Graph Handling
BioCypher Node
Handoff class to represent biomedical entities as Neo4j nodes.
Has id, label, property dict; id and label (in the Neo4j sense of a label, ie, the entity descriptor after the colon, such as ":Protein") are non-optional and called node_id and node_label to avoid confusion with "label" properties. Node labels are written in PascalCase and as nouns, as per Neo4j consensus.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
node_id
|
string
|
consensus "best" id for biological entity |
required |
node_label
|
string
|
primary type of entity, capitalised |
required |
**properties
|
kwargs
|
collection of all other properties to be passed to neo4j for the respective node (dict) |
dict()
|
Todo
- check and correct small inconsistencies such as capitalisation of ID names ("uniprot" vs "UniProt")
- check for correct ID patterns (eg "ENSG" + string of numbers, uniprot length)
- ID conversion using pypath translation facilities for now
Source code in biocypher/_create.py
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 |
|
__post_init__()
Add id field to properties.
Check for reserved keywords.
Replace unwanted characters in properties.
Source code in biocypher/_create.py
get_dict()
Return dict of id, labels, and properties.
Returns:
Name | Type | Description |
---|---|---|
dict |
dict
|
node_id and node_label as top-level key-value pairs, |
dict
|
properties as second-level dict. |
Source code in biocypher/_create.py
get_id()
get_label()
get_preferred_id()
get_properties()
Returns all other node properties apart from primary id and label as key-value pairs.
Returns:
Name | Type | Description |
---|---|---|
dict |
dict
|
properties |
BioCypher Edge
Handoff class to represent biomedical relationships in Neo4j.
Has source and target ids, label, property dict; ids and label (in the Neo4j sense of a label, ie, the entity descriptor after the colon, such as ":TARGETS") are non-optional and called source_id, target_id, and relationship_label to avoid confusion with properties called "label", which usually denotes the human-readable form. Relationship labels are written in UPPERCASE and as verbs, as per Neo4j consensus.
Args:
source_id (string): consensus "best" id for biological entity
target_id (string): consensus "best" id for biological entity
relationship_label (string): type of interaction, UPPERCASE
properties (dict): collection of all other properties of the
respective edge
Source code in biocypher/_create.py
165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 |
|
__post_init__()
Check for reserved keywords.
Source code in biocypher/_create.py
get_dict()
Return dict of ids, label, and properties.
Returns:
Name | Type | Description |
---|---|---|
dict |
dict
|
source_id, target_id and relationship_label as top-level key-value pairs, properties as second-level dict. |
Source code in biocypher/_create.py
get_id()
Returns primary node identifier or None.
Returns:
Name | Type | Description |
---|---|---|
str |
Union[str, None]
|
node_id |
get_label()
get_properties()
Returns all other relationship properties apart from primary ids and label as key-value pairs.
Returns:
Name | Type | Description |
---|---|---|
dict |
dict
|
properties |
get_source_id()
Returns primary node identifier of relationship source.
Returns:
Name | Type | Description |
---|---|---|
str |
str
|
source_id |
get_target_id()
Returns primary node identifier of relationship target.
Returns:
Name | Type | Description |
---|---|---|
str |
str
|
target_id |
BioCypher RelAsNode
Class to represent relationships as nodes (with in- and outgoing edges) as a triplet of a BioCypherNode and two BioCypherEdges. Main usage in type checking (instances where the receiving function needs to check whether it receives a relationship as a single edge or as a triplet).
Args:
node (BioCypherNode): node representing the relationship
source_edge (BioCypherEdge): edge representing the source of the
relationship
target_edge (BioCypherEdge): edge representing the target of the
relationship