This document describes the JSON schema structure for the Virtual Fly Brain (VFB) term information API.
The base schema returned by term info queries:
{
"Name": "String (term name)",
"Id": "String (term ID/short form)",
"SuperTypes": ["String (class hierarchies)"],
"Meta": {
"Name": "String (markdown link)",
"Description": "String (description)",
"Comment": "String (additional information)",
"Types": "String (class information)",
"Relationships": "String (relationships)",
"Cross References": "String (external links)",
"Synonyms": "String (alternative names)"
},
"Tags": ["String (tag names)"],
"Technique": ["String (imaging techniques, Individual only)"],
"Queries": [
{
"query": "String (query identifier)",
"label": "String (human-readable query name)",
"function": "String (backend function name)",
"takes": {
"short_form": {"$and": ["String (required type constraints)"]},
"default": {"parameter_key": "parameter_value"}
},
"preview": "Integer (number of preview results, -1 for all)",
"preview_columns": ["String (column identifiers)"],
"preview_results": {
"headers": {
"column_id": {
"title": "String (display name)",
"type": "String (data type)",
"order": "Integer (display order)",
"sort": {"Integer (priority)": "String (direction)"}
}
},
"rows": [
{
"id": "String (entity ID)",
"column_name": "Value (column data)",
// Additional columns...
}
]
},
"output_format": "String (table/ribbon)",
"count": "Integer (total result count)"
}
],
"IsIndividual": "Boolean",
"IsClass": "Boolean",
"IsTemplate": "Boolean",
"Publications": [
{
"title": "String (publication title)",
"short_form": "String (publication ID)",
"microref": "String (short citation)",
"refs": ["String (URL to external reference)"]
}
]
}VFB entities fall into three main types, each with specific fields beyond the core schema:
Individual instances (neurons, expression patterns, anatomical instances):
"Technique": ["String (imaging techniques used)"],
"Images": {
"template_id": [
{
"id": "String (image ID)",
"label": "String (image label)",
"thumbnail": "String (URL to thumbnail)",
"thumbnail_transparent": "String (URL to transparent thumbnail)",
"nrrd": "String (URL to NRRD volume)",
"wlz": "String (URL to Woolz volume)",
"obj": "String (URL to OBJ model)",
"swc": "String (URL to SWC file)",
"index": "Integer (sorting order)",
"center": {"X": "Float", "Y": "Float", "Z": "Float"},
"extent": {"X": "Float", "Y": "Float", "Z": "Float"},
"voxel": {"X": "Float", "Y": "Float", "Z": "Float"},
"orientation": "String (orientation code)",
"type_label": "String (anatomical type)",
"type_id": "String (anatomical type ID)"
}
]
},
"Publications": [
{
"title": "String (publication title)",
"short_form": "String (publication ID)",
"microref": "String (short citation)",
"refs": ["String (URL to external reference)"]
}
],
"Licenses": {
"index": {
"iri": "String (license IRI)",
"short_form": "String (license ID)",
"label": "String (license name)",
"icon": "String (URL to license icon)",
"source": "String (dataset source)",
"source_iri": "String (dataset source IRI)"
}
}Ontology classes (anatomical structures, neuron types):
"Examples": {
"template_id": [
{
// Same structure as Images objects
}
]
},
"Publications": [
{
"title": "String (publication title)",
"short_form": "String (publication ID)",
"microref": "String (short citation)",
"refs": ["String (URL to external reference)"]
}
],
"Synonyms": [
{
"label": "String (synonym text)",
"scope": "String (synonym scope)",
"type": "String (synonym type)",
"publication": "String (publication reference)"
}
]Template brains and reference images:
"Images": {
"template_id": [
{
// Same structure as individual images
}
]
},
"Domains": {
"index": {
"id": "String (domain ID)",
"label": "String (domain label)",
"thumbnail": "String (URL to thumbnail)",
"thumbnail_transparent": "String (URL to transparent thumbnail)",
"index": "Integer (sorting order)",
"center": {"X": "Float", "Y": "Float", "Z": "Float"} | null,
"type_label": "String (anatomical type)",
"type_id": "String (anatomical type ID)"
}
},
"Licenses": {
"index": {
"iri": "String (license IRI)",
"short_form": "String (license ID)",
"label": "String (license name)",
"icon": "String (URL to license icon)",
"source": "String (dataset source)",
"source_iri": "String (dataset source IRI)"
}
}These objects appear in multiple places throughout the schema:
Represents 3D coordinates in space:
{
"X": "Float",
"Y": "Float",
"Z": "Float"
}Basic information about any entity:
{
"short_form": "String (entity ID)",
"iri": "String (full IRI)",
"label": "String (display name)",
"types": ["String (entity types)"],
"unique_facets": ["String (special classifications)"],
"symbol": "String (alternate identifier)"
}Basic information about relationships:
{
"short_form": "String (relation ID)",
"iri": "String (full IRI)",
"label": "String (relation name)",
"type": "String (relation type)"
}Publication information:
{
"core": {
// MinimalEntityInfo
},
"microref": "String (short citation)",
"PubMed": "String (PubMed ID)",
"FlyBase": "String (FlyBase ID)",
"DOI": "String (DOI)",
"ISBN": "String (ISBN)"
}License information:
{
"core": {
// MinimalEntityInfo
},
"link": "String (URL to license)",
"icon": "String (URL to license icon)",
"is_bespoke": "String (custom license flag)"
}Cross-reference to external resources:
{
"site": {
// MinimalEntityInfo
},
"homepage": "String (site homepage)",
"link_base": "String (base URL for links)",
"link_postfix": "String (URL suffix)",
"accession": "String (ID in external system)",
"link_text": "String (display text)",
"icon": "String (URL to site icon)"
}The system supports several query types:
Returns all available images for a term.
{
"query": "ListAllAvailableImages",
"label": "List all images for [term]",
"function": "get_images",
"takes": {
"short_form": {"$and": ["has_image"]},
"default": {"term": "TERM_ID"}
}
}Finds neurons with similar morphology.
{
"query": "SimilarMorphologyTo",
"label": "Find similar neurons to [neuron]",
"function": "get_similar_neurons",
"takes": {
"short_form": {"$and": ["Individual", "Neuron"]},
"default": {
"neuron": "NEURON_ID",
"similarity_score": "NBLAST_score"
}
}
}Finds neurons with synapses into the target.
{
"query": "NeuronInputsTo",
"label": "Find neurons with inputs to [neuron]",
"function": "get_individual_neuron_inputs",
"takes": {
"short_form": {"$and": ["Individual", "Neuron"]},
"default": {
"neuron_short_form": "NEURON_ID",
"summary_mode": true
}
}
}Finds instances classified as a specific type.
{
"query": "ClassifiedAs",
"label": "Find instances of [class]",
"function": "get_instances",
"takes": {
"short_form": {"$and": ["Class"]},
"default": {"short_form": "CLASS_ID"}
}
}Finds individuals related to a template.
{
"query": "RelatedIndividuals",
"label": "Find instances in [template]",
"function": "get_related_anatomy",
"takes": {
"short_form": {"$and": ["Template"]},
"default": {"template_short_form": "TEMPLATE_ID"}
}
}{
"Name": "fru-M-200266",
"Id": "VFB_00000001",
"SuperTypes": [
"Entity", "Adult", "Anatomy", "Cell", "Expression_pattern_fragment",
"Individual", "Nervous_system", "Neuron", "VFB", "has_image",
"FlyCircuit", "NBLAST"
],
"Meta": {
"Name": "[fru-M-200266](VFB_00000001)",
"Comment": "OutAge: Adult 5~15 days",
"Types": "[adult DM6 lineage neuron](FBbt_00050144); [expression pattern fragment](VFBext_0000004)",
"Relationships": "[expresses](RO_0002292): [Scer\\GAL4[fru.P1.D]](FBal0276838); [is part of](BFO_0000050): [Scer\\GAL4[fru.P1.D] expression pattern](VFBexp_FBal0276838), [adult brain](FBbt_00003624), [male organism](FBbt_00007004)",
"Cross References": "[FlyCircuit 1.0](http://flycircuit.tw): [fru-M-200266](http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&neuron=fru-M-200266)"
},
"Tags": ["Adult", "Expression_pattern_fragment", "Nervous_system", "Neuron"],
"Queries": [
{
"query": "SimilarMorphologyTo",
"label": "Find similar neurons to fru-M-200266",
"function": "get_similar_neurons",
"takes": {
"short_form": {"$and": ["Individual", "Neuron"]},
"default": {
"neuron": "VFB_00000001",
"similarity_score": "NBLAST_score"
}
},
"preview": 5,
"preview_columns": ["id", "score", "name", "tags", "thumbnail"],
"preview_results": {
"headers": {
"id": {"title": "Add", "type": "selection_id", "order": -1},
"score": {"title": "Score", "type": "numeric", "order": 1, "sort": {"0": "Desc"}},
"name": {"title": "Name", "type": "markdown", "order": 1, "sort": {"1": "Asc"}},
"tags": {"title": "Tags", "type": "tags", "order": 2},
"thumbnail": {"title": "Thumbnail", "type": "markdown", "order": 9}
},
"rows": []
},
"output_format": "table",
"count": 60
}
],
"IsIndividual": true,
"Images": {
"VFB_00017894": [
{
"id": "VFB_00000001",
"label": "fru-M-200266",
"thumbnail": "https://virtualflybrain.org/reports/VFB_00000001/thumbnail.png",
"thumbnail_transparent": "https://virtualflybrain.org/reports/VFB_00000001/thumbnailT.png",
"nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.nrrd",
"wlz": "https://virtualflybrain.org/reports/VFB_00000001/volume.wlz",
"obj": "https://virtualflybrain.org/reports/VFB_00000001/volume.obj",
"swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.swc"
}
]
},
"IsClass": false,
"IsTemplate": false,
"Licenses": {
"0": {
"iri": "http://virtualflybrain.org/reports/VFBlicense_FlyCircuit_License",
"short_form": "VFBlicense_FlyCircuit_License",
"label": "FlyCircuit License",
"icon": "",
"source": "FlyCircuit 1.0 - single neurons (Chiang2010)",
"source_iri": "http://virtualflybrain.org/reports/Chiang2010"
}
}
}{
"Name": "JRC2018Unisex",
"Id": "VFB_00101567",
"SuperTypes": [
"Entity", "Adult", "Anatomy", "Individual",
"Nervous_system", "Template", "has_image"
],
"Meta": {
"Name": "[JRC2018Unisex](VFB_00101567)",
"Description": "Janelia 2018 unisex, averaged adult brain template",
"Types": "[adult brain](FBbt_00003624)"
},
"Tags": ["Adult", "Nervous_system"],
"Queries": [],
"IsIndividual": true,
"Images": {
"VFBc_00101567": [{
"id": "VFBc_00101567",
"label": "JRC2018Unisex_c",
"thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnail.png",
"thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnailT.png",
"nrrd": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/volume.nrrd",
"wlz": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/volume.wlz",
"obj": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/volume_man.obj",
"index": 0,
"center": {"X": 605.0, "Y": 283.0, "Z": 87.0},
"extent": {"X": 1211.0, "Y": 567.0, "Z": 175.0},
"voxel": {"X": 0.5189161, "Y": 0.5189161, "Z": 1.0},
"orientation": "LPS"
}]
},
"IsClass": false,
"IsTemplate": true,
"Domains": {
"0": {
"id": "VFB_00101567",
"label": "JRC2018Unisex",
"thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnail.png",
"thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnailT.png",
"index": 0,
"type_label": "adult brain",
"type_id": "FBbt_00003624"
}
},
"Licenses": {
"0": {
"iri": "http://virtualflybrain.org/reports/VFBlicense_CC_BY_NC_SA_4_0",
"short_form": "VFBlicense_CC_BY_NC_SA_4_0",
"label": "CC-BY-NC-SA_4.0",
"icon": "http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-nc-sa.png",
"source": "JRC 2018 templates & ROIs",
"source_iri": "http://virtualflybrain.org/reports/JRC2018"
}
}
}{
"Name": "adult antennal lobe projection neuron",
"Id": "FBbt_00007354",
"SuperTypes": [
"Entity", "Adult", "Anatomy", "Class", "Nervous_system", "Neuron"
],
"Meta": {
"Name": "[adult antennal lobe projection neuron](FBbt_00007354)",
"Description": "Any adult secondary olfactory neuron that has branched terminals in the antennal lobe and elsewhere (generally the protocerebrum).",
"Relationships": "[is a](is_a): [adult antennal lobe neuron](FBbt_00007363), [adult projection neuron](FBbt_00007353); [synonyms](has_exact_synonym): olfactory projection neuron, antennal lobe projection neuron, AL projection neuron, secondary olfactory neuron, ALPN",
"Classification": "[adult neuron](FBbt_00005106) > [adult intrinsic neuron](FBbt_00005116) > [adult central nervous system neuron](FBbt_00005125) > [adult cerebrum neuron](FBbt_00047698) > [adult antennal lobe neuron](FBbt_00007363) > adult antennal lobe projection neuron",
"Types": "[adult antennal lobe neuron](FBbt_00007363); [adult projection neuron](FBbt_00007353)"
},
"Tags": ["Adult", "Nervous_system", "Neuron"],
"Queries": [
{
"query": "ClassifiedAs",
"label": "Find instances of adult antennal lobe projection neuron",
"function": "get_instances",
"takes": {
"short_form": {"$and": ["Class"]},
"default": {"short_form": "FBbt_00007354"}
},
"preview": 5,
"preview_columns": ["id", "name", "driver", "thumbnail"],
"preview_results": {
"headers": {
"id": {"title": "Add", "type": "selection_id", "order": -1},
"name": {"title": "Name", "type": "markdown", "order": 1, "sort": {"0": "Asc"}},
"driver": {"title": "Driver", "type": "markdown", "order": 2},
"thumbnail": {"title": "Thumbnail", "type": "markdown", "order": 9}
},
"rows": []
},
"output_format": "table",
"count": 387
}
],
"IsIndividual": false,
"IsClass": true,
"Examples": {
"VFB_00017894": [
{
"id": "VFB_jrchc2b",
"label": "PN v-L-Ad3",
"thumbnail": "https://www.virtualflybrain.org/data/VFB/i/00jc/hc2b/VFB_jrchc2b/thumbnail.png",
"type_label": "adult antennal lobe projection neuron",
"type_id": "FBbt_00007354"
}
]
},
"Synonyms": [
{
"label": "olfactory projection neuron",
"scope": "exact",
"type": "synonym"
},
{
"label": "antennal lobe projection neuron",
"scope": "exact",
"type": "synonym"
},
{
"label": "AL projection neuron",
"scope": "exact",
"type": "synonym"
},
{
"label": "secondary olfactory neuron",
"scope": "exact",
"type": "synonym"
},
{
"label": "ALPN",
"scope": "exact",
"type": "synonym"
}
]
}{
"Name": "Chiang et al., 2011",
"Id": "FBrf0213510",
"SuperTypes": ["Entity", "Publication"],
"Meta": {
"Name": "[Chiang et al., 2011](FBrf0213510)",
"Description": "Chiang AS, Lin CY, Chuang CC, Chang HM, Hsieh CH, Yeh CW, Shih CT, Wu JJ, Wang GT, Chen YC et al. 2011. Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr. Biol. 21(1):1--11.",
"Cross References": "[PubMed](https://www.ncbi.nlm.nih.gov/pubmed/): [21129968](http://www.ncbi.nlm.nih.gov/pubmed/?term=21129968); [FlyBase](http://flybase.org/): [FBrf0213510](http://flybase.org/reports/FBrf0213510); [DOI](https://doi.org/): [10.1016/j.cub.2010.11.056](https://doi.org/10.1016/j.cub.2010.11.056)"
},
"IsIndividual": true,
"IsClass": false,
"IsTemplate": false,
"Publications": [
{
"title": "Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution",
"short_form": "FBrf0213510",
"microref": "Chiang et al., 2011",
"refs": [
"http://www.ncbi.nlm.nih.gov/pubmed/?term=21129968",
"http://flybase.org/reports/FBrf0213510",
"https://doi.org/10.1016/j.cub.2010.11.056"
]
}
]
}