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corrected BEL schema, details follow
- moved evidence inside definitions section - moved edge inside graph/properties - fixed evidence JSON pointer in edge metadata - fixed citation/type string enumeration - added BEL test to validate child schema and an example BEL network
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Lines changed: 580 additions & 78 deletions

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‎.build/test/test-bel.rb‎

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require 'json'
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require 'json-schema'
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require 'pathname'
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require 'pp'
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require 'minitest/autorun'
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require 'minitest/unit'
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class ExtTest < Minitest::Test
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def test_validate_schema
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root = Pathname(File.dirname(File.expand_path __FILE__)) + '..' + '..' + 'child-schemas'
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schema = JSON.parse File.read(root + 'bel-json-graph.schema.json')
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errors = JSON::Validator.fully_validate_schema(schema)
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assert errors.empty?, errors.join("\n")
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root = Pathname(File.dirname(File.expand_path __FILE__)) + '..' + '..'
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data = JSON.parse File.open(root + 'examples' + 'test.network.json', 'r:UTF-8', &:read)
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errors = JSON::Validator.fully_validate(schema, data, :insert_defaults => true, :errors_as_objects => true)
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if ENV['JGS_VERBOSE']
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puts "\n\nValidated JSON for example: examples/test.network.json"
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pp data
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end
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assert errors.empty?, errors.join("\n")
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end
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end
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# vim: ts=2 sts=2 sw=2

‎child-schemas/bel-json-graph.schema.json‎

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{
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"$schema": "http://json-schema.org/draft-04/schema",
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"oneOf": [{
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"type": "object",
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"properties": {
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"graph": {
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"$ref": "#/definitions/graph"
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}
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},
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"additionalProperties": false,
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"required": ["graph"]
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}, {
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"type": "object",
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"properties": {
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"label": {
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"type": "string",
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"title": "Graph Set Label",
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"description": "Graph Set label",
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"name": "graph_set_label"
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},
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"type": {
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"type": "string",
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"title": "Type of Graphs in Set",
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"description": "Graph types in graph set",
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"name": "graph_set_type"
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},
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"metadata": {
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"type": ["object", "null"],
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"title": "Graph Set Metadata",
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"description": "Graph set metadata",
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"name": "graph_set_metadata"
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},
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"graphs": {
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"type": "array",
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"items": {
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"description": "Graph data description. Please note that all field keys are to be lowercase and use snake-case (e.g. words are separated by underscores like ncbi_tax_id). Some of the metadata fields are not required but are included as exemplars for generating interoperable BEL JGF files. You may need to provide additional validation programmatically to confirm that the metadata you need for your application exists.",
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"oneOf": [
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{
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"type": "object",
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"properties": {
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"graph": {
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"$ref": "#/definitions/graph"
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}
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}
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},
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"additionalProperties": false,
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"required": [
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"graph"
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]
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},
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"additionalProperties": false
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}],
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{
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"type": "object",
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"properties": {
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"label": {
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"type": "string",
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"title": "Graph Set Label",
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"description": "Graph Set label"
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},
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"type": {
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"type": "string",
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"title": "Type of Graphs in Set",
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"description": "Graph types in graph set"
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},
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"metadata": {
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"type": [
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"object",
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"null"
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],
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"title": "Graph Set Metadata",
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"description": "Graph set metadata"
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},
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"graphs": {
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"type": "array",
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"items": {
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"$ref": "#/definitions/graph"
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}
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}
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},
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"additionalProperties": false
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}
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],
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"definitions": {
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"graph": {
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"type": "object",
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"additionalProperties": false,
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"title": "Graph or Network data",
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"properties": {
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"label": {
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"type": "string",
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"title": "Graph Label",
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"description": "Graph label",
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"name": "graph_label"
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"description": "Graph label"
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},
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"directed": {
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"type": ["boolean", "null"],
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"type": [
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"boolean",
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"null"
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],
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"description": "Directed or undirected graph",
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"default": true
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},
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"type": {
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"type": "string",
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"title": "Type of Graph",
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"description": "Graph type",
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"name": "graph_type"
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"description": "BEL Versioned Graph type"
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},
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"metadata": {
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"type": ["object", "null"],
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"type": [
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"object",
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"null"
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],
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"additionalProperties": true,
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"properties": {
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"ncbi_tax_id": {
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"type": "integer",
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"title": "NCBI Taxonomy ID - ",
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"title": "NCBI Taxonomy ID",
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"description": "NCBI Taxonomy ID - http://www.ncbi.nlm.nih.gov/taxonomy"
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},
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"species_common_name": {
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"type": "string",
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"title": "Graph description",
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"description": "Graph description"
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},
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"version": {
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"type": "string",
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"description": "Version of the graph"
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}
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}
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},
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"nodes": {
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"type": ["array", "null"],
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"type": [
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"array",
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"null"
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],
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"items": {
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"type": "object",
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"additionalProperties": false,
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"type": "string"
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},
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"metadata": {
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"type": ["object", "null"],
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"type": [
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"object",
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"null"
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],
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"additionalProperties": true,
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"properties": {
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"x": {
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"type": "number",
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"title": "X coordinate",
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"description": "x coordinate of node location"
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},
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"y": {
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"type": "number",
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"title": "Y coordinate",
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"description": "y coordinate of node location"
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"coordinate": {
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"type": "array",
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"items": {
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"type": "number"
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},
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"minItems": 2,
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"title": "Node coordinates",
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"description": "Node coordinates as either an (x, y) or (x, y, z) tuple, the tuple is unbounded to allow additional dimensions to be used in addition to x, y and z coordinates"
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},
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"z": {
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"type": "number",
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"title": "Z coordinate",
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"description": "z coordinate of node location - not needed for 2D visualizations"
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"bel_function_type": {
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"type": "string",
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"description": "BEL function types such as proteinAbundance, trancriptionalActivity, etc"
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}
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}
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}
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},
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"required": ["id"]
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}
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}
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},
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"required": [
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"id"
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]
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},
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"edges": {
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"type": ["array", "null"],
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"type": [
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"array",
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"null"
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],
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"items": {
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"type": "object",
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"additionalProperties": false,
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"properties": {
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"id": {
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"type": "string"
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},
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"source": {
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"type": "string",
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"title": "Source Node",
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"description": "Relationship between nodes in edge - may be directed or undirected"
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},
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"directed": {
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"type": ["boolean", "null"],
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"type": [
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"boolean",
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"null"
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],
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"default": true
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},
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"label": {
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"type": "string"
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},
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"metadata": {
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"type": ["object", "null"],
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"type": [
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"object",
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"null"
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],
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"additionalProperties": true,
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"properties": {
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"causal": {
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"type": "boolean",
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"description": "True if a BEL causal edge type"
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},
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"evidences": {
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"type": "array",
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"items": {
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}
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}
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},
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"required": ["source", "target"]
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"required": [
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"source",
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"target"
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]
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}
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}
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}
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},
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"evidence": {
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"type": "object",
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"required": [
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"bel_statement",
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"citation"
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],
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"properties": {
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"bel_statement": {
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"type": "string",
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"citation": {
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"type": "object",
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"properties": {
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"reference_type": {
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"type": {
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"type": "string",
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"title": "Reference Type",
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"description": "The reference type of this citation."
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"enum": [
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"PubMed",
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"Book",
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"Journal",
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"Online Resource",
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"Other"
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],
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"title": "Citation Type",
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"description": "The citation type"
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},
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"reference_id": {
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"id": {
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"type": "string",
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"title": "Reference ID",
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"description": "Identifier of the reference, e.g. PubMed ID"
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"title": "Citation ID",
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"description": "Identifier of the citation, e.g. PubMed ID"
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},
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"name": {
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"type": "string",
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"title": "Reference Name",
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"description": "Name or citation string for the citation."
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"title": "Citation Name",
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"description": "Name or citation string for the reference."
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}
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},
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"title": "Citation for Edge Evidence",
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"description": "Reference to support the evidence presented for the Edge"
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"description": "Citation to support the evidence presented for the Edge"
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},
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"biological_context": {
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"type": "object",

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