-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathexperiment_valid-1.json
216 lines (216 loc) · 7.98 KB
/
experiment_valid-1.json
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
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
{
"data": {
"assayTechnology": {
"assayInstrument": "array",
"assayInstrumentPlatform": "[HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]"
},
"assayType": {
"termId": "EFO:0002764",
"termLabel": "ChIP-chip by SNP array"
},
"assayedBiologicalMacromolecule": {
"termId": "EFO:0008479",
"termLabel": "genomic DNA"
},
"experimentAttributes": [
{
"tag": "sub_project",
"value": "CB4-1UD"
},
{
"tag": "experiments_budget",
"units": "GBP",
"value": 20500
}
],
"experimentRelationships": [
{
"rSource": {
"objectId": {
"egaAccession": "EGAS00002045411"
},
"objectType": "study"
},
"rType": "referencedBy"
},
{
"rTarget": {
"objectId": {
"egaAccession": "EGAZ00001051423"
},
"objectType": "analysis"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"alias": "Patient's blood collection protocol",
"egaAccession": "EGAO00001031671"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"alias": "Extraction of the RNA",
"egaAccession": "EGAO00001031672"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rLabel": "Differed from the general protocol by using parameters X and Y with values ...",
"rSource": {
"objectId": {
"alias": "Protocol to label extracted RNA",
"egaAccession": "EGAO00001031673"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"alias": "Hibridization of the RNA to the array",
"egaAccession": "EGAO00001031674"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"alias": "Scanning of the array",
"egaAccession": "EGAO00001031675"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"alias": "Normalization of the data",
"egaAccession": "EGAO00001031676"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"egaAccession": "EGAB00002045411"
},
"objectType": "submission"
},
"rType": "referencedBy"
}
],
"experimentTypeSpecifications": {
"arrayExperiment": {
"adfFiles": [
{
"checksumMethod": "MD5",
"encryptedChecksum": "c6779ec2960296ed9a04f08d67f64423",
"filename": "myADF-file.xlsx",
"filetype": "XLSX",
"unencryptedChecksum": "c6779ec2960296ed9a04f08d67f64423"
}
],
"arrayLabels": [
{
"arrayLabelIdentifier": {
"termId": "CHEBI:15956",
"termLabel": "Biotin"
}
},
{
"arrayLabelIdentifier": {
"termId": "CHEBI:37987",
"termLabel": "Cy3 dye"
},
"arrayLabelDescription": "This label was use to dye the control samples"
}
]
}
},
"objectDescription": "Example array experiment's description of my experiment N13.",
"objectId": {
"alias": "My_ChIP_arrayExperiment_13",
"centerName": "EBI-TEST"
},
"objectTitle": "Example array experiment title",
"schemaDescriptor": {
"commonSchemaVersion": "0.0.0",
"describedBySchemaUri": "https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.experiment.json",
"objectSchemaVersion": "0.0.0",
"objectType": "experiment"
},
"targetedLoci": [
{
"lociDescriptor": [
{
"geneDescriptor": {
"geneIdentifier": {
"termId": "HGNC:11998",
"termLabel": "TP53"
}
},
"locusAdditionalDescription": "The locus of TP53 within the array corresponds to a variant version of the defined gene, only existing in patients with the pulmonary disease."
},
{
"genomicSequenceDescriptor": {
"assemblyDescriptor": {
"ncbiAssembly": {
"termId": "assembly:GCA_000001405.29",
"termLabel": "GRCh38.p14"
},
"ncbiAssemblyUnit": {
"termId": "refseq:NC_000017.11",
"termLabel": "chr17"
}
},
"dnaSequenceStrand": "forward",
"nucleicAcidSequence": "CTTGTTCAGTG",
"sequenceCoordinates": {
"sequenceInterval": {
"end": 7669460,
"start": 7669450
}
}
}
},
{
"locusAdditionalDescription": "Additional locus that was placed in the array for SNP scanning for the purpose of individuals identification as tags...",
"locusExternalReference": {
"objectExternalAccessionIdentifier": {
"termLabel": "EST89992 Human Small intestine Homo sapiens cDNA 5' end",
"termId": "nucleotide:T35715.1"
}
}
}
],
"organismDescriptor": {
"organismTaxon": {
"termId": "NCBITaxon:9606",
"termLabel": "homo sapiens"
},
"commonName": "human"
}
}
],
"typesOfOutputData": [
"genomic data"
]
},
"schema": {
"$ref": "https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.experiment.json"
}
}