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
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
|
$base: http://biohackathon.org/bh20-seq-schema
$namespaces:
sch: https://schema.org/
efo: http://www.ebi.ac.uk/efo/
obo: http://purl.obolibrary.org/obo/
sio: http://semanticscience.org/resource/
edam: http://edamontology.org/
evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
$graph:
- name: hostSchema
type: record
fields:
host_species:
doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens
type: string
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000532
_type: "@id"
noLinkCheck: true
host_id:
doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
host_sex:
doc: Sex of the host as defined in PATO, expect Male (http://purl.obolibrary.org/obo/PATO_0000384) or Female (http://purl.obolibrary.org/obo/PATO_0000383) or in Intersex (http://purl.obolibrary.org/obo/PATO_0001340)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
_type: "@id"
noLinkCheck: true
host_age:
doc: Age of the host as number (e.g. 50)
type: int?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000011
host_age_unit:
doc: Unit of host age e.g. http://purl.obolibrary.org/obo/UO_0000036
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42574
_type: "@id"
noLinkCheck: true
host_health_status:
doc: A condition or state at a particular time, must be one of the following (obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C25688
_type: "@id"
noLinkCheck: true
host_treatment:
doc: Process in which the act is intended to modify or alter host status
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000727
host_vaccination:
doc: List of vaccines given to the host
type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/VO_0000002
ethnicity:
doc: Ethinicity of the host e.g. http://purl.obolibrary.org/obo/HANCESTRO_0010
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001014
_type: "@id"
noLinkCheck: true
additional_host_information:
doc: Field for additional host information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- name: sampleSchema
type: record
fields:
sample_id:
doc: Unique sample identifier as defined by the submitter
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
collection_date:
doc: Date when the sample was taken
type: string
jsonldPredicate:
_id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
collection_location:
doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/GAZ_00000448
_type: "@id"
noLinkCheck: true
collector_name:
doc: Name of the person that took the sample
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001895
collecting_institution:
doc: Institute that was responsible for sampeling
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C41206
specimen_source:
doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155831 (=nasopharyngeal swab)
type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
_type: "@id"
noLinkCheck: true
sample_storage_conditions:
doc: Information about storage of a specified type, e.g. frozen specimen, paraffin, fresh ....
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001472
additional_collection_information:
doc: Add additional comment about the circumstances that a sample was taken
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
source_database_accession:
doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here. Please use a resolveable URL (e.g. http://identifiers.org/insdc/LC522350.1#sequence)
type: string[]?
jsonldPredicate:
_id: http://edamontology.org/data_2091
_type: "@id"
noLinkCheck: true
- name: virusSchema
type: record
fields:
virus_species:
doc: The name of virus species from the NCBI taxonomy database, e.g. http://purl.obolibrary.org/obo/NCBITaxon_2697049 for Severe acute respiratory syndrome coronavirus 2
type: string
jsonldPredicate:
_id: http://edamontology.org/data_1875
_type: "@id"
noLinkCheck: true
virus_strain:
doc: Name of the virus strain
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_010055
- name: technologySchema
type: record
fields:
sample_sequencing_technology:
doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
type: string[]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0600047
_type: "@id"
noLinkCheck: true
sequence_assembly_method:
doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0002699
sequencing_coverage:
doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
type: double[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
additional_technology_information:
doc: Field for additional technology information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- name: submitterSchema
type: record
fields:
authors:
doc: Name(s) of the author(s)
type: string[]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42781
submitter_name:
doc: Name of the submitter(s)
type: string[]?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000116
submitter_address:
doc: Address of the submitter
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000172
originating_lab:
doc: Name of the laboratory that took the sample
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C37984
lab_address:
doc: Address of the laboratory where the sample was taken
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C37900
provider_sample_id:
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0001741
submitter_sample_id:
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42781
publication:
doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C19026
submitter_orcid:
doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097
type: string[]?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
_type: "@id"
noLinkCheck: true
additional_submitter_information:
doc: Field for additional submitter information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- name: MainSchema
type: record
documentRoot: true
fields:
host: hostSchema
sample: sampleSchema
virus: virusSchema
technology: technologySchema
submitter: submitterSchema
id:
doc: The subject (eg the fasta/fastq file) that the metadata describes
type: string
jsonldPredicate:
_id: "@id"
_type: "@id"
noLinkCheck: true
|
