phenopackets 0.2.2-post2

Rust bindings for Phenopacket Schema
Documentation 
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

// This file is @generated by prost-build.

#[cfg(feature = "serde")]
use serde::{Deserialize, Serialize};

/// An anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses.
///
/// This is a bundle of high-level concepts with no specifically defined relational concepts. It is expected that the
/// resources sharing the phenopackets will define and enforce their own semantics and level of requirements for included
/// fields.
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct Phenopacket {
    /// An identifier specific for this phenopacket.
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub id: ::prost::alloc::string::String,
    /// The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
    #[prost(message, optional, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub subject:
        ::core::option::Option<crate::generated::org_phenopackets_schema_v2_core::Individual>,
    /// Phenotypic features relating to the subject of the phenopacket
    #[prost(message, repeated, tag = "3")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub phenotypic_features: ::prost::alloc::vec::Vec<
        crate::generated::org_phenopackets_schema_v2_core::PhenotypicFeature,
    >,
    /// Quantifiable measurements related to the individual
    #[prost(message, repeated, tag = "4")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub measurements:
        ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::Measurement>,
    /// Biosample(s) derived from the patient or a collection of biosamples in isolation
    #[prost(message, repeated, tag = "5")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub biosamples:
        ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::Biosample>,
    #[prost(message, repeated, tag = "6")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub interpretations:
        ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::Interpretation>,
    /// Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The
    /// resources using these fields should define what this represents in their context.
    #[prost(message, repeated, tag = "7")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub diseases:
        ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::Disease>,
    #[prost(message, repeated, tag = "9")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub medical_actions:
        ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::MedicalAction>,
    /// Pointer to the relevant file(s) for the individual
    #[prost(message, repeated, tag = "10")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub files: ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::File>,
    /// Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
    #[prost(message, optional, tag = "11")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub meta_data:
        ::core::option::Option<crate::generated::org_phenopackets_schema_v2_core::MetaData>,
}
/// Phenotype, sample and pedigree data required for a genomic diagnosis.
/// Equivalent to the Genomics England InterpretationRequestRD
/// <https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl>
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct Family {
    /// An identifier specific for this family.
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub id: ::prost::alloc::string::String,
    /// The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
    #[prost(message, optional, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub proband: ::core::option::Option<Phenopacket>,
    /// Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
    /// be members of a cohort. If this field is used, then  it is expected that a pedigree will be included for
    /// genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
    /// describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
    /// the cohort.
    #[prost(message, repeated, tag = "3")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub relatives: ::prost::alloc::vec::Vec<Phenopacket>,
    /// flag to indicate that the parents of the proband are consanguinous
    #[prost(bool, tag = "7")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "std::ops::Not::not", default)
    )]
    pub consanguinous_parents: bool,
    /// The pedigree defining the relations between the proband and their relatives. Pedigree.individual_id should
    /// map to the PhenoPacket.Individual.id
    #[prost(message, optional, tag = "4")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub pedigree:
        ::core::option::Option<crate::generated::org_phenopackets_schema_v2_core::Pedigree>,
    /// Pointer to the relevant file(s) for the family. These should be files relating to one or more of the family
    /// members e.g a multi-sample VCF. Files relating exclusively to individual phenopackets should be contained in the
    /// Phenopacket.
    #[prost(message, repeated, tag = "5")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub files: ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::File>,
    /// Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
    #[prost(message, optional, tag = "6")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub meta_data:
        ::core::option::Option<crate::generated::org_phenopackets_schema_v2_core::MetaData>,
}
/// A group of individuals related in some phenotypic or genotypic aspect.
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct Cohort {
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub id: ::prost::alloc::string::String,
    #[prost(string, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub description: ::prost::alloc::string::String,
    #[prost(message, repeated, tag = "3")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub members: ::prost::alloc::vec::Vec<Phenopacket>,
    /// Pointer to relevant file(s) for the cohort. Files relating exclusively to individual phenopackets should be
    /// contained in the Phenopacket.
    #[prost(message, repeated, tag = "4")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub files: ::prost::alloc::vec::Vec<crate::generated::org_phenopackets_schema_v2_core::File>,
    /// Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
    #[prost(message, optional, tag = "5")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub meta_data:
        ::core::option::Option<crate::generated::org_phenopackets_schema_v2_core::MetaData>,
}