GeneService geneService;
 
 	@Transactional
 	public void loadExonLocationAssociations(ImmutablePair<Gff3DTO, Map<String, String>> gffEntryPair, List<Long> idsAdded, BackendBulkDataProvider dataProvider, String assemblyId) throws ValidationException {
@@ -140,6 +146,42 @@ public void loadTranscriptLocationAssociations(ImmutablePair<Gff3DTO, Map<String
 		}
 	}
 
+	@Transactional
+	public void loadGeneLocationAssociations(ImmutablePair<Gff3DTO, Map<String, String>> gffEntryPair, List<Long> idsAdded, BackendBulkDataProvider dataProvider, String assemblyId) throws ValidationException {
+		Gff3DTO gffEntry = gffEntryPair.getKey();
+		Map<String, String> attributes = gffEntryPair.getValue();
+		if (StringUtils.isBlank(assemblyId)) {
+			throw new ObjectValidationException(gffEntry, "Cannot load associations without assembly");
+		}
+
+		if (!Gff3Constants.GENE_TYPES.contains(gffEntry.getType())) {
+			throw new ObjectValidationException(gffEntry, "Invalid Type: " + gffEntry.getType() + " for Gene Location");
+		}
+
+		String geneCurie;
+		String identifyingAttribute;
+		if (attributes.containsKey("gene_id")) {
+			geneCurie = attributes.get("gene_id");
+			identifyingAttribute = "gene_id";
+		} else if (attributes.containsKey("ID")) {
+			geneCurie = attributes.get("ID");
+			identifyingAttribute = "ID";
+		} else {
+			throw new ObjectValidationException(gffEntry, "attributes - ID - " + ValidationConstants.REQUIRED_MESSAGE);
+		}
+		
+		Gene gene = geneService.findByIdentifierString(geneCurie);
+		if (gene == null) {
+			throw new KnownIssueValidationException(ValidationConstants.UNRECOGNIZED_MESSAGE + " (" + attributes.get(identifyingAttribute) + ")");
+		}
+
+		GeneGenomicLocationAssociation geneLocation = gff3DtoValidator.validateGeneLocation(gffEntry, gene, assemblyId, dataProvider);
+		if (geneLocation != null) {
+			idsAdded.add(geneLocation.getId());
+			geneLocationService.addAssociationToSubject(geneLocation);
+		}
+	}
+
 	@Transactional
 	public void loadExonParentChildAssociations(ImmutablePair<Gff3DTO, Map<String, String>> gffEntryPair, List<Long> idsAdded, BackendBulkDataProvider dataProvider) throws ValidationException {
 		Gff3DTO gffEntry = gffEntryPair.getKey();
@@ -216,7 +258,7 @@ public Map<String, String> getGeneIdCurieMap(List<Gff3DTO> gffData, BackendBulkD
 		Map<String, String> geneIdCurieMap = new HashMap<>();
 
 		for (Gff3DTO gffEntry : gffData) {
-			if (gffEntry.getType().contains("gene")) {
+			if (Gff3Constants.GENE_TYPES.contains(gffEntry.getType())) {
 				Map<String, String> attributes = Gff3AttributesHelper.getAttributes(gffEntry, dataProvider);
 				if (attributes.containsKey("gene_id") && attributes.containsKey("ID")) {
 					geneIdCurieMap.put(attributes.get("ID"), attributes.get("gene_id"));
diff --git a/src/main/java/org/alliancegenome/curation_api/services/HTPExpressionDatasetSampleAnnotationService.java b/src/main/java/org/alliancegenome/curation_api/services/HTPExpressionDatasetSampleAnnotationService.java
new file mode 100644
index 000000000..6b0097203
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/HTPExpressionDatasetSampleAnnotationService.java
@@ -0,0 +1,46 @@
+package org.alliancegenome.curation_api.services;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import org.alliancegenome.curation_api.constants.EntityFieldConstants;
+import org.alliancegenome.curation_api.dao.HTPExpressionDatasetSampleAnnotationDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.interfaces.crud.BaseUpsertServiceInterface;
+import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetSampleAnnotation;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetSampleAnnotationFmsDTO;
+import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
+import org.alliancegenome.curation_api.services.validation.dto.fms.HTPExpressionDatasetSampleAnnotationFmsDTOValidator;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+
+@RequestScoped
+public class HTPExpressionDatasetSampleAnnotationService extends BaseEntityCrudService<HTPExpressionDatasetSampleAnnotation, HTPExpressionDatasetSampleAnnotationDAO> implements BaseUpsertServiceInterface<HTPExpressionDatasetSampleAnnotation, HTPExpressionDatasetSampleAnnotationFmsDTO> {
+	
+	@Inject HTPExpressionDatasetSampleAnnotationDAO htpExpressionDatasetSampleAnnotationDAO;
+	@Inject HTPExpressionDatasetSampleAnnotationFmsDTOValidator htpExpressionDatasetSampleAnnotationFmsDtoValidator;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setSQLDao(htpExpressionDatasetSampleAnnotationDAO);
+	}
+	@Transactional
+	public HTPExpressionDatasetSampleAnnotation upsert(HTPExpressionDatasetSampleAnnotationFmsDTO htpExpressionDatasetSampleAnnotationData, BackendBulkDataProvider backendBulkDataProvider) throws ValidationException {
+		return htpExpressionDatasetSampleAnnotationFmsDtoValidator.validateHTPExpressionDatasetSampleAnnotationFmsDTO(htpExpressionDatasetSampleAnnotationData, backendBulkDataProvider);
+	}
+
+	public List<Long> getAnnotationIdsByDataProvider(String dataProvider) {
+		Map<String, Object> params = new HashMap<>();
+		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider);
+		List<Long> ids = htpExpressionDatasetSampleAnnotationDAO.findIdsByParams(params);
+		ids.removeIf(Objects::isNull);
+		return ids;
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/InformationContentEntityService.java b/src/main/java/org/alliancegenome/curation_api/services/InformationContentEntityService.java
index 645bdacb0..2f74097e0 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/InformationContentEntityService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/InformationContentEntityService.java
@@ -28,4 +28,5 @@ public InformationContentEntity retrieveFromDbOrLiteratureService(String curieOr
 
 		return ice;
 	}
+
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/services/OrganizationService.java b/src/main/java/org/alliancegenome/curation_api/services/OrganizationService.java
index 3b4d20b4b..672c720e9 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/OrganizationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/OrganizationService.java
@@ -1,23 +1,23 @@
 package org.alliancegenome.curation_api.services;
 
-import java.util.Date;
-import java.util.HashMap;
-
+import io.quarkus.logging.Log;
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.dao.OrganizationDAO;
 import org.alliancegenome.curation_api.model.entities.Organization;
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
 
-import io.quarkus.logging.Log;
-import jakarta.annotation.PostConstruct;
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
+import java.util.Date;
+import java.util.HashMap;
 
 @RequestScoped
 public class OrganizationService extends BaseEntityCrudService<Organization, OrganizationDAO> {
 
-	@Inject OrganizationDAO organizationDAO;
+	@Inject
+	OrganizationDAO organizationDAO;
 
 	Date orgRequest;
 	HashMap<Long, Organization> orgIdCacheMap = new HashMap<>();
@@ -54,7 +54,7 @@ public ObjectResponse<Organization> getById(Long id) {
 	public ObjectResponse<Organization> getByAbbr(String abbr) {
 
 		Organization org = null;
-		SearchResponse<Organization> orgResponse = null;
+		SearchResponse<Organization> orgResponse;
 
 		if (orgRequest != null) {
 			if (orgAbbrCacheMap.containsKey(abbr)) {
diff --git a/src/main/java/org/alliancegenome/curation_api/services/PredictedVariantConsequenceService.java b/src/main/java/org/alliancegenome/curation_api/services/PredictedVariantConsequenceService.java
new file mode 100644
index 000000000..e1b241bb6
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/PredictedVariantConsequenceService.java
@@ -0,0 +1,100 @@
+package org.alliancegenome.curation_api.services;
+
+import java.time.OffsetDateTime;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import org.alliancegenome.curation_api.constants.EntityFieldConstants;
+import org.alliancegenome.curation_api.dao.PredictedVariantConsequenceDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.interfaces.crud.BaseUpsertServiceInterface;
+import org.alliancegenome.curation_api.model.entities.Person;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
+import org.alliancegenome.curation_api.services.validation.dto.fms.VepGeneFmsDTOValidator;
+import org.alliancegenome.curation_api.services.validation.dto.fms.VepTranscriptFmsDTOValidator;
+import org.apache.commons.lang.StringUtils;
+
+import io.quarkus.logging.Log;
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+
+@RequestScoped
+public class PredictedVariantConsequenceService extends BaseEntityCrudService<PredictedVariantConsequence, PredictedVariantConsequenceDAO> implements BaseUpsertServiceInterface<PredictedVariantConsequence, VepTxtDTO> {
+
+	@Inject PredictedVariantConsequenceDAO predictedVariantConsequenceDAO;
+	@Inject VepTranscriptFmsDTOValidator vepTranscriptFmsDtoValidator;
+	@Inject VepGeneFmsDTOValidator vepGeneFmsDtoValidator;
+	@Inject PersonService personService;
+	
+	@Override
+	@PostConstruct
+	protected void init() {
+		setSQLDao(predictedVariantConsequenceDAO);
+	}
+
+	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
+		Map<String, Object> params = new HashMap<>();
+		params.put("variantTranscript." + EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+			params.put("variantTranscript." + EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
+		}
+		List<Long> ids = predictedVariantConsequenceDAO.findIdsByParams(params);
+		ids.removeIf(Objects::isNull);
+		return ids;
+	}
+
+	public List<Long> getGeneLevelIdsByDataProvider(BackendBulkDataProvider dataProvider) {
+		Map<String, Object> params = new HashMap<>();
+		params.put("variantTranscript." + EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+			params.put("variantTranscript." + EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
+		}
+		params.put("geneLevelConsequence", true);
+		List<Long> ids = predictedVariantConsequenceDAO.findIdsByParams(params);
+		ids.removeIf(Objects::isNull);
+		return ids;
+	}
+
+	@Override
+	@Transactional
+	public PredictedVariantConsequence upsert(VepTxtDTO dto, BackendBulkDataProvider dataProvider)
+			throws ValidationException {
+		return vepTranscriptFmsDtoValidator.validateTranscriptLevelConsequence(dto, dataProvider);
+	}
+
+	@Transactional
+	public Long updateGeneLevelConsequence(VepTxtDTO dto) throws ValidationException {
+		return vepGeneFmsDtoValidator.validateGeneLevelConsequence(dto);
+	}
+	
+	@Transactional
+	public PredictedVariantConsequence resetGeneLevelConsequence(Long id, String requestSource) {
+		PredictedVariantConsequence pvc = predictedVariantConsequenceDAO.find(id);
+		
+		if (pvc == null) {
+			String errorMessage = "Could not find PredictedVariantConsequence with id: " + id;
+			Log.error(errorMessage);
+			return null;
+		}
+
+		if (pvc.getGeneLevelConsequence()) {
+			pvc.setGeneLevelConsequence(true);
+			if (authenticatedPerson.getUniqueId() != null) {
+				requestSource = authenticatedPerson.getUniqueId();
+			}
+			Person updatedBy = personService.fetchByUniqueIdOrCreate(requestSource);
+				pvc.setUpdatedBy(updatedBy);
+				pvc.setDateUpdated(OffsetDateTime.now());
+			return predictedVariantConsequenceDAO.persist(pvc);
+		}
+		
+		return pvc;
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/ReferenceService.java b/src/main/java/org/alliancegenome/curation_api/services/ReferenceService.java
index 4d8d97576..daa706d9f 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/ReferenceService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/ReferenceService.java
@@ -1,10 +1,10 @@
 package org.alliancegenome.curation_api.services;
 
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-
+import io.quarkus.logging.Log;
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
 import org.alliancegenome.curation_api.dao.ReferenceDAO;
 import org.alliancegenome.curation_api.model.entities.Reference;
 import org.alliancegenome.curation_api.response.ObjectResponse;
@@ -12,20 +12,23 @@
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
 import org.alliancegenome.curation_api.services.helpers.references.ReferenceSynchronisationHelper;
 
-import io.quarkus.logging.Log;
-import jakarta.annotation.PostConstruct;
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
-import jakarta.transaction.Transactional;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
 
 @RequestScoped
 public class ReferenceService extends BaseEntityCrudService<Reference, ReferenceDAO> {
 
-	@Inject ReferenceDAO referenceDAO;
-	@Inject ReferenceSynchronisationHelper refSyncHelper;
-	
+	@Inject
+	ReferenceDAO referenceDAO;
+	@Inject
+	ReferenceSynchronisationHelper refSyncHelper;
+
 	Date referenceRequest;
+	Date referenceRequestShallow;
 	HashMap<String, Reference> referenceCacheMap = new HashMap<>();
+	HashMap<String, Reference> shallowReferenceCacheMap = new HashMap<>();
 
 	@Override
 	@PostConstruct
@@ -52,6 +55,9 @@ public ObjectResponse<Reference> getByCurie(String curie) {
 	public Reference retrieveFromDbOrLiteratureService(String curieOrXref) {
 		Reference reference = null;
 		if (referenceRequest != null) {
+			if (referenceCacheMap.isEmpty()) {
+				referenceCacheMap = referenceDAO.getReferenceMap();
+			}
 			if (referenceCacheMap.containsKey(curieOrXref)) {
 				reference = referenceCacheMap.get(curieOrXref);
 			} else {
@@ -65,7 +71,25 @@ public Reference retrieveFromDbOrLiteratureService(String curieOrXref) {
 		}
 		return reference;
 	}
-	
+
+	@Transactional
+	public Reference retrieveShallowReferenceFromDbOrLiteratureService(String curieOrXref) {
+		Reference reference = null;
+		if (shallowReferenceCacheMap.containsKey(curieOrXref)) {
+			reference = shallowReferenceCacheMap.get(curieOrXref);
+		} else {
+			Log.debug("Reference not cached, caching reference: (" + curieOrXref + ")");
+			if (shallowReferenceCacheMap.isEmpty()) {
+				shallowReferenceCacheMap = referenceDAO.getShallowReferenceMap();
+				reference = shallowReferenceCacheMap.get(curieOrXref);
+			} else {
+				reference = findOrCreateReference(curieOrXref);
+				referenceCacheMap.put(curieOrXref, reference);
+			}
+		}
+		return reference;
+	}
+
 	private Reference findOrCreateReference(String curieOrXref) {
 		Reference reference = null;
 
diff --git a/src/main/java/org/alliancegenome/curation_api/services/TranscriptService.java b/src/main/java/org/alliancegenome/curation_api/services/TranscriptService.java
index abc9f8fbf..4c8816b8e 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/TranscriptService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/TranscriptService.java
@@ -34,7 +34,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> ids = transcriptDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/codingSequenceAssociations/CodingSequenceGenomicLocationAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/codingSequenceAssociations/CodingSequenceGenomicLocationAssociationService.java
index 0ca58b1fb..2af2decd9 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/codingSequenceAssociations/CodingSequenceGenomicLocationAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/codingSequenceAssociations/CodingSequenceGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.CODING_SEQUENCE_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.CODING_SEQUENCE_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = codingSequenceGenomicLocationAssociationDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/constructAssociations/ConstructGenomicEntityAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/constructAssociations/ConstructGenomicEntityAssociationService.java
index 7a0098d77..258396355 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/constructAssociations/ConstructGenomicEntityAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/constructAssociations/ConstructGenomicEntityAssociationService.java
@@ -1,13 +1,10 @@
 package org.alliancegenome.curation_api.services.associations.constructAssociations;
 
-import java.time.OffsetDateTime;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.stream.Collectors;
-
+import io.quarkus.logging.Log;
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
 import org.alliancegenome.curation_api.constants.EntityFieldConstants;
 import org.alliancegenome.curation_api.dao.ConstructDAO;
 import org.alliancegenome.curation_api.dao.GenomicEntityDAO;
@@ -18,7 +15,6 @@
 import org.alliancegenome.curation_api.exceptions.ValidationException;
 import org.alliancegenome.curation_api.interfaces.crud.BaseUpsertServiceInterface;
 import org.alliancegenome.curation_api.model.entities.Construct;
-import org.alliancegenome.curation_api.model.entities.GenomicEntity;
 import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.model.ingest.dto.associations.constructAssociations.ConstructGenomicEntityAssociationDTO;
 import org.alliancegenome.curation_api.response.ObjectResponse;
@@ -28,23 +24,27 @@
 import org.alliancegenome.curation_api.services.validation.associations.constructAssociations.ConstructGenomicEntityAssociationValidator;
 import org.alliancegenome.curation_api.services.validation.dto.associations.constructAssociations.ConstructGenomicEntityAssociationDTOValidator;
 
-import io.quarkus.logging.Log;
-import jakarta.annotation.PostConstruct;
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
-import jakarta.transaction.Transactional;
+import java.util.*;
+import java.util.stream.Collectors;
 
 @RequestScoped
 public class ConstructGenomicEntityAssociationService extends BaseAssociationDTOCrudService<ConstructGenomicEntityAssociation, ConstructGenomicEntityAssociationDTO, ConstructGenomicEntityAssociationDAO>
 	implements BaseUpsertServiceInterface<ConstructGenomicEntityAssociation, ConstructGenomicEntityAssociationDTO> {
 
-	@Inject ConstructGenomicEntityAssociationDAO constructGenomicEntityAssociationDAO;
-	@Inject ConstructGenomicEntityAssociationValidator constructGenomicEntityAssociationValidator;
-	@Inject ConstructGenomicEntityAssociationDTOValidator constructGenomicEntityAssociationDtoValidator;
-	@Inject ConstructDAO constructDAO;
-	@Inject GenomicEntityDAO genomicEntityDAO;
-	@Inject PersonService personService;
-	@Inject PersonDAO personDAO;
+	@Inject
+	ConstructGenomicEntityAssociationDAO constructGenomicEntityAssociationDAO;
+	@Inject
+	ConstructGenomicEntityAssociationValidator constructGenomicEntityAssociationValidator;
+	@Inject
+	ConstructGenomicEntityAssociationDTOValidator constructGenomicEntityAssociationDtoValidator;
+	@Inject
+	ConstructDAO constructDAO;
+	@Inject
+	GenomicEntityDAO genomicEntityDAO;
+	@Inject
+	PersonService personService;
+	@Inject
+	PersonDAO personDAO;
 
 	@Override
 	@PostConstruct
@@ -59,9 +59,11 @@ public ObjectResponse<ConstructGenomicEntityAssociation> upsert(ConstructGenomic
 			return null;
 		}
 		dbEntity = constructGenomicEntityAssociationDAO.persist(dbEntity);
+/*
 		addAssociationToConstruct(dbEntity);
 		addAssociationToGenomicEntity(dbEntity);
-		return new ObjectResponse<ConstructGenomicEntityAssociation>(dbEntity);
+*/
+		return new ObjectResponse<>(dbEntity);
 	}
 
 	public ObjectResponse<ConstructGenomicEntityAssociation> validate(ConstructGenomicEntityAssociation uiEntity) {
@@ -85,11 +87,11 @@ public List<Long> getAssociationsByDataProvider(BackendBulkDataProvider dataProv
 	}
 
 	@Transactional
-	public ConstructGenomicEntityAssociation deprecateOrDeleteAssociation(Long id, Boolean throwApiError, String loadDescription, Boolean deprecate) {
-		ConstructGenomicEntityAssociation association = constructGenomicEntityAssociationDAO.find(id);
+	public ConstructGenomicEntityAssociation deprecateOrDelete(Long id, Boolean throwApiError, String requestSource, Boolean deprecate) {
+		ConstructGenomicEntityAssociation object = dao.getShallowEntity(ConstructGenomicEntityAssociation.class, id);
 
-		if (association == null) {
-			String errorMessage = "Could not find ConstructGenomicEntityAssociation with id: " + id;
+		if (object == null) {
+			String errorMessage = "Could not find entity with id: " + id;
 			if (throwApiError) {
 				ObjectResponse<ConstructGenomicEntityAssociation> response = new ObjectResponse<>();
 				response.addErrorMessage("id", errorMessage);
@@ -98,21 +100,7 @@ public ConstructGenomicEntityAssociation deprecateOrDeleteAssociation(Long id, B
 			Log.error(errorMessage);
 			return null;
 		}
-		if (deprecate) {
-			if (!association.getObsolete()) {
-				association.setObsolete(true);
-				if (authenticatedPerson != null) {
-					association.setUpdatedBy(personDAO.find(authenticatedPerson.getId()));
-				} else {
-					association.setUpdatedBy(personService.fetchByUniqueIdOrCreate(loadDescription));
-				}
-				association.setDateUpdated(OffsetDateTime.now());
-				return constructGenomicEntityAssociationDAO.persist(association);
-			}
-		}
-
-		constructGenomicEntityAssociationDAO.remove(association.getId());
-
+		dao.remove(id);
 		return null;
 	}
 
@@ -150,6 +138,7 @@ private void addAssociationToConstruct(ConstructGenomicEntityAssociation associa
 		constructDAO.persist(construct);
 	}
 
+/*
 	private void addAssociationToGenomicEntity(ConstructGenomicEntityAssociation association) {
 		GenomicEntity genomicEntity = association.getConstructGenomicEntityAssociationObject();
 		List<ConstructGenomicEntityAssociation> currentAssociations = genomicEntity.getConstructGenomicEntityAssociations();
@@ -164,4 +153,5 @@ private void addAssociationToGenomicEntity(ConstructGenomicEntityAssociation ass
 		genomicEntity.setConstructGenomicEntityAssociations(currentAssociations);
 		genomicEntityDAO.persist(genomicEntity);
 	}
+*/
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/exonAssociations/ExonGenomicLocationAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/exonAssociations/ExonGenomicLocationAssociationService.java
index d6840d409..adb1a45c7 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/exonAssociations/ExonGenomicLocationAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/exonAssociations/ExonGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.EXON_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.EXON_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = exonGenomicLocationAssociationDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/geneAssociations/GeneGenomicLocationAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/geneAssociations/GeneGenomicLocationAssociationService.java
new file mode 100644
index 000000000..da6b25f85
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/geneAssociations/GeneGenomicLocationAssociationService.java
@@ -0,0 +1,124 @@
+package org.alliancegenome.curation_api.services.associations.geneAssociations;
+
+import java.time.OffsetDateTime;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+import org.alliancegenome.curation_api.constants.EntityFieldConstants;
+import org.alliancegenome.curation_api.dao.PersonDAO;
+import org.alliancegenome.curation_api.dao.associations.geneAssociations.GeneGenomicLocationAssociationDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.ApiErrorException;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.services.PersonService;
+import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
+import org.apache.commons.lang.StringUtils;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+import lombok.extern.jbosslog.JBossLog;
+
+@JBossLog
+@RequestScoped
+public class GeneGenomicLocationAssociationService extends BaseEntityCrudService<GeneGenomicLocationAssociation, GeneGenomicLocationAssociationDAO> {
+
+	@Inject GeneGenomicLocationAssociationDAO geneGenomicLocationAssociationDAO;
+	@Inject PersonDAO personDAO;
+	@Inject PersonService personService;
+	
+	@Override
+	@PostConstruct
+	protected void init() {
+		setSQLDao(geneGenomicLocationAssociationDAO);
+	}
+
+
+	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
+		Map<String, Object> params = new HashMap<>();
+		params.put(EntityFieldConstants.GENE_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
+			params.put(EntityFieldConstants.GENE_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
+		}
+		List<Long> associationIds = geneGenomicLocationAssociationDAO.findIdsByParams(params);
+		associationIds.removeIf(Objects::isNull);
+
+		return associationIds;
+	}
+
+	@Override
+	@Transactional
+	public GeneGenomicLocationAssociation deprecateOrDelete(Long id, Boolean throwApiError, String loadDescription, Boolean deprecate) {
+		GeneGenomicLocationAssociation association = geneGenomicLocationAssociationDAO.find(id);
+
+		if (association == null) {
+			String errorMessage = "Could not find GeneGenomicLocationAssociation with id: " + id;
+			if (throwApiError) {
+				ObjectResponse<GeneGenomicLocationAssociation> response = new ObjectResponse<>();
+				response.addErrorMessage("id", errorMessage);
+				throw new ApiErrorException(response);
+			}
+			log.error(errorMessage);
+			return null;
+		}
+		if (deprecate) {
+			if (!association.getObsolete()) {
+				association.setObsolete(true);
+				if (authenticatedPerson.getId() != null) {
+					association.setUpdatedBy(personDAO.find(authenticatedPerson.getId()));
+				} else {
+					association.setUpdatedBy(personService.fetchByUniqueIdOrCreate(loadDescription));
+				}
+				association.setDateUpdated(OffsetDateTime.now());
+				return geneGenomicLocationAssociationDAO.persist(association);
+			}
+			return association;
+		}
+		
+		geneGenomicLocationAssociationDAO.remove(association.getId());
+		
+		return null;
+	}
+
+	public ObjectResponse<GeneGenomicLocationAssociation> getLocationAssociation(Long geneId, Long assemblyComponentId) {
+		GeneGenomicLocationAssociation association = null;
+
+		Map<String, Object> params = new HashMap<>();
+		params.put(EntityFieldConstants.GENE_ASSOCIATION_SUBJECT + ".id", geneId);
+		params.put("geneGenomicLocationAssociationObject.id", assemblyComponentId);
+
+		SearchResponse<GeneGenomicLocationAssociation> resp = geneGenomicLocationAssociationDAO.findByParams(params);
+		if (resp != null && resp.getSingleResult() != null) {
+			association = resp.getSingleResult();
+		}
+
+		ObjectResponse<GeneGenomicLocationAssociation> response = new ObjectResponse<>();
+		response.setEntity(association);
+
+		return response;
+	}
+	
+	public void addAssociationToSubject(GeneGenomicLocationAssociation association) {
+		Gene gene = association.getGeneAssociationSubject();
+		
+		List<GeneGenomicLocationAssociation> currentSubjectAssociations = gene.getGeneGenomicLocationAssociations();
+		if (currentSubjectAssociations == null) {
+			currentSubjectAssociations = new ArrayList<>();
+		}
+		
+		List<Long> currentSubjectAssociationIds = currentSubjectAssociations.stream()
+				.map(GeneGenomicLocationAssociation::getId).collect(Collectors.toList());
+		
+		if (!currentSubjectAssociationIds.contains(association.getId())) {
+			currentSubjectAssociations.add(association);
+		}
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptCodingSequenceAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptCodingSequenceAssociationService.java
index ca9bc103e..b859c62b8 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptCodingSequenceAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptCodingSequenceAssociationService.java
@@ -46,7 +46,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptCodingSequenceAssociationDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptExonAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptExonAssociationService.java
index 57602635c..34cbbff5d 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptExonAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptExonAssociationService.java
@@ -46,7 +46,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptExonAssociationDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGeneAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGeneAssociationService.java
index 256d9a003..c0cf3d08f 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGeneAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGeneAssociationService.java
@@ -46,7 +46,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptGeneAssociationDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGenomicLocationAssociationService.java b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGenomicLocationAssociationService.java
index babdc301f..34cb99c19 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGenomicLocationAssociationService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/associations/transcriptAssociations/TranscriptGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptGenomicLocationAssociationDAO.findIdsByParams(params);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/base/BaseOntologyTermService.java b/src/main/java/org/alliancegenome/curation_api/services/base/BaseOntologyTermService.java
index a612843b6..01d798db8 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/base/BaseOntologyTermService.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/base/BaseOntologyTermService.java
@@ -222,9 +222,9 @@ private void handleSynonyms(OntologyTerm dbTerm, OntologyTerm incomingTerm) {
 		} else {
 			newSynonyms = incomingTerm.getSynonyms().stream().collect(Collectors.toSet());
 		}
-		List<String> newSynonymNames = currentSynonyms.stream().map(Synonym::getName).collect(Collectors.toList());
+		List<String> newSynonymNames = newSynonyms.stream().map(Synonym::getName).collect(Collectors.toList());
 
-		newSynonyms.forEach(syn -> {
+		for (Synonym syn: newSynonyms) {
 			if (!currentSynonymNames.contains(syn.getName())) {
 				SearchResponse<Synonym> response = synonymDAO.findByField("name", syn.getName());
 				Synonym synonym;
@@ -235,13 +235,12 @@ private void handleSynonyms(OntologyTerm dbTerm, OntologyTerm incomingTerm) {
 				}
 				dbTerm.getSynonyms().add(synonym);
 			}
-		});
-
-		currentSynonyms.forEach(syn -> {
+		}
+		for (Synonym syn: currentSynonyms) {
 			if (!newSynonymNames.contains(syn.getName())) {
 				dbTerm.getSynonyms().remove(syn);
 			}
-		});
+		}
 
 	}
 
diff --git a/src/main/java/org/alliancegenome/curation_api/services/helpers/GenericOntologyLoadHelper.java b/src/main/java/org/alliancegenome/curation_api/services/helpers/GenericOntologyLoadHelper.java
index 05e8e35c1..613371037 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/helpers/GenericOntologyLoadHelper.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/helpers/GenericOntologyLoadHelper.java
@@ -17,6 +17,7 @@
 import org.alliancegenome.curation_api.model.entities.ontology.OntologyTerm;
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
 import org.apache.commons.collections.CollectionUtils;
+import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLAnnotation;
@@ -30,7 +31,6 @@
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.search.EntitySearcher;
-import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 
 import io.quarkus.logging.Log;
 
@@ -317,7 +317,7 @@ private T parseAnnotation(OWLAnnotation annotation, OWLClass node, T term, Strin
 			term.setObsolete(getBoolean(annotation.getValue()));
 		} else if (key.equals("hasOBONamespace")) {
 			term.setNamespace(getString(annotation.getValue()));
-		} else if (key.equals("hasExactSynonym") || key.equals("hasRelatedSynonym")) {
+		} else if (key.equals("hasExactSynonym") || key.equals("hasRelatedSynonym") || key.equals("hasNarrowSynonym") || key.equals("hasBroadSynonym")) {
 			if (term.getSynonyms() == null) {
 				term.setSynonyms(new ArrayList<>());
 			}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/helpers/annotations/GeneExpressionAnnotationUniqueIdHelper.java b/src/main/java/org/alliancegenome/curation_api/services/helpers/annotations/GeneExpressionAnnotationUniqueIdHelper.java
index 25174699f..a243051a6 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/helpers/annotations/GeneExpressionAnnotationUniqueIdHelper.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/helpers/annotations/GeneExpressionAnnotationUniqueIdHelper.java
@@ -14,11 +14,24 @@ public String generateUniqueId(GeneExpressionFmsDTO geneExpressionFmsDTO, String
 		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getAssay());
 		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getGeneId());
 		uniqueIdGeneratorHelper.add(referenceCurie);
-		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhenExpressed().getStageTermId());
-		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhenExpressed().getStageName());
-		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhereExpressed().getWhereExpressedStatement());
-		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureTermId());
-		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhereExpressed().getCellularComponentTermId());
+		if (geneExpressionFmsDTO.getWhenExpressed() != null) {
+			uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhenExpressed().getStageTermId());
+			uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhenExpressed().getStageName());
+		}
+		if (geneExpressionFmsDTO.getWhereExpressed() != null) {
+			uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhereExpressed().getWhereExpressedStatement());
+			uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureTermId());
+			uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getWhereExpressed().getCellularComponentTermId());
+		}
+		return uniqueIdGeneratorHelper.getUniqueId();
+	}
+
+	//	UniqueID =	geneId | evidenceReferenceCurie | assayId
+	public String generateExperimentId(GeneExpressionFmsDTO geneExpressionFmsDTO, String referenceCurie) {
+		UniqueIdGeneratorHelper uniqueIdGeneratorHelper = new UniqueIdGeneratorHelper();
+		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getGeneId());
+		uniqueIdGeneratorHelper.add(referenceCurie);
+		uniqueIdGeneratorHelper.add(geneExpressionFmsDTO.getAssay());
 		return uniqueIdGeneratorHelper.getUniqueId();
 	}
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/services/helpers/gff3/Gff3AttributesHelper.java b/src/main/java/org/alliancegenome/curation_api/services/helpers/gff3/Gff3AttributesHelper.java
index 7d5872df1..4444cc999 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/helpers/gff3/Gff3AttributesHelper.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/helpers/gff3/Gff3AttributesHelper.java
@@ -27,7 +27,7 @@ public static Map<String, String> getAttributes(Gff3DTO dto, BackendBulkDataProv
 		}
 
 		// Ensure identifiers have MOD prefix
-		for (String key : List.of("ID", "Parent")) {
+		for (String key : List.of("ID", "Parent", "gene_id")) {
 			if (attributes.containsKey(key)) {
 				String idsString = attributes.get(key);
 				if (StringUtils.equals(dataProvider.sourceOrganization, "WB")) {
@@ -98,6 +98,21 @@ public static List<ImmutablePair<Gff3DTO, Map<String, String>>> getTranscriptGff
 		ph.finishProcess();
 		return retGffData;
 	}
+	
+	
+	public static List<ImmutablePair<Gff3DTO, Map<String, String>>> getGeneGffData(List<Gff3DTO> gffData, BackendBulkDataProvider dataProvider) {
+		List<ImmutablePair<Gff3DTO, Map<String, String>>> retGffData = new ArrayList<>();
+		ProcessDisplayHelper ph = new ProcessDisplayHelper();
+		ph.startProcess("GFF Gene pre-processing for " + dataProvider.name(), gffData.size());
+		for (Gff3DTO originalGffEntry : gffData) {
+			if (Gff3Constants.GENE_TYPES.contains(originalGffEntry.getType())) {
+				processGffEntry(originalGffEntry, retGffData, dataProvider);
+			}
+			ph.progressProcess();
+		}
+		ph.finishProcess();
+		return retGffData;
+	}
 
 	private static void processGffEntry(Gff3DTO originalGffEntry, List<ImmutablePair<Gff3DTO, Map<String, String>>> retGffData, BackendBulkDataProvider dataProvider) {
 		Map<String, String> attributes = getAttributes(originalGffEntry, dataProvider);
diff --git a/src/main/java/org/alliancegenome/curation_api/services/helpers/variants/HgvsIdentifierHelper.java b/src/main/java/org/alliancegenome/curation_api/services/helpers/variants/HgvsIdentifierHelper.java
index 331712250..bc2f04e05 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/helpers/variants/HgvsIdentifierHelper.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/helpers/variants/HgvsIdentifierHelper.java
@@ -1,5 +1,7 @@
 package org.alliancegenome.curation_api.services.helpers.variants;
 
+import java.util.Objects;
+
 import org.alliancegenome.curation_api.model.ingest.dto.fms.VariantFmsDTO;
 import org.apache.commons.lang3.StringUtils;
 
@@ -15,9 +17,16 @@ public static String getHgvsIdentifier(VariantFmsDTO dto) {
 		if (dto.getEnd() != null) {
 			end = Integer.toString(dto.getEnd());
 		}
+	
+		String refSeq = "";
+		if (StringUtils.isNotBlank(dto.getGenomicReferenceSequence()) && !Objects.equals(dto.getGenomicReferenceSequence(), "N/A")) {
+			refSeq = StringUtils.deleteWhitespace(dto.getGenomicReferenceSequence().toUpperCase());
+		}
 		
-		String varSeq = StringUtils.isBlank(dto.getGenomicVariantSequence()) ? "" : dto.getGenomicVariantSequence();
-		String refSeq = StringUtils.isBlank(dto.getGenomicReferenceSequence()) ? "" : dto.getGenomicReferenceSequence();
+		String varSeq = "";
+		if (StringUtils.isNotBlank(dto.getGenomicVariantSequence()) && !Objects.equals(dto.getGenomicVariantSequence(), "N/A")) {
+			varSeq = StringUtils.deleteWhitespace(dto.getGenomicVariantSequence().toUpperCase());
+		}
 		
 		String chrAccession = "";
 		if (StringUtils.isNotBlank(dto.getSequenceOfReferenceAccessionNumber())) {
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/Gff3DtoValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/Gff3DtoValidator.java
index 430cec249..b856cd886 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/Gff3DtoValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/Gff3DtoValidator.java
@@ -13,6 +13,7 @@
 import org.alliancegenome.curation_api.dao.TranscriptDAO;
 import org.alliancegenome.curation_api.dao.associations.codingSequenceAssociations.CodingSequenceGenomicLocationAssociationDAO;
 import org.alliancegenome.curation_api.dao.associations.exonAssociations.ExonGenomicLocationAssociationDAO;
+import org.alliancegenome.curation_api.dao.associations.geneAssociations.GeneGenomicLocationAssociationDAO;
 import org.alliancegenome.curation_api.dao.associations.transcriptAssociations.TranscriptCodingSequenceAssociationDAO;
 import org.alliancegenome.curation_api.dao.associations.transcriptAssociations.TranscriptExonAssociationDAO;
 import org.alliancegenome.curation_api.dao.associations.transcriptAssociations.TranscriptGeneAssociationDAO;
@@ -30,6 +31,7 @@
 import org.alliancegenome.curation_api.model.entities.Transcript;
 import org.alliancegenome.curation_api.model.entities.associations.codingSequenceAssociations.CodingSequenceGenomicLocationAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.exonAssociations.ExonGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptCodingSequenceAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptExonAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptGeneAssociation;
@@ -60,6 +62,7 @@ public class Gff3DtoValidator {
 	@Inject GeneService geneService;
 	@Inject ExonGenomicLocationAssociationDAO exonLocationDAO;
 	@Inject TranscriptGenomicLocationAssociationDAO transcriptLocationDAO;
+	@Inject GeneGenomicLocationAssociationDAO geneLocationDAO;
 	@Inject TranscriptGeneAssociationDAO transcriptGeneDAO;
 	@Inject TranscriptExonAssociationDAO transcriptExonDAO;
 	@Inject TranscriptCodingSequenceAssociationDAO transcriptCdsDAO;
@@ -164,6 +167,8 @@ public void validateTranscriptEntry(Gff3DTO dto, Map<String, String> attributes,
 		
 		if (attributes.containsKey("Name")) {
 			transcript.setName(attributes.get("Name"));
+		} else {
+			transcript.setName(null);
 		}
 		
 		ObjectResponse<Transcript> transcriptResponse = validateGenomicEntity(transcript, dto, attributes, dataProvider);
@@ -171,6 +176,12 @@ public void validateTranscriptEntry(Gff3DTO dto, Map<String, String> attributes,
 			transcriptResponse.addErrorMessage("attributes - ID", ValidationConstants.REQUIRED_MESSAGE);
 		}
 		
+		if (attributes.containsKey("transcript_id")) {
+			transcript.setTranscriptId(attributes.get("transcript_id"));
+		} else {
+			transcript.setTranscriptId(null);
+		}
+		
 		if (transcriptResponse.hasErrors()) {
 			throw new ObjectValidationException(dto, transcriptResponse.errorMessagesString());
 		}
@@ -273,6 +284,33 @@ public TranscriptGenomicLocationAssociation validateTranscriptLocation(Gff3DTO g
 		
 		return transcriptLocationDAO.persist(locationResponse.getEntity());
 	}
+
+	@Transactional
+	public GeneGenomicLocationAssociation validateGeneLocation(Gff3DTO gffEntry, Gene gene, String assemblyId, BackendBulkDataProvider dataProvider) throws ObjectValidationException {
+		AssemblyComponent assemblyComponent = null;
+		GeneGenomicLocationAssociation locationAssociation = new GeneGenomicLocationAssociation();
+		if (StringUtils.isNotBlank(gffEntry.getSeqId())) {
+			assemblyComponent = assemblyComponentService.fetchOrCreate(gffEntry.getSeqId(), assemblyId, dataProvider.canonicalTaxonCurie, dataProvider);
+			Map<String, Object> params = new HashMap<>();
+			params.put(EntityFieldConstants.GENE_ASSOCIATION_SUBJECT + ".id", gene.getId());
+			params.put(EntityFieldConstants.GENE_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY, assemblyId);
+			SearchResponse<GeneGenomicLocationAssociation> locationSearchResponse = geneLocationDAO.findByParams(params);
+			if (locationSearchResponse != null && locationSearchResponse.getSingleResult() != null) {
+				locationAssociation = locationSearchResponse.getSingleResult();
+			}
+			locationAssociation.setGeneGenomicLocationAssociationObject(assemblyComponent);
+		}
+		locationAssociation.setGeneAssociationSubject(gene);
+		
+		locationAssociation.setStrand(gffEntry.getStrand());
+		
+		ObjectResponse<GeneGenomicLocationAssociation> locationResponse = validateLocationAssociation(locationAssociation, gffEntry, assemblyComponent);
+		if (locationResponse.hasErrors()) {
+			throw new ObjectValidationException(gffEntry, locationResponse.errorMessagesString());
+		}
+		
+		return geneLocationDAO.persist(locationResponse.getEntity());
+	}
 	
 	@Transactional
 	public TranscriptGeneAssociation validateTranscriptGeneAssociation(Gff3DTO gffEntry, Transcript transcript, Map<String, String> attributes, Map<String, String> geneIdCurieMap) throws ObjectValidationException {
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/EvidenceAssociationDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/EvidenceAssociationDTOValidator.java
index 4441063db..cdddf074d 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/EvidenceAssociationDTOValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/EvidenceAssociationDTOValidator.java
@@ -1,8 +1,7 @@
 package org.alliancegenome.curation_api.services.validation.dto.associations;
 
-import java.util.ArrayList;
-import java.util.List;
-
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.constants.ValidationConstants;
 import org.alliancegenome.curation_api.model.entities.EvidenceAssociation;
 import org.alliancegenome.curation_api.model.entities.InformationContentEntity;
@@ -12,18 +11,19 @@
 import org.alliancegenome.curation_api.services.validation.dto.base.BaseDTOValidator;
 import org.apache.commons.collections.CollectionUtils;
 
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
+import java.util.ArrayList;
+import java.util.List;
 
 @RequestScoped
 public class EvidenceAssociationDTOValidator extends BaseDTOValidator {
 
-	@Inject InformationContentEntityService informationContentEntityService;
+	@Inject
+	InformationContentEntityService informationContentEntityService;
 
 	public <E extends EvidenceAssociation, D extends EvidenceAssociationDTO> ObjectResponse<E> validateEvidenceAssociationDTO(E association, D dto) {
 		ObjectResponse<E> assocResponse = validateAuditedObjectDTO(association, dto);
 		association = assocResponse.getEntity();
-
+		
 		if (CollectionUtils.isNotEmpty(dto.getEvidenceCuries())) {
 			List<InformationContentEntity> evidence = new ArrayList<>();
 			for (String evidenceCurie : dto.getEvidenceCuries()) {
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/alleleAssociations/AlleleGeneAssociationDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/alleleAssociations/AlleleGeneAssociationDTOValidator.java
index bfd87c332..6351aa369 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/alleleAssociations/AlleleGeneAssociationDTOValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/alleleAssociations/AlleleGeneAssociationDTOValidator.java
@@ -57,7 +57,7 @@ public AlleleGeneAssociation validateAlleleGeneAssociationDTO(AlleleGeneAssociat
 		}
 
 		AlleleGeneAssociation association = null;
-		if (subjectIds != null && subjectIds.size() == 1 && objectIds != null || objectIds.size() == 1 && StringUtils.isNotBlank(dto.getRelationName())) {
+		if (subjectIds != null && subjectIds.size() == 1 && objectIds != null && objectIds.size() == 1 && StringUtils.isNotBlank(dto.getRelationName())) {
 			HashMap<String, Object> params = new HashMap<>();
 
 			params.put("alleleAssociationSubject.id", subjectIds.get(0));
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/constructAssociations/ConstructGenomicEntityAssociationDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/constructAssociations/ConstructGenomicEntityAssociationDTOValidator.java
index 62f269466..39b11c42e 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/constructAssociations/ConstructGenomicEntityAssociationDTOValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/constructAssociations/ConstructGenomicEntityAssociationDTOValidator.java
@@ -1,9 +1,7 @@
 package org.alliancegenome.curation_api.services.validation.dto.associations.constructAssociations;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.constants.ValidationConstants;
 import org.alliancegenome.curation_api.constants.VocabularyConstants;
 import org.alliancegenome.curation_api.dao.associations.constructAssociations.ConstructGenomicEntityAssociationDAO;
@@ -27,17 +25,23 @@
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
 
 @RequestScoped
 public class ConstructGenomicEntityAssociationDTOValidator extends EvidenceAssociationDTOValidator {
 
-	@Inject ConstructService constructService;
-	@Inject GenomicEntityService genomicEntityService;
-	@Inject NoteDTOValidator noteDtoValidator;
-	@Inject VocabularyTermService vocabularyTermService;
-	@Inject ConstructGenomicEntityAssociationDAO constructGenomicEntityAssociationDAO;
+	@Inject
+	ConstructService constructService;
+	@Inject
+	GenomicEntityService genomicEntityService;
+	@Inject
+	NoteDTOValidator noteDtoValidator;
+	@Inject
+	VocabularyTermService vocabularyTermService;
+	@Inject
+	ConstructGenomicEntityAssociationDAO constructGenomicEntityAssociationDAO;
 
 	private ObjectResponse<ConstructGenomicEntityAssociation> assocResponse;
 
@@ -53,6 +57,7 @@ public ConstructGenomicEntityAssociation validateConstructGenomicEntityAssociati
 			} else {
 				if (beDataProvider != null && !construct.getDataProvider().getSourceOrganization().getAbbreviation().equals(beDataProvider.sourceOrganization)) {
 					assocResponse.addErrorMessage("construct_identifier", ValidationConstants.INVALID_MESSAGE + " for " + beDataProvider.name() + " load");
+					return null;
 				}
 			}
 		} else {
@@ -68,7 +73,6 @@ public ConstructGenomicEntityAssociation validateConstructGenomicEntityAssociati
 				assocResponse.addErrorMessage("genomic_entity_identifier", ValidationConstants.INVALID_MESSAGE + " (" + dto.getGenomicEntityIdentifier() + ")");
 			}
 		}
-
 		ConstructGenomicEntityAssociation association = null;
 		if (construct != null && StringUtils.isNotBlank(dto.getGenomicEntityRelationName()) && genomicEntity != null) {
 			HashMap<String, Object> params = new HashMap<>();
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/GeneExpressionAnnotationFmsDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/GeneExpressionAnnotationFmsDTOValidator.java
index 203bd6d5b..89d849ac1 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/GeneExpressionAnnotationFmsDTOValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/GeneExpressionAnnotationFmsDTOValidator.java
@@ -6,12 +6,14 @@
 import org.alliancegenome.curation_api.constants.VocabularyConstants;
 import org.alliancegenome.curation_api.dao.GeneExpressionAnnotationDAO;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
-import org.alliancegenome.curation_api.exceptions.ValidationException;
 import org.alliancegenome.curation_api.exceptions.ObjectValidationException;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
 import org.alliancegenome.curation_api.model.entities.*;
 import org.alliancegenome.curation_api.model.entities.ontology.*;
 import org.alliancegenome.curation_api.model.ingest.dto.fms.GeneExpressionFmsDTO;
 import org.alliancegenome.curation_api.model.ingest.dto.fms.UberonSlimTermDTO;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.WhenExpressedFmsDTO;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.WhereExpressedFmsDTO;
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.DataProviderService;
@@ -25,8 +27,7 @@
 
 import java.time.OffsetDateTime;
 import java.time.format.DateTimeParseException;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
 
 @RequestScoped
 public class GeneExpressionAnnotationFmsDTOValidator {
@@ -44,30 +45,31 @@ public class GeneExpressionAnnotationFmsDTOValidator {
 	@Inject StageTermService stageTermService;
 	@Inject OntologyTermService ontologyTermService;
 
-	public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpressionFmsDTO, BackendBulkDataProvider dataProvider) throws ValidationException {
+	public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpressionFmsDTO, BackendBulkDataProvider dataProvider, Map<String, Set<String>> experiments) throws ValidationException {
 		ObjectResponse<GeneExpressionAnnotation> response = new ObjectResponse<>();
-		GeneExpressionAnnotation geneExpressionAnnotation;
+		GeneExpressionAnnotation geneExpressionAnnotation = new GeneExpressionAnnotation();
+		String uniqueId = "empty";
+		String referenceCurie = "empty";
 
 		ObjectResponse<Reference> singleReferenceResponse = validateEvidence(geneExpressionFmsDTO);
 		if (singleReferenceResponse.hasErrors()) {
 			response.addErrorMessage("singleReference", singleReferenceResponse.errorMessagesString());
-			throw new ObjectValidationException(geneExpressionFmsDTO, response.errorMessagesString());
 		} else {
-			String referenceCurie = singleReferenceResponse.getEntity().getCurie();
-			String uniqueId = geneExpressionAnnotationUniqueIdHelper.generateUniqueId(geneExpressionFmsDTO, referenceCurie);
+			referenceCurie = singleReferenceResponse.getEntity().getCurie();
+			uniqueId = geneExpressionAnnotationUniqueIdHelper.generateUniqueId(geneExpressionFmsDTO, referenceCurie);
 			SearchResponse<GeneExpressionAnnotation> annotationDB = geneExpressionAnnotationDAO.findByField("uniqueId", uniqueId);
 			if (annotationDB != null && annotationDB.getSingleResult() != null) {
 				geneExpressionAnnotation = annotationDB.getSingleResult();
 			} else {
-				geneExpressionAnnotation = new GeneExpressionAnnotation();
 				geneExpressionAnnotation.setUniqueId(uniqueId);
 			}
-			if (geneExpressionAnnotation.getExpressionPattern() == null) {
-				geneExpressionAnnotation.setExpressionPattern(new ExpressionPattern());
-			}
 			geneExpressionAnnotation.setSingleReference(singleReferenceResponse.getEntity());
 		}
 
+		if (geneExpressionAnnotation.getExpressionPattern() == null) {
+			geneExpressionAnnotation.setExpressionPattern(new ExpressionPattern());
+		}
+
 		if (ObjectUtils.isEmpty(geneExpressionFmsDTO.getGeneId())) {
 			response.addErrorMessage("geneId - ", ValidationConstants.REQUIRED_MESSAGE + " (" + geneExpressionFmsDTO.getGeneId() + ")");
 		} else {
@@ -102,21 +104,21 @@ public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpr
 			}
 		}
 
-		ObjectResponse<AnatomicalSite> anatomicalSiteObjectResponse = validateAnatomicalSite(geneExpressionFmsDTO);
+		ObjectResponse<AnatomicalSite> anatomicalSiteObjectResponse = validateAnatomicalSite(geneExpressionFmsDTO.getWhereExpressed());
 		if (anatomicalSiteObjectResponse.hasErrors()) {
 			response.addErrorMessage("expressionPattern", anatomicalSiteObjectResponse.errorMessagesString());
 		} else {
 			geneExpressionAnnotation.setWhereExpressedStatement(geneExpressionFmsDTO.getWhereExpressed().getWhereExpressedStatement());
-			AnatomicalSite anatomicalSite = updateAnatomicalSite(anatomicalSiteObjectResponse, geneExpressionAnnotation);
+			AnatomicalSite anatomicalSite = updateAnatomicalSite(anatomicalSiteObjectResponse, geneExpressionAnnotation.getExpressionPattern().getWhereExpressed());
 			geneExpressionAnnotation.getExpressionPattern().setWhereExpressed(anatomicalSite);
 		}
 
-		ObjectResponse<TemporalContext> temporalContextObjectResponse = validateTemporalContext(geneExpressionFmsDTO);
+		ObjectResponse<TemporalContext> temporalContextObjectResponse = validateTemporalContext(geneExpressionFmsDTO.getWhenExpressed());
 		if (temporalContextObjectResponse.hasErrors()) {
 			response.addErrorMessage("expressionPattern", temporalContextObjectResponse.errorMessagesString());
 		} else {
 			geneExpressionAnnotation.setWhenExpressedStageName(geneExpressionFmsDTO.getWhenExpressed().getStageName());
-			TemporalContext temporalContext = updateTemporalContext(temporalContextObjectResponse, geneExpressionAnnotation);
+			TemporalContext temporalContext = updateTemporalContext(temporalContextObjectResponse, geneExpressionAnnotation.getExpressionPattern().getWhenExpressed());
 			geneExpressionAnnotation.getExpressionPattern().setWhenExpressed(temporalContext);
 		}
 
@@ -128,21 +130,29 @@ public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpr
 		if (response.hasErrors()) {
 			throw new ObjectValidationException(geneExpressionFmsDTO, response.errorMessagesString());
 		}
+		String experimentId = geneExpressionAnnotationUniqueIdHelper.generateExperimentId(geneExpressionFmsDTO, referenceCurie);
+		if (experiments.containsKey(experimentId)) {
+			experiments.get(experimentId).add(uniqueId);
+		} else {
+			Set<String> expressionIds = new HashSet<>();
+			expressionIds.add(uniqueId);
+			experiments.put(experimentId, expressionIds);
+		}
 		return geneExpressionAnnotation;
 	}
 
-	private ObjectResponse<TemporalContext> validateTemporalContext(GeneExpressionFmsDTO geneExpressionFmsDTO) {
+	protected ObjectResponse<TemporalContext> validateTemporalContext(WhenExpressedFmsDTO whenExpressedDTO) {
 		ObjectResponse<TemporalContext> response = new ObjectResponse<>();
 		TemporalContext temporalContext = new TemporalContext();
-		if (ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhenExpressed())) {
-			response.addErrorMessage("whenExpressed - ", ValidationConstants.REQUIRED_MESSAGE + " (" + geneExpressionFmsDTO.getWhenExpressed() + ")");
+		if (ObjectUtils.isEmpty(whenExpressedDTO)) {
+			response.addErrorMessage("whenExpressed - ", ValidationConstants.REQUIRED_MESSAGE + " (" + whenExpressedDTO + ")");
 			return response;
 		} else {
-			String stageName = geneExpressionFmsDTO.getWhenExpressed().getStageName();
+			String stageName = whenExpressedDTO.getStageName();
 			if (ObjectUtils.isEmpty(stageName)) {
 				response.addErrorMessage("whenExpressed - whenExpressedStageName", ValidationConstants.REQUIRED_MESSAGE + " (" + stageName + ")");
 			}
-			String stageTermId = geneExpressionFmsDTO.getWhenExpressed().getStageTermId();
+			String stageTermId = whenExpressedDTO.getStageTermId();
 			if (!ObjectUtils.isEmpty(stageTermId)) {
 				StageTerm stageTerm = stageTermService.findByCurie(stageTermId);
 				if (stageTerm == null) {
@@ -151,9 +161,9 @@ private ObjectResponse<TemporalContext> validateTemporalContext(GeneExpressionFm
 					temporalContext.setDevelopmentalStageStart(stageTerm);
 				}
 			}
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhenExpressed().getStageUberonSlimTerm())) {
-				if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhenExpressed().getStageUberonSlimTerm().getUberonTerm())) {
-					String stageUberonSlimTermId = geneExpressionFmsDTO.getWhenExpressed().getStageUberonSlimTerm().getUberonTerm();
+			if (!ObjectUtils.isEmpty(whenExpressedDTO.getStageUberonSlimTerm())) {
+				if (!ObjectUtils.isEmpty(whenExpressedDTO.getStageUberonSlimTerm().getUberonTerm())) {
+					String stageUberonSlimTermId = whenExpressedDTO.getStageUberonSlimTerm().getUberonTerm();
 					if (!ObjectUtils.isEmpty(stageUberonSlimTermId)) {
 						VocabularyTerm stageUberonSlimTerm = vocabularyTermService.getTermInVocabulary(VocabularyConstants.STAGE_UBERON_SLIM_TERMS, stageUberonSlimTermId).getEntity();
 						if (stageUberonSlimTerm == null) {
@@ -169,47 +179,47 @@ private ObjectResponse<TemporalContext> validateTemporalContext(GeneExpressionFm
 		return response;
 	}
 
-	private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsDTO geneExpressionFmsDTO) {
+	protected ObjectResponse<AnatomicalSite> validateAnatomicalSite(WhereExpressedFmsDTO whereExpressedDTO) {
 		ObjectResponse<AnatomicalSite> response = new ObjectResponse<>();
 		AnatomicalSite anatomicalSite = new AnatomicalSite();
-		if (ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed())) {
-			response.addErrorMessage("whereExpressed - ", ValidationConstants.REQUIRED_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed() + ")");
+		if (ObjectUtils.isEmpty(whereExpressedDTO)) {
+			response.addErrorMessage("whereExpressed - ", ValidationConstants.REQUIRED_MESSAGE + " (" + whereExpressedDTO + ")");
 		} else {
-			if (ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getWhereExpressedStatement())) {
-				response.addErrorMessage("whereExpressed - whereExpressedStatement", ValidationConstants.REQUIRED_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getWhereExpressedStatement() + ")");
+			if (ObjectUtils.isEmpty(whereExpressedDTO.getWhereExpressedStatement())) {
+				response.addErrorMessage("whereExpressed - whereExpressedStatement", ValidationConstants.REQUIRED_MESSAGE + " (" + whereExpressedDTO.getWhereExpressedStatement() + ")");
 				return response;
 			}
 
-			boolean lackAnatomicalStructureTermId = ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureTermId());
-			boolean lackStructureUberonSlimTermIds = ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureUberonSlimTermIds());
-			boolean lackCellularComponentId = ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getCellularComponentTermId());
+			boolean lackAnatomicalStructureTermId = ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalStructureTermId());
+			boolean lackStructureUberonSlimTermIds = ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalStructureUberonSlimTermIds());
+			boolean lackCellularComponentId = ObjectUtils.isEmpty(whereExpressedDTO.getCellularComponentTermId());
 
 			if ((lackAnatomicalStructureTermId || lackStructureUberonSlimTermIds) && lackCellularComponentId) {
-				response.addErrorMessage("whereExpressed - MUST HAVe (anatomicalStructureTermId and anatomicalStructureUberonSlimTermIds) or cellularComponentTermId", ValidationConstants.REQUIRED_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed() + ")");
+				response.addErrorMessage("whereExpressed - MUST HAVe (anatomicalStructureTermId and anatomicalStructureUberonSlimTermIds) or cellularComponentTermId", ValidationConstants.REQUIRED_MESSAGE + " (" + whereExpressedDTO + ")");
 			}
 
 			if (!lackAnatomicalStructureTermId) {
-				AnatomicalTerm anatomicalStructureTerm = anatomicalTermService.findByCurie(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureTermId());
+				AnatomicalTerm anatomicalStructureTerm = anatomicalTermService.findByCurie(whereExpressedDTO.getAnatomicalStructureTermId());
 				if (anatomicalStructureTerm == null) {
-					response.addErrorMessage("whereExpressed - anatomicalStructureTermId", ValidationConstants.INVALID_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureTermId() + ")");
+					response.addErrorMessage("whereExpressed - anatomicalStructureTermId", ValidationConstants.INVALID_MESSAGE + " (" + whereExpressedDTO.getAnatomicalStructureTermId() + ")");
 				} else {
 					anatomicalSite.setAnatomicalStructure(anatomicalStructureTerm);
 				}
 			}
 
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureTermId())) {
-				AnatomicalTerm anatomicalSubStructureTerm = anatomicalTermService.findByCurie(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureTermId());
+			if (!ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalSubStructureTermId())) {
+				AnatomicalTerm anatomicalSubStructureTerm = anatomicalTermService.findByCurie(whereExpressedDTO.getAnatomicalSubStructureTermId());
 				if (anatomicalSubStructureTerm == null) {
-					response.addErrorMessage("whereExpressed - anatomicalSubStructureTermId", ValidationConstants.INVALID_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureTermId() + ")");
+					response.addErrorMessage("whereExpressed - anatomicalSubStructureTermId", ValidationConstants.INVALID_MESSAGE + " (" + whereExpressedDTO.getAnatomicalSubStructureTermId() + ")");
 				} else {
 					anatomicalSite.setAnatomicalSubstructure(anatomicalSubStructureTerm);
 				}
 			}
 
 			if (!lackCellularComponentId) {
-				GOTerm cellularComponent = goTermService.findByCurie(geneExpressionFmsDTO.getWhereExpressed().getCellularComponentTermId());
+				GOTerm cellularComponent = goTermService.findByCurie(whereExpressedDTO.getCellularComponentTermId());
 				if (cellularComponent == null) {
-					response.addErrorMessage("whereExpressed - cellularComponentTermId", ValidationConstants.INVALID_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getCellularComponentTermId() + ")");
+					response.addErrorMessage("whereExpressed - cellularComponentTermId", ValidationConstants.INVALID_MESSAGE + " (" + whereExpressedDTO.getCellularComponentTermId() + ")");
 				} else {
 					GOTerm cellularComponentRibbon = goTermService.findSubsetTerm(cellularComponent, "goslim_agr");
 					if (cellularComponentRibbon == null) {
@@ -222,8 +232,8 @@ private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsD
 				}
 			}
 
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureQualifierTermId())) {
-				String anatomicalstructurequalifiertermId = geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureQualifierTermId();
+			if (!ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalStructureQualifierTermId())) {
+				String anatomicalstructurequalifiertermId = whereExpressedDTO.getAnatomicalStructureQualifierTermId();
 				if (vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.ANATOMICAL_STRUCTURE_QUALIFIER, anatomicalstructurequalifiertermId) != null) {
 					OntologyTerm anatomicalStructureQualifierTerm = ontologyTermService.findByCurieOrSecondaryId(anatomicalstructurequalifiertermId);
 					if (anatomicalStructureQualifierTerm == null) {
@@ -234,8 +244,8 @@ private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsD
 				}
 			}
 
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureQualifierTermId())) {
-				String anatomicalsubstructurequalifierId = geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureQualifierTermId();
+			if (!ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalSubStructureQualifierTermId())) {
+				String anatomicalsubstructurequalifierId = whereExpressedDTO.getAnatomicalSubStructureQualifierTermId();
 				if (vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.ANATOMICAL_SUBSTRUCTURE_QUALIFIER, anatomicalsubstructurequalifierId) != null) {
 					OntologyTerm anatomicalSubStructureQualifierTerm = ontologyTermService.findByCurieOrSecondaryId(anatomicalsubstructurequalifierId);
 					if (anatomicalSubStructureQualifierTerm == null) {
@@ -246,8 +256,8 @@ private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsD
 				}
 			}
 
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getCellularComponentQualifierTermId())) {
-				String cellularComponentQualifierTermId = geneExpressionFmsDTO.getWhereExpressed().getCellularComponentQualifierTermId();
+			if (!ObjectUtils.isEmpty(whereExpressedDTO.getCellularComponentQualifierTermId())) {
+				String cellularComponentQualifierTermId = whereExpressedDTO.getCellularComponentQualifierTermId();
 				if (vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.CELLULAR_COMPONENT_QUALIFIER, cellularComponentQualifierTermId) != null) {
 					OntologyTerm cellularComponentQualifierTerm = ontologyTermService.findByCurieOrSecondaryId(cellularComponentQualifierTermId);
 					if (cellularComponentQualifierTerm == null) {
@@ -258,8 +268,8 @@ private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsD
 				}
 			}
 
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureUberonSlimTermIds())) {
-				List<UberonSlimTermDTO> anatomicalStructureUberonSlimTermIds = geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureUberonSlimTermIds();
+			if (!ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalStructureUberonSlimTermIds())) {
+				List<UberonSlimTermDTO> anatomicalStructureUberonSlimTermIds = whereExpressedDTO.getAnatomicalStructureUberonSlimTermIds();
 				List<UBERONTerm> uberonTerms = new ArrayList<>();
 				for (UberonSlimTermDTO uberonSlimTermDTO: anatomicalStructureUberonSlimTermIds) {
 					if (!uberonSlimTermDTO.getUberonTerm().equals("Other")) {
@@ -274,8 +284,8 @@ private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsD
 				anatomicalSite.setAnatomicalStructureUberonTerms(uberonTerms);
 			}
 
-			if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureUberonSlimTermIds())) {
-				List<UberonSlimTermDTO> anatomicalSubStructureUberonSlimTermIds = geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureUberonSlimTermIds();
+			if (!ObjectUtils.isEmpty(whereExpressedDTO.getAnatomicalSubStructureUberonSlimTermIds())) {
+				List<UberonSlimTermDTO> anatomicalSubStructureUberonSlimTermIds = whereExpressedDTO.getAnatomicalSubStructureUberonSlimTermIds();
 				List<UBERONTerm> uberonTerms = new ArrayList<>();
 				for (UberonSlimTermDTO uberonSlimTermDTO : anatomicalSubStructureUberonSlimTermIds) {
 					if (!uberonSlimTermDTO.getUberonTerm().equals("Other")) {
@@ -314,9 +324,9 @@ private ObjectResponse<Reference> validateEvidence(GeneExpressionFmsDTO geneExpr
 		return response;
 	}
 
-	private TemporalContext updateTemporalContext(ObjectResponse<TemporalContext> temporalContextObjectResponse, GeneExpressionAnnotation geneExpressionAnnotation) {
+	protected TemporalContext updateTemporalContext(ObjectResponse<TemporalContext> temporalContextObjectResponse, TemporalContext whenExpressed) {
 		TemporalContext temporalContext = temporalContextObjectResponse.getEntity();
-		TemporalContext temporalContextDB = geneExpressionAnnotation.getExpressionPattern().getWhenExpressed();
+		TemporalContext temporalContextDB = whenExpressed;
 		if (temporalContextDB == null) {
 			temporalContextDB = new TemporalContext();
 		}
@@ -325,9 +335,9 @@ private TemporalContext updateTemporalContext(ObjectResponse<TemporalContext> te
 		return temporalContextDB;
 	}
 
-	private AnatomicalSite updateAnatomicalSite(ObjectResponse<AnatomicalSite> anatomicalSiteObjectResponse, GeneExpressionAnnotation geneExpressionAnnotation) {
+	private AnatomicalSite updateAnatomicalSite(ObjectResponse<AnatomicalSite> anatomicalSiteObjectResponse, AnatomicalSite whereExpressed) {
 		AnatomicalSite anatomicalSite = anatomicalSiteObjectResponse.getEntity();
-		AnatomicalSite anatomicalSiteDB = geneExpressionAnnotation.getExpressionPattern().getWhereExpressed();
+		AnatomicalSite anatomicalSiteDB = whereExpressed;
 		if (anatomicalSiteDB == null) {
 			anatomicalSiteDB = new AnatomicalSite();
 		}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTOValidator.java
new file mode 100644
index 000000000..be5cbcf1c
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTOValidator.java
@@ -0,0 +1,307 @@
+package org.alliancegenome.curation_api.services.validation.dto.fms;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.alliancegenome.curation_api.constants.ValidationConstants;
+import org.alliancegenome.curation_api.constants.VocabularyConstants;
+import org.alliancegenome.curation_api.dao.AnatomicalSiteDAO;
+import org.alliancegenome.curation_api.dao.HTPExpressionDatasetSampleAnnotationDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.ObjectValidationException;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.model.entities.AffectedGenomicModel;
+import org.alliancegenome.curation_api.model.entities.Allele;
+import org.alliancegenome.curation_api.model.entities.AnatomicalSite;
+import org.alliancegenome.curation_api.model.entities.BioSampleAge;
+import org.alliancegenome.curation_api.model.entities.BioSampleGenomicInformation;
+import org.alliancegenome.curation_api.model.entities.ExternalDataBaseEntity;
+import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetSampleAnnotation;
+import org.alliancegenome.curation_api.model.entities.MicroarraySampleDetails;
+import org.alliancegenome.curation_api.model.entities.Note;
+import org.alliancegenome.curation_api.model.entities.TemporalContext;
+import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
+import org.alliancegenome.curation_api.model.entities.ontology.MMOTerm;
+import org.alliancegenome.curation_api.model.entities.ontology.NCBITaxonTerm;
+import org.alliancegenome.curation_api.model.entities.ontology.OBITerm;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.BioSampleGenomicInformationFmsDTO;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetSampleAnnotationFmsDTO;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.WhereExpressedFmsDTO;
+import org.alliancegenome.curation_api.model.input.Pagination;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.services.AffectedGenomicModelService;
+import org.alliancegenome.curation_api.services.AlleleService;
+import org.alliancegenome.curation_api.services.DataProviderService;
+import org.alliancegenome.curation_api.services.ExternalDataBaseEntityService;
+import org.alliancegenome.curation_api.services.VocabularyTermService;
+import org.alliancegenome.curation_api.services.ontology.MmoTermService;
+import org.alliancegenome.curation_api.services.ontology.NcbiTaxonTermService;
+import org.alliancegenome.curation_api.services.ontology.ObiTermService;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang.StringUtils;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+
+@RequestScoped
+public class HTPExpressionDatasetSampleAnnotationFmsDTOValidator {
+
+	@Inject ExternalDataBaseEntityFmsDTOValidator externalDataBaseEntityFmsDtoValidator;
+	@Inject GeneExpressionAnnotationFmsDTOValidator geneExpressionAnnotationFmsDTOValidator;
+	@Inject HTPExpressionDatasetSampleAnnotationDAO htpExpressionDatasetSampleAnnotationDAO;
+	@Inject VocabularyTermService vocabularyTermService;
+	@Inject ExternalDataBaseEntityService externalDataBaseEntityService;
+	@Inject DataProviderService dataProviderService;
+	@Inject ObiTermService obiTermService;
+	@Inject MmoTermService mmoTermService;
+	@Inject AlleleService alleleService;
+	@Inject AffectedGenomicModelService affectedGenomicModelService;
+	@Inject NcbiTaxonTermService ncbiTaxonTermService;
+	@Inject AnatomicalSiteDAO anatomicalSiteDAO;
+
+	@Transactional
+	public HTPExpressionDatasetSampleAnnotation validateHTPExpressionDatasetSampleAnnotationFmsDTO(HTPExpressionDatasetSampleAnnotationFmsDTO dto, BackendBulkDataProvider backendBulkDataProvider) throws ValidationException {
+		ObjectResponse<HTPExpressionDatasetSampleAnnotation> htpSampleAnnotationResponse = new ObjectResponse<>();
+		HTPExpressionDatasetSampleAnnotation htpSampleAnnotation;
+
+		Boolean sampleExists = dto.getSampleId() != null && StringUtils.isNotEmpty(dto.getSampleId().getPrimaryId()) || StringUtils.isNotEmpty(dto.getSampleTitle());
+
+		if (!sampleExists) {
+			htpSampleAnnotationResponse.addErrorMessage("SampleId or Sample Title", ValidationConstants.REQUIRED_MESSAGE);
+		}
+		
+		if (dto.getSampleId() != null && StringUtils.isNotBlank(dto.getSampleId().getPrimaryId())) {
+			String curie = dto.getSampleId().getPrimaryId();
+			ExternalDataBaseEntity externalDbEntity = externalDataBaseEntityFmsDtoValidator.validateExternalDataBaseEntityFmsDTO(dto.getSampleId());
+			if (externalDbEntity != null) {
+				Long htpSampleId = externalDbEntity.getId();
+				Map<String, Object> params = new HashMap<>();
+				params.put("htpExpressionSample.id", htpSampleId);
+				SearchResponse<HTPExpressionDatasetSampleAnnotation> searchResponse = htpExpressionDatasetSampleAnnotationDAO.findByParams(params);
+				if (searchResponse == null || searchResponse.getSingleResult() == null) {
+					htpSampleAnnotation = new HTPExpressionDatasetSampleAnnotation();
+					htpSampleAnnotation.setHtpExpressionSample(externalDbEntity);
+				} else {
+					htpSampleAnnotation = searchResponse.getSingleResult();
+				}
+			} else {
+				htpSampleAnnotation = new HTPExpressionDatasetSampleAnnotation();
+			}
+		} else {
+			htpSampleAnnotation = new HTPExpressionDatasetSampleAnnotation();
+		}
+
+		if (StringUtils.isNotEmpty(dto.getSampleTitle())) {
+			htpSampleAnnotation.setHtpExpressionSampleTitle(dto.getSampleTitle());
+		}
+
+		if (StringUtils.isNotEmpty(dto.getAbundance())) {
+			htpSampleAnnotation.setAbundance(dto.getAbundance());
+		}
+		
+		if (StringUtils.isNotEmpty(dto.getSampleType())) {
+			String curie = dto.getSampleType();
+			OBITerm obiTerm = obiTermService.findByCurie(curie);
+			if (obiTerm != null) {
+				htpSampleAnnotation.setHtpExpressionSampleType(obiTerm);
+			} else {
+				htpSampleAnnotationResponse.addErrorMessage("SampleType", ValidationConstants.INVALID_MESSAGE + " (" + curie + ")");
+			}
+		} else {
+			htpSampleAnnotationResponse.addErrorMessage("SampleType", ValidationConstants.REQUIRED_MESSAGE);
+		}
+
+		if (dto.getSampleAge() != null) {
+			if (htpSampleAnnotation.getHtpExpressionSampleAge() == null) {
+				htpSampleAnnotation.setHtpExpressionSampleAge(new BioSampleAge());
+			}
+			ObjectResponse<TemporalContext> temporalContextObjectResponse = geneExpressionAnnotationFmsDTOValidator.validateTemporalContext(dto.getSampleAge().getStage());
+			if (temporalContextObjectResponse.hasErrors()) {
+				htpSampleAnnotationResponse.addErrorMessage("Sample Age - Stage", temporalContextObjectResponse.errorMessagesString());
+			} else {
+				TemporalContext temporalContext = geneExpressionAnnotationFmsDTOValidator.updateTemporalContext(temporalContextObjectResponse, htpSampleAnnotation.getHtpExpressionSampleAge().getStage());
+				htpSampleAnnotation.getHtpExpressionSampleAge().setAge(dto.getSampleAge().getAge());
+				htpSampleAnnotation.getHtpExpressionSampleAge().setWhenExpressedStageName(dto.getSampleAge().getStage().getStageName());
+				htpSampleAnnotation.getHtpExpressionSampleAge().setStage(temporalContext);
+			}
+		}
+
+		List<Long> idsToRemove = new ArrayList<>();
+		if (CollectionUtils.isNotEmpty(dto.getSampleLocations())) {
+			if (CollectionUtils.isNotEmpty(htpSampleAnnotation.getHtpExpressionSampleLocations())) {
+				for (AnatomicalSite anatomicalSite : htpSampleAnnotation.getHtpExpressionSampleLocations()) {
+					idsToRemove.add(anatomicalSite.getId());
+				}
+			}
+			List<AnatomicalSite> htpSampleLocations = new ArrayList<>();
+			for (WhereExpressedFmsDTO whereExpressedDTO : dto.getSampleLocations()) {
+				ObjectResponse<AnatomicalSite> anatomicalSiteObjectResponse = geneExpressionAnnotationFmsDTOValidator.validateAnatomicalSite(whereExpressedDTO);
+				if (anatomicalSiteObjectResponse.hasErrors()) {
+					htpSampleAnnotationResponse.addErrorMessage("SampleLocations", anatomicalSiteObjectResponse.errorMessagesString());
+				} else {
+					htpSampleLocations.add(anatomicalSiteObjectResponse.getEntity());
+				}
+			}
+			htpSampleAnnotation.setHtpExpressionSampleLocations(htpSampleLocations);
+		}
+
+		if (dto.getGenomicInformation() != null) {
+			Boolean genomicInformationExists = StringUtils.isNotEmpty(dto.getGenomicInformation().getBioSampleText()) || StringUtils.isNotEmpty(dto.getGenomicInformation().getBiosampleId());
+			if (genomicInformationExists) {
+				if (htpSampleAnnotation.getGenomicInformation() == null) {
+					htpSampleAnnotation.setGenomicInformation(new BioSampleGenomicInformation());
+					if (StringUtils.isNotEmpty(dto.getGenomicInformation().getBiosampleId())) {
+						validateGenomicInformation(dto.getGenomicInformation(), htpSampleAnnotation, htpSampleAnnotationResponse);
+					}
+					if (StringUtils.isNotEmpty(dto.getGenomicInformation().getBioSampleText())) {
+						htpSampleAnnotation.getGenomicInformation().setBioSampleText(dto.getGenomicInformation().getBioSampleText());
+					}
+				} else {
+					if (StringUtils.isNotEmpty(dto.getGenomicInformation().getBiosampleId())) {
+						String identifierString = null;
+						if (htpSampleAnnotation.getGenomicInformation().getBioSampleAgm() != null) {
+							identifierString = htpSampleAnnotation.getGenomicInformation().getBioSampleAgm().getIdentifier();
+						} else if (htpSampleAnnotation.getGenomicInformation().getBioSampleAllele() != null) {
+							identifierString = htpSampleAnnotation.getGenomicInformation().getBioSampleAllele().getIdentifier();
+						}
+						if (!identifierString.equals(dto.getGenomicInformation().getBiosampleId()) || htpSampleAnnotation.getGenomicInformation().getBioSampleAgmType() == null && StringUtils.isNotEmpty(dto.getGenomicInformation().getIdType())) {
+							validateGenomicInformation(dto.getGenomicInformation(), htpSampleAnnotation, htpSampleAnnotationResponse);
+						}
+						if (StringUtils.isNotEmpty(dto.getGenomicInformation().getBioSampleText())) {
+							htpSampleAnnotation.getGenomicInformation().setBioSampleText(dto.getGenomicInformation().getBioSampleText());
+						}
+					}
+				}
+			} else {
+				htpSampleAnnotationResponse.addErrorMessage("GenomicInformation - BioSampleId or BioSampleText", ValidationConstants.REQUIRED_MESSAGE);
+			}
+		}
+
+		if (StringUtils.isNotEmpty(dto.getSex())) {
+			Map<String, Object> params = new HashMap<>();
+			params.put("name", dto.getSex());
+			params.put("query_operator", "or");
+			params.put("synonyms", dto.getSex());
+			SearchResponse<VocabularyTerm> searchResponse = vocabularyTermService.findByParams(new Pagination(), params);
+			boolean added = false;
+			if (searchResponse.getTotalResults() > 0) {
+				for (VocabularyTerm tag : searchResponse.getResults()) {
+					if (tag.getVocabulary().getVocabularyLabel().equals("genetic_sex") && (tag.getName().equals(dto.getSex()) || tag.getSynonyms().contains(dto.getSex()))) {
+						htpSampleAnnotation.setGeneticSex(tag);
+						added = true;
+					}
+				}
+			}
+			if (!added) {
+				htpSampleAnnotationResponse.addErrorMessage("Sex", ValidationConstants.INVALID_MESSAGE + " (" + dto.getSex() + ")");
+			}
+		}
+
+		if (StringUtils.isNotEmpty(dto.getAssayType())) {
+			String curie = dto.getAssayType();
+			MMOTerm mmoTerm = mmoTermService.findByCurie(curie);
+			if (mmoTerm != null) {
+				htpSampleAnnotation.setExpressionAssayUsed(mmoTerm);
+			} else {
+				htpSampleAnnotationResponse.addErrorMessage("AssayType", ValidationConstants.INVALID_MESSAGE + " (" + curie + ")");
+			}
+		} else {
+			htpSampleAnnotationResponse.addErrorMessage("AssayType", ValidationConstants.REQUIRED_MESSAGE);
+		}
+
+		if (CollectionUtils.isNotEmpty(dto.getAssemblyVersions())) {
+			List<String> assemblyVersions = new ArrayList<>();
+			for (String assemblyVersion : dto.getAssemblyVersions()) {
+				assemblyVersions.add(assemblyVersion);
+			}
+			htpSampleAnnotation.setAssemblyVersions(assemblyVersions);
+		}
+
+		if (CollectionUtils.isNotEmpty(dto.getDatasetIds())) {
+			List<ExternalDataBaseEntity> datasetIds = new ArrayList<>();
+			for (String datasetId : dto.getDatasetIds()) {
+				ExternalDataBaseEntity externalDbEntity = externalDataBaseEntityService.findByCurie(datasetId);
+				if (externalDbEntity != null) {
+					datasetIds.add(externalDbEntity);
+				}
+			}
+			htpSampleAnnotation.setDatasetIds(datasetIds);
+		} else {
+			htpSampleAnnotationResponse.addErrorMessage("DatasetIds", ValidationConstants.REQUIRED_MESSAGE);
+		}
+
+		if (StringUtils.isNotEmpty(dto.getSequencingFormat())) {
+			VocabularyTerm sequencingFormat = vocabularyTermService.getTermInVocabulary(VocabularyConstants.HTP_DATASET_SAMPLE_SEQUENCE_FORMAT_VOCABULARY, dto.getSequencingFormat()).getEntity();
+			if (sequencingFormat != null) {
+				htpSampleAnnotation.setSequencingFormat(sequencingFormat);
+			}
+		}
+
+		if (StringUtils.isNotEmpty(dto.getTaxonId())) {
+			ObjectResponse<NCBITaxonTerm> taxonResponse = ncbiTaxonTermService.getByCurie(dto.getTaxonId());
+			if (taxonResponse.getEntity() == null || backendBulkDataProvider != null && (backendBulkDataProvider.name().equals("RGD") || backendBulkDataProvider.name().equals("HUMAN")) && !taxonResponse.getEntity().getCurie().equals(backendBulkDataProvider.canonicalTaxonCurie)) {
+				htpSampleAnnotationResponse.addErrorMessage("taxonId", ValidationConstants.INVALID_MESSAGE + " (" + dto.getTaxonId() + ") for " + backendBulkDataProvider.name() + " load");
+			}
+			htpSampleAnnotation.setTaxon(taxonResponse.getEntity());
+		}
+
+		if (dto.getMicroarraySampleDetails() != null) {
+			if (htpSampleAnnotation.getMicroarraySampleDetails() == null && (dto.getMicroarraySampleDetails().getChannelId() != null || dto.getMicroarraySampleDetails().getChannelNum() != null)) {
+				htpSampleAnnotation.setMicroarraySampleDetails(new MicroarraySampleDetails());
+			}
+			if (StringUtils.isNotEmpty(dto.getMicroarraySampleDetails().getChannelId())) {
+				htpSampleAnnotation.getMicroarraySampleDetails().setChannelId(dto.getMicroarraySampleDetails().getChannelId());
+			}
+			if (dto.getMicroarraySampleDetails().getChannelNum() != null) {
+				htpSampleAnnotation.getMicroarraySampleDetails().setChannelNumber(dto.getMicroarraySampleDetails().getChannelNum());
+			}
+		}
+
+		if (StringUtils.isNotEmpty(dto.getNotes())) {
+			List<Note> relatedNotes = new ArrayList<>();
+			Note relatedNote = new Note();
+			relatedNote.setFreeText(dto.getNotes());
+			relatedNote.setNoteType(vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.HTP_DATASET_SAMPLE_NOTE_TYPE_VOCABULARY_TERM_SET, "htp_expression_dataset_sample_note_type").getEntity());
+			relatedNotes.add(relatedNote);
+			htpSampleAnnotation.setRelatedNotes(relatedNotes);
+		}
+		
+		htpSampleAnnotation.setDataProvider(dataProviderService.getDefaultDataProvider(backendBulkDataProvider.sourceOrganization));
+
+		if (htpSampleAnnotationResponse.hasErrors()) {
+			throw new ObjectValidationException(dto, htpSampleAnnotationResponse.errorMessagesString());
+		}
+
+		HTPExpressionDatasetSampleAnnotation htp = htpExpressionDatasetSampleAnnotationDAO.persist(htpSampleAnnotation);
+		for (Long id : idsToRemove) {
+			anatomicalSiteDAO.remove(id);
+		}
+		return htp;
+	}
+
+	protected void validateGenomicInformation(BioSampleGenomicInformationFmsDTO dto, HTPExpressionDatasetSampleAnnotation htpSampleAnnotation, ObjectResponse<HTPExpressionDatasetSampleAnnotation> htpSampleAnnotationResponse) {
+		if (StringUtils.isNotEmpty(dto.getBiosampleId())) {
+			String identifierString = dto.getBiosampleId();
+			Allele allele = alleleService.findByIdentifierString(identifierString);
+			if (allele != null) {
+				htpSampleAnnotation.getGenomicInformation().setBioSampleAllele(allele);
+			} else {
+				AffectedGenomicModel agm = affectedGenomicModelService.findByIdentifierString(identifierString);
+				if (agm == null) {
+					htpSampleAnnotationResponse.addErrorMessage("GenomicInformation - BioSampleId", ValidationConstants.INVALID_MESSAGE + " (" + identifierString + ")");
+				} else {
+					htpSampleAnnotation.getGenomicInformation().setBioSampleAgm(agm);
+					VocabularyTerm agmType = vocabularyTermService.getTermInVocabulary(VocabularyConstants.AGM_SUBTYPE_VOCABULARY, dto.getIdType()).getEntity();
+					if (agmType != null) {
+						htpSampleAnnotation.getGenomicInformation().setBioSampleAgmType(agmType);
+					} else {
+						htpSampleAnnotationResponse.addErrorMessage("GenomicInformation - IdType", ValidationConstants.INVALID_MESSAGE + " (" + dto.getIdType() + ")");
+					}
+				}
+			}
+		}
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/ParalogyFmsDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/ParalogyFmsDTOValidator.java
index c0c6060f3..bc0c8ac39 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/ParalogyFmsDTOValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/ParalogyFmsDTOValidator.java
@@ -75,7 +75,7 @@ public GeneToGeneParalogy validateParalogyFmsDTO(ParalogyFmsDTO dto) throws Vali
 			if (subjectGene == null) {
 				paralogyResponse.addErrorMessage("gene1", ValidationConstants.INVALID_MESSAGE + " (" + subjectGeneIdentifier + ")");
 			} else {
-				if (!sameGenus(speciesTaxon, subjectGene.getTaxon())) {
+				if (speciesTaxon != null && !sameGenus(speciesTaxon, subjectGene.getTaxon())) {
 					paralogyResponse.addErrorMessage("Species", ValidationConstants.INVALID_MESSAGE + " (" + dto.getSpecies() + ") for gene " + subjectGene.getCurie());
 				}
 			}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java
index 5cbd0a331..d8594b880 100644
--- a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java
@@ -110,7 +110,7 @@ public Long validateVariant(VariantFmsDTO dto, List<Long> idsAdded, BackendBulkD
 		}
 		
 		String hgvs = HgvsIdentifierHelper.getHgvsIdentifier(dto);
-		String modInternalId = DigestUtils.md5Hex(hgvs);
+		String modInternalId = hgvs == null ? null : DigestUtils.md5Hex(hgvs);
 		
 		if (StringUtils.isNotBlank(hgvs) && !variantResponse.hasErrors()) {
 			SearchResponse<Variant> searchResponse = variantDAO.findByField("modInternalId", modInternalId);
@@ -256,11 +256,17 @@ public void validateCuratedVariantGenomicLocationAssociation(VariantFmsDTO dto,
 		association.setStart(dto.getStart());
 		association.setEnd(dto.getEnd());
 		association.setRelation(vocabularyTermService.getTermInVocabulary(VocabularyConstants.LOCATION_ASSOCIATION_RELATION_VOCABULARY, "located_on").getEntity());
-		if (StringUtils.isNotBlank(dto.getGenomicReferenceSequence())) {
-			association.setReferenceSequence(dto.getGenomicReferenceSequence());
+		
+		if (StringUtils.isNotBlank(dto.getGenomicReferenceSequence()) && !Objects.equals(dto.getGenomicReferenceSequence(), "N/A")) {
+			association.setReferenceSequence(StringUtils.deleteWhitespace(dto.getGenomicReferenceSequence()));
+		} else {
+			association.setReferenceSequence(null);
 		}
-		if (StringUtils.isNotBlank(dto.getGenomicVariantSequence())) {
-			association.setVariantSequence(dto.getGenomicVariantSequence());
+		
+		if (StringUtils.isNotBlank(dto.getGenomicVariantSequence()) && !Objects.equals(dto.getGenomicVariantSequence(), "N/A")) {
+			association.setVariantSequence(StringUtils.deleteWhitespace(dto.getGenomicVariantSequence()));
+		} else {
+			association.setVariantSequence(null);
 		}
 		
 		if (variantId == null) {
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VepGeneFmsDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VepGeneFmsDTOValidator.java
new file mode 100644
index 000000000..b163a08e9
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VepGeneFmsDTOValidator.java
@@ -0,0 +1,86 @@
+package org.alliancegenome.curation_api.services.validation.dto.fms;
+
+import org.alliancegenome.curation_api.constants.ValidationConstants;
+import org.alliancegenome.curation_api.dao.PredictedVariantConsequenceDAO;
+import org.alliancegenome.curation_api.exceptions.KnownIssueValidationException;
+import org.alliancegenome.curation_api.exceptions.ObjectValidationException;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+import org.alliancegenome.curation_api.model.entities.Transcript;
+import org.alliancegenome.curation_api.model.entities.associations.variantAssociations.CuratedVariantGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.services.TranscriptService;
+import org.alliancegenome.curation_api.services.associations.variantAssociations.CuratedVariantGenomicLocationAssociationService;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
+
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class VepGeneFmsDTOValidator {
+
+	@Inject PredictedVariantConsequenceDAO predictedVariantConsequenceDAO;
+	@Inject CuratedVariantGenomicLocationAssociationService cvglaService;
+	@Inject TranscriptService transcriptService;
+	
+	public Long validateGeneLevelConsequence(VepTxtDTO dto) throws ValidationException {
+		ObjectResponse<PredictedVariantConsequence> response = new ObjectResponse<>();
+		PredictedVariantConsequence predictedVariantConsequence = null;
+
+		CuratedVariantGenomicLocationAssociation variantLocation = null;
+		if (StringUtils.isBlank(dto.getUploadedVariation())) {
+			response.addErrorMessage("uploadedVariant", ValidationConstants.REQUIRED_MESSAGE);
+		} else {
+			SearchResponse<CuratedVariantGenomicLocationAssociation> cvglaResponse = cvglaService.findByField("hgvs", dto.getUploadedVariation());
+			if (cvglaResponse != null && cvglaResponse.getSingleResult() != null) {
+				variantLocation = cvglaResponse.getSingleResult();
+			} else {
+				response.addErrorMessage("uploadedVariant", ValidationConstants.INVALID_MESSAGE + " (" + dto.getUploadedVariation() + ")");
+			}
+		}
+		
+		Transcript transcript = null;
+		if (StringUtils.isBlank(dto.getFeature())) {
+			if (dto.getConsequence().contains("intergenic_variant")) {
+				throw new KnownIssueValidationException("Intergenic variant consequences not currently supported");
+			}
+			response.addErrorMessage("feature", ValidationConstants.REQUIRED_MESSAGE);
+		} else {
+			SearchResponse<Transcript> searchResponse = transcriptService.findByField("transcriptId", dto.getFeature());
+			if (searchResponse == null || searchResponse.getSingleResult() == null) {
+				response.addErrorMessage("feature", ValidationConstants.INVALID_MESSAGE + " (" + dto.getFeature() + ")");
+			} else if (searchResponse.getReturnedRecords() > 1) {
+				response.addErrorMessage("feature", ValidationConstants.AMBIGUOUS_MESSAGE + " (" + dto.getFeature() + ")");
+			} else {
+				transcript = searchResponse.getSingleResult();
+			}
+		}
+		
+		if (variantLocation != null && CollectionUtils.isNotEmpty(variantLocation.getPredictedVariantConsequences()) && transcript != null) {
+			for (PredictedVariantConsequence existingPvc : variantLocation.getPredictedVariantConsequences()) {
+				if (transcript.getId() == existingPvc.getVariantTranscript().getId()) {
+					predictedVariantConsequence = existingPvc;
+					break;
+				}
+			}
+		}
+
+		if (predictedVariantConsequence == null) {
+			response.addErrorMessage("uploadedVariant / feature", ValidationConstants.INVALID_MESSAGE + " ("
+					+ dto.getUploadedVariation() + " / " + dto.getFeature() + ")");
+		} else {
+			predictedVariantConsequence.setGeneLevelConsequence(true);
+		}
+		
+		if (response.hasErrors()) {
+			throw new ObjectValidationException(dto, response.errorMessagesString());
+		}
+		
+		predictedVariantConsequence = predictedVariantConsequenceDAO.persist(predictedVariantConsequence);
+			
+		return predictedVariantConsequence.getId();
+	}
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VepTranscriptFmsDTOValidator.java b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VepTranscriptFmsDTOValidator.java
new file mode 100644
index 000000000..523d0272d
--- /dev/null
+++ b/src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VepTranscriptFmsDTOValidator.java
@@ -0,0 +1,338 @@
+package org.alliancegenome.curation_api.services.validation.dto.fms;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.alliancegenome.curation_api.constants.ValidationConstants;
+import org.alliancegenome.curation_api.constants.VocabularyConstants;
+import org.alliancegenome.curation_api.dao.PredictedVariantConsequenceDAO;
+import org.alliancegenome.curation_api.dao.TranscriptDAO;
+import org.alliancegenome.curation_api.dao.associations.variantAssociations.CuratedVariantGenomicLocationAssociationDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.exceptions.KnownIssueValidationException;
+import org.alliancegenome.curation_api.exceptions.ObjectValidationException;
+import org.alliancegenome.curation_api.exceptions.ValidationException;
+import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
+import org.alliancegenome.curation_api.model.entities.Transcript;
+import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
+import org.alliancegenome.curation_api.model.entities.associations.variantAssociations.CuratedVariantGenomicLocationAssociation;
+import org.alliancegenome.curation_api.model.entities.ontology.SOTerm;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.VepTxtDTO;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.services.VocabularyTermService;
+import org.alliancegenome.curation_api.services.associations.variantAssociations.CuratedVariantGenomicLocationAssociationService;
+import org.alliancegenome.curation_api.services.ontology.SoTermService;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class VepTranscriptFmsDTOValidator {
+
+	@Inject PredictedVariantConsequenceDAO predictedVariantConsequenceDAO;
+	@Inject CuratedVariantGenomicLocationAssociationDAO cvglaDAO;
+	@Inject CuratedVariantGenomicLocationAssociationService cvglaService;
+	@Inject TranscriptDAO transcriptDAO;
+	@Inject VocabularyTermService vocabularyTermService;
+	@Inject SoTermService soTermService;
+	
+	private static final Pattern PATHOGENICITY_PREDICTION_RESULT = Pattern.compile("^([\\w]+)\\(([\\d\\.]+)\\)$");
+	private static final Pattern POSITION_STRING = Pattern.compile("^[\\d\\?\\-]+$");
+	
+	public PredictedVariantConsequence validateTranscriptLevelConsequence(VepTxtDTO dto, BackendBulkDataProvider dataProvider) throws ValidationException {
+		ObjectResponse<PredictedVariantConsequence> response = new ObjectResponse<>();
+		PredictedVariantConsequence predictedVariantConsequence = new PredictedVariantConsequence();
+
+		CuratedVariantGenomicLocationAssociation variantLocation = null;
+		if (StringUtils.isBlank(dto.getUploadedVariation())) {
+			response.addErrorMessage("uploadedVariant", ValidationConstants.REQUIRED_MESSAGE);
+		} else {
+			SearchResponse<CuratedVariantGenomicLocationAssociation> cvglaResponse = cvglaService.findByField("hgvs", dto.getUploadedVariation());
+			if (cvglaResponse != null && cvglaResponse.getSingleResult() != null) {
+				variantLocation = cvglaResponse.getSingleResult();
+			} else {
+				response.addErrorMessage("uploadedVariant", ValidationConstants.INVALID_MESSAGE + " (" + dto.getUploadedVariation() + ")");
+			}
+		}
+		
+		Transcript transcript = null;
+		if (StringUtils.isBlank(dto.getFeature())) {
+			if (dto.getConsequence().contains("intergenic_variant")) {
+				throw new KnownIssueValidationException("Intergenic variant consequences not currently supported");
+			}
+			response.addErrorMessage("feature", ValidationConstants.REQUIRED_MESSAGE);
+		} else {
+			HashMap<String, Object> params = new HashMap<>();
+			params.put("transcriptId", dto.getFeature());
+			params.put("obsolete", false);
+			
+			SearchResponse<Transcript> searchResponse = transcriptDAO.findByParams(params);
+			if (searchResponse == null || searchResponse.getSingleResult() == null) {
+				response.addErrorMessage("feature", ValidationConstants.INVALID_MESSAGE + " (" + dto.getFeature() + ")");
+			} else if (searchResponse.getReturnedRecords() > 1) {
+				response.addErrorMessage("feature", ValidationConstants.AMBIGUOUS_MESSAGE + " (" + dto.getFeature() + ")");
+			} else {
+				transcript = searchResponse.getSingleResult();
+			}
+		}
+		
+		Boolean isUpdate = false;
+		if (variantLocation != null && CollectionUtils.isNotEmpty(variantLocation.getPredictedVariantConsequences()) && transcript != null) {
+			for (PredictedVariantConsequence existingPvc : variantLocation.getPredictedVariantConsequences()) {
+				if (transcript.getId() == existingPvc.getVariantTranscript().getId()) {
+					predictedVariantConsequence = existingPvc;
+					isUpdate = true;
+					break;
+				}
+			}
+		}
+		
+		predictedVariantConsequence.setVariantGenomicLocation(variantLocation);
+		predictedVariantConsequence.setVariantTranscript(transcript);
+
+		Map<String, String> attributes = getExtraAttributes(dto);
+		
+		VocabularyTerm vepImpact = null;
+		if (!attributes.containsKey("IMPACT")) {
+			response.addErrorMessage("extra - IMPACT", ValidationConstants.REQUIRED_MESSAGE);
+		} else {
+			vepImpact = vocabularyTermService.getTermInVocabulary(VocabularyConstants.VEP_IMPACT_VOCABULARY, attributes.get("IMPACT")).getEntity();
+			if (vepImpact == null) {
+				response.addErrorMessage("extra - IMPACT", ValidationConstants.INVALID_MESSAGE + " (" + attributes.get("IMPACT") + ")");
+			}
+		}
+		predictedVariantConsequence.setVepImpact(vepImpact);
+		
+		List<SOTerm> vepConsequences = null;
+		if (StringUtils.isBlank(dto.getConsequence())) {
+			response.addErrorMessage("consequence", ValidationConstants.REQUIRED_MESSAGE);
+		} else {
+			vepConsequences = new ArrayList<>();
+			for (String consequence : dto.getConsequence().split(",")) {
+				SearchResponse<SOTerm> soTermResponse = soTermService.findByField("name", consequence);
+				SOTerm vepConsequence = null;
+				if (soTermResponse != null && soTermResponse.getSingleResult() != null
+						&& vocabularyTermService.getTermInVocabulary(VocabularyConstants.VEP_CONSEQUENCE_VOCABULARY, consequence).getEntity() != null) {
+					vepConsequence = soTermResponse.getSingleResult();
+				}
+				if (vepConsequence == null) {
+					response.addErrorMessage("consequence", ValidationConstants.INVALID_MESSAGE + " (" + consequence + ")");
+					break;
+				} else {
+					vepConsequences.add(vepConsequence);
+				}
+			}
+		}
+		predictedVariantConsequence.setVepConsequences(vepConsequences);
+		
+		String hgvsCodingNomenclature = null;
+		if (attributes.containsKey("HGVSc")) {
+			hgvsCodingNomenclature = attributes.get("HGVSc");
+		}
+		predictedVariantConsequence.setHgvsCodingNomenclature(hgvsCodingNomenclature);
+		
+		String hgvsProteinNomenclature = null;
+		if (attributes.containsKey("HGVSp")) {
+			hgvsProteinNomenclature = attributes.get("HGVSp");
+		}
+		predictedVariantConsequence.setHgvsProteinNomenclature(hgvsProteinNomenclature);
+			
+		String referenceCodon = null;
+		String variantCodon = null;
+		if (StringUtils.isNotBlank(dto.getCodons())) {
+			String[] refVarCodons = dto.getCodons().split("/");
+			if (refVarCodons.length == 1 && dto.getConsequence().contains("synonymous_variant")) {
+				referenceCodon = dto.getCodons();
+				variantCodon = dto.getCodons();
+			} else if (refVarCodons.length == 2) {
+				referenceCodon = refVarCodons[0];
+				variantCodon = refVarCodons[1];
+			} else {
+				response.addErrorMessage("codons", ValidationConstants.INVALID_MESSAGE + " (" + dto.getCodons() + ")");
+			}
+		}
+		predictedVariantConsequence.setCodonReference(referenceCodon);
+		predictedVariantConsequence.setCodonVariant(variantCodon);
+		
+		String referenceAminoAcids = null;
+		String variantAminoAcids = null;
+		if (StringUtils.isNotBlank(dto.getAminoAcids())) {
+			String[] refVarAminoAcids = dto.getAminoAcids().split("/");
+			if (refVarAminoAcids.length == 1) {
+				referenceAminoAcids = refVarAminoAcids[0];
+				variantAminoAcids = refVarAminoAcids[0];
+			} else if (refVarAminoAcids.length == 2) {
+				referenceAminoAcids = refVarAminoAcids[0];
+				variantAminoAcids = refVarAminoAcids[1];
+			} else {
+				response.addErrorMessage("aminoAcids", ValidationConstants.INVALID_MESSAGE + " (" + dto.getAminoAcids() + ")");
+			}
+		}
+		predictedVariantConsequence.setAminoAcidReference(referenceAminoAcids);
+		predictedVariantConsequence.setAminoAcidVariant(variantAminoAcids);
+		
+		VocabularyTerm polyphenPrediction = null;
+		Float polyphenScore = null;
+		if (attributes.containsKey("PolyPhen")) {
+			Pair<VocabularyTerm, Float> polyphenResult = parsePathogenicityPredictionScore(attributes.get("PolyPhen"), VocabularyConstants.POLYPHEN_PREDICTION_VOCABULARY);
+			if (polyphenResult == null) {
+				response.addErrorMessage("extra - PolyPhen", ValidationConstants.INVALID_MESSAGE + " (" + attributes.get("PolyPhen") + ")");
+			
+			} else {
+				polyphenPrediction = polyphenResult.getLeft();
+				polyphenScore = polyphenResult.getRight();
+			}
+		}
+		predictedVariantConsequence.setPolyphenPrediction(polyphenPrediction);
+		predictedVariantConsequence.setPolyphenScore(polyphenScore);
+		
+		VocabularyTerm siftPrediction = null;
+		Float siftScore = null;
+		if (attributes.containsKey("SIFT")) {
+			Pair<VocabularyTerm, Float> siftResult = parsePathogenicityPredictionScore(attributes.get("SIFT"), VocabularyConstants.SIFT_PREDICTION_VOCABULARY);
+			if (siftResult == null) {
+				response.addErrorMessage("extra - SIFT", ValidationConstants.INVALID_MESSAGE + " (" + attributes.get("SIFT") + ")");
+			
+			} else {
+				siftPrediction = siftResult.getLeft();
+				siftScore = siftResult.getRight();
+			}
+		}
+		predictedVariantConsequence.setSiftPrediction(siftPrediction);
+		predictedVariantConsequence.setSiftScore(siftScore);
+		
+		Integer cdnaStart = null;
+		Integer cdnaEnd = null;
+		if (StringUtils.isNotBlank(dto.getCdnaPosition())) {
+			Pair<Integer, Integer> cdnaStartEnd = parseStartEnd(dto.getCdnaPosition());
+			if (cdnaStartEnd == null) {
+				response.addErrorMessage("cdnaPosition", ValidationConstants.INVALID_MESSAGE + " (" + dto.getCdnaPosition() + ")");
+			} else {
+				cdnaStart = cdnaStartEnd.getLeft();
+				cdnaEnd = cdnaStartEnd.getRight();
+			}
+		}
+		predictedVariantConsequence.setCalculatedCdnaStart(cdnaStart);
+		predictedVariantConsequence.setCalculatedCdnaEnd(cdnaEnd);
+		
+		Integer cdsStart = null;
+		Integer cdsEnd = null;
+		if (StringUtils.isNotBlank(dto.getCdsPosition())) {
+			Pair<Integer, Integer> cdsStartEnd = parseStartEnd(dto.getCdsPosition());
+			if (cdsStartEnd == null) {
+				response.addErrorMessage("cdsPosition", ValidationConstants.INVALID_MESSAGE + " (" + dto.getCdsPosition() + ")");
+			} else {
+				cdsStart = cdsStartEnd.getLeft();
+				cdsEnd = cdsStartEnd.getRight();
+			}
+		}
+		predictedVariantConsequence.setCalculatedCdsStart(cdsStart);
+		predictedVariantConsequence.setCalculatedCdsEnd(cdsEnd);
+		
+		Integer proteinStart = null;
+		Integer proteinEnd = null;
+		if (StringUtils.isNotBlank(dto.getProteinPosition())) {
+			Pair<Integer, Integer> proteinStartEnd = parseStartEnd(dto.getProteinPosition());
+			if (proteinStartEnd == null) {
+				response.addErrorMessage("proteinPosition", ValidationConstants.INVALID_MESSAGE + " (" + dto.getProteinPosition() + ")");
+			} else {
+				proteinStart = proteinStartEnd.getLeft();
+				proteinEnd = proteinStartEnd.getRight();
+			}
+		}
+		predictedVariantConsequence.setCalculatedProteinStart(proteinStart);
+		predictedVariantConsequence.setCalculatedProteinEnd(proteinEnd);
+		
+		if (response.hasErrors()) {
+			throw new ObjectValidationException(dto, response.errorMessagesString());
+		}
+		
+		predictedVariantConsequence = predictedVariantConsequenceDAO.persist(predictedVariantConsequence);
+			
+		if (!isUpdate) {
+			if (variantLocation.getPredictedVariantConsequences() == null) {
+				variantLocation.setPredictedVariantConsequences(new ArrayList<>());
+			}
+			variantLocation.getPredictedVariantConsequences().add(predictedVariantConsequence);
+		}
+		cvglaDAO.persist(variantLocation);
+		
+		return predictedVariantConsequence;
+	}
+	
+	private Map<String, String> getExtraAttributes(VepTxtDTO dto) {
+		Map<String, String> attributes = new HashMap<String, String>();
+		if (CollectionUtils.isNotEmpty(dto.getExtra())) {
+			for (String keyValue : dto.getExtra()) {
+				String[] parts = keyValue.split("=");
+				if (parts.length == 2) {
+					attributes.put(parts[0], parts[1]);
+				}
+			}
+		}
+		
+		return attributes;
+	}
+	
+	private Pair<VocabularyTerm, Float> parsePathogenicityPredictionScore(String result, String vocabularyName) {
+		
+		if (StringUtils.isBlank(result)) {
+			return null;
+		}
+		
+		Matcher matcher = PATHOGENICITY_PREDICTION_RESULT.matcher(result);
+		if (!matcher.find()) {
+			return null;
+		}
+		
+		VocabularyTerm consequence = vocabularyTermService.getTermInVocabulary(vocabularyName, matcher.group(1)).getEntity();
+		if (consequence == null) {
+			return null;
+		}
+		
+		ImmutablePair<VocabularyTerm, Float> parsedResult = new ImmutablePair<>(consequence, Float.parseFloat(matcher.group(2)));
+		
+		return parsedResult;
+	}
+	
+	private Pair<Integer, Integer> parseStartEnd(String position) {
+		Matcher matcher = POSITION_STRING.matcher(position);
+		if (!matcher.find()) {
+			return null;
+		}
+		
+		Integer start = null;
+		Integer end = null;
+		String[] positions = position.split("-");
+		
+		if (positions.length > 2) {
+			return null;
+		}
+		
+		if (positions.length == 1) {
+			start = Integer.parseInt(position);
+			end = start;
+		} else {
+			if (!Objects.equals("?", positions[0])) {
+				start = Integer.parseInt(positions[0]);
+			}
+			if (!Objects.equals("?", positions[1])) {
+				end = Integer.parseInt(positions[1]);
+			}
+		}
+		
+		ImmutablePair<Integer, Integer> startEnd = new ImmutablePair<>(start, end);
+		
+		return startEnd;
+	}
+}
diff --git a/src/main/resources/application.properties.defaults b/src/main/resources/application.properties.defaults
index f1cf5b070..6134b28e9 100644
--- a/src/main/resources/application.properties.defaults
+++ b/src/main/resources/application.properties.defaults
@@ -84,7 +84,7 @@ okta.url = ""
 okta.client.secret = ""
 okta.api.token = ""
 okta.scopes = ""
-mati.url = ""
+mati.url = http://localhost:8081
 %dev.okta.authentication = false
 %test.okta.authentication = false
 
diff --git a/src/main/resources/db/migration/v0.37.0.65__htpdatasample_adding_vocab_terms.sql b/src/main/resources/db/migration/v0.37.0.65__htpdatasample_adding_vocab_terms.sql
new file mode 100644
index 000000000..5665d0c99
--- /dev/null
+++ b/src/main/resources/db/migration/v0.37.0.65__htpdatasample_adding_vocab_terms.sql
@@ -0,0 +1,3 @@
+INSERT INTO vocabulary (id, name, vocabularylabel) VALUES (nextval('vocabulary_seq'), 'HTP Data Sample Sequencing Format','htp_data_sample_sequencing_format');
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'single',id FROM vocabulary WHERE vocabularylabel = 'htp_data_sample_sequencing_format';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'paired',id FROM vocabulary WHERE vocabularylabel = 'htp_data_sample_sequencing_format';
diff --git a/src/main/resources/db/migration/v0.38.0.10__gaf-load.sql b/src/main/resources/db/migration/v0.38.0.10__gaf-load.sql
new file mode 100644
index 000000000..6818da615
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.10__gaf-load.sql
@@ -0,0 +1,90 @@
+-- delete old bulk URL load
+delete
+from bulkurlload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkfmsload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete
+from bulkscheduledload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkloadfilehistory
+where bulkload_id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkloadgroup where name = 'File Management System (FMS) GAF Loads';
+-- Create bulk loads got the GAF load
+INSERT INTO bulkloadgroup (id, name)
+VALUES (nextval('bulkloadgroup_seq'), 'File Management System (FMS) GAF Loads');
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'FB GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'HUMAN GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'MGI GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'RGD GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'SGD GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'WB GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'XB GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'ZFIN GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', false
+FROM bulkload
+WHERE backendbulkloadtype = 'GAF';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'FB'
+FROM bulkload
+WHERE name = 'FB GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'HUMAN'
+FROM bulkload
+WHERE name = 'HUMAN GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'MGI'
+FROM bulkload
+WHERE name = 'MGI GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'RGD'
+FROM bulkload
+WHERE name = 'RGD GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'SGD'
+FROM bulkload
+WHERE name = 'SGD GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'WB'
+FROM bulkload
+WHERE name = 'WB GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'XB'
+FROM bulkload
+WHERE name = 'XB GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'ZFIN'
+FROM bulkload
+WHERE name = 'ZFIN GAF Load';
diff --git a/src/main/resources/db/migration/v0.38.0.12__gene_expression_xbxl.sql b/src/main/resources/db/migration/v0.38.0.12__gene_expression_xbxl.sql
new file mode 100644
index 000000000..9fd5fd29b
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.12__gene_expression_xbxl.sql
@@ -0,0 +1,8 @@
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'EXPRESSION', 'XBXL Expression Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) Expression Loads';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true FROM bulkload WHERE name = 'XBXL Expression Load';
+
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'EXPRESSION', 'XBXL' FROM bulkload WHERE name = 'XBXL Expression Load';
diff --git a/src/main/resources/db/migration/v0.38.0.1__predictedvariantconsequence.sql b/src/main/resources/db/migration/v0.38.0.1__predictedvariantconsequence.sql
new file mode 100644
index 000000000..0bda5e377
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.1__predictedvariantconsequence.sql
@@ -0,0 +1,185 @@
+ALTER TABLE transcript ADD COLUMN transcriptid VARCHAR(255);
+
+CREATE INDEX transcript_transcriptid_index ON transcript USING btree (transcriptid);
+
+CREATE TABLE predictedvariantconsequence (
+	id bigint PRIMARY KEY,
+	datecreated timestamp(6) with time zone,
+	dateupdated timestamp(6) with time zone,
+	dbdatecreated timestamp(6) with time zone,
+	dbdateupdated timestamp(6) with time zone,
+	internal boolean DEFAULT false NOT NULL,
+	obsolete boolean DEFAULT false NOT NULL,
+	createdby_id bigint,
+	updatedby_id bigint,
+	variantgenomiclocation_id bigint,
+	varianttranscript_id bigint,
+	vepimpact_id bigint,
+	polyphenprediction_id bigint,
+	polyphenscore real,
+	siftprediction_id bigint,
+	siftscore real,
+	aminoacidreference text,
+	aminoacidvariant text,
+	codonreference text,
+	codonvariant text,
+	calculatedcdnastart integer,
+	calculatedcdnaend integer,
+	calculatedcdsstart integer,
+	calculatedcdsend integer,
+	calculatedproteinstart integer,
+	calculatedproteinend integer,
+	hgvsproteinnomenclature text,
+	hgvscodingnomenclature text,
+	genelevelconsequence boolean DEFAULT false NOT NULL
+);
+
+CREATE SEQUENCE predictedvariantconsequence_seq
+	START WITH 1
+	INCREMENT BY 50
+	NO MINVALUE
+	NO MAXVALUE
+	CACHE 1;
+
+CREATE INDEX predictedvariantconsequence_varianttranscript_index ON predictedvariantconsequence USING btree (varianttranscript_id);
+CREATE INDEX predictedvariantconsequence_vepimpact_index ON predictedvariantconsequence USING btree (vepimpact_id);
+CREATE INDEX predictedvariantconsequence_polyphenprediction_index ON predictedvariantconsequence USING btree (polyphenprediction_id);
+CREATE INDEX predictedvariantconsequence_siftprediction_index ON predictedvariantconsequence USING btree (siftprediction_id);
+CREATE INDEX predictedvariantconsequence_createdby_index ON predictedvariantconsequence USING btree (createdby_id);
+CREATE INDEX predictedvariantconsequence_updatedby_index ON predictedvariantconsequence USING btree (updatedby_id);
+CREATE INDEX predictedvariantconsequence_hgvsproteinnomenclature_index ON predictedvariantconsequence USING btree (hgvsProteinNomenclature);
+CREATE INDEX predictedvariantconsequence_hgvscodingnomenclature_index ON predictedvariantconsequence USING btree (hgvsCodingNomenclature);
+CREATE INDEX predictedvariantconsequence_variantgenomiclocation_index ON predictedvariantconsequence USING btree (variantGenomicLocation_id);
+
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_createdby_id_fk FOREIGN KEY (createdby_id) REFERENCES person(id);
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_updatedby_id_fk FOREIGN KEY (updatedby_id) REFERENCES person(id);
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_variantgenomiclocation_id_fk FOREIGN KEY (variantgenomiclocation_id) REFERENCES curatedvariantgenomiclocation(id);
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_varianttranscript_id_fk FOREIGN KEY (varianttranscript_id) REFERENCES transcript(id);
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_vepimpact_id_fk FOREIGN KEY (vepimpact_id) REFERENCES vocabularyterm(id);
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_polyphenprediction_id_fk FOREIGN KEY (polyphenprediction_id) REFERENCES vocabularyterm(id);
+ALTER TABLE ONLY predictedvariantconsequence ADD CONSTRAINT predictedvariantconsequence_polyphenscore_id_fk FOREIGN KEY (siftprediction_id) REFERENCES vocabularyterm(id);
+
+CREATE TABLE predictedvariantconsequence_ontologyterm (
+	predictedvariantconsequence_id bigint,
+	vepconsequences_id bigint
+);
+
+CREATE INDEX predictedvariantconsequence_ontologyterm_pvc_index ON predictedvariantconsequence_ontologyterm USING btree (predictedvariantconsequence_id);
+CREATE INDEX predictedvariantconsequence_ontologyterm_vc_index ON predictedvariantconsequence_ontologyterm USING btree (vepconsequences_id);
+
+ALTER TABLE ONLY predictedvariantconsequence_ontologyterm ADD CONSTRAINT predictedvariantconsequence_ontologyterm_pvc_id_fk FOREIGN KEY (predictedvariantconsequence_id) REFERENCES predictedvariantconsequence (id);
+ALTER TABLE ONLY predictedvariantconsequence_ontologyterm ADD CONSTRAINT predictedvariantconsequence_ontologyterm_vc_id_fk FOREIGN KEY (vepconsequences_id) REFERENCES ontologyterm (id);
+
+INSERT INTO bulkloadgroup (id, name) VALUES (nextval('bulkloadgroup_seq'), 'File Management System (FMS) VEP Transcript Loads');
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPTRANSCRIPT', 'FB VEP Transcript Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Transcript Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPTRANSCRIPT', 'MGI VEP Transcript Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Transcript Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPTRANSCRIPT', 'RGD VEP Transcript Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Transcript Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPTRANSCRIPT', 'WB VEP Transcript Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Transcript Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPTRANSCRIPT', 'ZFIN VEP Transcript Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Transcript Loads';
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+	SELECT id, '0 0 20 ? * SUN-THU', false FROM bulkload WHERE backendbulkloadtype = 'VEPTRANSCRIPT';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPTRANSCRIPT', 'FB' FROM bulkload WHERE name = 'FB VEP Transcript Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPTRANSCRIPT', 'MGI' FROM bulkload WHERE name = 'MGI VEP Transcript Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPTRANSCRIPT', 'RGD' FROM bulkload WHERE name = 'RGD VEP Transcript Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPTRANSCRIPT', 'WB' FROM bulkload WHERE name = 'WB VEP Transcript Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPTRANSCRIPT', 'ZFIN' FROM bulkload WHERE name = 'ZFIN VEP Transcript Load';
+
+INSERT INTO bulkloadgroup (id, name) VALUES (nextval('bulkloadgroup_seq'), 'File Management System (FMS) VEP Gene Loads');
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPGENE', 'FB VEP Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Gene Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPGENE', 'MGI VEP Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Gene Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPGENE', 'RGD VEP Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Gene Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPGENE', 'WB VEP Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Gene Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'VEPGENE', 'ZFIN VEP Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) VEP Gene Loads';
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+	SELECT id, '0 0 23 ? * SUN-THU', false FROM bulkload WHERE backendbulkloadtype = 'VEPGENE';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPGENE', 'FB' FROM bulkload WHERE name = 'FB VEP Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPGENE', 'MGI' FROM bulkload WHERE name = 'MGI VEP Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPGENE', 'RGD' FROM bulkload WHERE name = 'RGD VEP Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPGENE', 'WB' FROM bulkload WHERE name = 'WB VEP Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'VEPGENE', 'ZFIN' FROM bulkload WHERE name = 'ZFIN VEP Gene Load';
+	
+INSERT INTO vocabulary (id, name, vocabularydescription, vocabularylabel)
+	VALUES (nextval('vocabulary_seq'), 'SIFT Prediction', 'SIFT prediction of impact of missense variation', 'sift_prediction');
+INSERT INTO vocabulary (id, name, vocabularydescription, vocabularylabel)
+	VALUES (nextval('vocabulary_seq'), 'PolyPhen-2 Prediction', 'Polyphen-2 prediction of impact of missense variation', 'polyphen_prediction');
+INSERT INTO vocabulary (id, name, vocabularydescription, vocabularylabel)
+	VALUES (nextval('vocabulary_seq'), 'VEP Impact', 'Ensembl VEP predicted impact rating of variant', 'vep_impact');
+INSERT INTO vocabulary (id, name, vocabularydescription, vocabularylabel)
+	VALUES (nextval('vocabulary_seq'), 'VEP Consequence', 'Names of SOTerms used to report predicted consequence of variant by Ensembl VEP', 'vep_consequence');
+
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'deleterious', id FROM vocabulary WHERE vocabularylabel = 'sift_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'deleterious_low_confidence', id FROM vocabulary WHERE vocabularylabel = 'sift_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'tolerated', id FROM vocabulary WHERE vocabularylabel = 'sift_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'tolerated_low_confidence', id FROM vocabulary WHERE vocabularylabel = 'sift_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'no_prediction', id FROM vocabulary WHERE vocabularylabel = 'sift_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'benign', id FROM vocabulary WHERE vocabularylabel = 'polyphen_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'possibly_damaging', id FROM vocabulary WHERE vocabularylabel = 'polyphen_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'probably_damaging', id FROM vocabulary WHERE vocabularylabel = 'polyphen_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'unknown', id FROM vocabulary WHERE vocabularylabel = 'polyphen_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'no_prediction', id FROM vocabulary WHERE vocabularylabel = 'polyphen_prediction';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'HIGH', id FROM vocabulary WHERE vocabularylabel = 'vep_impact';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'MODERATE', id FROM vocabulary WHERE vocabularylabel = 'vep_impact';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'LOW', id FROM vocabulary WHERE vocabularylabel = 'vep_impact';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'MODIFIER', id FROM vocabulary WHERE vocabularylabel = 'vep_impact';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'transcript_ablation', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'splice_acceptor_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'splice_donor_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'stop_gained', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'frameshift_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'stop_lost', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'start_lost', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'transcript_amplification', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'feature_elongation', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'feature_truncation', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'inframe_insertion', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'inframe_deletion', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'missense_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'protein_altering_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'splice_donor_5th_base_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'splice_region_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'splice_donor_region_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'splice_polypyrimidine_tract_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'incomplete_terminal_codon_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'start_retained_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'stop_retained_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'synonymous_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'coding_sequence_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'mature_miRNA_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), '5_prime_UTR_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), '3_prime_UTR_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'non_coding_transcript_exon_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'intron_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'NMD_transcript_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'non_coding_transcript_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'coding_transcript_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'upstream_gene_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'downstream_gene_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'TFBS_ablation', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'TFBS_amplification', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'TF_binding_site_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'regulatory_region_ablation', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'regulatory_region_amplification', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'regulatory_region_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'intergenic_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'sequence_variant', id FROM vocabulary WHERE vocabularylabel = 'vep_consequence';
+	
diff --git a/src/main/resources/db/migration/v0.38.0.2__gaf-load.sql b/src/main/resources/db/migration/v0.38.0.2__gaf-load.sql
new file mode 100644
index 000000000..3f8d1ba2e
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.2__gaf-load.sql
@@ -0,0 +1,222 @@
+insert into bulkloadgroup (id, name, internal, obsolete, dbdatecreated)
+values (nextval('bulkloadgroup_seq'), 'GAF Load', false, false, now());
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'ZFIN GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'SGD GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'WB GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'MGI GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'FB GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'RGD GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'HUMAN GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+insert into bulkload (id, backendbulkloadtype, name, internal, obsolete, group_id, dbdatecreated, bulkloadstatus)
+select nextval('bulkload_seq'),
+       'GAF',
+       'XB GAF',
+       false,
+       false,
+       id,
+       now(),
+       'STOPPED'
+from bulkloadgroup
+where name = 'GAF Load';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'ZFIN GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'SGD GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'MGI GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'WB GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'FB GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'RGD GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'HUMAN GAF';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', true
+FROM bulkload
+WHERE name = 'XB GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/zfin.gaf.gz'
+from bulkload
+where name = 'ZFIN GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/sgd.gaf.gz'
+from bulkload
+where name = 'SGD GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/wb.gaf.gz'
+from bulkload
+where name = 'WB GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/mgi.gaf.gz'
+from bulkload
+where name = 'MGI GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/fb.gaf.gz'
+from bulkload
+where name = 'FB GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/rgd.gaf.gz'
+from bulkload
+where name = 'RGD GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'https://www.ebi.ac.uk/gxa/species/Homo_sapiens/sitemap.xml?allEntries=true'
+from bulkload
+where name = 'HUMAN GAF';
+
+insert into bulkurlload (id, bulkloadurl)
+select id, 'http://current.geneontology.org/annotations/xenbase.gaf.gz'
+from bulkload
+where name = 'XB GAF';
+
+create table GeneOntologyAnnotation
+(
+    id            bigint PRIMARY KEY,
+    singlegene_id bigint,
+    goterm_id     bigint,
+    dateCreated   timestamp default now(),
+    dateUpdated   timestamp,
+    dbDateUpdated timestamp,
+    dbDateCreated timestamp,
+    createdBy_id  bigint,
+    updatedBy_id  bigint,
+    internal      boolean   DEFAULT false,
+    obsolete      boolean   DEFAULT false
+);
+
+CREATE SEQUENCE public.GeneOntologyAnnotation_SEQ START WITH 1 INCREMENT BY 50 NO MINVALUE NO MAXVALUE CACHE 1;
+
+ALTER TABLE GeneOntologyAnnotation
+    ADD CONSTRAINT GeneOntologyAnnotation_gene_fk
+        FOREIGN KEY (singlegene_id) REFERENCES biologicalentity (id);
+
+ALTER TABLE GeneOntologyAnnotation
+    ADD CONSTRAINT GeneOntologyAnnotation_goterm_fk
+        FOREIGN KEY (goterm_id) REFERENCES ontologyterm (id);
+
+ALTER TABLE GeneOntologyAnnotation
+    ADD CONSTRAINT GeneOntologyAnnotation_createdBy_fk
+        FOREIGN KEY (createdBy_id) REFERENCES person (id);
+
+ALTER TABLE GeneOntologyAnnotation
+    ADD CONSTRAINT GeneOntologyAnnotation_updatedBy_fk
+        FOREIGN KEY (updatedBy_id) REFERENCES person (id);
+
+ALTER TABLE GeneOntologyAnnotation
+    ADD UNIQUE (singlegene_id, goterm_id);
+
+CREATE INDEX GeneOntologyAnnotation_createdby_index ON GeneOntologyAnnotation USING btree (createdby_id);
+
+CREATE INDEX GeneOntologyAnnotation_updatedby_index ON GeneOntologyAnnotation USING btree (updatedBy_id);
+
+CREATE INDEX GeneOntologyAnnotation_singlegeneId_index ON GeneOntologyAnnotation USING btree (singlegene_id);
+
+CREATE INDEX GeneOntologyAnnotation_gotermId_index ON GeneOntologyAnnotation USING btree (goterm_id);
diff --git a/src/main/resources/db/migration/v0.38.0.3__gene_genomic_location_association.sql b/src/main/resources/db/migration/v0.38.0.3__gene_genomic_location_association.sql
new file mode 100644
index 000000000..43045f7a5
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.3__gene_genomic_location_association.sql
@@ -0,0 +1,108 @@
+CREATE TABLE genegenomiclocationassociation (
+	id bigint CONSTRAINT genegenomiclocationassociation_pkey PRIMARY KEY,
+	datecreated timestamp(6) with time zone,
+	dateupdated timestamp(6) with time zone,
+	dbdatecreated timestamp(6) with time zone,
+	dbdateupdated timestamp(6) with time zone,
+	internal boolean DEFAULT false NOT NULL,
+	obsolete boolean DEFAULT false NOT NULL,
+	createdby_id bigint,
+	updatedby_id bigint,
+	"start" integer,
+	"end" integer,
+	strand varchar(1),
+	relation_id bigint,
+	geneassociationsubject_id bigint,
+	genegenomiclocationassociationobject_id bigint
+);
+
+ALTER TABLE genegenomiclocationassociation ADD CONSTRAINT genegenomiclocationassociation_relation_id_fk
+	FOREIGN KEY (relation_id) REFERENCES vocabularyterm(id);
+ALTER TABLE genegenomiclocationassociation ADD CONSTRAINT genegenomiclocationassociation_gasubject_id_fk
+	FOREIGN KEY (geneassociationsubject_id) REFERENCES gene(id);
+ALTER TABLE genegenomiclocationassociation ADD CONSTRAINT genegenomiclocationassociation_gglaobject_id_fk
+	FOREIGN KEY (genegenomiclocationassociationobject_id) REFERENCES assemblycomponent(id);
+ALTER TABLE genegenomiclocationassociation ADD CONSTRAINT genegenomiclocationassociation_createdby_id_fk
+	FOREIGN KEY (createdby_id) REFERENCES person(id);
+ALTER TABLE genegenomiclocationassociation ADD CONSTRAINT genegenomiclocationassociation_updatedby_id_fk
+	FOREIGN KEY (updatedby_id) REFERENCES person(id);
+
+CREATE INDEX geneGenomicLocationAssociation_internal_index ON genegenomiclocationassociation
+	USING btree (internal);
+CREATE INDEX geneGenomicLocationAssociation_obsolete_index ON genegenomiclocationassociation
+	USING btree (obsolete);
+CREATE INDEX geneGenomicLocationAssociation_strand_index ON genegenomiclocationassociation
+	USING btree (strand);
+CREATE INDEX geneGenomicLocationAssociation_createdBy_index ON genegenomiclocationassociation
+	USING btree (createdby_id);
+CREATE INDEX geneGenomicLocationAssociation_updatedBy_index ON genegenomiclocationassociation
+	USING btree (updatedby_id);
+CREATE INDEX geneGenomicLocationAssociation_relation_index ON genegenomiclocationassociation
+	USING btree (relation_id);
+CREATE INDEX geneGenomicLocationAssociation_subject_index ON genegenomiclocationassociation
+	USING btree (geneassociationsubject_id);
+CREATE INDEX geneGenomicLocationAssociation_object_index ON genegenomiclocationassociation
+	USING btree (genegenomiclocationassociationobject_id);
+	
+CREATE SEQUENCE genegenomiclocationassociation_seq
+	START WITH 1
+	INCREMENT BY 50
+	NO MINVALUE
+	NO MAXVALUE
+	CACHE 1;
+	
+CREATE TABLE genegenomiclocationassociation_informationcontententity (
+	association_id bigint NOT NULL,
+	evidence_id bigint NOT NULL
+);
+
+ALTER TABLE genegenomiclocationassociation_informationcontententity ADD CONSTRAINT genegla_ice_association_id_fk
+	FOREIGN KEY (association_id) REFERENCES genegenomiclocationassociation(id);
+ALTER TABLE genegenomiclocationassociation_informationcontententity ADD CONSTRAINT genegla_ice_evidence_id_fk
+	FOREIGN KEY (association_id) REFERENCES informationcontententity(id);
+	
+CREATE INDEX idxiqhlffl5a2w5p3rkqb7wbqp1m ON genegenomiclocationassociation_informationcontententity
+	USING btree (association_id);
+CREATE INDEX idx35kn4cryxq4hb1h46lqrnixbm ON genegenomiclocationassociation_informationcontententity
+	USING btree (evidence_id);
+
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'FB GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'Human GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'MGI GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'RGD GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'SGD GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'WB GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'XBXL GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'XBXT GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+	SELECT nextval('bulkload_seq'), 'GFF_GENE', 'ZFIN GFF Gene Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'File Management System (FMS) GFF Loads';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+	SELECT id, '0 0 22 ? * SUN-THU', false FROM bulkload WHERE backendbulkloadtype = 'GFF_GENE';
+
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'FB' FROM bulkload WHERE name = 'FB GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'HUMAN' FROM bulkload WHERE name = 'Human GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'MGI' FROM bulkload WHERE name = 'MGI GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'RGD' FROM bulkload WHERE name = 'RGD GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'SGD' FROM bulkload WHERE name = 'SGD GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'WB' FROM bulkload WHERE name = 'WB GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'XBXL' FROM bulkload WHERE name = 'XBXL GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'XBXT' FROM bulkload WHERE name = 'XBXT GFF Gene Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+	SELECT id, 'GFF', 'ZFIN' FROM bulkload WHERE name = 'ZFIN GFF Gene Load';
\ No newline at end of file
diff --git a/src/main/resources/db/migration/v0.38.0.4__adding_synonyms_htpsample_genetic_sex.sql b/src/main/resources/db/migration/v0.38.0.4__adding_synonyms_htpsample_genetic_sex.sql
new file mode 100644
index 000000000..38311b0f4
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.4__adding_synonyms_htpsample_genetic_sex.sql
@@ -0,0 +1,2 @@
+INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'unknown' FROM vocabularyterm WHERE name = 'unknown sex';
+INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'pooled' FROM vocabularyterm WHERE name = 'pooled sexes';
diff --git a/src/main/resources/db/migration/v0.38.0.5__fixing_htpdataset_table.sql b/src/main/resources/db/migration/v0.38.0.5__fixing_htpdataset_table.sql
new file mode 100644
index 000000000..aeea0b6e3
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.5__fixing_htpdataset_table.sql
@@ -0,0 +1 @@
+ALTER TABLE htpexpressiondatasetannotation ALTER COLUMN name TYPE text;
\ No newline at end of file
diff --git a/src/main/resources/db/migration/v0.38.0.6__dataprovider_cleanup.sql b/src/main/resources/db/migration/v0.38.0.6__dataprovider_cleanup.sql
new file mode 100644
index 000000000..bfe245581
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.6__dataprovider_cleanup.sql
@@ -0,0 +1,20 @@
+CREATE TABLE tmp_unattached_dataproviders (
+	id bigint
+	);
+	
+INSERT INTO tmp_unattached_dataproviders (id) SELECT id FROM dataprovider;
+
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM biologicalentity);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM diseaseannotation);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM geneexpressionannotation);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM htpexpressiondatasetannotation);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM htpexpressiondatasetsampleannotation);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM phenotypeannotation);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM reagent);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT dataprovider_id FROM species);
+DELETE FROM tmp_unattached_dataproviders WHERE id IN (SELECT DISTINCT secondarydataprovider_id FROM diseaseannotation);
+
+DELETE FROM dataprovider WHERE id IN (SELECT DISTINCT id FROM tmp_unattached_dataproviders);
+	
+DROP TABLE tmp_unattached_dataproviders;
+
diff --git a/src/main/resources/db/migration/v0.38.0.7__fix_bulkloadhistory_set_counts_bug.sql b/src/main/resources/db/migration/v0.38.0.7__fix_bulkloadhistory_set_counts_bug.sql
new file mode 100644
index 000000000..e45c15e04
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.7__fix_bulkloadhistory_set_counts_bug.sql
@@ -0,0 +1 @@
+UPDATE bulkloadfilehistory SET counts = '{}' WHERE counts IS NULL;
\ No newline at end of file
diff --git a/src/main/resources/db/migration/v0.38.0.8__gene_expression_experiment.sql b/src/main/resources/db/migration/v0.38.0.8__gene_expression_experiment.sql
new file mode 100644
index 000000000..dbf6a1a9f
--- /dev/null
+++ b/src/main/resources/db/migration/v0.38.0.8__gene_expression_experiment.sql
@@ -0,0 +1,46 @@
+CREATE SEQUENCE geneexpressionexperiment_seq START WITH 1 INCREMENT BY 50 NO MINVALUE NO MAXVALUE CACHE 1;
+
+CREATE TABLE geneexpressionexperiment (
+	id BIGINT CONSTRAINT expressionexperiment_pkey PRIMARY KEY,
+	uniqueid varchar(3500),
+	curie VARCHAR(255),
+	modentityid VARCHAR(255),
+	modinternalid VARCHAR(255),
+	singlereference_id BIGINT REFERENCES public.reference (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+	entityassayed_id BIGINT  REFERENCES public.gene (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+	expressionassayused_id BIGINT  REFERENCES public.ontologyterm (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+	specimengenomicmodel_id BIGINT REFERENCES public.allele (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+	dataprovider_id BIGINT REFERENCES public.dataprovider (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+	datecreated timestamp without time zone,
+	dbdatecreated timestamp without time zone,
+	dateupdated timestamp without time zone,
+	dbdateupdated timestamp without time zone,
+	internal boolean DEFAULT false,
+	obsolete boolean DEFAULT false,
+	createdby_id bigint REFERENCES public.person (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+	updatedby_id bigint REFERENCES public.person (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION
+);
+
+CREATE INDEX geneexpressionexperiment_uniqueid_index ON geneexpressionexperiment USING btree (uniqueid);
+CREATE INDEX geneexpressionexperiment_curie_index ON geneexpressionexperiment USING btree (curie);
+CREATE INDEX geneexpressionexperiment_modentityid_index ON geneexpressionexperiment USING btree (modentityid);
+CREATE INDEX geneexpressionexperiment_modinternalid_index ON geneexpressionexperiment USING btree (modinternalid);
+CREATE INDEX geneexpressionexperiment_singlereference_index ON geneexpressionexperiment USING btree (singlereference_id);
+CREATE INDEX geneexpressionexperiment_entityassayedused_index ON geneexpressionexperiment USING btree (entityassayed_id);
+CREATE INDEX geneexpressionexperiment_expressionassayused_index ON geneexpressionexperiment USING btree (expressionassayused_id);
+CREATE INDEX geneexpressionexperiment_dataprovider_index ON geneexpressionexperiment USING btree (dataprovider_id);
+CREATE INDEX geneexpressionexperiment_internal_index ON geneexpressionexperiment USING btree (internal);
+CREATE INDEX geneexpressionexperiment_obsolete_index ON geneexpressionexperiment USING btree (obsolete);
+CREATE INDEX geneexpressionexperiment_createdby_index ON geneexpressionexperiment USING btree (createdby_id);
+CREATE INDEX geneexpressionexperiment_updatedby_index ON geneexpressionexperiment USING btree (updatedby_id);
+
+CREATE TABLE IF NOT EXISTS geneexpressionexperiment_geneexpressionannotation (
+    geneexpressionexperiment_id bigint NOT NULL,
+    expressionannotations_id bigint NOT NULL,
+
+	CONSTRAINT geexperiment_geannotation_geexperiment_id_fk FOREIGN KEY (geneexpressionexperiment_id) REFERENCES geneexpressionexperiment (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION,
+    CONSTRAINT geexperiment_geannotation_geannotation_id_fk FOREIGN KEY (expressionannotations_id)  REFERENCES geneexpressionannotation (id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION
+);
+
+CREATE INDEX geneexpressionexperiment_gea_experiment_index ON geneexpressionexperiment_geneexpressionannotation USING btree (geneexpressionexperiment_id);
+CREATE INDEX geneexpressionexperiment_gea_annotations_index ON geneexpressionexperiment_geneexpressionannotation USING btree (expressionannotations_id);
diff --git a/src/test/java/org/alliancegenome/curation_api/BiogridOrcBulkUploadFmsITCase.java b/src/test/java/org/alliancegenome/curation_api/BiogridOrcBulkUploadFmsITCase.java
new file mode 100644
index 000000000..54e1a1f4b
--- /dev/null
+++ b/src/test/java/org/alliancegenome/curation_api/BiogridOrcBulkUploadFmsITCase.java
@@ -0,0 +1,85 @@
+package org.alliancegenome.curation_api;
+
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.is;
+
+import org.alliancegenome.curation_api.base.BaseITCase;
+import org.alliancegenome.curation_api.model.entities.ResourceDescriptor;
+import org.alliancegenome.curation_api.model.entities.ResourceDescriptorPage;
+import org.alliancegenome.curation_api.resources.TestContainerResource;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.DisplayName;
+import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Order;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestMethodOrder;
+
+import io.quarkus.test.common.QuarkusTestResource;
+import io.quarkus.test.junit.QuarkusIntegrationTest;
+import io.restassured.RestAssured;
+import io.restassured.config.HttpClientConfig;
+import io.restassured.config.RestAssuredConfig;
+
+@QuarkusIntegrationTest
+@QuarkusTestResource(TestContainerResource.Initializer.class)
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@DisplayName("612 - Biogrid Orc bulk upload - FMS")
+@Order(612)
+public class BiogridOrcBulkUploadFmsITCase extends BaseITCase {
+
+	@BeforeEach
+	public void init() {
+		RestAssured.config = RestAssuredConfig.config()
+				.httpClient(HttpClientConfig.httpClientConfig()
+						.setParam("http.socket.timeout", 100000)
+						.setParam("http.connection.timeout", 100000));
+	}
+
+	ResourceDescriptorPage resourceDescriptorPage;
+
+	private final String biogridOrcBulkPostEndpoint = "/api/biogrid-orc/bulk/FB/biogridfile";
+	private final String biogridOrcTestFilePath = "src/test/resources/bulk/fms/12_biogrid/";
+	private final String biogridOrcFindEndpoint = "/api/cross-reference/find?limit=100&page=0";
+
+	private void loadRequiredEntities() throws Exception {
+		ResourceDescriptor rd = createResourceDescriptor("FB");
+		createResourceDescriptorPage("biogrid/orcs", "http://test.org", rd);
+	}
+
+	@Test
+	@Order(1)
+	public void biogridOrcBulkUploadCheckFields() throws Exception {
+		loadRequiredEntities();
+		checkSuccessfulBulkLoad(biogridOrcBulkPostEndpoint, biogridOrcTestFilePath + "AF_01_all_fields.json", 1);
+
+		RestAssured.given()
+				.when()
+				.header("Content-Type", "application/json")
+				.body("{\"referencedCurie\": \"NCBI_Gene:108101\"}").post(biogridOrcFindEndpoint)
+				.then().statusCode(200)
+				.body("totalResults", is(1))
+				.body("results", hasSize(1))
+				.body("results[0].referencedCurie", is("NCBI_Gene:108101"))
+				.body("results[0].displayName", is("BioGRID CRISPR Screen Cell Line Phenotypes"));
+	}
+
+	@Test
+	@Order(2)
+	public void biogridOrcBulkUploadDuplicateEntries() throws Exception {
+		checkBulkLoadRecordCounts(biogridOrcBulkPostEndpoint, biogridOrcTestFilePath + "DE_01_duplicate_entries.json",
+				"Records", 2, 0, 1, 0);
+
+		RestAssured.given()
+				.when()
+				.header("Content-Type", "application/json")
+				.body("{\"referencedCurie\": \"NCBI_Gene:100001\"}").post(biogridOrcFindEndpoint)
+				.then().statusCode(200)
+				.body("totalResults", is(1))
+				.body("results", hasSize(1))
+				.body("results[0].referencedCurie", is("NCBI_Gene:100001"))
+				.body("results[0].displayName", is("BioGRID CRISPR Screen Cell Line Phenotypes"));
+	}
+
+}
diff --git a/src/test/java/org/alliancegenome/curation_api/ExpressionBulkUploadFmsITCase.java b/src/test/java/org/alliancegenome/curation_api/ExpressionBulkUploadFmsITCase.java
index 9d9d9ab02..7b4430edf 100644
--- a/src/test/java/org/alliancegenome/curation_api/ExpressionBulkUploadFmsITCase.java
+++ b/src/test/java/org/alliancegenome/curation_api/ExpressionBulkUploadFmsITCase.java
@@ -13,6 +13,7 @@
 import org.junit.jupiter.api.*;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 import static org.hamcrest.Matchers.hasSize;
@@ -30,6 +31,7 @@ public class ExpressionBulkUploadFmsITCase extends BaseITCase {
 	private final String expressionBulkPostEndpoint = "/api/gene-expression-annotation/bulk/ZFIN/annotationFile";
 	private final String expressionTestFilePath = "src/test/resources/bulk/fms/07_expression/";
 	private final String expressionFindEndpoint = "/api/gene-expression-annotation/find?limit=100&page=0";
+	private final String experimentFindEndpoint = "/api/gene-expression-experiment/find?limit=100&page=0";
 	private final String taxon = "NCBITaxon:7955";
 	private final String gene = "GEXPTEST:GENE001";
 	private final String mmoTerm = "GEXPTEST:assay001";
@@ -37,10 +39,10 @@ public class ExpressionBulkUploadFmsITCase extends BaseITCase {
 	private final String agrReferenceId = "AGRKB:101000000668377";
 	private final String publicationId = "PMID:009";
 	private final String agrPublicationId = "AGRKB:101000000668376";
-
+	private final String pipe = "|";
+	private final String experimentUniqueIdExpected = gene + pipe + agrPublicationId + pipe + mmoTerm;
 	private final String stageTermId = "ZFS:001";
 	private final String stageUberonTermId = "UBERON:001";
-
 	private final String anatomicalStructureTermId = "ANAT:001";
 	private final String anatomicalSubstructureTermId = "ANAT:002";
 	private final String cellularComponentTermId = "GOTEST:0012";
@@ -52,6 +54,8 @@ public class ExpressionBulkUploadFmsITCase extends BaseITCase {
 	private final String anatomicalStructureUberonTermId2 = "UBERON:005";
 	private final String anatomicalSubstructureUberonTermId1 = "UBERON:006";
 	private final String anatomicalSubstructureUberonTermId2 = "UBERON:007";
+	private final String annotationUniqueIdExpected = String.join(pipe, mmoTerm, gene, agrPublicationId, stageTermId,
+		"stage1", "trunk", anatomicalStructureTermId, cellularComponentTermId);
 
 	@BeforeEach
 	public void init() {
@@ -65,7 +69,31 @@ public void init() {
 	@Order(1)
 	public void expressionBulkUploadAllFields() throws Exception {
 		loadRequiredEntities();
-		checkSuccessfulBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "AF_01_all_fields.json");
+		
+		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
+		params.put("Annotations", createCountParams(1, 0, 1, 0));
+		params.put("Experiments", createCountParams(1, 0, 1, 0));
+
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "AF_01_all_fields.json", params);
+
+		RestAssured.given().when()
+			.header("Content-Type", "application/json")
+			.body("{}")
+			.post(experimentFindEndpoint)
+			.then()
+			.statusCode(200)
+			.body("totalResults", is(1))
+			.body("results", hasSize(1))
+			.body("results[0].dataProvider.sourceOrganization.abbreviation", is("ZFIN"))
+			.body("results[0].uniqueId", is(experimentUniqueIdExpected))
+			.body("results[0].expressionAnnotations.size()", is(1))
+			.body("results[0].entityAssayed.modEntityId", is(gene))
+			.body("results[0].singleReference.crossReferences[0].referencedCurie", is(publicationId))
+			.body("results[0].expressionAssayUsed.curie", is(mmoTerm))
+			.body("results[0].obsolete", is(false))
+			.body("results[0].internal", is(false))
+			.body("results[0].expressionAnnotations[0].uniqueId", is(annotationUniqueIdExpected));
+
 		RestAssured.given().when()
 			.header("Content-Type", "application/json")
 			.body("{}")
@@ -101,43 +129,52 @@ public void expressionBulkUploadAllFields() throws Exception {
 	@Test
 	@Order(2)
 	public void expressionBulkUploadMissingRequiredFields() throws Exception {
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_01_no_geneId.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_02_no_dateAssigned.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_03_no_evidence.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_04_no_assay.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_05_no_whenExpressed.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_06_no_whereExpressed.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_07_nowhenExpressedStageName.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_08_nowhereExpressedStatement.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "MR_09_norCellComponentNORanatStructure.json");
+		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
+		params.put("Annotations", createCountParams(1, 1, 0, 0));
+
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_01_no_geneId.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_02_no_dateAssigned.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_03_no_evidence.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_04_no_assay.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_05_no_whenExpressed.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_06_no_whereExpressed.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_07_nowhenExpressedStageName.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_08_nowhereExpressedStatement.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "MR_09_norCellComponentNORanatStructure.json", params);
 	}
 
 	@Test
 	@Order(3)
 	public void expressionBulkUploadEmptyRequiredFields() throws Exception {
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "ER_01_empty_geneId.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "ER_02_empty_dateAssigned.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "ER_03_empty_assay.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "ER_04_empty_whenExpressedStageName.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "ER_05_empty_whereExpressedStatement.json");
+		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
+		params.put("Annotations", createCountParams(1, 1, 0, 0));
+
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "ER_01_empty_geneId.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "ER_02_empty_dateAssigned.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "ER_03_empty_assay.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "ER_04_empty_whenExpressedStageName.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "ER_05_empty_whereExpressedStatement.json", params);
 	}
 
 	@Test
 	@Order(4)
 	public void expressionBulkUploadInvalidFields() throws Exception {
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_01_invalid_geneId.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_02_invalid_dateAssigned.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_03_invalid_assay.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_04_invalid_publicationId.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_05_invalid_stageterm.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_06_invalid_anatomical_structure.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_07_invalid_anatomical_substructure.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_08_invalid_cellularcomponent.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_09_invalid_anatomicalstructurequalifier.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_10_invalid_anatomicalsubstructurequalifier.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_11_invalid_cellularcomponentqualifier.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_12_invalid_anatomicalstructureuberonslimterms.json");
-		checkFailedBulkLoad(expressionBulkPostEndpoint, expressionTestFilePath + "IV_13_invalid_anatomicalsubstructureuberonslimterms.json");
+		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
+		params.put("Annotations", createCountParams(1, 1, 0, 0));
+
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_01_invalid_geneId.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_02_invalid_dateAssigned.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_03_invalid_assay.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_04_invalid_publicationId.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_05_invalid_stageterm.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_06_invalid_anatomical_structure.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_07_invalid_anatomical_substructure.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_08_invalid_cellularcomponent.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_09_invalid_anatomicalstructurequalifier.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_10_invalid_anatomicalsubstructurequalifier.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_11_invalid_cellularcomponentqualifier.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_12_invalid_anatomicalstructureuberonslimterms.json", params);
+		checkBulkLoadRecordCounts(expressionBulkPostEndpoint, expressionTestFilePath + "IV_13_invalid_anatomicalsubstructureuberonslimterms.json", params);
 	}
 
 	private void loadRequiredEntities() throws Exception {
@@ -154,7 +191,7 @@ private void loadRequiredEntities() throws Exception {
 		Vocabulary vocabulary2 = createVocabulary(VocabularyConstants.GENE_EXPRESSION_VOCABULARY, false);
 		createVocabularyTerm(vocabulary2, VocabularyConstants.GENE_EXPRESSION_RELATION_TERM, false);
 		Vocabulary stageUberonTermVocabulary = getVocabulary(VocabularyConstants.STAGE_UBERON_SLIM_TERMS);
-		Vocabulary spatialExpressionQualififerVocabulary = getVocabulary(VocabularyConstants.SPATIAL_EXPRESSION_QUALIFIERS);
+		Vocabulary spatialExpressionQualifierVocabulary = getVocabulary(VocabularyConstants.SPATIAL_EXPRESSION_QUALIFIERS);
 		VocabularyTermSet anatatomicalStructureQualifierTermset = getVocabularyTermSet(VocabularyConstants.ANATOMICAL_STRUCTURE_QUALIFIER);
 		VocabularyTermSet anatatomicalSubstructureQualifierTermset = getVocabularyTermSet(VocabularyConstants.ANATOMICAL_SUBSTRUCTURE_QUALIFIER);
 		VocabularyTermSet cellularComponentQualifierTermset = getVocabularyTermSet(VocabularyConstants.CELLULAR_COMPONENT_QUALIFIER);
diff --git a/src/test/java/org/alliancegenome/curation_api/Gff3BulkUploadITCase.java b/src/test/java/org/alliancegenome/curation_api/Gff3BulkUploadITCase.java
index 13f5ae5a9..9d166187c 100644
--- a/src/test/java/org/alliancegenome/curation_api/Gff3BulkUploadITCase.java
+++ b/src/test/java/org/alliancegenome/curation_api/Gff3BulkUploadITCase.java
@@ -43,20 +43,23 @@ public void init() {
 	private final String transcriptBulkPostEndpoint = "/api/transcript/bulk/WB_WBcel235/transcripts";
 	private final String exonBulkPostEndpoint = "/api/exon/bulk/WB_WBcel235/exons";
 	private final String cdsBulkPostEndpoint = "/api/cds/bulk/WB_WBcel235/codingSequences";
+	private final String geneLocationBulkPostEndpoint = "/api/genegenomiclocation/bulk/WB_WBcel235/geneLocations";
 	private final String gffDataTestFilePath = "src/test/resources/bulk/fms/08_gff_data/";
 	private final String transcriptGetEndpoint = "/api/transcript/";
 	private final String exonGetEndpoint = "/api/exon/";
 	private final String cdsGetEndpoint = "/api/cds/";
+	private final String geneGetEndpoint = "/api/gene/";
 	private final String transcriptId = "WB:Y74C9A.2a.1";
 	private final String exonUniqueId = "WB:Y74C9A.2a_exon|WB:Y74C9A.2a.1|I|1|100|+";
 	private final String cdsUniqueId = "WB:Y74C9A.2a|WB:Y74C9A.2a.1|I|10|100|+";
+	private final String geneCurie = "WB:WBGene00022276";
 	
 	private void loadRequiredEntities() throws Exception {
 		createSoTerm("SO:0000234", "mRNA", false);
 		createSoTerm("SO:0001035", "piRNA", false);
 		createSoTerm("SO:0000147", "exon", false);
 		createSoTerm("SO:0000316", "CDS", false);
-		createGene("WB:WBGene00022276", "NCBITaxon:6239", getVocabularyTerm(getVocabulary(VocabularyConstants.NAME_TYPE_VOCABULARY), "nomenclature_symbol"), false);
+		createGene(geneCurie, "NCBITaxon:6239", getVocabularyTerm(getVocabulary(VocabularyConstants.NAME_TYPE_VOCABULARY), "nomenclature_symbol"), false);
 	}
 	
 	@Test
@@ -78,6 +81,7 @@ public void gff3DataBulkUploadTranscriptEntity() throws Exception {
 			statusCode(200).
 			body("entity.modInternalId", is(transcriptId)).
 			body("entity.name", is("Y74C9A.2a.1")).
+			body("entity.transcriptId", is("WB:Y74C9A.2a.1")).
 			body("entity.taxon.curie", is("NCBITaxon:6239")).
 			body("entity.dataProvider.sourceOrganization.abbreviation", is("WB")).
 			body("entity.transcriptType.curie", is("SO:0000234")).
@@ -92,7 +96,7 @@ public void gff3DataBulkUploadTranscriptEntity() throws Exception {
 			body("entity.transcriptGenomicLocationAssociations[0].strand", is("+")).
 			body("entity.transcriptGeneAssociations", hasSize(1)).
 			body("entity.transcriptGeneAssociations[0].relation.name", is("is_child_of")).
-			body("entity.transcriptGeneAssociations[0].transcriptGeneAssociationObject.modEntityId", is("WB:WBGene00022276"));
+			body("entity.transcriptGeneAssociations[0].transcriptGeneAssociationObject.modEntityId", is(geneCurie));
 
 	}
 
@@ -192,6 +196,7 @@ public void gff3DataBulkUploadUpdateTranscriptEntity() throws Exception {
 			statusCode(200).
 			body("entity.modInternalId", is(transcriptId)).
 			body("entity.name", is("Y74C9A.2a.1")).
+			body("entity.transcriptId", is("RefSeq:Y74C9A.2a.1")).
 			body("entity.taxon.curie", is("NCBITaxon:6239")).
 			body("entity.dataProvider.sourceOrganization.abbreviation", is("WB")).
 			body("entity.transcriptType.curie", is("SO:0001035")).
@@ -265,5 +270,38 @@ public void gff3DataBulkUploadInvalidFields() throws Exception {
 		checkBulkLoadRecordCounts(exonBulkPostEndpoint, gffDataTestFilePath + "IV_04_invalid_exon_parent.json", params);
 		checkBulkLoadRecordCounts(cdsBulkPostEndpoint, gffDataTestFilePath + "IV_05_invalid_cds_parent.json", params);
 	}
+	
+	@Test
+	@Order(8)
+	public void gff3DataBulkUploadGeneLocation() throws Exception {
+		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
+		params.put("Locations", createCountParams(1, 0, 1, 0));
+		
+		checkBulkLoadRecordCounts(geneLocationBulkPostEndpoint, gffDataTestFilePath + "GFF_04_gene.json", params);
+		
+		RestAssured.given().
+			when().
+			get(geneGetEndpoint + geneCurie).
+			then().
+			statusCode(200).
+			body("entity.modEntityId", is(geneCurie)).
+			body("entity.geneGenomicLocationAssociations", hasSize(1)).
+			body("entity.geneGenomicLocationAssociations[0].relation.name", is("located_on")).
+			body("entity.geneGenomicLocationAssociations[0].geneGenomicLocationAssociationObject.name", is("I")).
+			body("entity.geneGenomicLocationAssociations[0].geneGenomicLocationAssociationObject.modEntityId", is("RefSeq:NC_003279.8")).
+			body("entity.geneGenomicLocationAssociations[0].geneGenomicLocationAssociationObject.taxon.curie", is("NCBITaxon:6239")).
+			body("entity.geneGenomicLocationAssociations[0].start", is(1)).
+			body("entity.geneGenomicLocationAssociations[0].end", is(1005)).
+			body("entity.geneGenomicLocationAssociations[0].strand", is("+"));
+
+	}
+	
+	@Test
+	@Order(9)
+	public void gff3SkipUnrecognisedGene() throws Exception {
+		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
+		params.put("Locations", createCountParams(1, 0, 0, 1));
+		checkBulkLoadRecordCounts(geneLocationBulkPostEndpoint, gffDataTestFilePath + "UR_01_unrecognised_gene.json", params);
+	}
 
 }
diff --git a/src/test/java/org/alliancegenome/curation_api/HTPExpressionDatasetSampleAnnotationFmsITCase.java b/src/test/java/org/alliancegenome/curation_api/HTPExpressionDatasetSampleAnnotationFmsITCase.java
new file mode 100644
index 000000000..74827885f
--- /dev/null
+++ b/src/test/java/org/alliancegenome/curation_api/HTPExpressionDatasetSampleAnnotationFmsITCase.java
@@ -0,0 +1,152 @@
+package org.alliancegenome.curation_api;
+
+import org.alliancegenome.curation_api.base.BaseITCase;
+import org.alliancegenome.curation_api.resources.TestContainerResource;
+import org.junit.jupiter.api.Order;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.DisplayName;
+import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestMethodOrder;
+
+import io.quarkus.test.common.QuarkusTestResource;
+import io.quarkus.test.junit.QuarkusIntegrationTest;
+import io.restassured.RestAssured;
+import io.restassured.config.HttpClientConfig;
+import io.restassured.config.RestAssuredConfig;
+
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.hasKey;
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.not;
+
+@QuarkusIntegrationTest
+@QuarkusTestResource(TestContainerResource.Initializer.class)
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@DisplayName("612 - HTPExpressionDatasetSampleAnnotation bulk upload - FMS")
+@Order(612)
+public class HTPExpressionDatasetSampleAnnotationFmsITCase extends BaseITCase {
+
+	@BeforeEach
+	public void init() {
+		RestAssured.config = RestAssuredConfig.config()
+				.httpClient(HttpClientConfig.httpClientConfig()
+						.setParam("http.socket.timeout", 100000)
+						.setParam("http.connection.timeout", 100000));
+	}
+
+	private final String htpDatasetSampleBulkPostEndpoint = "/api/htpexpressiondatasetsampleannotation/bulk/FB/htpexpressiondatasetsampleannotationfile";
+	private final String htpDatasetSampleTestFilePath = "src/test/resources/bulk/fms/12_htp_dataset_sample/";
+	private final String htpDatasetSampleFindEndpoint = "/api/htpexpressiondatasetsampleannotation/find?limit=100&page=0";
+	private final String mmoTerm = "HTPMMO:assay001";
+	private final String obiTermCurie = "HTPOBI:sample001";
+
+
+	private void loadRequiredEntities() throws Exception {
+		createMmoTerm(mmoTerm, "assay001");
+		createObiTerm(obiTermCurie, "sample001");
+	}
+
+	@Test
+	@Order(1)
+	public void htpDatasetSampleBulkUploadCheckFields() throws Exception {
+		loadRequiredEntities();
+		checkSuccessfulBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "AF_01_all_fields.json");
+
+		RestAssured.given().when().header("Content-Type", "application/json").body("{}")
+				.post(htpDatasetSampleFindEndpoint)
+				.then().statusCode(200).body("totalResults", is(1)).body("results", hasSize(1))
+				.body("results[0].htpExpressionSample.curie", is("GEO:GSE38764"))
+				.body("results[0].datasetIds", hasSize(1))
+				.body("results[0].datasetIds[0].curie", is("GEO:GSE38764"))
+				.body("results[0].htpExpressionSampleTitle", is("TEST TITLE"))
+				.body("results[0].expressionAssayUsed.curie", is("HTPMMO:assay001"))
+				.body("results[0].htpExpressionSampleType.curie", is("HTPOBI:sample001"))
+				.body("results[0].htpExpressionSampleAge.stage.developmentalStageStart.curie", is("ZFS:001"))
+				.body("results[0].genomicInformation.bioSampleAllele.modEntityId", is("AGA:Allele0001"))
+				.body("results[0].microarraySampleDetails.channelId", is("WB:[cgc4349]:fem-3:A"))
+				.body("results[0].microarraySampleDetails.channelNumber", is(1))
+				.body("results[0].geneticSex.name", is("hermaphrodite"))
+				.body("results[0].sequencingFormat.name", is("single"))
+				.body("results[0].htpExpressionSampleLocations[0].anatomicalStructure.curie", is("ANAT:001"))
+				.body("results[0].htpExpressionSampleLocations[0].anatomicalSubstructure.curie", is("ANAT:002"))
+				.body("results[0].htpExpressionSampleLocations[0].cellularComponentTerm.curie", is("GOTEST:0012"))
+				.body("results[0].htpExpressionSampleLocations[0].cellularComponentRibbonTerm.curie", is("GOSLIMTEST:0012"))
+				.body("results[0].taxon.curie", is("NCBITaxon:6239"))
+				.body("results[0].abundance", is("abundance test"))
+				.body("results[0].assemblyVersions[0]", is("Zv9"));
+	}
+
+	@Test
+	@Order(2)
+	public void htpDatasetSampleBulkUploadMissingRequiredFields() throws Exception {
+
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "MR_01_no_sample_id_and_sample_title.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "MR_02_no_sample_type.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "MR_03_no_biosample_id_and_biosample_text.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "MR_04_no_assay_type.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "MR_05_no_dataset_ids.json");
+	}
+
+	@Test
+	@Order(3)
+	public void htpDatasetSampleBulkUploadEmptyRequiredFields() throws Exception {
+
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "ER_01_empty_sample_id_and_sample_title.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "ER_02_empty_sample_type.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "ER_03_empty_biosample_id_and_biosample_text.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "ER_04_empty_assay_type.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "ER_05_empty_dataset_ids.json");
+	}
+
+	@Test
+	@Order(4)
+	public void htpDatasetSampleBulkUploadInvalidFields() throws Exception {
+
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "IV_01_invalid_sex.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "IV_02_invalid_assay_type.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "IV_03_invalid_sample_type.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "IV_04_invalid_taxon_id.json");
+		checkFailedBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "IV_05_invalid_genomic_information_biosample_id.json");
+	}
+
+	@Test
+	@Order(5)
+	public void htpDatasetSampleBulkUploadUpdateMissingNonRequiredFields() throws Exception {
+
+		checkSuccessfulBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "UM_01_update_no_non_required_fields.json");
+
+		RestAssured.given().when().header("Content-Type", "application/json").body("{}")
+				.post(htpDatasetSampleFindEndpoint).then().statusCode(200).body("totalResults", is(2))
+				.body("results[2]", not(hasKey("abundance")))
+				.body("results[2]", not(hasKey("htpExpressionSampleTitle")))
+				.body("results[2]", not(hasKey("taxon")))
+				.body("results[2]", not(hasKey("geneticSex")))
+				.body("results[2]", not(hasKey("sequencingFormat")))
+				.body("results[2]", not(hasKey("microarraySampleDetails")))
+				.body("results[2]", not(hasKey("htpExpressionSampleLocations")));
+	}
+
+	@Test
+	@Order(6)
+	public void htpDatasetSampleBulkUploadUpdateEmptyNonRequiredFields() throws Exception {
+
+		checkSuccessfulBulkLoad(htpDatasetSampleBulkPostEndpoint, htpDatasetSampleTestFilePath + "UE_01_update_empty_non_required_fields.json");
+
+		RestAssured.given().when().header("Content-Type", "application/json").body("{}")
+				.post(htpDatasetSampleFindEndpoint).then().statusCode(200).body("totalResults", is(3))
+				.body("results", hasSize(3))
+				.body("results[2]", not(hasKey("htpExpressionSampleAge")))
+				.body("results[2]", not(hasKey("abundance")))
+				.body("results[2]", not(hasKey("htpExpressionSampleTitle")))
+				.body("results[2]", not(hasKey("taxon")))
+				.body("results[2]", not(hasKey("geneticSex")))
+				.body("results[2]", not(hasKey("sequencingFormat")))
+				.body("results[2]", not(hasKey("microarraySampleDetails")))
+				.body("results[2]", not(hasKey("htpExpressionSampleLocations")));
+	}
+
+
+}
diff --git a/src/test/java/org/alliancegenome/curation_api/VepFmsITCase.java b/src/test/java/org/alliancegenome/curation_api/VepFmsITCase.java
new file mode 100644
index 000000000..e68759c39
--- /dev/null
+++ b/src/test/java/org/alliancegenome/curation_api/VepFmsITCase.java
@@ -0,0 +1,206 @@
+package org.alliancegenome.curation_api;
+
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.hasKey;
+
+import org.alliancegenome.curation_api.base.BaseITCase;
+import org.alliancegenome.curation_api.resources.TestContainerResource;
+import org.apache.commons.codec.digest.DigestUtils;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.DisplayName;
+import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Order;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestMethodOrder;
+
+import io.quarkus.test.common.QuarkusTestResource;
+import io.quarkus.test.junit.QuarkusIntegrationTest;
+import io.restassured.RestAssured;
+import io.restassured.config.HttpClientConfig;
+import io.restassured.config.RestAssuredConfig;
+
+@QuarkusIntegrationTest
+@QuarkusTestResource(TestContainerResource.Initializer.class)
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@DisplayName("611 - VEP data bulk upload - FMS")
+@Order(611)
+public class VepFmsITCase extends BaseITCase {
+
+	// These tests require: GeneBulkUploadITCase and VocabularyTermITCase
+	
+	@BeforeEach
+	public void init() {
+		RestAssured.config = RestAssuredConfig.config()
+				.httpClient(HttpClientConfig.httpClientConfig()
+					.setParam("http.socket.timeout", 100000)
+					.setParam("http.connection.timeout", 100000));
+	}
+
+	private final String vepFmsTestFilePath = "src/test/resources/bulk/fms/11_vep/";
+	private final String vepTranscriptFmsBulkPostEndpoint = "/api/predictedvariantconsequence/bulk/WB/transcriptConsequenceFile";
+	private final String vepGeneFmsBulkPostEndpoint = "/api/predictedvariantconsequence/bulk/WB/geneConsequenceFile";
+	private final String variantHgvs = "NC_003279.8:g.1A>T";
+	private final String variantId = DigestUtils.md5Hex(variantHgvs);
+	private final String variantGetEndpoint = "/api/variant/";
+	
+	private void loadRequiredEntities() throws Exception {
+		createSoTerm("SO:0001574", "splice_acceptor_variant", false);
+		createSoTerm("SO:0001630", "splice_donor_5th_base_variant", false);
+	}
+	
+	@Test
+	@Order(1)
+	public void vepTranscriptFmsBulkUpload() throws Exception {
+		loadRequiredEntities();
+		
+		checkSuccessfulBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "AF_01_all_fields.json");
+		
+		RestAssured.given().
+			when().
+			get(variantGetEndpoint + variantId).
+			then().
+			statusCode(200).
+			body("entity.modInternalId", is(variantId)).
+			body("entity.curatedVariantGenomicLocations[0].hgvs", is("NC_003279.8:g.1A>T")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences", hasSize(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].variantTranscript.modInternalId", is("WB:Y74C9A.2a.1")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepImpact.name", is("MODERATE")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepConsequences", hasSize(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepConsequences[0].name", is("splice_acceptor_variant")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].polyphenPrediction.name", is("probably_damaging")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].polyphenScore", is(0.993F)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].siftPrediction.name", is("tolerated")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].siftScore", is(0F)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].aminoAcidReference", is("T")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].aminoAcidVariant", is("I")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].codonReference", is("aCc")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].codonVariant", is("aTc")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdnaStart", is(3)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdnaEnd", is(800)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdsStart", is(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdsEnd", is(600)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedProteinStart", is(246)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0]", not(hasKey("calculatedProteinEnd"))).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].hgvsProteinNomenclature", is("WB:CE49439:p.Thr10Ile")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].hgvsCodingNomenclature", is("WB:Y74C9A.2a.1:c.29T>I")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].geneLevelConsequence", is(false));
+	}
+	
+	@Test
+	@Order(2)
+	public void vepGeneBulkUpload() throws Exception {
+		checkSuccessfulBulkLoad(vepGeneFmsBulkPostEndpoint, vepFmsTestFilePath + "AF_01_all_fields.json");
+		
+		RestAssured.given().
+			when().
+			get(variantGetEndpoint + variantId).
+			then().
+			statusCode(200).
+			body("entity.modInternalId", is(variantId)).
+			body("entity.curatedVariantGenomicLocations[0].hgvs", is("NC_003279.8:g.1A>T")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].variantTranscript.modInternalId", is("WB:Y74C9A.2a.1")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepImpact.name", is("MODERATE")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepConsequences", hasSize(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepConsequences[0].name", is("splice_acceptor_variant")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].polyphenPrediction.name", is("probably_damaging")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].polyphenScore", is(0.993F)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].siftPrediction.name", is("tolerated")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].siftScore", is(0F)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].aminoAcidReference", is("T")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].aminoAcidVariant", is("I")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].codonReference", is("aCc")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].codonVariant", is("aTc")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdnaStart", is(3)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdnaEnd", is(800)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdsStart", is(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdsEnd", is(600)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedProteinStart", is(246)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0]", not(hasKey("calculatedProteinEnd"))).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].hgvsProteinNomenclature", is("WB:CE49439:p.Thr10Ile")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].hgvsCodingNomenclature", is("WB:Y74C9A.2a.1:c.29T>I")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].geneLevelConsequence", is(true));
+	}
+	
+	@Test
+	@Order(3)
+	public void vepTranscriptMissingRequiredFields() throws Exception {
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "MR_01_no_uploaded_variation.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "MR_02_no_feature.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "MR_03_no_consequence.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "MR_04_no_impact.json");
+	}
+	
+	@Test
+	@Order(4)
+	public void vepTranscriptEmptyRequiredFields() throws Exception {
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "ER_01_empty_uploaded_variation.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "ER_02_empty_feature.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "ER_03_empty_consequence.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "ER_04_empty_impact.json");
+	}
+	
+	@Test
+	@Order(5)
+	public void vepTranscriptInvalidFields() throws Exception {
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_01_invalid_uploaded_variation.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_02_invalid_feature.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_03_invalid_consequence.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_04_invalid_cdna_position.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_05_invalid_cds_position.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_06_invalid_protein_position.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_07_invalid_amino_acids.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_08_invalid_codons.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_09_invalid_impact.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_10_invalid_polyphen.json");
+		checkFailedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_11_invalid_sift.json");
+		checkFailedBulkLoad(vepGeneFmsBulkPostEndpoint, vepFmsTestFilePath + "IV_12_invalid_variant_transcript_pair.json");
+	}
+	
+	@Test
+	@Order(6)
+	public void vepTranscriptUpdate() throws Exception {
+		checkSuccessfulBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "UD_01_update.json");
+		
+		RestAssured.given().
+			when().
+			get(variantGetEndpoint + variantId).
+			then().
+			statusCode(200).
+			body("entity.modInternalId", is(variantId)).
+			body("entity.curatedVariantGenomicLocations[0].hgvs", is("NC_003279.8:g.1A>T")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences", hasSize(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].variantTranscript.modInternalId", is("WB:Y74C9A.2a.1")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepImpact.name", is("MODIFIER")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepConsequences", hasSize(1)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].vepConsequences[0].name", is("splice_donor_5th_base_variant")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].polyphenPrediction.name", is("possibly_damaging")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].polyphenScore", is(0.8F)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].siftPrediction.name", is("deleterious_low_confidence")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].siftScore", is(0.767F)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].aminoAcidReference", is("M")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].aminoAcidVariant", is("N")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].codonReference", is("aCt")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].codonVariant", is("aTt")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdnaStart", is(2)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdnaEnd", is(900)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdsStart", is(3)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedCdsEnd", is(500)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedProteinStart", is(247)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].calculatedProteinEnd", is(250)).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].hgvsProteinNomenclature", is("WB:CE49439:p.Met10Neo")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].hgvsCodingNomenclature", is("WB:Y74C9A.2a.1:c.29M>N")).
+			body("entity.curatedVariantGenomicLocations[0].predictedVariantConsequences[0].geneLevelConsequence", is(true));
+	}
+	
+	@Test
+	@Order(7)
+	public void vepSkipIntergenic() throws Exception {
+		checkSkippedBulkLoad(vepTranscriptFmsBulkPostEndpoint, vepFmsTestFilePath + "US_01_unsupported_intergenic.json");
+		checkSkippedBulkLoad(vepGeneFmsBulkPostEndpoint, vepFmsTestFilePath + "US_01_unsupported_intergenic.json");
+	}
+	
+}
diff --git a/src/test/java/org/alliancegenome/curation_api/base/BaseITCase.java b/src/test/java/org/alliancegenome/curation_api/base/BaseITCase.java
index 34bb40b0a..bb0b3b981 100644
--- a/src/test/java/org/alliancegenome/curation_api/base/BaseITCase.java
+++ b/src/test/java/org/alliancegenome/curation_api/base/BaseITCase.java
@@ -50,6 +50,7 @@
 import org.alliancegenome.curation_api.model.entities.ontology.GOTerm;
 import org.alliancegenome.curation_api.model.entities.ontology.MITerm;
 import org.alliancegenome.curation_api.model.entities.ontology.MMOTerm;
+import org.alliancegenome.curation_api.model.entities.ontology.OBITerm;
 import org.alliancegenome.curation_api.model.entities.ontology.MPTerm;
 import org.alliancegenome.curation_api.model.entities.ontology.NCBITaxonTerm;
 import org.alliancegenome.curation_api.model.entities.ontology.OntologyTerm;
@@ -604,6 +605,25 @@ public MMOTerm createMmoTerm(String curie, String name) throws Exception {
 		return response.getEntity();
 	}
 
+	public OBITerm createObiTerm(String curie, String name) throws Exception {
+		OBITerm obiTerm = new OBITerm();
+		obiTerm.setCurie(curie);
+		obiTerm.setName(name);
+		obiTerm.setObsolete(false);
+		obiTerm.setSecondaryIdentifiers(List.of(curie + "secondary"));
+
+		ObjectResponse<OBITerm> response = RestAssured.given().
+			contentType("application/json").
+			body(obiTerm).
+			when().
+			put("/api/obiterm").
+			then().
+			statusCode(200).
+			extract().body().as(getObjectResponseTypeRefOBITerm());
+
+		return response.getEntity();
+	}
+
 	public MPTerm createMpTerm(String curie, String name) {
 		return createMpTerm(curie, name, false);
 	}
@@ -1308,6 +1328,11 @@ private TypeRef<ObjectResponse<MMOTerm>> getObjectResponseTypeRefMMOTerm() {
 		};
 	}
 
+	private TypeRef<ObjectResponse<OBITerm>> getObjectResponseTypeRefOBITerm() {
+		return new TypeRef<ObjectResponse<OBITerm>>() {
+		};
+	}
+
 	private TypeRef<ObjectResponse<MPTerm>> getObjectResponseTypeRefMPTerm() {
 		return new TypeRef<ObjectResponse<MPTerm>>() {
 		};
diff --git a/src/test/resources/bulk/fms/08_gff_data/ER_01_empty_seq_id.json b/src/test/resources/bulk/fms/08_gff_data/ER_01_empty_seq_id.json
index a691479e6..8cf67b6a4 100644
--- a/src/test/resources/bulk/fms/08_gff_data/ER_01_empty_seq_id.json
+++ b/src/test/resources/bulk/fms/08_gff_data/ER_01_empty_seq_id.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/ER_02_empty_strand.json b/src/test/resources/bulk/fms/08_gff_data/ER_02_empty_strand.json
index 32a9ac0ec..495bfdb3c 100644
--- a/src/test/resources/bulk/fms/08_gff_data/ER_02_empty_strand.json
+++ b/src/test/resources/bulk/fms/08_gff_data/ER_02_empty_strand.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/ER_03_empty_transcript_parent.json b/src/test/resources/bulk/fms/08_gff_data/ER_03_empty_transcript_parent.json
index 3e262c924..de0dc15de 100644
--- a/src/test/resources/bulk/fms/08_gff_data/ER_03_empty_transcript_parent.json
+++ b/src/test/resources/bulk/fms/08_gff_data/ER_03_empty_transcript_parent.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/GFF_01_transcript.json b/src/test/resources/bulk/fms/08_gff_data/GFF_01_transcript.json
index ef30adafe..e4157e0f5 100644
--- a/src/test/resources/bulk/fms/08_gff_data/GFF_01_transcript.json
+++ b/src/test/resources/bulk/fms/08_gff_data/GFF_01_transcript.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/GFF_04_gene.json b/src/test/resources/bulk/fms/08_gff_data/GFF_04_gene.json
new file mode 100644
index 000000000..911bec308
--- /dev/null
+++ b/src/test/resources/bulk/fms/08_gff_data/GFF_04_gene.json
@@ -0,0 +1,15 @@
+[
+	{
+		"seqId": "I",
+		"source": "WormBase",
+		"type": "gene",
+		"start": 1,
+		"end": 1005,
+		"strand": "+",
+		"attributes": [
+			"ID=Gene:WBGene00022276",
+			"Name=TestGene",
+			"gene_id=WB:WBGene00022276"
+		]
+	}
+]
diff --git a/src/test/resources/bulk/fms/08_gff_data/IV_01_invalid_strand.json b/src/test/resources/bulk/fms/08_gff_data/IV_01_invalid_strand.json
index 920bde5f5..9d832b705 100644
--- a/src/test/resources/bulk/fms/08_gff_data/IV_01_invalid_strand.json
+++ b/src/test/resources/bulk/fms/08_gff_data/IV_01_invalid_strand.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/IV_02_invalid_phase.json b/src/test/resources/bulk/fms/08_gff_data/IV_02_invalid_phase.json
index e6f751326..788af87dd 100644
--- a/src/test/resources/bulk/fms/08_gff_data/IV_02_invalid_phase.json
+++ b/src/test/resources/bulk/fms/08_gff_data/IV_02_invalid_phase.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/IV_03_invalid_transcript_parent.json b/src/test/resources/bulk/fms/08_gff_data/IV_03_invalid_transcript_parent.json
index 8d524dd08..71503f4fd 100644
--- a/src/test/resources/bulk/fms/08_gff_data/IV_03_invalid_transcript_parent.json
+++ b/src/test/resources/bulk/fms/08_gff_data/IV_03_invalid_transcript_parent.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:Invalid",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/MR_01_no_seq_id.json b/src/test/resources/bulk/fms/08_gff_data/MR_01_no_seq_id.json
index e9651e61e..554c08d40 100644
--- a/src/test/resources/bulk/fms/08_gff_data/MR_01_no_seq_id.json
+++ b/src/test/resources/bulk/fms/08_gff_data/MR_01_no_seq_id.json
@@ -9,7 +9,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/MR_02_no_start.json b/src/test/resources/bulk/fms/08_gff_data/MR_02_no_start.json
index 0997e4e33..6065ed59b 100644
--- a/src/test/resources/bulk/fms/08_gff_data/MR_02_no_start.json
+++ b/src/test/resources/bulk/fms/08_gff_data/MR_02_no_start.json
@@ -9,7 +9,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/MR_03_no_end.json b/src/test/resources/bulk/fms/08_gff_data/MR_03_no_end.json
index 7284de1d8..fe1480334 100644
--- a/src/test/resources/bulk/fms/08_gff_data/MR_03_no_end.json
+++ b/src/test/resources/bulk/fms/08_gff_data/MR_03_no_end.json
@@ -9,7 +9,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/MR_04_no_strand.json b/src/test/resources/bulk/fms/08_gff_data/MR_04_no_strand.json
index 3a6cdcbd6..d2162706f 100644
--- a/src/test/resources/bulk/fms/08_gff_data/MR_04_no_strand.json
+++ b/src/test/resources/bulk/fms/08_gff_data/MR_04_no_strand.json
@@ -9,7 +9,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/MR_05_no_transcript_parent.json b/src/test/resources/bulk/fms/08_gff_data/MR_05_no_transcript_parent.json
index 123f5e739..1a76034db 100644
--- a/src/test/resources/bulk/fms/08_gff_data/MR_05_no_transcript_parent.json
+++ b/src/test/resources/bulk/fms/08_gff_data/MR_05_no_transcript_parent.json
@@ -9,7 +9,8 @@
 		"phase": 0,
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=WB:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/UD_01_update_transcript.json b/src/test/resources/bulk/fms/08_gff_data/UD_01_update_transcript.json
index ed9d9e98e..227ff22ce 100644
--- a/src/test/resources/bulk/fms/08_gff_data/UD_01_update_transcript.json
+++ b/src/test/resources/bulk/fms/08_gff_data/UD_01_update_transcript.json
@@ -10,7 +10,8 @@
 		"attributes": [
 			"ID=Transcript:Y74C9A.2a.1",
 			"Parent=Gene:WBGene00022276",
-			"Name=Y74C9A.2a.1"
+			"Name=Y74C9A.2a.1",
+			"transcript_id=RefSeq:Y74C9A.2a.1"
 		]
 	}
 ]
diff --git a/src/test/resources/bulk/fms/08_gff_data/UR_01_unrecognised_gene.json b/src/test/resources/bulk/fms/08_gff_data/UR_01_unrecognised_gene.json
new file mode 100644
index 000000000..dfec3c293
--- /dev/null
+++ b/src/test/resources/bulk/fms/08_gff_data/UR_01_unrecognised_gene.json
@@ -0,0 +1,15 @@
+[
+	{
+		"seqId": "I",
+		"source": "WormBase",
+		"type": "gene",
+		"start": 1,
+		"end": 1005,
+		"strand": "+",
+		"attributes": [
+			"ID=Gene:WBGeneNotLoaded",
+			"Name=TestGene",
+			"gene_id=WB:WBGeneNotLoaded"
+		]
+	}
+]
diff --git a/src/test/resources/bulk/fms/11_vep/AF_01_all_fields.json b/src/test/resources/bulk/fms/11_vep/AF_01_all_fields.json
new file mode 100644
index 000000000..f68f032b4
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/AF_01_all_fields.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/ER_01_empty_uploaded_variation.json b/src/test/resources/bulk/fms/11_vep/ER_01_empty_uploaded_variation.json
new file mode 100644
index 000000000..a50d2f5bf
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/ER_01_empty_uploaded_variation.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/ER_02_empty_feature.json b/src/test/resources/bulk/fms/11_vep/ER_02_empty_feature.json
new file mode 100644
index 000000000..623ee5311
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/ER_02_empty_feature.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/ER_03_empty_consequence.json b/src/test/resources/bulk/fms/11_vep/ER_03_empty_consequence.json
new file mode 100644
index 000000000..56ff42450
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/ER_03_empty_consequence.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/ER_04_empty_impact.json b/src/test/resources/bulk/fms/11_vep/ER_04_empty_impact.json
new file mode 100644
index 000000000..5a4ff658b
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/ER_04_empty_impact.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_01_invalid_uploaded_variation.json b/src/test/resources/bulk/fms/11_vep/IV_01_invalid_uploaded_variation.json
new file mode 100644
index 000000000..7bb5766d4
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_01_invalid_uploaded_variation.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "Invalid",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_02_invalid_feature.json b/src/test/resources/bulk/fms/11_vep/IV_02_invalid_feature.json
new file mode 100644
index 000000000..010eb35b1
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_02_invalid_feature.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Invalid",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_03_invalid_consequence.json b/src/test/resources/bulk/fms/11_vep/IV_03_invalid_consequence.json
new file mode 100644
index 000000000..1984520a5
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_03_invalid_consequence.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "invalid",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_04_invalid_cdna_position.json b/src/test/resources/bulk/fms/11_vep/IV_04_invalid_cdna_position.json
new file mode 100644
index 000000000..e8b70e196
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_04_invalid_cdna_position.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3 - 800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_05_invalid_cds_position.json b/src/test/resources/bulk/fms/11_vep/IV_05_invalid_cds_position.json
new file mode 100644
index 000000000..697fdc926
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_05_invalid_cds_position.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1 to 600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_06_invalid_protein_position.json b/src/test/resources/bulk/fms/11_vep/IV_06_invalid_protein_position.json
new file mode 100644
index 000000000..fbd4db078
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_06_invalid_protein_position.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "unknown",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_07_invalid_amino_acids.json b/src/test/resources/bulk/fms/11_vep/IV_07_invalid_amino_acids.json
new file mode 100644
index 000000000..a430c671d
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_07_invalid_amino_acids.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I/A",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_08_invalid_codons.json b/src/test/resources/bulk/fms/11_vep/IV_08_invalid_codons.json
new file mode 100644
index 000000000..c80c0bdd4
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_08_invalid_codons.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCcaTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_09_invalid_impact.json b/src/test/resources/bulk/fms/11_vep/IV_09_invalid_impact.json
new file mode 100644
index 000000000..854d16908
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_09_invalid_impact.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=INVALID",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_10_invalid_polyphen.json b/src/test/resources/bulk/fms/11_vep/IV_10_invalid_polyphen.json
new file mode 100644
index 000000000..76638b5ed
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_10_invalid_polyphen.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=invalid(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_11_invalid_sift.json b/src/test/resources/bulk/fms/11_vep/IV_11_invalid_sift.json
new file mode 100644
index 000000000..d61d901d9
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_11_invalid_sift.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=invalid(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/IV_12_invalid_variant_transcript_pair.json b/src/test/resources/bulk/fms/11_vep/IV_12_invalid_variant_transcript_pair.json
new file mode 100644
index 000000000..6728068eb
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/IV_12_invalid_variant_transcript_pair.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "VARIANTTEST:Variant0001",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/MR_01_no_uploaded_variation.json b/src/test/resources/bulk/fms/11_vep/MR_01_no_uploaded_variation.json
new file mode 100644
index 000000000..20b35b4f2
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/MR_01_no_uploaded_variation.json
@@ -0,0 +1,21 @@
+[
+	{
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/MR_02_no_feature.json b/src/test/resources/bulk/fms/11_vep/MR_02_no_feature.json
new file mode 100644
index 000000000..6bc3d351f
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/MR_02_no_feature.json
@@ -0,0 +1,21 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/MR_03_no_consequence.json b/src/test/resources/bulk/fms/11_vep/MR_03_no_consequence.json
new file mode 100644
index 000000000..512fd10b1
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/MR_03_no_consequence.json
@@ -0,0 +1,21 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"IMPACT=MODERATE",
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/MR_04_no_impact.json b/src/test/resources/bulk/fms/11_vep/MR_04_no_impact.json
new file mode 100644
index 000000000..89430906d
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/MR_04_no_impact.json
@@ -0,0 +1,21 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_acceptor_variant",
+		"cdnaPosition": "3-800",
+		"cdsPosition": "1-600",
+		"proteinPosition": "246-?",
+		"aminoAcids": "T/I",
+		"codons": "aCc/aTc",
+		"extra": [
+			"HGVSc=WB:Y74C9A.2a.1:c.29T>I",
+			"HGVSp=WB:CE49439:p.Thr10Ile",
+			"PolyPhen=probably_damaging(0.993)",
+			"SIFT=tolerated(0)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/UD_01_update.json b/src/test/resources/bulk/fms/11_vep/UD_01_update.json
new file mode 100644
index 000000000..1fb48758c
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/UD_01_update.json
@@ -0,0 +1,22 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:2-1000",
+		"feature": "WB:Y74C9A.2a.1",
+		"featureType": "Transcript",
+		"consequence": "splice_donor_5th_base_variant",
+		"cdnaPosition": "2-900",
+		"cdsPosition": "3-500",
+		"proteinPosition": "247-250",
+		"aminoAcids": "M/N",
+		"codons": "aCt/aTt",
+		"extra": [
+			"IMPACT=MODIFIER",
+			"HGVSc=WB:Y74C9A.2a.1:c.29M>N",
+			"HGVSp=WB:CE49439:p.Met10Neo",
+			"PolyPhen=possibly_damaging(0.8)",
+			"SIFT=deleterious_low_confidence(0.767)"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/11_vep/US_01_unsupported_intergenic.json b/src/test/resources/bulk/fms/11_vep/US_01_unsupported_intergenic.json
new file mode 100644
index 000000000..0738f2893
--- /dev/null
+++ b/src/test/resources/bulk/fms/11_vep/US_01_unsupported_intergenic.json
@@ -0,0 +1,11 @@
+[
+	{
+		"uploadedVariation": "NC_003279.8:g.1A>T",
+		"location": "I:1-1000",
+		"consequence": "intergenic_variant",
+		"extra": [
+			"IMPACT=LOW"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/12_biogrid/AF_01_all_fields.json b/src/test/resources/bulk/fms/12_biogrid/AF_01_all_fields.json
new file mode 100644
index 000000000..44ffa6cb6
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_biogrid/AF_01_all_fields.json
@@ -0,0 +1,32 @@
+{
+  "data": [
+    {
+      "screenId": 1888,
+      "identifierId": "108101",
+      "identifierType": "ENTREZ_GENE",
+      "officialSymbol": "Fermt3",
+      "aliases": "C79673|Kindlin3",
+      "organismId": 10090,
+      "organismOfficial": "Mus musculus",
+      "score1": 205.0, 
+      "score2": -2.2,   
+      "score3": 1e-05,
+      "score4": null,
+      "score5": null,
+      "hit": "YES",
+      "source": "BioGRID ORCS"
+    }
+  ],
+  "metaData": {
+    "dateProduced": "2024-04-18T20:10:35-07:00",
+    "dataProvider": {
+      "crossReference": {
+        "id": "FB",
+        "pages": [
+          "biogrid/orc"
+        ]
+      },
+      "type": "curated"
+    }
+  }
+}
diff --git a/src/test/resources/bulk/fms/12_biogrid/DE_01_duplicate_entries.json b/src/test/resources/bulk/fms/12_biogrid/DE_01_duplicate_entries.json
new file mode 100644
index 000000000..677cb545b
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_biogrid/DE_01_duplicate_entries.json
@@ -0,0 +1,49 @@
+{
+    "data": [
+      {
+        "screenId": 1888,
+        "identifierId": "100001",
+        "identifierType": "ENTREZ_GENE",
+        "officialSymbol": "Fermt3",
+        "aliases": "C79673|Kindlin3",
+        "organismId": 10090,
+        "organismOfficial": "Mus musculus",
+        "score1": 205.0, 
+        "score2": -2.2,   
+        "score3": 1e-05,
+        "score4": null,
+        "score5": null,
+        "hit": "YES",
+        "source": "BioGRID ORCS"
+      }, 
+      {
+        "screenId": 1888,
+        "identifierId": "100001",
+        "identifierType": "ENTREZ_GENE",
+        "officialSymbol": "Fermt3",
+        "aliases": "C79673|Kindlin3",
+        "organismId": 10090,
+        "organismOfficial": "Mus musculus",
+        "score1": 205.0, 
+        "score2": -2.2,   
+        "score3": 1e-05,
+        "score4": null,
+        "score5": null,
+        "hit": "YES",
+        "source": "BioGRID ORCS"
+      }
+    ],
+    "metaData": {
+      "dateProduced": "2024-04-18T20:10:35-07:00",
+      "dataProvider": {
+        "crossReference": {
+          "id": "FB",
+          "pages": [
+            "biogrid/orc"
+          ]
+        },
+        "type": "curated"
+      }
+    }
+  }
+  
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/AF_01_all_fields.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/AF_01_all_fields.json
new file mode 100644
index 000000000..334f007dc
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/AF_01_all_fields.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_01_empty_sample_id_and_sample_title.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_01_empty_sample_id_and_sample_title.json
new file mode 100644
index 000000000..8cd99c768
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_01_empty_sample_id_and_sample_title.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_02_empty_sample_type.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_02_empty_sample_type.json
new file mode 100644
index 000000000..4b06ff68b
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_02_empty_sample_type.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_03_empty_biosample_id_and_biosample_text.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_03_empty_biosample_id_and_biosample_text.json
new file mode 100644
index 000000000..317d58e59
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_03_empty_biosample_id_and_biosample_text.json
@@ -0,0 +1,70 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "",
+                "idType" : "fish",
+                "bioSampleText": ""
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_04_empty_assay_type.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_04_empty_assay_type.json
new file mode 100644
index 000000000..71eadb24b
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_04_empty_assay_type.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_05_empty_dataset_ids.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_05_empty_dataset_ids.json
new file mode 100644
index 000000000..c8fd4bfff
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/ER_05_empty_dataset_ids.json
@@ -0,0 +1,67 @@
+{
+    "data": [
+        {
+            "datasetIds" : [],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_01_invalid_sex.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_01_invalid_sex.json
new file mode 100644
index 000000000..6d252b133
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_01_invalid_sex.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "invalid",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_02_invalid_assay_type.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_02_invalid_assay_type.json
new file mode 100644
index 000000000..c47b06986
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_02_invalid_assay_type.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "invalid_assay_type",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_03_invalid_sample_type.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_03_invalid_sample_type.json
new file mode 100644
index 000000000..50b876cc1
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_03_invalid_sample_type.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "invalid_sample_type",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_04_invalid_taxon_id.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_04_invalid_taxon_id.json
new file mode 100644
index 000000000..243fc0ece
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_04_invalid_taxon_id.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "INVALID_TAXON_ID",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_05_invalid_genomic_information_biosample_id.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_05_invalid_genomic_information_biosample_id.json
new file mode 100644
index 000000000..b3abe5cad
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/IV_05_invalid_genomic_information_biosample_id.json
@@ -0,0 +1,69 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "invalid_biosample_id",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_01_no_sample_id_and_sample_title.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_01_no_sample_id_and_sample_title.json
new file mode 100644
index 000000000..2f0abfbf5
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_01_no_sample_id_and_sample_title.json
@@ -0,0 +1,65 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_02_no_sample_type.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_02_no_sample_type.json
new file mode 100644
index 000000000..d7ec1f06d
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_02_no_sample_type.json
@@ -0,0 +1,68 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_03_no_biosample_id_and_biosample_text.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_03_no_biosample_id_and_biosample_text.json
new file mode 100644
index 000000000..84c94759c
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_03_no_biosample_id_and_biosample_text.json
@@ -0,0 +1,68 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_04_no_assay_type.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_04_no_assay_type.json
new file mode 100644
index 000000000..f0768d72c
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_04_no_assay_type.json
@@ -0,0 +1,68 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:GSE38764"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_05_no_dataset_ids.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_05_no_dataset_ids.json
new file mode 100644
index 000000000..7f91b8efd
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/MR_05_no_dataset_ids.json
@@ -0,0 +1,66 @@
+{
+    "data": [
+        {
+            "sampleId" : {
+              "primaryId" : "GEO:GSE38764"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "sampleAge" : {
+                "stage" : {
+                  "stageName" : "stage1",
+                  "stageTermId" : "ZFS:001",
+                  "stageUberonSlimTerm" : {
+                    "uberonTerm" : "UBERON:001"
+                  }
+                }
+              },
+            "abundance" : "abundance test",
+            "sampleTitle" : "TEST TITLE",
+            "taxonId" : "NCBITaxon:6239",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "hermaphrodite",
+            "assemblyVersions" : [ "Zv9" ],
+            "sequencingFormat" : "single",
+            "microarraySampleDetails" : {
+                "channelId" : "WB:[cgc4349]:fem-3:A",
+                "channelNum" : 1
+             },
+            "sampleLocations" : [ 
+                {
+                    "whereExpressedStatement" : "trunk",
+                    "anatomicalStructureTermId" : "ANAT:001",
+                    "anatomicalSubStructureTermId" : "ANAT:002",
+                    "cellularComponentTermId" : "GOTEST:0012",
+                    "anatomicalStructureQualifierTermId": "UBERON:002",
+                    "anatomicalSubStructureQualifierTermId": "UBERON:003",
+                    "cellularComponentQualifierTermId": "FBCV:001",
+                    "anatomicalStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:004"},
+                        {"uberonTerm" : "UBERON:005"}
+                    ],
+                    "anatomicalSubStructureUberonSlimTermIds" : [
+                        {"uberonTerm" : "UBERON:006"},
+                        {"uberonTerm" : "UBERON:007"}
+                    ]
+                }
+            ]
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/UE_01_update_empty_non_required_fields.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/UE_01_update_empty_non_required_fields.json
new file mode 100644
index 000000000..eb074dd42
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/UE_01_update_empty_non_required_fields.json
@@ -0,0 +1,39 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                "GEO:TEST2"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:TEST2"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "abundance" : "",
+            "sampleTitle" : "",
+            "taxonId" : "",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              },
+            "sex" : "",
+            "sequencingFormat" : "",
+            "microarraySampleDetails" : {
+             },
+            "sampleLocations" : []
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file
diff --git a/src/test/resources/bulk/fms/12_htp_dataset_sample/UM_01_update_no_non_required_fields.json b/src/test/resources/bulk/fms/12_htp_dataset_sample/UM_01_update_no_non_required_fields.json
new file mode 100644
index 000000000..6dc5ccbe4
--- /dev/null
+++ b/src/test/resources/bulk/fms/12_htp_dataset_sample/UM_01_update_no_non_required_fields.json
@@ -0,0 +1,31 @@
+{
+    "data": [
+        {
+            "datasetIds" : [
+                 "GEO:TEST1"
+            ],
+            "sampleId" : {
+              "primaryId" : "GEO:TEST1"
+            },
+            "assayType" : "HTPMMO:assay001",
+            "sampleType" : "HTPOBI:sample001",
+            "genomicInformation" : {
+                "biosampleId" : "AGA:Allele0001",
+                "idType" : "fish"
+              }
+        }
+    ],
+    "metaData": {
+        "dataProvider": {
+        "crossReference": {
+            "id": "FB",
+            "pages": [
+            "homepage"
+            ]
+        },
+        "type": "curated"
+        },
+        "dateProduced": "2024-07-12T12:36:21-04:00",
+        "release": "2024_03"
+    }
+}
\ No newline at end of file