<commit_before>{
    "title": "Experiment Type",
    "description": "Schema for experiment type",
    "id": "/profiles/experiment_type.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["title", "lab", "award"],
    "identifyingProperties": ["experiment_name", "uuid"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/static_embeds" },
        { "$ref": "mixins.json#/notes" }
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "status": {
            "title": "Status",
            "type": "string",
            "default": "in review by lab",
            "enum" : [
                "released",
                "in review by lab",
                "deleted"
            ]
        },
        "title": {
            "title": "Experiment Type",
            "description": "The display name for the experiment type",
            "type": "string",
            "lookup": 20
        },
        "experiment_name": {
            "title": "Experiment Name",
            "description": "DON'T SUBMIT, auto-generated",
            "type": "string",
            "pattern": "^[a-z0-9\\-]+$",
            "uniqueKey": true,
            "exclude_from": ["submit4dn", "FFedit-create"]
        },
        "controlled_term": {
            "title": "Ontology Term",
            "description": "Ontology term that matches this experiment type",
            "type": "string",
            "linkTo": "OntologyTerm"
        },
        "experiment_category": {
            "title": "Experiment Category",
            "description": "General category of the experiment type",
            "type": "string",
            "enum": ["Sequencing", "Microscopy"],
            "lookup": 100
        },
        "assay_classification": {
            "title": "Assay Classification",
            "description": "Classification of assay type",
            "type": "string",
            "lookup": 110,
            "suggested_enum": [
                "Linear DNA Enrichment",
                "3C via Ligation",
                "Ligation-free Multi-fragment 3C",
                "RNA Quantification",
                "RNA-DNA Proximity Capture",
                "Fluorescence Localization"
            ]
        },
        "assay_subclassification": {
            "title": "Assay Purpose",
            "description": "Sub-classification of assay based on what is measured",
            "type": "string",
            "lookup": 120,
            "suggested_enum": [
                "Replication Timing",
                "Proximity to Organelle",
                "DNA Binding",
                "Open Chromatin",
                "DNA-DNA Pairwise Interactions",
                "DNA-DNA Pairwise Interactions - Single Cell",
                "DNA-DNA Multi-way Interactions",
                "DNA-DNA Multi-way Interactions of Selected Loci",
                "DNA-DNA Pairwise Interactions of Enriched Regions",
                "DNA-DNA Pairwise Interactions of Selected Loci",
                "RNA-DNA Multi-way Interactions",
                "RNA-DNA Pairwise Interactions",
                "Fixed Sample DNA Localization",
                "Fixed Sample RNA Localization",
                "Single Particle Tracking"
            ]
        },
        "other_tags": {
            "title": "Tags",
            "description": "Additional categories for characterizing this experiment type",
            "type": "array",
            "lookup": 150,
            "items": {
                "title": "Tag",
                "description": "A tag for the item.",
                "type":  "string",
                "suggested_enum": [
                    "DNA-DNA",
                    "RNA-DNA",
                    "DNA-Protein",
                    "Single Cell",
                    "Multi-contact",
                    "Pairwise",
                    "1D",
                    "3D"
                ]
            }
        },
        "raw_file_types": {
            "title": "Raw Files",
            "description": "The type of raw files typically associated with the experiment type in the portal",
            "type": "string",
            "lookup": 160,
            "suggested_enum": ["Reads (fastq) provided by lab"]
        },
        "sop": {
            "title": "SOP",
            "description": "Approved SOP for the experiment type",
            "type": "string",
            "lookup": 170,
            "linkTo": "Protocol"
        },
        "reference_pubs": {
            "title": "Reference Publications",
            "description": "Reference publication(s) for the experiment type",
            "type": "array",
            "lookup": 180,
            "items": {
                "title": "Publication",
                "description": "Publication metadata",
                "type": "string",
                "linkTo": "Publication"
            }
        },
        "valid_item_types": {
            "title": "Valid Item Types",
            "description": "Types of items that can utilize this experiment type",
            "type": "array",
            "permission": "import_items",
            "items": {
                "title": "Item Type",
                "description": "Item class name (e.g. ExperimentHiC)",
                "type": "string"
            }
        }
    },
    "facets": {
        "experiment_category": {
            "title": "Experiment Category"
        },
        "assay_subclass_short": {
            "title": "Assay Type"
        },
        "other_tags": {
            "title": "Additional Categories"
        }
    },
    "columns": {
        "experiment_category": {
            "title": "Experiment Category"
        },
        "assay_classification": {
            "title": "Assay Classification"
        },
        "assay_subclassification": {
            "title": "Assay Subclassification"
        }
    }
}
<commit_msg>And added the category to the suggested enum<commit_after>{
    "title": "Experiment Type",
    "description": "Schema for experiment type",
    "id": "/profiles/experiment_type.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["title", "lab", "award"],
    "identifyingProperties": ["experiment_name", "uuid"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/static_embeds" },
        { "$ref": "mixins.json#/notes" }
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "status": {
            "title": "Status",
            "type": "string",
            "default": "in review by lab",
            "enum" : [
                "released",
                "in review by lab",
                "deleted"
            ]
        },
        "title": {
            "title": "Experiment Type",
            "description": "The display name for the experiment type",
            "type": "string",
            "lookup": 20
        },
        "experiment_name": {
            "title": "Experiment Name",
            "description": "DON'T SUBMIT, auto-generated",
            "type": "string",
            "pattern": "^[a-z0-9\\-]+$",
            "uniqueKey": true,
            "exclude_from": ["submit4dn", "FFedit-create"]
        },
        "controlled_term": {
            "title": "Ontology Term",
            "description": "Ontology term that matches this experiment type",
            "type": "string",
            "linkTo": "OntologyTerm"
        },
        "experiment_category": {
            "title": "Experiment Category",
            "description": "General category of the experiment type",
            "type": "string",
            "enum": ["Sequencing", "Microscopy"],
            "lookup": 100
        },
        "assay_classification": {
            "title": "Assay Classification",
            "description": "Classification of assay type",
            "type": "string",
            "lookup": 110,
            "suggested_enum": [
                "Linear DNA Enrichment",
                "3C via Ligation",
                "Ligation-free Multi-fragment 3C",
                "RNA Quantification",
                "RNA-DNA Proximity Capture",
                "Fluorescence Localization"
            ]
        },
        "assay_subclassification": {
            "title": "Assay Purpose",
            "description": "Sub-classification of assay based on what is measured",
            "type": "string",
            "lookup": 120,
            "suggested_enum": [
                "Replication Timing",
                "Proximity to Organelle",
                "DNA Binding",
                "Open Chromatin",
                "DNA-DNA Pairwise Interactions",
                "DNA-DNA Pairwise Interactions - Single Cell",
                "DNA-DNA Multi-way Interactions",
                "DNA-DNA Multi-way Interactions of Selected Loci",
                "DNA-DNA Pairwise Interactions of Enriched Regions",
                "DNA-DNA Pairwise Interactions of Selected Loci",
                "RNA-DNA Multi-way Interactions",
                "RNA-DNA Pairwise Interactions",
                "Fixed Sample DNA Localization",
                "Fixed Sample RNA Localization",
                "Single Particle Tracking",
                "Context-dependent Reporter Expression"
            ]
        },
        "other_tags": {
            "title": "Tags",
            "description": "Additional categories for characterizing this experiment type",
            "type": "array",
            "lookup": 150,
            "items": {
                "title": "Tag",
                "description": "A tag for the item.",
                "type":  "string",
                "suggested_enum": [
                    "DNA-DNA",
                    "RNA-DNA",
                    "DNA-Protein",
                    "Single Cell",
                    "Multi-contact",
                    "Pairwise",
                    "1D",
                    "3D"
                ]
            }
        },
        "raw_file_types": {
            "title": "Raw Files",
            "description": "The type of raw files typically associated with the experiment type in the portal",
            "type": "string",
            "lookup": 160,
            "suggested_enum": ["Reads (fastq) provided by lab"]
        },
        "sop": {
            "title": "SOP",
            "description": "Approved SOP for the experiment type",
            "type": "string",
            "lookup": 170,
            "linkTo": "Protocol"
        },
        "reference_pubs": {
            "title": "Reference Publications",
            "description": "Reference publication(s) for the experiment type",
            "type": "array",
            "lookup": 180,
            "items": {
                "title": "Publication",
                "description": "Publication metadata",
                "type": "string",
                "linkTo": "Publication"
            }
        },
        "valid_item_types": {
            "title": "Valid Item Types",
            "description": "Types of items that can utilize this experiment type",
            "type": "array",
            "permission": "import_items",
            "items": {
                "title": "Item Type",
                "description": "Item class name (e.g. ExperimentHiC)",
                "type": "string"
            }
        }
    },
    "facets": {
        "experiment_category": {
            "title": "Experiment Category"
        },
        "assay_subclass_short": {
            "title": "Assay Type"
        },
        "other_tags": {
            "title": "Additional Categories"
        }
    },
    "columns": {
        "experiment_category": {
            "title": "Experiment Category"
        },
        "assay_classification": {
            "title": "Assay Classification"
        },
        "assay_subclassification": {
            "title": "Assay Subclassification"
        }
    }
}

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