working_fusion_model.js

//
// top level qs:
// * any Array-style components require members?
// * any scalar-style components require values? (ie can be Optional?)
const example = {
    // ** reading frame preserved
    // mandatory?
    // how to (if needed?) represent 'unknown'?
    // not required to be included -- fusor // null
    // curation tool -- should be yes or no
    "r_frame_preserved": true,

    // ** reg elements
    "regulatory_elements": [
        {
            "type": "promoter",
            "value_id": "hgnc:100",
            "label": "ASIC1"
        },
        {
            "type": "enhancer",
            "value_id": "hgnc:200",
            "label": "G1"
        },
        
        // DO THIS:
        // * either fill in gene descriptor or gene descriptor ID
        // * fill in optional
        // what if not normalize?
        //  * have to provide valid gene
        {
            "type": "enhancer",
            "gene_descriptor_id": "fusion.gene:G1"
        }
        // should do something like this instead?
        // just include gene descriptor id and have a GeneDescriptors property below including them
        {
            "type": "enhancer",
            "gene": { // name the field 'gene'?
                "type": "GeneDescriptor"
                "id": "fusion.gene:G1", // id should be "fusion.gene:
                "value_id": "hgnc:200",
                "label": "G1",
            }
        }
    ],

    // ** protein domains
    // what if domain name doesn't normalize to an interpro ID? leave as unknown?
    // what if gene symbol doesn't normalize to a gene concept ID?
    // what should we put for `id`? something like "fusion.gene:NTRK1"?
    // gene descriptor id is just "gene:NTRK1"
    // for protein domain, we should already ask for gene, give preloaded list of possible domain names
    "protein_domains": [
        {
            "status": "preserved",
            "name": "tyrosine kinase catalytic domain",
            "id": "interpro:IPR020635",
            "gene": {
                // id field here --- "id": "fusion.gene:NTRK1"?
                "value_id": "hgnc:8031",
                "label": "NTRK1",
                "type": "GeneDescriptor"
            }
        }
    ],

    // ** causative event
    // option for 'unknown'? no need
    "causative_event": {
        "event_type": "rearrangement" // enum: {'rearrangement', 'read-through', 'trans-splicing'}
    },

    // ** transcript components
    //
    // components to add/fit?
    //  * gene (just known gene symbol)
    //  * unknown
    // 
    // always at least
        
    // gene component:
        // make it a descriptor
    // unknown_gene: unknown
        
    // must be length >= 2
    "transcript_components": [
        // unknown genes
        //    * front end: user chooses either ChromosomeLocation or SequenceLocation?
        {
            "component_type": "unknown_gene"
            "region": {
                "sequence_id": "ncbi:NC_000001.11",
                "interval": {
                    "type": "SimpleInterval"
                    "start": 1000,
                    "end": 5000,
                },
                "type": "SequenceLocation"
            },
        },
        {
            "component_type": "unknown_gene"
            "region": {
                "species_id": "<whatever>",
                "interval": {
                    "type": "CytobandInterval"
                    "start": "p12.1",
                    "end": "p12.16",
                },
                "chr": "12",
                "type": "ChromosomeLocation"
            },
        },
        {
            "component_type": "unknown_gene"
            "region": null, // use for "unknown" component?
        },

        // linker
        {
            "component_type": "linker_sequence",
            "linker_sequence": "ATTATTA" // rename property to "sequence"?
        },

        // transcript segment component
        {
            "component_type": "transcript_segment",
            "transcript": "NM:002529.3",
            "exon_start": 10,
            "exon_start_offset": -8,
            "exon_end": 17,
            "exon_end_offset": 8,
            "gene": {
                "id": "fusion.gene:NTRK1"
                "value_id": "hgnc:8031",
                "label": "NTRK1",
                "type": "GeneDescriptor"
            },
            "component_genomic_region": {
                "type": "LocationDescription"
                "description": null,   // ??
                "value": {
                    "seq_id": "ncbi:NC_000001.13",
                    "start": 154170401,
                    "end": 1556346348,
                    "type": "SequenceLocation" // any case where this is ever a ChromosomeLocation? NO
                },
            },
        }
    ]
}