rna-interaction-format/rna-interaction-schema_v1.json at main · RNABioInfo/rna-interaction-format · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
{
	"$schema": "https://json-schema.org/draft/2020-12/schema",
	"$id": "https://raw.githubusercontent.com/RNABioInfo/rna-interaction-specification/rna-interaction-schema_v1.json",
	"title": "RNA-RNA/Protein Interaction Format",
	"description": "The RNA Interaction Format (RIF) is focused on capturing RNA interactions in a convenient to use format.",
	"type": "array",
	"minItems": 1,
	"uniqueItems": true,
	"items": {
		"type": "object",
		"properties": {
			"ID": {
				"description": "The unique identifier for an interaction",
				"type": "string"
			},
            "version": {
                "description": "The file version of RIF. Currently only RIFv1.0 allowed",
                "type": "string",
                "pattern": "^RIFv1.0$"
            },
			"class": {
                "description": "The class of the described interaction",
				"enum": ["RNA-RNA", "RNA-Protein", "RNA-RNA-Protein"]
			},
			"type": {
                "description": "The type of interaction, i.e. molecular mechanism",
				"type": "string"
			},
			"evidence": {
				"description": "Evidence that supports the interaction",
				"type": "array",
				"minItems": 1,
				"uniqueItems": true,
				"items": {
					"type": "object",
					"properties": {
						"type": {
							"description": "Type of evidence (e.g., prediction, experimental)",
							"type": "string"
						},
						"method": {
							"description": "Tools or laboratory techniques used",
							"type": "string"
						},
						"command": {
							"description": "Command of the computational method",
							"type": "string"
						},
						"data": {
                            "description": "Data that supports the interaction",
                            "type": "object",
                            "additionalProperties": {
                                "oneOf": [
                                    {
                                        "type": "object",
                                        "additionalProperties": {
                                            "not": { "type": "object" }
                                        }
                                    },
                                    {
                                        "not": { "type": "object" }
                                    }
                                ]
                            }
						}
					},
                    "additionalProperties": false,
					"required": ["type", "method", "data"]
				}
			},
			"partners": {
                "description": "RNA/Proteins involved in the interaction",
				"type": "array",
				"items": {
					"type": "object",
					"properties": {
						"name": {
							"description": "Description of the RNA/Protein",
							"type": "string"
						},
						"symbol": {
							"description": "Scientific naming of the RNA/protein",
							"type": "string"
						},
						"type": {
							"description": "Type of the of the RNA/Protein. Should match entry in sequence ontology",
							"type": "string"
						},
						"sequence_type": {
							"description": "Type of sequence which can be either DNA, RNA or Protein",
							"enum": ["dna","rna","protein"]
						},
						"genomic_coordinates": {
							"description": "chromosome, strand and genomic coordinates of the RNA/Protein",
							"type": "string",
                            "pattern": "[a-zA-Z0-9]+:[+-]:[0-9]+-[0-9]+"
						},
						"organism_name": {
							"description": "Name of the organism",
							"type": "string"
						},
                        "organism_acc": {
							"description": "Unique accession id of the organism",
							"type": "string"
                        },
						"local_sites": {
                            "description": "Interaction sites of the organism",
							"type": "object",
                            "patternProperties": {
								"^.*$": {
                                    "type": "array",
                                    "items": {
                                        "type": "array",
                                        "minItems": 2,
                                        "maxItems": 2,
                                        "items": {
                                            "type": "number"
                                        }
                                    }
                                }
                            }
						},
						"info": {
                            "description": "Optional properties of the interaction partner",
							"type": "object",
                            "properties": {
                                "description": {
                                    "description": "Details on the function of gene/transcript/protein",
                                    "type": "string"
                                },
                                "sequence": {
                                    "description": "Sequence of the gene/transcript/protein as specified in genomic coordinates",
                                    "type": "string",
                                    "pattern": "^([ATGC]*|[ARNDCQEGHILKMFPSTWYV]*)$"
                                },
                                "structure": {
                                    "description": "Representation of the RNA secondary structure in dot-bracket notation",
                                    "type": "string",
                                    "pattern": "^[.()]*$"
                                },
                                "note": {
                                    "description": "Arbitrary information",
                                    "type": "string"
                                }
                            },
                            "additionalProperties": true
						},
						"custom": {
							"type": "object"
						}
					},
                    "additionalProperties": false,
					"required": ["name", "type", "local_sites"]
				}
			}
		},
        "additionalProperties": false,
		"required": ["ID", "version", "class", "type", "evidence", "partners"]
	}
}