0
|
1 {
|
|
2 "software_result": {
|
|
3 "type": "software_result",
|
|
4 "key": "string*",
|
|
5 "software_name": "string*",
|
|
6 "software_version": "string*",
|
|
7 "software_branch": "string",
|
|
8 "software_commit": "string",
|
|
9 "software_log": "string",
|
|
10 "run_id": "string",
|
|
11 "run_date": "date",
|
|
12 "databases": "dict database:class",
|
|
13 "genes": "dict gene:class",
|
|
14 "seq_variations": "dict seq_variation:class",
|
|
15 "phenotypes": "dict phenotype:class"
|
|
16 },
|
|
17 "database": {
|
|
18 "type": "database",
|
|
19 "key": "string*",
|
|
20 "database_name": "string*",
|
|
21 "database_version": "string",
|
|
22 "database_branch": "string",
|
|
23 "database_commit": "string",
|
|
24 "checksum_sha256": "char64"
|
|
25 },
|
|
26 "gene": {
|
|
27 "type": "gene",
|
|
28 "key": "string*",
|
|
29 "name": "string*",
|
|
30 "identity": "percentage",
|
|
31 "alignment_length": "integer",
|
|
32 "ref_gene_lenght": "integer",
|
|
33 "coverage": "percentage",
|
|
34 "depth": "float",
|
|
35 "ref_id": "string*",
|
|
36 "ref_acc": "string",
|
|
37 "ref_start_pos": "integer",
|
|
38 "ref_end_pos": "integer",
|
|
39 "query_id": "string",
|
|
40 "query_start_pos": "integer",
|
|
41 "query_end_pos": "integer",
|
|
42 "phenotypes": "array phenotype.key",
|
|
43 "ref_database": "database.key"
|
|
44 },
|
|
45 "seq_region": {
|
|
46 "type": "seq_region",
|
|
47 "key": "string*",
|
|
48 "name": "string*",
|
|
49 "gene": "bool_or_unknown",
|
|
50 "identity": "percentage",
|
|
51 "alignment_length": "integer",
|
|
52 "ref_gene_lenght": "integer",
|
|
53 "coverage": "percentage",
|
|
54 "depth": "float",
|
|
55 "ref_id": "string*",
|
|
56 "ref_acc": "string",
|
|
57 "ref_start_pos": "integer",
|
|
58 "ref_end_pos": "integer",
|
|
59 "query_id": "string",
|
|
60 "query_start_pos": "integer",
|
|
61 "query_end_pos": "integer",
|
|
62 "phenotypes": "array phenotype.key",
|
|
63 "ref_database": "database.key"
|
|
64 },
|
|
65 "seq_variation": {
|
|
66 "type": "seq_variation",
|
|
67 "key": "string*",
|
|
68 "ref_id": "string*",
|
|
69 "seq_var": "seq_var_string",
|
|
70 "codon_change": "codon_change_string",
|
|
71 "ref_codon": "nucleotides",
|
|
72 "var_codon": "nucleotides",
|
|
73 "ref_aa": "aminoacid_1_char",
|
|
74 "var_aa": "aminoacid_1_char",
|
|
75 "ref_start_pos": "integer",
|
|
76 "ref_end_pos": "integer",
|
|
77 "substitution": "bool",
|
|
78 "insertion": "bool",
|
|
79 "deletion": "bool",
|
|
80 "ref_database": "database.key",
|
|
81 "genes": "array gene.key",
|
|
82 "phenotypes": "array phenotype.key"
|
|
83 },
|
|
84 "phenotype": {
|
|
85 "type": "phenotype",
|
|
86 "key": "string*",
|
|
87 "category": "vocabulary*",
|
|
88 "amr_classes": "array vocabulary",
|
|
89 "amr_resistance": "vocabulary",
|
|
90 "amr_resistant": "bool_or_unknown",
|
|
91 "genes": "array gene.key",
|
|
92 "seq_variations": "array seq_variation.key",
|
|
93 "ref_database": "database.key"
|
|
94 }
|
|
95 }
|