<commit_before>{
    "title": "Biological Feature",
    "description": "A biological feature like a Gene, Protein, Cellular Structure.",
    "id": "/profiles/bio_feature.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["award", "lab", "description", "feature_type"],
    "identifyingProperties": ["uuid", "aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/notes" },
        { "$ref": "mixins.json#/status"} ,
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/release_dates" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/tags" },
        { "$ref": "mixins.json#/dbxrefs" },
        { "$ref": "mixins.json#/static_embeds" }
    ],
    "mixinFacets" : [
        { "$ref": "mixins.json#/facets_common" }
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "description": {
            "title": "Description",
            "description": "A short description of the feature",
            "type": "string",
            "lookup": 20,
            "formInput": "textarea"
        },
        "preferred_label": {
            "title": "Preferred label",
            "description": "A provided label that can override the automatically calculated display_title - only submit if the calculated title does not work",
            "type": "string",
            "lookup": 40
        },
        "feature_type": {
            "title": "Feature Type",
            "description": "An (usually sequence) ontology term indicating the type of feature - eg. gene, protein, region",
            "type": "string",
            "linkTo": "OntologyTerm",
            "lookup": 10
        },
        "organism_name": {
            "title": "Species",
            "type": "string",
            "description": "The organism that is the source of the BioFeature",
            "lookup": 30,
            "suggested_enum": [
                "human",
                "mouse",
                "rat",
                "fruit fly",
                "roundworm",
                "chicken",
                "multiple organisms"
            ]
        },
        "genome_location": {
            "title": "Genomic Location",
            "description": "The location(s) of the feature on the genome",
            "comment": "A BioFeature can be a simple location and if so must have this field and appropriate type from SO",
            "type": "array",
            "lookup": 60,
            "items": {
                "title": "Genomic Region",
                "description": "Item indicating genome assembly, chromosome and coordinates of the region",
                "type": "string",
                "linkTo": "GenomicRegion"
            }
        },
        "relevant_genes": {
            "title": "Gene",
            "description": "Gene or Gene(s) that a feature can be linked to.",
            "type": "array",
            "lookup": 50,
            "comment": "Usually a single ID but in some cases such as Histones that have multiple gene clusters or a region that contains more than one relevant gene can use multiple IDs",
            "items": {
                  "title": "Gene ID",
                  "description": "Entrez Gene ID",
                  "type": "string",
                  "linkTo": "Gene"
            }
        },
        "cellular_structure": {
            "title": "Cellular Structure",
            "description": "If the feature is a cellular structure such as a chromosome use this field and set type to 'cellular_component'",
            "type": "string",
            "lookup": 70,
            "enum": [
                "Cell membrane",
                "Nucleolus",
                "Nuclear pore complex",
                "Microtubules",
                "Endoplasmic reticulum",
                "Chromosomes"
            ]
        },
        "feature_mods": {
            "type": "array",
            "uniqueItems": true,
            "comment": "This property will be used to calculate the display_title of the feature - however a submitted preferred_label overrides this info.",
            "items": {
                "title": "Modification",
                "description": "A modification to the feature.",
                "type": "object",
                "required": ["mod_type"],
                "lookup": 80,
                "properties": {
                    "mod_type": {
                        "title": "Type of modification",
                        "description": "One specific modification - list has suggested values.",
                        "type": "string",
                        "suggested_enum": [
                            "3xFLAG",
                            "6XHis",
                            "DsRed",
                            "eGFP",
                            "ER",
                            "FLAG",
                            "GFP",
                            "HA",
                            "mCherry",
                            "T2A",
                            "TRE",
                            "V5",
                            "YFP",
                            "Methylation",
                            "Monomethylation",
                            "Dimethylation",
                            "Trimethylation",
                            "Acetylation",
                            "Phosphorylation"
                        ]
                    },
                    "mod_position": {
                        "title": "Modified Position",
                        "description": "The position relative to the feature - aa residue, base position or descriptive (eg. N-terminus)",
                        "type": "string"
                    }
                }
            }
        }
    },
    "facets": {
        "feature_type.preferred_name": {
            "title": "Feature Type"
        },
        "organism_name": {
            "title": "Species"
        }
    },
    "columns": {
        "feature_type.preferred_name": {
            "title": "Feature Type"
        },
        "organism_name": {
            "title": "Species"
        }
    }
}
<commit_msg>Added a couple new choices to biofeature organism_name suggested enum<commit_after>{
    "title": "Biological Feature",
    "description": "A biological feature like a Gene, Protein, Cellular Structure.",
    "id": "/profiles/bio_feature.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["award", "lab", "description", "feature_type"],
    "identifyingProperties": ["uuid", "aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/notes" },
        { "$ref": "mixins.json#/status"} ,
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/release_dates" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/tags" },
        { "$ref": "mixins.json#/dbxrefs" },
        { "$ref": "mixins.json#/static_embeds" }
    ],
    "mixinFacets" : [
        { "$ref": "mixins.json#/facets_common" }
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "description": {
            "title": "Description",
            "description": "A short description of the feature",
            "type": "string",
            "lookup": 20,
            "formInput": "textarea"
        },
        "preferred_label": {
            "title": "Preferred label",
            "description": "A provided label that can override the automatically calculated display_title - only submit if the calculated title does not work",
            "type": "string",
            "lookup": 40
        },
        "feature_type": {
            "title": "Feature Type",
            "description": "An (usually sequence) ontology term indicating the type of feature - eg. gene, protein, region",
            "type": "string",
            "linkTo": "OntologyTerm",
            "lookup": 10
        },
        "organism_name": {
            "title": "Species",
            "type": "string",
            "description": "The organism that is the source of the BioFeature",
            "lookup": 30,
            "suggested_enum": [
                "human",
                "mouse",
                "rat",
                "fruit fly",
                "roundworm",
                "chicken",
                "multiple organisms",
                "unspecified",
                "engineered reagent"
            ]
        },
        "genome_location": {
            "title": "Genomic Location",
            "description": "The location(s) of the feature on the genome",
            "comment": "A BioFeature can be a simple location and if so must have this field and appropriate type from SO",
            "type": "array",
            "lookup": 60,
            "items": {
                "title": "Genomic Region",
                "description": "Item indicating genome assembly, chromosome and coordinates of the region",
                "type": "string",
                "linkTo": "GenomicRegion"
            }
        },
        "relevant_genes": {
            "title": "Gene",
            "description": "Gene or Gene(s) that a feature can be linked to.",
            "type": "array",
            "lookup": 50,
            "comment": "Usually a single ID but in some cases such as Histones that have multiple gene clusters or a region that contains more than one relevant gene can use multiple IDs",
            "items": {
                  "title": "Gene ID",
                  "description": "Entrez Gene ID",
                  "type": "string",
                  "linkTo": "Gene"
            }
        },
        "cellular_structure": {
            "title": "Cellular Structure",
            "description": "If the feature is a cellular structure such as a chromosome use this field and set type to 'cellular_component'",
            "type": "string",
            "lookup": 70,
            "enum": [
                "Cell membrane",
                "Nucleolus",
                "Nuclear pore complex",
                "Microtubules",
                "Endoplasmic reticulum",
                "Chromosomes"
            ]
        },
        "feature_mods": {
            "type": "array",
            "uniqueItems": true,
            "comment": "This property will be used to calculate the display_title of the feature - however a submitted preferred_label overrides this info.",
            "items": {
                "title": "Modification",
                "description": "A modification to the feature.",
                "type": "object",
                "required": ["mod_type"],
                "lookup": 80,
                "properties": {
                    "mod_type": {
                        "title": "Type of modification",
                        "description": "One specific modification - list has suggested values.",
                        "type": "string",
                        "suggested_enum": [
                            "3xFLAG",
                            "6XHis",
                            "DsRed",
                            "eGFP",
                            "ER",
                            "FLAG",
                            "GFP",
                            "HA",
                            "mCherry",
                            "T2A",
                            "TRE",
                            "V5",
                            "YFP",
                            "Methylation",
                            "Monomethylation",
                            "Dimethylation",
                            "Trimethylation",
                            "Acetylation",
                            "Phosphorylation"
                        ]
                    },
                    "mod_position": {
                        "title": "Modified Position",
                        "description": "The position relative to the feature - aa residue, base position or descriptive (eg. N-terminus)",
                        "type": "string"
                    }
                }
            }
        }
    },
    "facets": {
        "feature_type.preferred_name": {
            "title": "Feature Type"
        },
        "organism_name": {
            "title": "Species"
        }
    },
    "columns": {
        "feature_type.preferred_name": {
            "title": "Feature Type"
        },
        "organism_name": {
            "title": "Species"
        }
    }
}

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