Package Bio :: Package Phylo :: Module _cdao_owl
[hide private]
[frames] | no frames]

Source Code for Module Bio.Phylo._cdao_owl

   1  # Copyright (C) 2013 by Ben Morris (ben@bendmorris.com) 
   2  # This code is part of the Biopython distribution and governed by its 
   3  # license. Please see the LICENSE file that should have been included 
   4  # as part of this package. 
   5   
   6  import xml.etree.ElementTree as ET 
   7   
   8  cdao_namespaces = { 
   9                     'cdao': 'http://purl.obolibrary.org/obo/cdao.owl#', 
  10                     'obo': 'http://purl.obolibrary.org/obo/', 
  11                     } 
  12   
13 -def resolve_uri(s, namespaces=cdao_namespaces, cdao_to_obo=True, xml_style=False):
14 '''Converts prefixed URIs to full URIs. Optionally, converts CDAO 15 named identifiers to OBO numeric identifiers.''' 16 17 if cdao_to_obo and s.startswith('cdao:'): 18 return resolve_uri('obo:%s' % cdao_elements[s[5:]], namespaces, cdao_to_obo) 19 20 for prefix in namespaces: 21 if xml_style: 22 s = s.replace(prefix+':', '{%s}' % namespaces[prefix]) 23 else: 24 s = s.replace(prefix+':', namespaces[prefix]) 25 26 return s
27 28 29 cdao_owl = '''<?xml version="1.0"?> 30 31 32 <!DOCTYPE rdf:RDF [ 33 <!ENTITY owl "http://www.w3.org/2002/07/owl#" > 34 <!ENTITY obo "http://purl.obolibrary.org/obo/" > 35 <!ENTITY dc "http://purl.org/dc/elements/1.1/" > 36 <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > 37 <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > 38 <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > 39 ]> 40 41 42 <rdf:RDF xmlns="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#" 43 xml:base="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl" 44 xmlns:dc="http://purl.org/dc/elements/1.1/" 45 xmlns:obo="http://purl.obolibrary.org/obo/" 46 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 47 xmlns:owl="http://www.w3.org/2002/07/owl#" 48 xmlns:xsd="http://www.w3.org/2001/XMLSchema#" 49 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> 50 <owl:Ontology rdf:about="&obo;cdao.owl"> 51 <dc:coverage rdf:datatype="&xsd;string">Comparison of two or more biological entities of the same class when the similarities and differences of the entities are treated explicitly as the product of an evolutionary process of descent with modification.</dc:coverage> 52 <dc:description rdf:datatype="&xsd;string">The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called &#39;OTUs&#39; (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the &#39;character-state data model&#39;. For a given character, such as &#39;beak length&#39;, each OTU has a state, such as &#39;short&#39; or &#39;long&#39;. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.</dc:description> 53 <dc:creator xml:lang="en">CDAO Team</dc:creator> 54 <dc:title xml:lang="en">Comparative Data Analysis Ontology</dc:title> 55 <dc:subject xml:lang="en">comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics</dc:subject> 56 <dc:rights rdf:resource="http://creativecommons.org/publicdomain/zero/1.0/"/> 57 <owl:versionIRI rdf:resource="&obo;cdao/2012-06-06/cdao.owl"/> 58 <owl:imports rdf:resource="&obo;iao/ontology-metadata.owl"/> 59 </owl:Ontology> 60 61 62 63 <!-- 64 /////////////////////////////////////////////////////////////////////////////////////// 65 // 66 // Annotation properties 67 // 68 /////////////////////////////////////////////////////////////////////////////////////// 69 --> 70 71 <owl:AnnotationProperty rdf:about="&dc;creator"/> 72 <owl:AnnotationProperty rdf:about="&dc;subject"/> 73 <owl:AnnotationProperty rdf:about="&dc;description"/> 74 <owl:AnnotationProperty rdf:about="&dc;coverage"/> 75 <owl:AnnotationProperty rdf:about="&dc;language"/> 76 <owl:AnnotationProperty rdf:about="&dc;identifier"/> 77 <owl:AnnotationProperty rdf:about="&dc;date"/> 78 <owl:AnnotationProperty rdf:about="&dc;source"/> 79 <owl:AnnotationProperty rdf:about="&dc;title"/> 80 <owl:AnnotationProperty rdf:about="&dc;rights"/> 81 82 83 84 85 86 87 <!-- 88 /////////////////////////////////////////////////////////////////////////////////////// 89 // 90 // Object Properties 91 // 92 /////////////////////////////////////////////////////////////////////////////////////// 93 --> 94 95 96 97 98 <!-- http://purl.obolibrary.org/obo/CDAO_0000142 --> 99 100 <owl:ObjectProperty rdf:about="&obo;CDAO_0000142"> 101 <rdfs:label rdf:datatype="&xsd;string">has_Character</rdfs:label> 102 <dc:description rdf:datatype="&xsd;string">This property associates a character data matrix with a character (a column) represented in the matrix.</dc:description> 103 <rdfs:domain rdf:resource="&obo;CDAO_0000056"/> 104 <rdfs:range rdf:resource="&obo;CDAO_0000071"/> 105 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 106 </owl:ObjectProperty> 107 108 109 110 <!-- http://purl.obolibrary.org/obo/CDAO_0000143 --> 111 112 <owl:ObjectProperty rdf:about="&obo;CDAO_0000143"> 113 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Edge_as_Child</rdfs:label> 114 <dc:description>The property links a Node to the Edge it belongs to in the child position.</dc:description> 115 <rdfs:range rdf:resource="&obo;CDAO_0000139"/> 116 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 117 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000146"/> 118 <owl:inverseOf rdf:resource="&obo;CDAO_0000209"/> 119 </owl:ObjectProperty> 120 121 122 123 <!-- http://purl.obolibrary.org/obo/CDAO_0000144 --> 124 125 <owl:ObjectProperty rdf:about="&obo;CDAO_0000144"> 126 <rdf:type rdf:resource="&owl;TransitiveProperty"/> 127 <rdfs:label rdf:datatype="&xsd;string">has_Ancestor</rdfs:label> 128 <dc:description>The property links a node to any of the other nodes that are its ancestors in a rooted tree.</dc:description> 129 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 130 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 131 <owl:inverseOf rdf:resource="&obo;CDAO_0000174"/> 132 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 133 </owl:ObjectProperty> 134 135 136 137 <!-- http://purl.obolibrary.org/obo/CDAO_0000145 --> 138 139 <owl:ObjectProperty rdf:about="&obo;CDAO_0000145"> 140 <rdfs:label rdf:datatype="&xsd;string">has_Nucleotide_State</rdfs:label> 141 <dc:description rdf:datatype="&xsd;string">This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states.</dc:description> 142 <rdfs:domain rdf:resource="&obo;CDAO_0000002"/> 143 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 144 <rdfs:range> 145 <owl:Class> 146 <owl:unionOf rdf:parseType="Collection"> 147 <rdf:Description rdf:about="&obo;CDAO_0000015"/> 148 <rdf:Description rdf:about="&obo;CDAO_0000133"/> 149 </owl:unionOf> 150 </owl:Class> 151 </rdfs:range> 152 </owl:ObjectProperty> 153 154 155 156 <!-- http://purl.obolibrary.org/obo/CDAO_0000146 --> 157 158 <owl:ObjectProperty rdf:about="&obo;CDAO_0000146"> 159 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Edge</rdfs:label> 160 <dc:description>The property links a Node to one of the edges that are incident on such node.</dc:description> 161 <rdfs:range rdf:resource="&obo;CDAO_0000099"/> 162 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 163 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 164 </owl:ObjectProperty> 165 166 167 168 <!-- http://purl.obolibrary.org/obo/CDAO_0000147 --> 169 170 <owl:ObjectProperty rdf:about="&obo;CDAO_0000147"> 171 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Character_State_Data_Matrix</rdfs:label> 172 <rdfs:range rdf:resource="&obo;CDAO_0000056"/> 173 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 174 <rdfs:domain> 175 <owl:Class> 176 <owl:unionOf rdf:parseType="Collection"> 177 <rdf:Description rdf:about="&obo;CDAO_0000071"/> 178 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 179 </owl:unionOf> 180 </owl:Class> 181 </rdfs:domain> 182 </owl:ObjectProperty> 183 184 185 186 <!-- http://purl.obolibrary.org/obo/CDAO_0000148 --> 187 188 <owl:ObjectProperty rdf:about="&obo;CDAO_0000148"> 189 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 190 <rdfs:label rdf:datatype="&xsd;string">has_Root</rdfs:label> 191 <dc:description>The property links a rooted tree to the specific node that represents the unique root of the tree.</dc:description> 192 <rdfs:domain rdf:resource="&obo;CDAO_0000012"/> 193 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 194 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 195 </owl:ObjectProperty> 196 197 198 199 <!-- http://purl.obolibrary.org/obo/CDAO_0000149 --> 200 201 <owl:ObjectProperty rdf:about="&obo;CDAO_0000149"> 202 <rdfs:label rdf:datatype="&xsd;string">has_Child</rdfs:label> 203 <dc:description>The property links a node to a node that is an immediate descendant in the tree.</dc:description> 204 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 205 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 206 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000174"/> 207 <owl:inverseOf rdf:resource="&obo;CDAO_0000179"/> 208 <owl:propertyChainAxiom rdf:parseType="Collection"> 209 <rdf:Description rdf:about="&obo;CDAO_0000177"/> 210 <rdf:Description rdf:about="&obo;CDAO_0000209"/> 211 </owl:propertyChainAxiom> 212 </owl:ObjectProperty> 213 214 215 216 <!-- http://purl.obolibrary.org/obo/CDAO_0000150 --> 217 218 <owl:ObjectProperty rdf:about="&obo;CDAO_0000150"> 219 <rdfs:label rdf:datatype="&xsd;string">has_First_Coordinate_Item</rdfs:label> 220 <dc:description rdf:datatype="&xsd;string">The property that relates a coordinate list to the first item in the list.</dc:description> 221 <rdfs:domain rdf:resource="&obo;CDAO_0000092"/> 222 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 223 <rdfs:range> 224 <owl:Class> 225 <owl:unionOf rdf:parseType="Collection"> 226 <rdf:Description rdf:about="&obo;CDAO_0000003"/> 227 <rdf:Description rdf:about="&obo;CDAO_0000095"/> 228 </owl:unionOf> 229 </owl:Class> 230 </rdfs:range> 231 </owl:ObjectProperty> 232 233 234 235 <!-- http://purl.obolibrary.org/obo/CDAO_0000151 --> 236 237 <owl:ObjectProperty rdf:about="&obo;CDAO_0000151"> 238 <rdfs:label rdf:datatype="&xsd;string">has_Coordinate</rdfs:label> 239 <rdfs:range rdf:resource="&obo;CDAO_0000022"/> 240 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 241 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 242 </owl:ObjectProperty> 243 244 245 246 <!-- http://purl.obolibrary.org/obo/CDAO_0000152 --> 247 248 <owl:ObjectProperty rdf:about="&obo;CDAO_0000152"> 249 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 250 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Continuous_Character</rdfs:label> 251 <rdfs:domain rdf:resource="&obo;CDAO_0000019"/> 252 <rdfs:range rdf:resource="&obo;CDAO_0000068"/> 253 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 254 </owl:ObjectProperty> 255 256 257 258 <!-- http://purl.obolibrary.org/obo/CDAO_0000153 --> 259 260 <owl:ObjectProperty rdf:about="&obo;CDAO_0000153"> 261 <rdfs:label rdf:datatype="&xsd;string">has_Datum</rdfs:label> 262 <dc:description rdf:datatype="&xsd;string">This property relates a character to a state datum for the character.</dc:description> 263 <rdfs:range rdf:resource="&obo;CDAO_0000098"/> 264 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 265 <rdfs:domain> 266 <owl:Class> 267 <owl:unionOf rdf:parseType="Collection"> 268 <rdf:Description rdf:about="&obo;CDAO_0000071"/> 269 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 270 </owl:unionOf> 271 </owl:Class> 272 </rdfs:domain> 273 </owl:ObjectProperty> 274 275 276 277 <!-- http://purl.obolibrary.org/obo/CDAO_0000154 --> 278 279 <owl:ObjectProperty rdf:about="&obo;CDAO_0000154"> 280 <rdfs:label rdf:datatype="&xsd;string">has_Standard_Datum</rdfs:label> 281 <rdfs:range rdf:resource="&obo;CDAO_0000008"/> 282 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000183"/> 283 <rdfs:domain> 284 <owl:Class> 285 <owl:unionOf rdf:parseType="Collection"> 286 <rdf:Description rdf:about="&obo;CDAO_0000075"/> 287 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 288 </owl:unionOf> 289 </owl:Class> 290 </rdfs:domain> 291 </owl:ObjectProperty> 292 293 294 295 <!-- http://purl.obolibrary.org/obo/CDAO_0000155 --> 296 297 <owl:ObjectProperty rdf:about="&obo;CDAO_0000155"> 298 <rdfs:label rdf:datatype="&xsd;string">subtree_of</rdfs:label> 299 <dc:description>This property links two networks where the latter is a substructure of the former</dc:description> 300 <rdfs:range rdf:resource="&obo;CDAO_0000006"/> 301 <rdfs:domain rdf:resource="&obo;CDAO_0000006"/> 302 </owl:ObjectProperty> 303 304 305 306 <!-- http://purl.obolibrary.org/obo/CDAO_0000156 --> 307 308 <owl:ObjectProperty rdf:about="&obo;CDAO_0000156"> 309 <rdfs:label rdf:datatype="&xsd;string">has_Amino_Acid_State</rdfs:label> 310 <dc:description rdf:datatype="&xsd;string">This property associates a amino acid character-state instance with a state value from the domain of amino acid states.</dc:description> 311 <rdfs:domain rdf:resource="&obo;CDAO_0000112"/> 312 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 313 <rdfs:range> 314 <owl:Class> 315 <owl:unionOf rdf:parseType="Collection"> 316 <rdf:Description rdf:about="&obo;CDAO_0000015"/> 317 <rdf:Description rdf:about="&obo;CDAO_0000076"/> 318 </owl:unionOf> 319 </owl:Class> 320 </rdfs:range> 321 </owl:ObjectProperty> 322 323 324 325 <!-- http://purl.obolibrary.org/obo/CDAO_0000157 --> 326 327 <owl:ObjectProperty rdf:about="&obo;CDAO_0000157"> 328 <rdfs:label rdf:datatype="&xsd;string">is_annotation_of</rdfs:label> 329 <rdfs:domain rdf:resource="&obo;CDAO_0000040"/> 330 <rdfs:range rdf:resource="&owl;Thing"/> 331 </owl:ObjectProperty> 332 333 334 335 <!-- http://purl.obolibrary.org/obo/CDAO_0000158 --> 336 337 <owl:ObjectProperty rdf:about="&obo;CDAO_0000158"> 338 <rdfs:label rdf:datatype="&xsd;string">has_RNA_Datum</rdfs:label> 339 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000206"/> 340 </owl:ObjectProperty> 341 342 343 344 <!-- http://purl.obolibrary.org/obo/CDAO_0000159 --> 345 346 <owl:ObjectProperty rdf:about="&obo;CDAO_0000159"> 347 <rdfs:label rdf:datatype="&xsd;string">has_Left_State</rdfs:label> 348 <dc:description rdf:datatype="&xsd;string">This property relates a transformation to a &#39;left&#39; state (the state associated with the &#39;left&#39; node).</dc:description> 349 <rdfs:range rdf:resource="&obo;CDAO_0000091"/> 350 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 351 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 352 </owl:ObjectProperty> 353 354 355 356 <!-- http://purl.obolibrary.org/obo/CDAO_0000160 --> 357 358 <owl:ObjectProperty rdf:about="&obo;CDAO_0000160"> 359 <rdfs:label rdf:datatype="&xsd;string">precedes</rdfs:label> 360 </owl:ObjectProperty> 361 362 363 364 <!-- http://purl.obolibrary.org/obo/CDAO_0000161 --> 365 366 <owl:ObjectProperty rdf:about="&obo;CDAO_0000161"> 367 <rdfs:label rdf:datatype="&xsd;string">exclude</rdfs:label> 368 </owl:ObjectProperty> 369 370 371 372 <!-- http://purl.obolibrary.org/obo/CDAO_0000162 --> 373 374 <owl:ObjectProperty rdf:about="&obo;CDAO_0000162"> 375 <rdfs:label rdf:datatype="&xsd;string">has_Node</rdfs:label> 376 <dc:description>Property that associates to each Edge the Nodes it connects.</dc:description> 377 <rdfs:domain rdf:resource="&obo;CDAO_0000099"/> 378 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 379 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 380 </owl:ObjectProperty> 381 382 383 384 <!-- http://purl.obolibrary.org/obo/CDAO_0000163 --> 385 386 <owl:ObjectProperty rdf:about="&obo;CDAO_0000163"> 387 <rdfs:label rdf:datatype="&xsd;string">nca_node_of</rdfs:label> 388 <rdfs:range rdf:resource="&obo;CDAO_0000059"/> 389 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 390 </owl:ObjectProperty> 391 392 393 394 <!-- http://purl.obolibrary.org/obo/CDAO_0000164 --> 395 396 <owl:ObjectProperty rdf:about="&obo;CDAO_0000164"> 397 <rdfs:label rdf:datatype="&xsd;string">has_External_Reference</rdfs:label> 398 <rdfs:comment rdf:datatype="&rdfs;Literal">Associates a TU to some external taxonomy reference.</rdfs:comment> 399 <rdfs:domain rdf:resource="&obo;CDAO_0000138"/> 400 <rdfs:range rdf:resource="&owl;Thing"/> 401 </owl:ObjectProperty> 402 403 404 405 <!-- http://purl.obolibrary.org/obo/CDAO_0000165 --> 406 407 <owl:ObjectProperty rdf:about="&obo;CDAO_0000165"> 408 <rdfs:label rdf:datatype="&xsd;string">has_Coordinate_System</rdfs:label> 409 <dc:description rdf:datatype="&xsd;string">This property links a coordinate to the coordinate system it references.</dc:description> 410 <rdfs:domain rdf:resource="&obo;CDAO_0000022"/> 411 <rdfs:range rdf:resource="&obo;CDAO_0000104"/> 412 </owl:ObjectProperty> 413 414 415 416 <!-- http://purl.obolibrary.org/obo/CDAO_0000166 --> 417 418 <owl:ObjectProperty rdf:about="&obo;CDAO_0000166"> 419 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 420 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Nucleotide_Character</rdfs:label> 421 <rdfs:domain rdf:resource="&obo;CDAO_0000002"/> 422 <rdfs:range rdf:resource="&obo;CDAO_0000094"/> 423 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 424 </owl:ObjectProperty> 425 426 427 428 <!-- http://purl.obolibrary.org/obo/CDAO_0000167 --> 429 430 <owl:ObjectProperty rdf:about="&obo;CDAO_0000167"> 431 <rdf:type rdf:resource="&owl;SymmetricProperty"/> 432 <rdfs:label rdf:datatype="&xsd;string">connects_to</rdfs:label> 433 <owl:inverseOf rdf:resource="&obo;CDAO_0000167"/> 434 </owl:ObjectProperty> 435 436 437 438 <!-- http://purl.obolibrary.org/obo/CDAO_0000168 --> 439 440 <owl:ObjectProperty rdf:about="&obo;CDAO_0000168"> 441 <rdfs:label rdf:datatype="&xsd;string">has_Amino_Acid_Datum</rdfs:label> 442 <dc:description rdf:datatype="&xsd;string">This property relates an amino acid character (a column in a protein sequence alignment) to a state datum for the character (an individual cell in the alignment column).</dc:description> 443 <rdfs:range rdf:resource="&obo;CDAO_0000112"/> 444 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000206"/> 445 <rdfs:domain> 446 <owl:Class> 447 <owl:unionOf rdf:parseType="Collection"> 448 <rdf:Description rdf:about="&obo;CDAO_0000131"/> 449 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 450 </owl:unionOf> 451 </owl:Class> 452 </rdfs:domain> 453 </owl:ObjectProperty> 454 455 456 457 <!-- http://purl.obolibrary.org/obo/CDAO_0000169 --> 458 459 <owl:ObjectProperty rdf:about="&obo;CDAO_0000169"> 460 <rdfs:label rdf:datatype="&xsd;string">hereditary_change_of</rdfs:label> 461 <dc:description rdf:datatype="&xsd;string">This property relates a type of evolutionary change (an Edge_Transformation) to the character that undergoes the change. The change is a transformation_of the affected character.</dc:description> 462 <rdfs:range rdf:resource="&obo;CDAO_0000071"/> 463 </owl:ObjectProperty> 464 465 466 467 <!-- http://purl.obolibrary.org/obo/CDAO_0000170 --> 468 469 <owl:ObjectProperty rdf:about="&obo;CDAO_0000170"> 470 <rdfs:label rdf:datatype="&xsd;string">has_Compound_Datum</rdfs:label> 471 <dc:description rdf:datatype="&xsd;string">This property relates a compound character (a character with some states that are subdividable) to a state datum for the character.</dc:description> 472 <rdfs:range rdf:resource="&obo;CDAO_0000136"/> 473 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000183"/> 474 <rdfs:domain> 475 <owl:Class> 476 <owl:unionOf rdf:parseType="Collection"> 477 <rdf:Description rdf:about="&obo;CDAO_0000078"/> 478 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 479 </owl:unionOf> 480 </owl:Class> 481 </rdfs:domain> 482 </owl:ObjectProperty> 483 484 485 486 <!-- http://purl.obolibrary.org/obo/CDAO_0000171 --> 487 488 <owl:ObjectProperty rdf:about="&obo;CDAO_0000171"> 489 <rdfs:label rdf:datatype="&xsd;string">has_Descendants</rdfs:label> 490 <rdfs:range rdf:resource="&obo;CDAO_0000059"/> 491 <rdfs:domain rdf:resource="&obo;CDAO_0000080"/> 492 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 493 </owl:ObjectProperty> 494 495 496 497 <!-- http://purl.obolibrary.org/obo/CDAO_0000172 --> 498 499 <owl:ObjectProperty rdf:about="&obo;CDAO_0000172"> 500 <rdfs:label rdf:datatype="&xsd;string">reconciliation_of</rdfs:label> 501 <rdfs:domain rdf:resource="&obo;CDAO_0000030"/> 502 <rdfs:range rdf:resource="&obo;CDAO_0000110"/> 503 </owl:ObjectProperty> 504 505 506 507 <!-- http://purl.obolibrary.org/obo/CDAO_0000173 --> 508 509 <owl:ObjectProperty rdf:about="&obo;CDAO_0000173"> 510 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 511 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Amino_Acid_Character</rdfs:label> 512 <rdfs:domain rdf:resource="&obo;CDAO_0000112"/> 513 <rdfs:range rdf:resource="&obo;CDAO_0000131"/> 514 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 515 </owl:ObjectProperty> 516 517 518 519 <!-- http://purl.obolibrary.org/obo/CDAO_0000174 --> 520 521 <owl:ObjectProperty rdf:about="&obo;CDAO_0000174"> 522 <rdf:type rdf:resource="&owl;TransitiveProperty"/> 523 <rdfs:label rdf:datatype="&xsd;string">has_Descendant</rdfs:label> 524 <dc:description>A property that links a node to any of its descendants in a rooted tree.</dc:description> 525 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 526 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 527 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 528 </owl:ObjectProperty> 529 530 531 532 <!-- http://purl.obolibrary.org/obo/CDAO_0000175 --> 533 534 <owl:ObjectProperty rdf:about="&obo;CDAO_0000175"> 535 <rdfs:label rdf:datatype="&xsd;string">has_Continuous_State</rdfs:label> 536 <dc:description rdf:datatype="&xsd;string">This property associates a character-state instance with a state value on a continuous numeric scale.</dc:description> 537 <rdfs:domain rdf:resource="&obo;CDAO_0000019"/> 538 <rdfs:range rdf:resource="&obo;CDAO_0000031"/> 539 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 540 </owl:ObjectProperty> 541 542 543 544 <!-- http://purl.obolibrary.org/obo/CDAO_0000176 --> 545 546 <owl:ObjectProperty rdf:about="&obo;CDAO_0000176"> 547 <rdfs:label rdf:datatype="&xsd;string">has_Type</rdfs:label> 548 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 549 </owl:ObjectProperty> 550 551 552 553 <!-- http://purl.obolibrary.org/obo/CDAO_0000177 --> 554 555 <owl:ObjectProperty rdf:about="&obo;CDAO_0000177"> 556 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Edge_as_Parent</rdfs:label> 557 <dc:description>The property links a Node to one of the Edges where the node appears in the parent position (i.e., closer to the root).</dc:description> 558 <rdfs:range rdf:resource="&obo;CDAO_0000139"/> 559 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 560 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000146"/> 561 <owl:inverseOf rdf:resource="&obo;CDAO_0000201"/> 562 </owl:ObjectProperty> 563 564 565 566 <!-- http://purl.obolibrary.org/obo/CDAO_0000178 --> 567 568 <owl:ObjectProperty rdf:about="&obo;CDAO_0000178"> 569 <rdfs:label rdf:datatype="&xsd;string">has</rdfs:label> 570 <dc:description>Generic &#39;has&#39; property.</dc:description> 571 </owl:ObjectProperty> 572 573 574 575 <!-- http://purl.obolibrary.org/obo/CDAO_0000179 --> 576 577 <owl:ObjectProperty rdf:about="&obo;CDAO_0000179"> 578 <rdfs:label rdf:datatype="&xsd;string">has_Parent</rdfs:label> 579 <dc:description>The property that links a node to its unique parent in a rooted tree.</dc:description> 580 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 581 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 582 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000144"/> 583 <owl:propertyChainAxiom rdf:parseType="Collection"> 584 <rdf:Description rdf:about="&obo;CDAO_0000143"/> 585 <rdf:Description rdf:about="&obo;CDAO_0000201"/> 586 </owl:propertyChainAxiom> 587 </owl:ObjectProperty> 588 589 590 591 <!-- http://purl.obolibrary.org/obo/CDAO_0000180 --> 592 593 <owl:ObjectProperty rdf:about="&obo;CDAO_0000180"> 594 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Compound_Character</rdfs:label> 595 <rdfs:range rdf:resource="&obo;CDAO_0000078"/> 596 <rdfs:domain rdf:resource="&obo;CDAO_0000136"/> 597 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 598 </owl:ObjectProperty> 599 600 601 602 <!-- http://purl.obolibrary.org/obo/CDAO_0000181 --> 603 604 <owl:ObjectProperty rdf:about="&obo;CDAO_0000181"> 605 <rdfs:label rdf:datatype="&xsd;string">homologous_to</rdfs:label> 606 <dc:description rdf:datatype="&xsd;string">This propery relates different instances of the same character, including the case when the states of the character differ (e.g., large_beak of beak_size_character of TU A is homologous_to small_beak of beak_size_character of TU B).</dc:description> 607 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 608 <rdfs:range rdf:resource="&obo;CDAO_0000098"/> 609 </owl:ObjectProperty> 610 611 612 613 <!-- http://purl.obolibrary.org/obo/CDAO_0000182 --> 614 615 <owl:ObjectProperty rdf:about="&obo;CDAO_0000182"> 616 <rdfs:label rdf:datatype="&xsd;string">has_Change_Component</rdfs:label> 617 <dc:description rdf:datatype="&xsd;string">This property relates a transformation to the components that compose it.</dc:description> 618 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 619 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 620 </owl:ObjectProperty> 621 622 623 624 <!-- http://purl.obolibrary.org/obo/CDAO_0000183 --> 625 626 <owl:ObjectProperty rdf:about="&obo;CDAO_0000183"> 627 <rdfs:label rdf:datatype="&xsd;string">has_Categorical_Datum</rdfs:label> 628 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000153"/> 629 </owl:ObjectProperty> 630 631 632 633 <!-- http://purl.obolibrary.org/obo/CDAO_0000184 --> 634 635 <owl:ObjectProperty rdf:about="&obo;CDAO_0000184"> 636 <rdfs:label rdf:datatype="&xsd;string">has_State</rdfs:label> 637 <dc:description rdf:datatype="&xsd;string">This property associates a character-state instance with its state value, e.g., a state value expressed in terms of an imported domain ontology.</dc:description> 638 <rdfs:range rdf:resource="&obo;CDAO_0000091"/> 639 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 640 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 641 </owl:ObjectProperty> 642 643 644 645 <!-- http://purl.obolibrary.org/obo/CDAO_0000185 --> 646 647 <owl:ObjectProperty rdf:about="&obo;CDAO_0000185"> 648 <rdfs:label rdf:datatype="&xsd;string">has_Left_Node</rdfs:label> 649 <dc:description rdf:datatype="&xsd;string">This property relates a transformation to a &#39;left&#39; node (the node that has the &#39;left&#39; state).</dc:description> 650 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 651 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 652 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 653 </owl:ObjectProperty> 654 655 656 657 <!-- http://purl.obolibrary.org/obo/CDAO_0000186 --> 658 659 <owl:ObjectProperty rdf:about="&obo;CDAO_0000186"> 660 <rdfs:label rdf:datatype="&xsd;string">has_Right_State</rdfs:label> 661 <dc:description rdf:datatype="&xsd;string">This property relates a transformation to a &#39;right&#39; state (the state associated with the &#39;right&#39; node).</dc:description> 662 <rdfs:range rdf:resource="&obo;CDAO_0000091"/> 663 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 664 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 665 </owl:ObjectProperty> 666 667 668 669 <!-- http://purl.obolibrary.org/obo/CDAO_0000187 --> 670 671 <owl:ObjectProperty rdf:about="&obo;CDAO_0000187"> 672 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 673 <rdfs:label rdf:datatype="&xsd;string">represents_TU</rdfs:label> 674 <dc:description rdf:datatype="&xsd;string">This property relates a TU or taxonomic unit (typically associated with character data) to a phylogenetic history (Tree).</dc:description> 675 <rdfs:range rdf:resource="&obo;CDAO_0000138"/> 676 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 677 </owl:ObjectProperty> 678 679 680 681 <!-- http://purl.obolibrary.org/obo/CDAO_0000188 --> 682 683 <owl:ObjectProperty rdf:about="&obo;CDAO_0000188"> 684 <rdfs:label rdf:datatype="&xsd;string">exclude_Node</rdfs:label> 685 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 686 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000161"/> 687 </owl:ObjectProperty> 688 689 690 691 <!-- http://purl.obolibrary.org/obo/CDAO_0000189 --> 692 693 <owl:ObjectProperty rdf:about="&obo;CDAO_0000189"> 694 <rdfs:label rdf:datatype="&xsd;string">has_Compound_State</rdfs:label> 695 <dc:description rdf:datatype="&xsd;string">This property associates a compound character-state instance with its compound state value.</dc:description> 696 <rdfs:domain rdf:resource="&obo;CDAO_0000136"/> 697 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 698 <rdfs:range> 699 <owl:Class> 700 <owl:unionOf rdf:parseType="Collection"> 701 <rdf:Description rdf:about="&obo;CDAO_0000015"/> 702 <rdf:Description rdf:about="&obo;CDAO_0000055"/> 703 </owl:unionOf> 704 </owl:Class> 705 </rdfs:range> 706 </owl:ObjectProperty> 707 708 709 710 <!-- http://purl.obolibrary.org/obo/CDAO_0000190 --> 711 712 <owl:ObjectProperty rdf:about="&obo;CDAO_0000190"> 713 <rdfs:label rdf:datatype="&xsd;string">belongs_to</rdfs:label> 714 <dc:description>Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of.</dc:description> 715 <owl:equivalentProperty rdf:resource="&obo;CDAO_0000194"/> 716 <rdfs:range rdf:resource="&owl;Thing"/> 717 <rdfs:domain rdf:resource="&owl;Thing"/> 718 </owl:ObjectProperty> 719 720 721 722 <!-- http://purl.obolibrary.org/obo/CDAO_0000191 --> 723 724 <owl:ObjectProperty rdf:about="&obo;CDAO_0000191"> 725 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 726 <rdfs:label rdf:datatype="&xsd;string">belongs_to_TU</rdfs:label> 727 <dc:description rdf:datatype="&xsd;string">This property relates a character-state datum to its TU.</dc:description> 728 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 729 <rdfs:range rdf:resource="&obo;CDAO_0000138"/> 730 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 731 </owl:ObjectProperty> 732 733 734 735 <!-- http://purl.obolibrary.org/obo/CDAO_0000192 --> 736 737 <owl:ObjectProperty rdf:about="&obo;CDAO_0000192"> 738 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Network</rdfs:label> 739 <rdfs:range rdf:resource="&obo;CDAO_0000006"/> 740 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 741 <rdfs:domain> 742 <owl:Class> 743 <owl:unionOf rdf:parseType="Collection"> 744 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 745 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 746 </owl:unionOf> 747 </owl:Class> 748 </rdfs:domain> 749 </owl:ObjectProperty> 750 751 752 753 <!-- http://purl.obolibrary.org/obo/CDAO_0000193 --> 754 755 <owl:ObjectProperty rdf:about="&obo;CDAO_0000193"> 756 <rdfs:label rdf:datatype="&xsd;string">has_Annotation</rdfs:label> 757 <rdfs:range rdf:resource="&obo;CDAO_0000040"/> 758 <owl:inverseOf rdf:resource="&obo;CDAO_0000157"/> 759 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 760 <rdfs:domain rdf:resource="&owl;Thing"/> 761 </owl:ObjectProperty> 762 763 764 765 <!-- http://purl.obolibrary.org/obo/CDAO_0000194 --> 766 767 <owl:ObjectProperty rdf:about="&obo;CDAO_0000194"> 768 <rdfs:label rdf:datatype="&xsd;string">part_of</rdfs:label> 769 <owl:inverseOf rdf:resource="&obo;CDAO_0000178"/> 770 </owl:ObjectProperty> 771 772 773 774 <!-- http://purl.obolibrary.org/obo/CDAO_0000195 --> 775 776 <owl:ObjectProperty rdf:about="&obo;CDAO_0000195"> 777 <rdfs:label rdf:datatype="&xsd;string">has_Nucleotide_Datum</rdfs:label> 778 <dc:description rdf:datatype="&xsd;string">This property relates a nucleotide character (a column in a nucleotide alignment) to a state datum for the character (an individual cell in the alignment column).</dc:description> 779 <rdfs:range rdf:resource="&obo;CDAO_0000002"/> 780 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000206"/> 781 <rdfs:domain> 782 <owl:Class> 783 <owl:unionOf rdf:parseType="Collection"> 784 <rdf:Description rdf:about="&obo;CDAO_0000094"/> 785 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 786 </owl:unionOf> 787 </owl:Class> 788 </rdfs:domain> 789 </owl:ObjectProperty> 790 791 792 793 <!-- http://purl.obolibrary.org/obo/CDAO_0000196 --> 794 795 <owl:ObjectProperty rdf:about="&obo;CDAO_0000196"> 796 <rdfs:label rdf:datatype="&xsd;string">represented_by_Node</rdfs:label> 797 <dc:description rdf:datatype="&xsd;string">This property relates a TU to a node that represents it in a network.</dc:description> 798 <rdfs:domain rdf:resource="&obo;CDAO_0000138"/> 799 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 800 <owl:inverseOf rdf:resource="&obo;CDAO_0000187"/> 801 </owl:ObjectProperty> 802 803 804 805 <!-- http://purl.obolibrary.org/obo/CDAO_0000197 --> 806 807 <owl:ObjectProperty rdf:about="&obo;CDAO_0000197"> 808 <rdfs:label rdf:datatype="&xsd;string">has_Remaining_Coordinate_List</rdfs:label> 809 <dc:description rdf:datatype="&xsd;string">The property that relates a coordinate list to the item in the list beyond the first item.</dc:description> 810 <rdfs:range rdf:resource="&obo;CDAO_0000092"/> 811 <rdfs:domain rdf:resource="&obo;CDAO_0000092"/> 812 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 813 </owl:ObjectProperty> 814 815 816 817 <!-- http://purl.obolibrary.org/obo/CDAO_0000198 --> 818 819 <owl:ObjectProperty rdf:about="&obo;CDAO_0000198"> 820 <rdfs:label rdf:datatype="&xsd;string">has_Element</rdfs:label> 821 <rdfs:domain rdf:resource="&obo;CDAO_0000118"/> 822 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 823 </owl:ObjectProperty> 824 825 826 827 <!-- http://purl.obolibrary.org/obo/CDAO_0000199 --> 828 829 <owl:ObjectProperty rdf:about="&obo;CDAO_0000199"> 830 <rdfs:label rdf:datatype="&xsd;string">exclude_Subtree</rdfs:label> 831 <rdfs:range rdf:resource="&obo;CDAO_0000070"/> 832 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000161"/> 833 </owl:ObjectProperty> 834 835 836 837 <!-- http://purl.obolibrary.org/obo/CDAO_0000200 --> 838 839 <owl:ObjectProperty rdf:about="&obo;CDAO_0000200"> 840 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Tree</rdfs:label> 841 <rdfs:range rdf:resource="&obo;CDAO_0000110"/> 842 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 843 <rdfs:domain> 844 <owl:Class> 845 <owl:unionOf rdf:parseType="Collection"> 846 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 847 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 848 </owl:unionOf> 849 </owl:Class> 850 </rdfs:domain> 851 </owl:ObjectProperty> 852 853 854 855 <!-- http://purl.obolibrary.org/obo/CDAO_0000201 --> 856 857 <owl:ObjectProperty rdf:about="&obo;CDAO_0000201"> 858 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 859 <rdfs:label rdf:datatype="&xsd;string">has_Parent_Node</rdfs:label> 860 <dc:description>Associates to a Directed Edge the Node that is in the parent position in the edge (i.e., the node touched by the edge and closer to the root of the tree)</dc:description> 861 <rdfs:domain rdf:resource="&obo;CDAO_0000139"/> 862 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 863 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000162"/> 864 </owl:ObjectProperty> 865 866 867 868 <!-- http://purl.obolibrary.org/obo/CDAO_0000202 --> 869 870 <owl:ObjectProperty rdf:about="&obo;CDAO_0000202"> 871 <rdfs:label rdf:datatype="&xsd;string">has_Lineage_node</rdfs:label> 872 <rdfs:domain rdf:resource="&obo;CDAO_0000004"/> 873 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 874 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 875 </owl:ObjectProperty> 876 877 878 879 <!-- http://purl.obolibrary.org/obo/CDAO_0000203 --> 880 881 <owl:ObjectProperty rdf:about="&obo;CDAO_0000203"> 882 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Tree_as_Root</rdfs:label> 883 <rdfs:range rdf:resource="&obo;CDAO_0000110"/> 884 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 885 <owl:inverseOf rdf:resource="&obo;CDAO_0000148"/> 886 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 887 </owl:ObjectProperty> 888 889 890 891 <!-- http://purl.obolibrary.org/obo/CDAO_0000204 --> 892 893 <owl:ObjectProperty rdf:about="&obo;CDAO_0000204"> 894 <rdfs:label rdf:datatype="&xsd;string">has_Hereditary_Change</rdfs:label> 895 <rdfs:range rdf:resource="&obo;CDAO_0000097"/> 896 <rdfs:domain rdf:resource="&obo;CDAO_0000099"/> 897 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 898 </owl:ObjectProperty> 899 900 901 902 <!-- http://purl.obolibrary.org/obo/CDAO_0000205 --> 903 904 <owl:ObjectProperty rdf:about="&obo;CDAO_0000205"> 905 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 906 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Character</rdfs:label> 907 <rdfs:range rdf:resource="&obo;CDAO_0000071"/> 908 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 909 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 910 </owl:ObjectProperty> 911 912 913 914 <!-- http://purl.obolibrary.org/obo/CDAO_0000206 --> 915 916 <owl:ObjectProperty rdf:about="&obo;CDAO_0000206"> 917 <rdfs:label rdf:datatype="&xsd;string">has_Molecular_Datum</rdfs:label> 918 <rdfs:range rdf:resource="&obo;CDAO_0000050"/> 919 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000183"/> 920 <rdfs:domain> 921 <owl:Class> 922 <owl:unionOf rdf:parseType="Collection"> 923 <rdf:Description rdf:about="&obo;CDAO_0000115"/> 924 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 925 </owl:unionOf> 926 </owl:Class> 927 </rdfs:domain> 928 </owl:ObjectProperty> 929 930 931 932 <!-- http://purl.obolibrary.org/obo/CDAO_0000207 --> 933 934 <owl:ObjectProperty rdf:about="&obo;CDAO_0000207"> 935 <rdfs:label rdf:datatype="&xsd;string">has_Continuous_Datum</rdfs:label> 936 <dc:description rdf:datatype="&xsd;string">This property relates a continuous character to a state datum for the character.</dc:description> 937 <rdfs:range rdf:resource="&obo;CDAO_0000019"/> 938 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000153"/> 939 <rdfs:domain> 940 <owl:Class> 941 <owl:unionOf rdf:parseType="Collection"> 942 <rdf:Description rdf:about="&obo;CDAO_0000068"/> 943 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 944 </owl:unionOf> 945 </owl:Class> 946 </rdfs:domain> 947 </owl:ObjectProperty> 948 949 950 951 <!-- http://purl.obolibrary.org/obo/CDAO_0000208 --> 952 953 <owl:ObjectProperty rdf:about="&obo;CDAO_0000208"> 954 <rdfs:label rdf:datatype="&xsd;string">has_TU</rdfs:label> 955 <dc:description rdf:datatype="&xsd;string">This property associates a character data matrix with a TU (a row) represented in the matrix.</dc:description> 956 <rdfs:domain rdf:resource="&obo;CDAO_0000056"/> 957 <rdfs:range rdf:resource="&obo;CDAO_0000138"/> 958 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 959 </owl:ObjectProperty> 960 961 962 963 <!-- http://purl.obolibrary.org/obo/CDAO_0000209 --> 964 965 <owl:ObjectProperty rdf:about="&obo;CDAO_0000209"> 966 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 967 <rdfs:label rdf:datatype="&xsd;string">has_Child_Node</rdfs:label> 968 <dc:description>The property associates to a Directed Edge the Node that is in the child position in the edge, i.e., the node touched by the edge and closer to the leaves of the tree.</dc:description> 969 <rdfs:domain rdf:resource="&obo;CDAO_0000139"/> 970 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 971 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000162"/> 972 </owl:ObjectProperty> 973 974 975 976 <!-- http://purl.obolibrary.org/obo/CDAO_0000210 --> 977 978 <owl:ObjectProperty rdf:about="&obo;CDAO_0000210"> 979 <rdfs:label rdf:datatype="&xsd;string">has_Right_Node</rdfs:label> 980 <dc:description rdf:datatype="&xsd;string">This property relates a transformation to a &#39;right&#39; node (the node that has the &#39;right&#39; state).</dc:description> 981 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 982 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 983 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 984 </owl:ObjectProperty> 985 986 987 988 <!-- 989 /////////////////////////////////////////////////////////////////////////////////////// 990 // 991 // Data properties 992 // 993 /////////////////////////////////////////////////////////////////////////////////////// 994 --> 995 996 997 998 999 <!-- http://purl.obolibrary.org/obo/CDAO_0000211 --> 1000 1001 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000211"> 1002 <rdfs:label rdf:datatype="&xsd;string">has_Precision</rdfs:label> 1003 <rdfs:range rdf:resource="&xsd;float"/> 1004 </owl:DatatypeProperty> 1005 1006 1007 1008 <!-- http://purl.obolibrary.org/obo/CDAO_0000212 --> 1009 1010 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000212"> 1011 <rdfs:label rdf:datatype="&xsd;string">has_Point_Coordinate_Value</rdfs:label> 1012 <rdfs:domain rdf:resource="&obo;CDAO_0000003"/> 1013 <rdfs:range rdf:resource="&xsd;integer"/> 1014 </owl:DatatypeProperty> 1015 1016 1017 1018 <!-- http://purl.obolibrary.org/obo/CDAO_0000213 --> 1019 1020 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000213"> 1021 <rdfs:label rdf:datatype="&xsd;string">has_Int_Value</rdfs:label> 1022 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000215"/> 1023 <rdfs:range rdf:resource="&xsd;int"/> 1024 </owl:DatatypeProperty> 1025 1026 1027 1028 <!-- http://purl.obolibrary.org/obo/CDAO_0000214 --> 1029 1030 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000214"> 1031 <rdfs:label rdf:datatype="&xsd;string">has_Support_Value</rdfs:label> 1032 <rdfs:range rdf:resource="&xsd;float"/> 1033 </owl:DatatypeProperty> 1034 1035 1036 1037 <!-- http://purl.obolibrary.org/obo/CDAO_0000215 --> 1038 1039 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000215"> 1040 <rdfs:label rdf:datatype="&xsd;string">has_Value</rdfs:label> 1041 </owl:DatatypeProperty> 1042 1043 1044 1045 <!-- http://purl.obolibrary.org/obo/CDAO_0000216 --> 1046 1047 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000216"> 1048 <rdfs:label rdf:datatype="&xsd;string">has_Uncertainty_Factor</rdfs:label> 1049 <rdfs:range rdf:resource="&xsd;float"/> 1050 </owl:DatatypeProperty> 1051 1052 1053 1054 <!-- http://purl.obolibrary.org/obo/CDAO_0000217 --> 1055 1056 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000217"> 1057 <rdfs:label rdf:datatype="&xsd;string">has_Range_End_Value</rdfs:label> 1058 <rdfs:domain rdf:resource="&obo;CDAO_0000095"/> 1059 <rdfs:range rdf:resource="&xsd;integer"/> 1060 </owl:DatatypeProperty> 1061 1062 1063 1064 <!-- http://purl.obolibrary.org/obo/CDAO_0000218 --> 1065 1066 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000218"> 1067 <rdfs:label rdf:datatype="&xsd;string">has_Float_Value</rdfs:label> 1068 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000215"/> 1069 <rdfs:range rdf:resource="&xsd;float"/> 1070 </owl:DatatypeProperty> 1071 1072 1073 1074 <!-- http://purl.obolibrary.org/obo/CDAO_0000219 --> 1075 1076 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000219"> 1077 <rdfs:label rdf:datatype="&xsd;string">has_Range_Start_Value</rdfs:label> 1078 <rdfs:domain rdf:resource="&obo;CDAO_0000095"/> 1079 <rdfs:range rdf:resource="&xsd;integer"/> 1080 </owl:DatatypeProperty> 1081 1082 1083 1084 <!-- 1085 /////////////////////////////////////////////////////////////////////////////////////// 1086 // 1087 // Classes 1088 // 1089 /////////////////////////////////////////////////////////////////////////////////////// 1090 --> 1091 1092 1093 1094 1095 <!-- http://purl.obolibrary.org/obo/CDAO_0000002 --> 1096 1097 <owl:Class rdf:about="&obo;CDAO_0000002"> 1098 <rdfs:label rdf:datatype="&xsd;string">DesoxiRibonucleotideResidueStateDatum</rdfs:label> 1099 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000050"/> 1100 </owl:Class> 1101 1102 1103 1104 <!-- http://purl.obolibrary.org/obo/CDAO_0000003 --> 1105 1106 <owl:Class rdf:about="&obo;CDAO_0000003"> 1107 <rdfs:label rdf:datatype="&xsd;string">CoordinatePoint</rdfs:label> 1108 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000022"/> 1109 </owl:Class> 1110 1111 1112 1113 <!-- http://purl.obolibrary.org/obo/CDAO_0000004 --> 1114 1115 <owl:Class rdf:about="&obo;CDAO_0000004"> 1116 <rdfs:label rdf:datatype="&xsd;string">Lineage</rdfs:label> 1117 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 1118 <rdfs:subClassOf> 1119 <owl:Restriction> 1120 <owl:onProperty rdf:resource="&obo;CDAO_0000202"/> 1121 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1122 </owl:Restriction> 1123 </rdfs:subClassOf> 1124 </owl:Class> 1125 1126 1127 1128 <!-- http://purl.obolibrary.org/obo/CDAO_0000005 --> 1129 1130 <owl:Class rdf:about="&obo;CDAO_0000005"> 1131 <rdfs:label rdf:datatype="&xsd;string">Phylo4Tree</rdfs:label> 1132 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1133 </owl:Class> 1134 1135 1136 1137 <!-- http://purl.obolibrary.org/obo/CDAO_0000006 --> 1138 1139 <owl:Class rdf:about="&obo;CDAO_0000006"> 1140 <rdfs:label rdf:datatype="&xsd;string">Network</rdfs:label> 1141 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1142 <rdfs:subClassOf> 1143 <owl:Restriction> 1144 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 1145 <owl:allValuesFrom> 1146 <owl:Class> 1147 <owl:unionOf rdf:parseType="Collection"> 1148 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 1149 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 1150 </owl:unionOf> 1151 </owl:Class> 1152 </owl:allValuesFrom> 1153 </owl:Restriction> 1154 </rdfs:subClassOf> 1155 </owl:Class> 1156 1157 1158 1159 <!-- http://purl.obolibrary.org/obo/CDAO_0000007 --> 1160 1161 <owl:Class rdf:about="&obo;CDAO_0000007"> 1162 <rdfs:label rdf:datatype="&xsd;string">ModelDescription</rdfs:label> 1163 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1164 <dc:description>Description of a model of transformations.</dc:description> 1165 <rdfs:comment>This is a non-computible description of a model, not the fully specified mathematical model, which typically relates the probability of a transformation to various parameters.</rdfs:comment> 1166 </owl:Class> 1167 1168 1169 1170 <!-- http://purl.obolibrary.org/obo/CDAO_0000008 --> 1171 1172 <owl:Class rdf:about="&obo;CDAO_0000008"> 1173 <rdfs:label rdf:datatype="&xsd;string">StandardStateDatum</rdfs:label> 1174 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000089"/> 1175 </owl:Class> 1176 1177 1178 1179 <!-- http://purl.obolibrary.org/obo/CDAO_0000009 --> 1180 1181 <owl:Class rdf:about="&obo;CDAO_0000009"> 1182 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharacterLengthType</rdfs:label> 1183 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 1184 </owl:Class> 1185 1186 1187 1188 <!-- http://purl.obolibrary.org/obo/CDAO_0000010 --> 1189 1190 <owl:Class rdf:about="&obo;CDAO_0000010"> 1191 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharBayesianLengthType</rdfs:label> 1192 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 1193 </owl:Class> 1194 1195 1196 1197 <!-- http://purl.obolibrary.org/obo/CDAO_0000011 --> 1198 1199 <owl:Class rdf:about="&obo;CDAO_0000011"> 1200 <rdfs:label rdf:datatype="&xsd;string">NEXUSTreeBlock</rdfs:label> 1201 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1202 </owl:Class> 1203 1204 1205 1206 <!-- http://purl.obolibrary.org/obo/CDAO_0000012 --> 1207 1208 <owl:Class rdf:about="&obo;CDAO_0000012"> 1209 <rdfs:label rdf:datatype="&xsd;string">RootedTree</rdfs:label> 1210 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1211 <rdfs:subClassOf> 1212 <owl:Restriction> 1213 <owl:onProperty rdf:resource="&obo;CDAO_0000155"/> 1214 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000012"/> 1215 </owl:Restriction> 1216 </rdfs:subClassOf> 1217 <rdfs:subClassOf> 1218 <owl:Restriction> 1219 <owl:onProperty rdf:resource="&obo;CDAO_0000148"/> 1220 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 1221 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1222 </owl:Restriction> 1223 </rdfs:subClassOf> 1224 <rdfs:subClassOf> 1225 <owl:Restriction> 1226 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 1227 <owl:allValuesFrom> 1228 <owl:Class> 1229 <owl:unionOf rdf:parseType="Collection"> 1230 <rdf:Description rdf:about="&obo;CDAO_0000139"/> 1231 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 1232 </owl:unionOf> 1233 </owl:Class> 1234 </owl:allValuesFrom> 1235 </owl:Restriction> 1236 </rdfs:subClassOf> 1237 <owl:disjointWith rdf:resource="&obo;CDAO_0000088"/> 1238 </owl:Class> 1239 1240 1241 1242 <!-- http://purl.obolibrary.org/obo/CDAO_0000013 --> 1243 1244 <owl:Class rdf:about="&obo;CDAO_0000013"> 1245 <rdfs:label rdf:datatype="&xsd;string">Kimura2Parameters</rdfs:label> 1246 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000020"/> 1247 </owl:Class> 1248 1249 1250 1251 <!-- http://purl.obolibrary.org/obo/CDAO_0000014 --> 1252 1253 <owl:Class rdf:about="&obo;CDAO_0000014"> 1254 <rdfs:label rdf:datatype="&xsd;string">TreeProcedure</rdfs:label> 1255 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000044"/> 1256 </owl:Class> 1257 1258 1259 1260 <!-- http://purl.obolibrary.org/obo/CDAO_0000015 --> 1261 1262 <owl:Class rdf:about="&obo;CDAO_0000015"> 1263 <rdfs:label rdf:datatype="&xsd;string">Generic_State</rdfs:label> 1264 <owl:equivalentClass> 1265 <owl:Class> 1266 <owl:oneOf rdf:parseType="Collection"> 1267 <rdf:Description rdf:about="&obo;CDAO_0000222"/> 1268 <rdf:Description rdf:about="&obo;CDAO_0000221"/> 1269 <rdf:Description rdf:about="&obo;CDAO_0000223"/> 1270 </owl:oneOf> 1271 </owl:Class> 1272 </owl:equivalentClass> 1273 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1274 <rdfs:comment>This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.</rdfs:comment> 1275 <dc:description>This concept is tied to the verbally ambiguous &#39;gap&#39; concept and to the use of a gap character (often the en dash &#39;-&#39;) in text representations of sequence alignments. In general, this represents the absence of any positively diagnosed Character-State. As such, the gap may be interpreted as an additional Character-State, as the absence of the Character, or as an unknown value. In some cases it is helpful to separate these.</dc:description> 1276 </owl:Class> 1277 1278 1279 1280 <!-- http://purl.obolibrary.org/obo/CDAO_0000016 --> 1281 1282 <owl:Class rdf:about="&obo;CDAO_0000016"> 1283 <rdfs:label rdf:datatype="&xsd;string">UnrootedSubtree</rdfs:label> 1284 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000070"/> 1285 </owl:Class> 1286 1287 1288 1289 <!-- http://purl.obolibrary.org/obo/CDAO_0000017 --> 1290 1291 <owl:Class rdf:about="&obo;CDAO_0000017"> 1292 <rdfs:label rdf:datatype="&xsd;string">UnresolvedTree</rdfs:label> 1293 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1294 </owl:Class> 1295 1296 1297 1298 <!-- http://purl.obolibrary.org/obo/CDAO_0000018 --> 1299 1300 <owl:Class rdf:about="&obo;CDAO_0000018"> 1301 <rdfs:label rdf:datatype="&xsd;string">BifurcatingTree</rdfs:label> 1302 <owl:equivalentClass rdf:resource="&obo;CDAO_0000130"/> 1303 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1304 </owl:Class> 1305 1306 1307 1308 <!-- http://purl.obolibrary.org/obo/CDAO_0000019 --> 1309 1310 <owl:Class rdf:about="&obo;CDAO_0000019"> 1311 <rdfs:label rdf:datatype="&xsd;string">ContinuousStateDatum</rdfs:label> 1312 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000098"/> 1313 </owl:Class> 1314 1315 1316 1317 <!-- http://purl.obolibrary.org/obo/CDAO_0000020 --> 1318 1319 <owl:Class rdf:about="&obo;CDAO_0000020"> 1320 <rdfs:label rdf:datatype="&xsd;string">SubstitutionModel</rdfs:label> 1321 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000007"/> 1322 </owl:Class> 1323 1324 1325 1326 <!-- http://purl.obolibrary.org/obo/CDAO_0000021 --> 1327 1328 <owl:Class rdf:about="&obo;CDAO_0000021"> 1329 <rdfs:label rdf:datatype="&xsd;string">JukesKantor</rdfs:label> 1330 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000020"/> 1331 </owl:Class> 1332 1333 1334 1335 <!-- http://purl.obolibrary.org/obo/CDAO_0000022 --> 1336 1337 <owl:Class rdf:about="&obo;CDAO_0000022"> 1338 <rdfs:label rdf:datatype="&xsd;string">DatumCoordinate</rdfs:label> 1339 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1340 <rdfs:subClassOf> 1341 <owl:Restriction> 1342 <owl:onProperty rdf:resource="&obo;CDAO_0000165"/> 1343 <owl:onClass rdf:resource="&obo;CDAO_0000104"/> 1344 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1345 </owl:Restriction> 1346 </rdfs:subClassOf> 1347 <dc:description>A positional coordinate giving the source of a character state, used for molecular sequences.</dc:description> 1348 <rdfs:comment>drawing from seqloc categories from NCBI at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on</rdfs:comment> 1349 </owl:Class> 1350 1351 1352 1353 <!-- http://purl.obolibrary.org/obo/CDAO_0000023 --> 1354 1355 <owl:Class rdf:about="&obo;CDAO_0000023"> 1356 <rdfs:label rdf:datatype="&xsd;string">UnresolvedRootedTree</rdfs:label> 1357 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 1358 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000017"/> 1359 </owl:Class> 1360 1361 1362 1363 <!-- http://purl.obolibrary.org/obo/CDAO_0000024 --> 1364 1365 <owl:Class rdf:about="&obo;CDAO_0000024"> 1366 <rdfs:label rdf:datatype="&xsd;string">Branch</rdfs:label> 1367 <owl:equivalentClass rdf:resource="&obo;CDAO_0000099"/> 1368 <dc:description>&#39;Branch&#39; is the domain-specific synonym for an edge of a (Phylogenetic) Tree or Network. Branches may have properties such as length and degree of support.</dc:description> 1369 </owl:Class> 1370 1371 1372 1373 <!-- http://purl.obolibrary.org/obo/CDAO_0000025 --> 1374 1375 <owl:Class rdf:about="&obo;CDAO_0000025"> 1376 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDataMatrixAnnotation</rdfs:label> 1377 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1378 <dc:description>Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.</dc:description> 1379 </owl:Class> 1380 1381 1382 1383 <!-- http://purl.obolibrary.org/obo/CDAO_0000026 --> 1384 1385 <owl:Class rdf:about="&obo;CDAO_0000026"> 1386 <rdfs:label rdf:datatype="&xsd;string">AncestralNode</rdfs:label> 1387 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000140"/> 1388 <rdfs:subClassOf> 1389 <owl:Restriction> 1390 <owl:onProperty rdf:resource="&obo;CDAO_0000174"/> 1391 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1392 </owl:Restriction> 1393 </rdfs:subClassOf> 1394 <rdfs:subClassOf> 1395 <owl:Restriction> 1396 <owl:onProperty rdf:resource="&obo;CDAO_0000194"/> 1397 <owl:onClass rdf:resource="&obo;CDAO_0000012"/> 1398 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 1399 </owl:Restriction> 1400 </rdfs:subClassOf> 1401 </owl:Class> 1402 1403 1404 1405 <!-- http://purl.obolibrary.org/obo/CDAO_0000027 --> 1406 1407 <owl:Class rdf:about="&obo;CDAO_0000027"> 1408 <rdfs:label rdf:datatype="&xsd;string">UnresolvedUnrootedTree</rdfs:label> 1409 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000017"/> 1410 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000088"/> 1411 </owl:Class> 1412 1413 1414 1415 <!-- http://purl.obolibrary.org/obo/CDAO_0000029 --> 1416 1417 <owl:Class rdf:about="&obo;CDAO_0000029"> 1418 <rdfs:label rdf:datatype="&xsd;string">UncertainStateDomain</rdfs:label> 1419 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1420 <rdfs:subClassOf> 1421 <owl:Restriction> 1422 <owl:onProperty rdf:resource="&obo;CDAO_0000216"/> 1423 <owl:someValuesFrom rdf:resource="&xsd;float"/> 1424 </owl:Restriction> 1425 </rdfs:subClassOf> 1426 </owl:Class> 1427 1428 1429 1430 <!-- http://purl.obolibrary.org/obo/CDAO_0000030 --> 1431 1432 <owl:Class rdf:about="&obo;CDAO_0000030"> 1433 <rdfs:label rdf:datatype="&xsd;string">ReconcileTree</rdfs:label> 1434 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1435 <rdfs:subClassOf> 1436 <owl:Restriction> 1437 <owl:onProperty rdf:resource="&obo;CDAO_0000172"/> 1438 <owl:onClass rdf:resource="&obo;CDAO_0000110"/> 1439 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:minQualifiedCardinality> 1440 </owl:Restriction> 1441 </rdfs:subClassOf> 1442 </owl:Class> 1443 1444 1445 1446 <!-- http://purl.obolibrary.org/obo/CDAO_0000031 --> 1447 1448 <owl:Class rdf:about="&obo;CDAO_0000031"> 1449 <rdfs:label rdf:datatype="&xsd;string">Continuous</rdfs:label> 1450 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1451 <rdfs:subClassOf> 1452 <owl:Restriction> 1453 <owl:onProperty rdf:resource="&obo;CDAO_0000215"/> 1454 <owl:cardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:cardinality> 1455 </owl:Restriction> 1456 </rdfs:subClassOf> 1457 <dc:description>This class describes a continuous value. The link to the actual float value is through the property has_Value. It could have also other properties attached (e.g., has_Precision).</dc:description> 1458 </owl:Class> 1459 1460 1461 1462 <!-- http://purl.obolibrary.org/obo/CDAO_0000032 --> 1463 1464 <owl:Class rdf:about="&obo;CDAO_0000032"> 1465 <rdfs:label rdf:datatype="&xsd;string">AlignmentProcedure</rdfs:label> 1466 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000025"/> 1467 </owl:Class> 1468 1469 1470 1471 <!-- http://purl.obolibrary.org/obo/CDAO_0000033 --> 1472 1473 <owl:Class rdf:about="&obo;CDAO_0000033"> 1474 <rdfs:label rdf:datatype="&xsd;string">Dichotomy</rdfs:label> 1475 <owl:equivalentClass rdf:resource="&obo;CDAO_0000124"/> 1476 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 1477 <owl:disjointWith rdf:resource="&obo;CDAO_0000042"/> 1478 </owl:Class> 1479 1480 1481 1482 <!-- http://purl.obolibrary.org/obo/CDAO_0000034 --> 1483 1484 <owl:Class rdf:about="&obo;CDAO_0000034"> 1485 <rdfs:label rdf:datatype="&xsd;string">Molecular</rdfs:label> 1486 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1487 </owl:Class> 1488 1489 1490 1491 <!-- http://purl.obolibrary.org/obo/CDAO_0000035 --> 1492 1493 <owl:Class rdf:about="&obo;CDAO_0000035"> 1494 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharParsimonyLengthType</rdfs:label> 1495 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 1496 </owl:Class> 1497 1498 1499 1500 <!-- http://purl.obolibrary.org/obo/CDAO_0000039 --> 1501 1502 <owl:Class rdf:about="&obo;CDAO_0000039"> 1503 <rdfs:label rdf:datatype="&xsd;string">Categorical</rdfs:label> 1504 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1505 </owl:Class> 1506 1507 1508 1509 <!-- http://purl.obolibrary.org/obo/CDAO_0000040 --> 1510 1511 <owl:Class rdf:about="&obo;CDAO_0000040"> 1512 <rdfs:label rdf:datatype="&xsd;string">CDAOAnnotation</rdfs:label> 1513 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1514 <rdfs:comment>Its possible that this base class should be discarded and that annotations should inherit from an imported base class if one exists.</rdfs:comment> 1515 <dc:description>The base class of annotations in CDAO.</dc:description> 1516 </owl:Class> 1517 1518 1519 1520 <!-- http://purl.obolibrary.org/obo/CDAO_0000041 --> 1521 1522 <owl:Class rdf:about="&obo;CDAO_0000041"> 1523 <rdfs:label rdf:datatype="&xsd;string">originationEvent</rdfs:label> 1524 <rdfs:subClassOf> 1525 <owl:Restriction> 1526 <owl:onProperty rdf:resource="&obo;CDAO_0000190"/> 1527 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000097"/> 1528 </owl:Restriction> 1529 </rdfs:subClassOf> 1530 </owl:Class> 1531 1532 1533 1534 <!-- http://purl.obolibrary.org/obo/CDAO_0000042 --> 1535 1536 <owl:Class rdf:about="&obo;CDAO_0000042"> 1537 <rdfs:label rdf:datatype="&xsd;string">Polytomy</rdfs:label> 1538 <owl:equivalentClass> 1539 <owl:Restriction> 1540 <owl:onProperty rdf:resource="&obo;CDAO_0000177"/> 1541 <owl:minCardinality rdf:datatype="&xsd;nonNegativeInteger">3</owl:minCardinality> 1542 </owl:Restriction> 1543 </owl:equivalentClass> 1544 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 1545 <owl:disjointWith rdf:resource="&obo;CDAO_0000124"/> 1546 </owl:Class> 1547 1548 1549 1550 <!-- http://purl.obolibrary.org/obo/CDAO_0000043 --> 1551 1552 <owl:Class rdf:about="&obo;CDAO_0000043"> 1553 <rdfs:label rdf:datatype="&xsd;string">PolymorphicStateDomain</rdfs:label> 1554 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1555 <rdfs:subClassOf> 1556 <owl:Restriction> 1557 <owl:onProperty rdf:resource="&obo;CDAO_0000216"/> 1558 <owl:hasValue rdf:datatype="&xsd;float">1.0</owl:hasValue> 1559 </owl:Restriction> 1560 </rdfs:subClassOf> 1561 </owl:Class> 1562 1563 1564 1565 <!-- http://purl.obolibrary.org/obo/CDAO_0000044 --> 1566 1567 <owl:Class rdf:about="&obo;CDAO_0000044"> 1568 <rdfs:label rdf:datatype="&xsd;string">TreeAnnotation</rdfs:label> 1569 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1570 <rdfs:subClassOf> 1571 <owl:Restriction> 1572 <owl:onProperty rdf:resource="&obo;CDAO_0000157"/> 1573 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000110"/> 1574 </owl:Restriction> 1575 </rdfs:subClassOf> 1576 </owl:Class> 1577 1578 1579 1580 <!-- http://purl.obolibrary.org/obo/CDAO_0000045 --> 1581 1582 <owl:Class rdf:about="&obo;CDAO_0000045"> 1583 <rdfs:label rdf:datatype="&xsd;string">Standard</rdfs:label> 1584 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1585 </owl:Class> 1586 1587 1588 1589 <!-- http://purl.obolibrary.org/obo/CDAO_0000046 --> 1590 1591 <owl:Class rdf:about="&obo;CDAO_0000046"> 1592 <rdfs:label rdf:datatype="&xsd;string">EdgeLength</rdfs:label> 1593 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000101"/> 1594 <rdfs:subClassOf> 1595 <owl:Restriction> 1596 <owl:onProperty rdf:resource="&obo;CDAO_0000176"/> 1597 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000063"/> 1598 </owl:Restriction> 1599 </rdfs:subClassOf> 1600 <rdfs:subClassOf> 1601 <owl:Restriction> 1602 <owl:onProperty rdf:resource="&obo;CDAO_0000215"/> 1603 <owl:someValuesFrom rdf:resource="&rdfs;Literal"/> 1604 </owl:Restriction> 1605 </rdfs:subClassOf> 1606 <rdfs:comment>Its possible that this should not be classed as an &#39;annotation&#39; since it contains data rather than meta-data.</rdfs:comment> 1607 <dc:description>The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character.</dc:description> 1608 </owl:Class> 1609 1610 1611 1612 <!-- http://purl.obolibrary.org/obo/CDAO_0000047 --> 1613 1614 <owl:Class rdf:about="&obo;CDAO_0000047"> 1615 <rdfs:label rdf:datatype="&xsd;string">RibonucleotideResidue</rdfs:label> 1616 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000034"/> 1617 </owl:Class> 1618 1619 1620 1621 <!-- http://purl.obolibrary.org/obo/CDAO_0000048 --> 1622 1623 <owl:Class rdf:about="&obo;CDAO_0000048"> 1624 <rdfs:label rdf:datatype="&xsd;string">Clade</rdfs:label> 1625 <owl:equivalentClass rdf:resource="&obo;CDAO_0000129"/> 1626 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1627 </owl:Class> 1628 1629 1630 1631 <!-- http://purl.obolibrary.org/obo/CDAO_0000049 --> 1632 1633 <owl:Class rdf:about="&obo;CDAO_0000049"> 1634 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharParsimonyLengthType</rdfs:label> 1635 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 1636 </owl:Class> 1637 1638 1639 1640 <!-- http://purl.obolibrary.org/obo/CDAO_0000050 --> 1641 1642 <owl:Class rdf:about="&obo;CDAO_0000050"> 1643 <rdfs:label rdf:datatype="&xsd;string">MolecularStateDatum</rdfs:label> 1644 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000089"/> 1645 </owl:Class> 1646 1647 1648 1649 <!-- http://purl.obolibrary.org/obo/CDAO_0000051 --> 1650 1651 <owl:Class rdf:about="&obo;CDAO_0000051"> 1652 <rdfs:label rdf:datatype="&xsd;string">PolyphyleticGroup</rdfs:label> 1653 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 1654 <rdfs:subClassOf> 1655 <owl:Restriction> 1656 <owl:onProperty rdf:resource="&obo;CDAO_0000188"/> 1657 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1658 </owl:Restriction> 1659 </rdfs:subClassOf> 1660 <owl:disjointWith rdf:resource="&obo;CDAO_0000127"/> 1661 </owl:Class> 1662 1663 1664 1665 <!-- http://purl.obolibrary.org/obo/CDAO_0000052 --> 1666 1667 <owl:Class rdf:about="&obo;CDAO_0000052"> 1668 <rdfs:label rdf:datatype="&xsd;string">NexusDataBlock</rdfs:label> 1669 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 1670 </owl:Class> 1671 1672 1673 1674 <!-- http://purl.obolibrary.org/obo/CDAO_0000053 --> 1675 1676 <owl:Class rdf:about="&obo;CDAO_0000053"> 1677 <rdfs:label rdf:datatype="&xsd;string">BranchingNode</rdfs:label> 1678 <owl:equivalentClass> 1679 <owl:Restriction> 1680 <owl:onProperty rdf:resource="&obo;CDAO_0000177"/> 1681 <owl:minCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:minCardinality> 1682 </owl:Restriction> 1683 </owl:equivalentClass> 1684 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 1685 </owl:Class> 1686 1687 1688 1689 <!-- http://purl.obolibrary.org/obo/CDAO_0000055 --> 1690 1691 <owl:Class rdf:about="&obo;CDAO_0000055"> 1692 <rdfs:label rdf:datatype="&xsd;string">Compound</rdfs:label> 1693 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1694 </owl:Class> 1695 1696 1697 1698 <!-- http://purl.obolibrary.org/obo/CDAO_0000056 --> 1699 1700 <owl:Class rdf:about="&obo;CDAO_0000056"> 1701 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDataMatrix</rdfs:label> 1702 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1703 <rdfs:subClassOf> 1704 <owl:Restriction> 1705 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 1706 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000025"/> 1707 </owl:Restriction> 1708 </rdfs:subClassOf> 1709 <rdfs:subClassOf> 1710 <owl:Restriction> 1711 <owl:onProperty rdf:resource="&obo;CDAO_0000208"/> 1712 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000138"/> 1713 </owl:Restriction> 1714 </rdfs:subClassOf> 1715 <rdfs:subClassOf> 1716 <owl:Restriction> 1717 <owl:onProperty rdf:resource="&obo;CDAO_0000142"/> 1718 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000071"/> 1719 </owl:Restriction> 1720 </rdfs:subClassOf> 1721 <dc:description>A matrix of character-state data, typically containing observed data, though in some cases the states in the matrix might be simulated or hypothetical. Synonyms: character Data matrix, character-state matrix</dc:description> 1722 </owl:Class> 1723 1724 1725 1726 <!-- http://purl.obolibrary.org/obo/CDAO_0000057 --> 1727 1728 <owl:Class rdf:about="&obo;CDAO_0000057"> 1729 <rdfs:label rdf:datatype="&xsd;string">RibonucleotideResidueStateDatum</rdfs:label> 1730 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000050"/> 1731 </owl:Class> 1732 1733 1734 1735 <!-- http://purl.obolibrary.org/obo/CDAO_0000058 --> 1736 1737 <owl:Class rdf:about="&obo;CDAO_0000058"> 1738 <rdfs:label rdf:datatype="&xsd;string">TimeCalibratedLengthType</rdfs:label> 1739 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 1740 </owl:Class> 1741 1742 1743 1744 <!-- http://purl.obolibrary.org/obo/CDAO_0000059 --> 1745 1746 <owl:Class rdf:about="&obo;CDAO_0000059"> 1747 <rdfs:label rdf:datatype="&xsd;string">SetOfNodes</rdfs:label> 1748 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000118"/> 1749 <rdfs:subClassOf> 1750 <owl:Restriction> 1751 <owl:onProperty rdf:resource="&obo;CDAO_0000198"/> 1752 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1753 </owl:Restriction> 1754 </rdfs:subClassOf> 1755 </owl:Class> 1756 1757 1758 1759 <!-- http://purl.obolibrary.org/obo/CDAO_0000060 --> 1760 1761 <owl:Class rdf:about="&obo;CDAO_0000060"> 1762 <rdfs:label rdf:datatype="&xsd;string">MRCANode</rdfs:label> 1763 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000080"/> 1764 <rdfs:subClassOf> 1765 <owl:Restriction> 1766 <owl:onProperty rdf:resource="&obo;CDAO_0000163"/> 1767 <owl:onClass rdf:resource="&obo;CDAO_0000118"/> 1768 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 1769 </owl:Restriction> 1770 </rdfs:subClassOf> 1771 </owl:Class> 1772 1773 1774 1775 <!-- http://purl.obolibrary.org/obo/CDAO_0000061 --> 1776 1777 <owl:Class rdf:about="&obo;CDAO_0000061"> 1778 <rdfs:label rdf:datatype="&xsd;string">FASTADataMatrix</rdfs:label> 1779 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 1780 </owl:Class> 1781 1782 1783 1784 <!-- http://purl.obolibrary.org/obo/CDAO_0000062 --> 1785 1786 <owl:Class rdf:about="&obo;CDAO_0000062"> 1787 <rdfs:label rdf:datatype="&xsd;string">evolutionaryTransition</rdfs:label> 1788 <owl:equivalentClass rdf:resource="&obo;CDAO_0000065"/> 1789 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000097"/> 1790 <rdfs:subClassOf> 1791 <owl:Restriction> 1792 <owl:onProperty rdf:resource="&obo;CDAO_0000159"/> 1793 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 1794 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1795 </owl:Restriction> 1796 </rdfs:subClassOf> 1797 <rdfs:subClassOf> 1798 <owl:Restriction> 1799 <owl:onProperty rdf:resource="&obo;CDAO_0000186"/> 1800 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 1801 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1802 </owl:Restriction> 1803 </rdfs:subClassOf> 1804 <rdfs:subClassOf> 1805 <owl:Restriction> 1806 <owl:onProperty rdf:resource="&obo;CDAO_0000169"/> 1807 <owl:onClass rdf:resource="&obo;CDAO_0000071"/> 1808 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1809 </owl:Restriction> 1810 </rdfs:subClassOf> 1811 </owl:Class> 1812 1813 1814 1815 <!-- http://purl.obolibrary.org/obo/CDAO_0000063 --> 1816 1817 <owl:Class rdf:about="&obo;CDAO_0000063"> 1818 <rdfs:label rdf:datatype="&xsd;string">EdgeLengthType</rdfs:label> 1819 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1820 </owl:Class> 1821 1822 1823 1824 <!-- http://purl.obolibrary.org/obo/CDAO_0000064 --> 1825 1826 <owl:Class rdf:about="&obo;CDAO_0000064"> 1827 <rdfs:label rdf:datatype="&xsd;string">cladogeneticChange</rdfs:label> 1828 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000097"/> 1829 </owl:Class> 1830 1831 1832 1833 <!-- http://purl.obolibrary.org/obo/CDAO_0000065 --> 1834 1835 <owl:Class rdf:about="&obo;CDAO_0000065"> 1836 <rdfs:label rdf:datatype="&xsd;string">anageneticChange</rdfs:label> 1837 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000097"/> 1838 </owl:Class> 1839 1840 1841 1842 <!-- http://purl.obolibrary.org/obo/CDAO_0000066 --> 1843 1844 <owl:Class rdf:about="&obo;CDAO_0000066"> 1845 <rdfs:label rdf:datatype="&xsd;string">TUAnnotation</rdfs:label> 1846 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1847 </owl:Class> 1848 1849 1850 1851 <!-- http://purl.obolibrary.org/obo/CDAO_0000067 --> 1852 1853 <owl:Class rdf:about="&obo;CDAO_0000067"> 1854 <rdfs:label rdf:datatype="&xsd;string">PhyloTree</rdfs:label> 1855 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1856 </owl:Class> 1857 1858 1859 1860 <!-- http://purl.obolibrary.org/obo/CDAO_0000068 --> 1861 1862 <owl:Class rdf:about="&obo;CDAO_0000068"> 1863 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharacter</rdfs:label> 1864 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000071"/> 1865 <rdfs:subClassOf> 1866 <owl:Restriction> 1867 <owl:onProperty rdf:resource="&obo;CDAO_0000207"/> 1868 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000019"/> 1869 </owl:Restriction> 1870 </rdfs:subClassOf> 1871 <rdfs:subClassOf> 1872 <owl:Restriction> 1873 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 1874 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000019"/> 1875 </owl:Restriction> 1876 </rdfs:subClassOf> 1877 </owl:Class> 1878 1879 1880 1881 <!-- http://purl.obolibrary.org/obo/CDAO_0000069 --> 1882 1883 <owl:Class rdf:about="&obo;CDAO_0000069"> 1884 <rdfs:label rdf:datatype="&xsd;string">PHYLIPTree</rdfs:label> 1885 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1886 </owl:Class> 1887 1888 1889 1890 <!-- http://purl.obolibrary.org/obo/CDAO_0000070 --> 1891 1892 <owl:Class rdf:about="&obo;CDAO_0000070"> 1893 <rdfs:label rdf:datatype="&xsd;string">Subtree</rdfs:label> 1894 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1895 <rdfs:subClassOf> 1896 <owl:Restriction> 1897 <owl:onProperty rdf:resource="&obo;CDAO_0000155"/> 1898 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000110"/> 1899 </owl:Restriction> 1900 </rdfs:subClassOf> 1901 </owl:Class> 1902 1903 1904 1905 <!-- http://purl.obolibrary.org/obo/CDAO_0000071 --> 1906 1907 <owl:Class rdf:about="&obo;CDAO_0000071"> 1908 <rdfs:label rdf:datatype="&xsd;string">Character</rdfs:label> 1909 <rdfs:subClassOf> 1910 <owl:Restriction> 1911 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 1912 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000098"/> 1913 </owl:Restriction> 1914 </rdfs:subClassOf> 1915 <rdfs:comment rdf:datatype="&xsd;string">Traits shown to be relevant for phylogenetic classification</rdfs:comment> 1916 </owl:Class> 1917 1918 1919 1920 <!-- http://purl.obolibrary.org/obo/CDAO_0000072 --> 1921 1922 <owl:Class rdf:about="&obo;CDAO_0000072"> 1923 <rdfs:label rdf:datatype="&xsd;string">GalledTree</rdfs:label> 1924 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 1925 </owl:Class> 1926 1927 1928 1929 <!-- http://purl.obolibrary.org/obo/CDAO_0000073 --> 1930 1931 <owl:Class rdf:about="&obo;CDAO_0000073"> 1932 <rdfs:label rdf:datatype="&xsd;string">SpeciesTree</rdfs:label> 1933 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1934 </owl:Class> 1935 1936 1937 1938 <!-- http://purl.obolibrary.org/obo/CDAO_0000074 --> 1939 1940 <owl:Class rdf:about="&obo;CDAO_0000074"> 1941 <rdfs:label rdf:datatype="&xsd;string">TreeFormat</rdfs:label> 1942 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000044"/> 1943 </owl:Class> 1944 1945 1946 1947 <!-- http://purl.obolibrary.org/obo/CDAO_0000075 --> 1948 1949 <owl:Class rdf:about="&obo;CDAO_0000075"> 1950 <rdfs:label rdf:datatype="&xsd;string">StandardCharacter</rdfs:label> 1951 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000111"/> 1952 </owl:Class> 1953 1954 1955 1956 <!-- http://purl.obolibrary.org/obo/CDAO_0000076 --> 1957 1958 <owl:Class rdf:about="&obo;CDAO_0000076"> 1959 <rdfs:label rdf:datatype="&xsd;string">AminoAcidResidue</rdfs:label> 1960 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000034"/> 1961 <dc:description>This class will be declared equivalent ot the amino acid class description imported</dc:description> 1962 </owl:Class> 1963 1964 1965 1966 <!-- http://purl.obolibrary.org/obo/CDAO_0000077 --> 1967 1968 <owl:Class rdf:about="&obo;CDAO_0000077"> 1969 <rdfs:label rdf:datatype="&xsd;string">geneDuplication</rdfs:label> 1970 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000064"/> 1971 </owl:Class> 1972 1973 1974 1975 <!-- http://purl.obolibrary.org/obo/CDAO_0000078 --> 1976 1977 <owl:Class rdf:about="&obo;CDAO_0000078"> 1978 <rdfs:label rdf:datatype="&xsd;string">CompoundCharacter</rdfs:label> 1979 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000111"/> 1980 <rdfs:subClassOf> 1981 <owl:Restriction> 1982 <owl:onProperty rdf:resource="&obo;CDAO_0000170"/> 1983 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000136"/> 1984 </owl:Restriction> 1985 </rdfs:subClassOf> 1986 <rdfs:subClassOf> 1987 <owl:Restriction> 1988 <owl:onProperty rdf:resource="&obo;CDAO_0000142"/> 1989 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000071"/> 1990 </owl:Restriction> 1991 </rdfs:subClassOf> 1992 <rdfs:subClassOf> 1993 <owl:Restriction> 1994 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 1995 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000136"/> 1996 </owl:Restriction> 1997 </rdfs:subClassOf> 1998 <dc:description>A character that could be divided into separate characters but is not due to the non-independence of changes that would result, e.g., as in the case of a subsequence that is either present or absent as a block.</dc:description> 1999 </owl:Class> 2000 2001 2002 2003 <!-- http://purl.obolibrary.org/obo/CDAO_0000079 --> 2004 2005 <owl:Class rdf:about="&obo;CDAO_0000079"> 2006 <rdfs:label rdf:datatype="&xsd;string">SIMMAPTree</rdfs:label> 2007 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 2008 </owl:Class> 2009 2010 2011 2012 <!-- http://purl.obolibrary.org/obo/CDAO_0000080 --> 2013 2014 <owl:Class rdf:about="&obo;CDAO_0000080"> 2015 <rdfs:label rdf:datatype="&xsd;string">CommonAncestralNode</rdfs:label> 2016 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 2017 <rdfs:subClassOf> 2018 <owl:Class> 2019 <owl:unionOf rdf:parseType="Collection"> 2020 <rdf:Description rdf:about="&obo;CDAO_0000053"/> 2021 <owl:Restriction> 2022 <owl:onProperty rdf:resource="&obo;CDAO_0000174"/> 2023 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000053"/> 2024 </owl:Restriction> 2025 </owl:unionOf> 2026 </owl:Class> 2027 </rdfs:subClassOf> 2028 </owl:Class> 2029 2030 2031 2032 <!-- http://purl.obolibrary.org/obo/CDAO_0000081 --> 2033 2034 <owl:Class rdf:about="&obo;CDAO_0000081"> 2035 <rdfs:label rdf:datatype="&xsd;string">NewickTree</rdfs:label> 2036 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 2037 </owl:Class> 2038 2039 2040 2041 <!-- http://purl.obolibrary.org/obo/CDAO_0000082 --> 2042 2043 <owl:Class rdf:about="&obo;CDAO_0000082"> 2044 <rdfs:label rdf:datatype="&xsd;string">TimeProportionalLengthType</rdfs:label> 2045 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 2046 </owl:Class> 2047 2048 2049 2050 <!-- http://purl.obolibrary.org/obo/CDAO_0000083 --> 2051 2052 <owl:Class rdf:about="&obo;CDAO_0000083"> 2053 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharDistanceLengthType</rdfs:label> 2054 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 2055 </owl:Class> 2056 2057 2058 2059 <!-- http://purl.obolibrary.org/obo/CDAO_0000084 --> 2060 2061 <owl:Class rdf:about="&obo;CDAO_0000084"> 2062 <rdfs:label rdf:datatype="&xsd;string">StarTree</rdfs:label> 2063 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 2064 <rdfs:subClassOf> 2065 <owl:Restriction> 2066 <owl:onProperty rdf:resource="&obo;CDAO_0000149"/> 2067 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000108"/> 2068 </owl:Restriction> 2069 </rdfs:subClassOf> 2070 </owl:Class> 2071 2072 2073 2074 <!-- http://purl.obolibrary.org/obo/CDAO_0000085 --> 2075 2076 <owl:Class rdf:about="&obo;CDAO_0000085"> 2077 <rdfs:label rdf:datatype="&xsd;string">FullyResolvedUnrootedTree</rdfs:label> 2078 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000018"/> 2079 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000088"/> 2080 </owl:Class> 2081 2082 2083 2084 <!-- http://purl.obolibrary.org/obo/CDAO_0000086 --> 2085 2086 <owl:Class rdf:about="&obo;CDAO_0000086"> 2087 <rdfs:label rdf:datatype="&xsd;string">ParaphyleticGroup</rdfs:label> 2088 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000127"/> 2089 <rdfs:subClassOf> 2090 <owl:Restriction> 2091 <owl:onProperty rdf:resource="&obo;CDAO_0000199"/> 2092 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000070"/> 2093 </owl:Restriction> 2094 </rdfs:subClassOf> 2095 <owl:disjointWith rdf:resource="&obo;CDAO_0000129"/> 2096 </owl:Class> 2097 2098 2099 2100 <!-- http://purl.obolibrary.org/obo/CDAO_0000087 --> 2101 2102 <owl:Class rdf:about="&obo;CDAO_0000087"> 2103 <rdfs:label rdf:datatype="&xsd;string">geneticEvent</rdfs:label> 2104 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000041"/> 2105 </owl:Class> 2106 2107 2108 2109 <!-- http://purl.obolibrary.org/obo/CDAO_0000088 --> 2110 2111 <owl:Class rdf:about="&obo;CDAO_0000088"> 2112 <rdfs:label rdf:datatype="&xsd;string">UnrootedTree</rdfs:label> 2113 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 2114 </owl:Class> 2115 2116 2117 2118 <!-- http://purl.obolibrary.org/obo/CDAO_0000089 --> 2119 2120 <owl:Class rdf:about="&obo;CDAO_0000089"> 2121 <rdfs:label rdf:datatype="&xsd;string">CategoricalStateDatum</rdfs:label> 2122 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000098"/> 2123 </owl:Class> 2124 2125 2126 2127 <!-- http://purl.obolibrary.org/obo/CDAO_0000090 --> 2128 2129 <owl:Class rdf:about="&obo;CDAO_0000090"> 2130 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharLikelihoodLengthType</rdfs:label> 2131 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 2132 </owl:Class> 2133 2134 2135 2136 <!-- http://purl.obolibrary.org/obo/CDAO_0000091 --> 2137 2138 <owl:Class rdf:about="&obo;CDAO_0000091"> 2139 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDomain</rdfs:label> 2140 <dc:description>The universe of possible states for a particular type of character, e.g., the states of an Amino_Acid character come from the Amino_Acid domain.</dc:description> 2141 </owl:Class> 2142 2143 2144 2145 <!-- http://purl.obolibrary.org/obo/CDAO_0000092 --> 2146 2147 <owl:Class rdf:about="&obo;CDAO_0000092"> 2148 <rdfs:label rdf:datatype="&xsd;string">CoordinateList</rdfs:label> 2149 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000022"/> 2150 </owl:Class> 2151 2152 2153 2154 <!-- http://purl.obolibrary.org/obo/CDAO_0000093 --> 2155 2156 <owl:Class rdf:about="&obo;CDAO_0000093"> 2157 <rdfs:label rdf:datatype="&xsd;string">GammaDistribution</rdfs:label> 2158 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000020"/> 2159 </owl:Class> 2160 2161 2162 2163 <!-- http://purl.obolibrary.org/obo/CDAO_0000094 --> 2164 2165 <owl:Class rdf:about="&obo;CDAO_0000094"> 2166 <rdfs:label rdf:datatype="&xsd;string">DesoxiRibonucleotideResidueCharacter</rdfs:label> 2167 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000115"/> 2168 <rdfs:subClassOf> 2169 <owl:Restriction> 2170 <owl:onProperty rdf:resource="&obo;CDAO_0000195"/> 2171 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000002"/> 2172 </owl:Restriction> 2173 </rdfs:subClassOf> 2174 <rdfs:subClassOf> 2175 <owl:Restriction> 2176 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 2177 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000002"/> 2178 </owl:Restriction> 2179 </rdfs:subClassOf> 2180 </owl:Class> 2181 2182 2183 2184 <!-- http://purl.obolibrary.org/obo/CDAO_0000095 --> 2185 2186 <owl:Class rdf:about="&obo;CDAO_0000095"> 2187 <rdfs:label rdf:datatype="&xsd;string">CoordinateRange</rdfs:label> 2188 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000022"/> 2189 </owl:Class> 2190 2191 2192 2193 <!-- http://purl.obolibrary.org/obo/CDAO_0000096 --> 2194 2195 <owl:Class rdf:about="&obo;CDAO_0000096"> 2196 <rdfs:label rdf:datatype="&xsd;string">ReticulateEvolution</rdfs:label> 2197 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 2198 </owl:Class> 2199 2200 2201 2202 <!-- http://purl.obolibrary.org/obo/CDAO_0000097 --> 2203 2204 <owl:Class rdf:about="&obo;CDAO_0000097"> 2205 <rdfs:label rdf:datatype="&xsd;string">hereditaryChange</rdfs:label> 2206 <rdfs:subClassOf> 2207 <owl:Restriction> 2208 <owl:onProperty rdf:resource="&obo;CDAO_0000186"/> 2209 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 2210 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2211 </owl:Restriction> 2212 </rdfs:subClassOf> 2213 <rdfs:subClassOf> 2214 <owl:Restriction> 2215 <owl:onProperty rdf:resource="&obo;CDAO_0000159"/> 2216 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 2217 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2218 </owl:Restriction> 2219 </rdfs:subClassOf> 2220 <rdfs:subClassOf> 2221 <owl:Restriction> 2222 <owl:onProperty rdf:resource="&obo;CDAO_0000169"/> 2223 <owl:onClass rdf:resource="&obo;CDAO_0000071"/> 2224 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2225 </owl:Restriction> 2226 </rdfs:subClassOf> 2227 </owl:Class> 2228 2229 2230 2231 <!-- http://purl.obolibrary.org/obo/CDAO_0000098 --> 2232 2233 <owl:Class rdf:about="&obo;CDAO_0000098"> 2234 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDatum</rdfs:label> 2235 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2236 <rdfs:subClassOf> 2237 <owl:Restriction> 2238 <owl:onProperty rdf:resource="&obo;CDAO_0000205"/> 2239 <owl:onClass rdf:resource="&obo;CDAO_0000071"/> 2240 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2241 </owl:Restriction> 2242 </rdfs:subClassOf> 2243 <rdfs:subClassOf> 2244 <owl:Restriction> 2245 <owl:onProperty rdf:resource="&obo;CDAO_0000191"/> 2246 <owl:onClass rdf:resource="&obo;CDAO_0000138"/> 2247 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2248 </owl:Restriction> 2249 </rdfs:subClassOf> 2250 <dc:description>The instance of a given character for a given TU. Its state is an object property drawn from a particular character state domain, e.g., the state of an Amino_Acid_State_Datum is an object property drawn from the domain Amino_Acid.</dc:description> 2251 </owl:Class> 2252 2253 2254 2255 <!-- http://purl.obolibrary.org/obo/CDAO_0000099 --> 2256 2257 <owl:Class rdf:about="&obo;CDAO_0000099"> 2258 <rdfs:label rdf:datatype="&xsd;string">Edge</rdfs:label> 2259 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2260 <rdfs:subClassOf> 2261 <owl:Restriction> 2262 <owl:onProperty rdf:resource="&obo;CDAO_0000193"/> 2263 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000101"/> 2264 </owl:Restriction> 2265 </rdfs:subClassOf> 2266 <rdfs:subClassOf> 2267 <owl:Restriction> 2268 <owl:onProperty rdf:resource="&obo;CDAO_0000162"/> 2269 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 2270 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:qualifiedCardinality> 2271 </owl:Restriction> 2272 </rdfs:subClassOf> 2273 <dc:description>An edge connecting two nodes in a (Phylogenetic) Tree or Network, also known as a &#39;branch&#39;. Edges may have attributes such as length, degree of support, and direction. An edge can be a surrogate for a &#39;split&#39; or bipartition, since each edge in a tree divides the terminal nodes into two sets.</dc:description> 2274 </owl:Class> 2275 2276 2277 2278 <!-- http://purl.obolibrary.org/obo/CDAO_0000100 --> 2279 2280 <owl:Class rdf:about="&obo;CDAO_0000100"> 2281 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharacterLengthType</rdfs:label> 2282 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 2283 </owl:Class> 2284 2285 2286 2287 <!-- http://purl.obolibrary.org/obo/CDAO_0000101 --> 2288 2289 <owl:Class rdf:about="&obo;CDAO_0000101"> 2290 <rdfs:label rdf:datatype="&xsd;string">EdgeAnnotation</rdfs:label> 2291 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 2292 </owl:Class> 2293 2294 2295 2296 <!-- http://purl.obolibrary.org/obo/CDAO_0000102 --> 2297 2298 <owl:Class rdf:about="&obo;CDAO_0000102"> 2299 <rdfs:label rdf:datatype="&xsd;string">FullyResolvedRootedTree</rdfs:label> 2300 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 2301 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000018"/> 2302 <rdfs:subClassOf> 2303 <owl:Restriction> 2304 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 2305 <owl:allValuesFrom> 2306 <owl:Class> 2307 <owl:unionOf rdf:parseType="Collection"> 2308 <rdf:Description rdf:about="&obo;CDAO_0000033"/> 2309 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 2310 <rdf:Description rdf:about="&obo;CDAO_0000108"/> 2311 </owl:unionOf> 2312 </owl:Class> 2313 </owl:allValuesFrom> 2314 </owl:Restriction> 2315 </rdfs:subClassOf> 2316 </owl:Class> 2317 2318 2319 2320 <!-- http://purl.obolibrary.org/obo/CDAO_0000103 --> 2321 2322 <owl:Class rdf:about="&obo;CDAO_0000103"> 2323 <rdfs:label rdf:datatype="&xsd;string">GrafenLengthType</rdfs:label> 2324 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 2325 </owl:Class> 2326 2327 2328 2329 <!-- http://purl.obolibrary.org/obo/CDAO_0000104 --> 2330 2331 <owl:Class rdf:about="&obo;CDAO_0000104"> 2332 <rdfs:label rdf:datatype="&xsd;string">CoordinateSystem</rdfs:label> 2333 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2334 <dc:description>A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.</dc:description> 2335 </owl:Class> 2336 2337 2338 2339 <!-- http://purl.obolibrary.org/obo/CDAO_0000105 --> 2340 2341 <owl:Class rdf:about="&obo;CDAO_0000105"> 2342 <rdfs:label rdf:datatype="&xsd;string">GenBankDataMatrix</rdfs:label> 2343 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 2344 </owl:Class> 2345 2346 2347 2348 <!-- http://purl.obolibrary.org/obo/CDAO_0000107 --> 2349 2350 <owl:Class rdf:about="&obo;CDAO_0000107"> 2351 <rdfs:label rdf:datatype="&xsd;string">DataMatrixFormat</rdfs:label> 2352 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000025"/> 2353 </owl:Class> 2354 2355 2356 2357 <!-- http://purl.obolibrary.org/obo/CDAO_0000108 --> 2358 2359 <owl:Class rdf:about="&obo;CDAO_0000108"> 2360 <rdfs:label rdf:datatype="&xsd;string">TerminalNode</rdfs:label> 2361 <owl:equivalentClass> 2362 <owl:Class> 2363 <owl:intersectionOf rdf:parseType="Collection"> 2364 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 2365 <owl:Restriction> 2366 <owl:onProperty rdf:resource="&obo;CDAO_0000149"/> 2367 <owl:allValuesFrom> 2368 <owl:Class> 2369 <owl:complementOf rdf:resource="&obo;CDAO_0000140"/> 2370 </owl:Class> 2371 </owl:allValuesFrom> 2372 </owl:Restriction> 2373 </owl:intersectionOf> 2374 </owl:Class> 2375 </owl:equivalentClass> 2376 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000140"/> 2377 </owl:Class> 2378 2379 2380 2381 <!-- http://purl.obolibrary.org/obo/CDAO_0000109 --> 2382 2383 <owl:Class rdf:about="&obo;CDAO_0000109"> 2384 <rdfs:label rdf:datatype="&xsd;string">RibonucleotideResidueCharacter</rdfs:label> 2385 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000115"/> 2386 <rdfs:subClassOf> 2387 <owl:Restriction> 2388 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 2389 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000057"/> 2390 </owl:Restriction> 2391 </rdfs:subClassOf> 2392 </owl:Class> 2393 2394 2395 2396 <!-- http://purl.obolibrary.org/obo/CDAO_0000110 --> 2397 2398 <owl:Class rdf:about="&obo;CDAO_0000110"> 2399 <rdfs:label rdf:datatype="&xsd;string">Tree</rdfs:label> 2400 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 2401 </owl:Class> 2402 2403 2404 2405 <!-- http://purl.obolibrary.org/obo/CDAO_0000111 --> 2406 2407 <owl:Class rdf:about="&obo;CDAO_0000111"> 2408 <rdfs:label rdf:datatype="&xsd;string">CategoricalCharacter</rdfs:label> 2409 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000071"/> 2410 </owl:Class> 2411 2412 2413 2414 <!-- http://purl.obolibrary.org/obo/CDAO_0000112 --> 2415 2416 <owl:Class rdf:about="&obo;CDAO_0000112"> 2417 <rdfs:label rdf:datatype="&xsd;string">AminoAcidResidueStateDatum</rdfs:label> 2418 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000050"/> 2419 </owl:Class> 2420 2421 2422 2423 <!-- http://purl.obolibrary.org/obo/CDAO_0000113 --> 2424 2425 <owl:Class rdf:about="&obo;CDAO_0000113"> 2426 <rdfs:label rdf:datatype="&xsd;string">PHYLIPDataMatrix</rdfs:label> 2427 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 2428 </owl:Class> 2429 2430 2431 2432 <!-- http://purl.obolibrary.org/obo/CDAO_0000114 --> 2433 2434 <owl:Class rdf:about="&obo;CDAO_0000114"> 2435 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharLikelihoodLengthType</rdfs:label> 2436 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 2437 </owl:Class> 2438 2439 2440 2441 <!-- http://purl.obolibrary.org/obo/CDAO_0000115 --> 2442 2443 <owl:Class rdf:about="&obo;CDAO_0000115"> 2444 <rdfs:label rdf:datatype="&xsd;string">MolecularCharacter</rdfs:label> 2445 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000111"/> 2446 </owl:Class> 2447 2448 2449 2450 <!-- http://purl.obolibrary.org/obo/CDAO_0000116 --> 2451 2452 <owl:Class rdf:about="&obo;CDAO_0000116"> 2453 <rdfs:label rdf:datatype="&xsd;string">hereditaryPersistance</rdfs:label> 2454 <rdfs:subClassOf> 2455 <owl:Restriction> 2456 <owl:onProperty rdf:resource="&obo;CDAO_0000190"/> 2457 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000097"/> 2458 </owl:Restriction> 2459 </rdfs:subClassOf> 2460 </owl:Class> 2461 2462 2463 2464 <!-- http://purl.obolibrary.org/obo/CDAO_0000117 --> 2465 2466 <owl:Class rdf:about="&obo;CDAO_0000117"> 2467 <rdfs:label rdf:datatype="&xsd;string">SetOfCharacters</rdfs:label> 2468 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000118"/> 2469 </owl:Class> 2470 2471 2472 2473 <!-- http://purl.obolibrary.org/obo/CDAO_0000118 --> 2474 2475 <owl:Class rdf:about="&obo;CDAO_0000118"> 2476 <rdfs:label rdf:datatype="&xsd;string">SetOfThings</rdfs:label> 2477 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2478 <rdfs:subClassOf> 2479 <owl:Restriction> 2480 <owl:onProperty rdf:resource="&obo;CDAO_0000198"/> 2481 <owl:allValuesFrom> 2482 <owl:Class> 2483 <owl:unionOf rdf:parseType="Collection"> 2484 <rdf:Description rdf:about="&obo;CDAO_0000071"/> 2485 <rdf:Description rdf:about="&obo;CDAO_0000117"/> 2486 </owl:unionOf> 2487 </owl:Class> 2488 </owl:allValuesFrom> 2489 </owl:Restriction> 2490 </rdfs:subClassOf> 2491 <dc:description>The class is used to describe either colletions of characters or higher order grouping (e.g., groups of groups of characters). This extends the CharSet block of NEXUS.</dc:description> 2492 </owl:Class> 2493 2494 2495 2496 <!-- http://purl.obolibrary.org/obo/CDAO_0000120 --> 2497 2498 <owl:Class rdf:about="&obo;CDAO_0000120"> 2499 <rdfs:label rdf:datatype="&xsd;string">Sequence</rdfs:label> 2500 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2501 <rdfs:subClassOf> 2502 <owl:Restriction> 2503 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 2504 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000098"/> 2505 </owl:Restriction> 2506 </rdfs:subClassOf> 2507 <rdfs:subClassOf> 2508 <owl:Restriction> 2509 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 2510 <owl:allValuesFrom> 2511 <owl:Restriction> 2512 <owl:onProperty rdf:resource="&obo;CDAO_0000151"/> 2513 <owl:onClass rdf:resource="&obo;CDAO_0000022"/> 2514 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 2515 </owl:Restriction> 2516 </owl:allValuesFrom> 2517 </owl:Restriction> 2518 </rdfs:subClassOf> 2519 <dc:description>A set of ordered states, typically the residues in a macromolecular sequence.</dc:description> 2520 </owl:Class> 2521 2522 2523 2524 <!-- http://purl.obolibrary.org/obo/CDAO_0000121 --> 2525 2526 <owl:Class rdf:about="&obo;CDAO_0000121"> 2527 <rdfs:label rdf:datatype="&xsd;string">speciation</rdfs:label> 2528 <owl:equivalentClass rdf:resource="&obo;CDAO_0000122"/> 2529 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000064"/> 2530 </owl:Class> 2531 2532 2533 2534 <!-- http://purl.obolibrary.org/obo/CDAO_0000122 --> 2535 2536 <owl:Class rdf:about="&obo;CDAO_0000122"> 2537 <rdfs:label rdf:datatype="&xsd;string">cladogenesis</rdfs:label> 2538 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000064"/> 2539 </owl:Class> 2540 2541 2542 2543 <!-- http://purl.obolibrary.org/obo/CDAO_0000124 --> 2544 2545 <owl:Class rdf:about="&obo;CDAO_0000124"> 2546 <rdfs:label rdf:datatype="&xsd;string">Bifurcation</rdfs:label> 2547 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 2548 <rdfs:subClassOf> 2549 <owl:Restriction> 2550 <owl:onProperty rdf:resource="&obo;CDAO_0000177"/> 2551 <owl:cardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:cardinality> 2552 </owl:Restriction> 2553 </rdfs:subClassOf> 2554 </owl:Class> 2555 2556 2557 2558 <!-- http://purl.obolibrary.org/obo/CDAO_0000125 --> 2559 2560 <owl:Class rdf:about="&obo;CDAO_0000125"> 2561 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharBayesianLengthType</rdfs:label> 2562 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 2563 </owl:Class> 2564 2565 2566 2567 <!-- http://purl.obolibrary.org/obo/CDAO_0000126 --> 2568 2569 <owl:Class rdf:about="&obo;CDAO_0000126"> 2570 <rdfs:label rdf:datatype="&xsd;string">TaxonomicLink</rdfs:label> 2571 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000066"/> 2572 <dc:description>Link to an externally defined taxonomic hierarchy.</dc:description> 2573 </owl:Class> 2574 2575 2576 2577 <!-- http://purl.obolibrary.org/obo/CDAO_0000127 --> 2578 2579 <owl:Class rdf:about="&obo;CDAO_0000127"> 2580 <rdfs:label rdf:datatype="&xsd;string">MonophyleticGroup</rdfs:label> 2581 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 2582 </owl:Class> 2583 2584 2585 2586 <!-- http://purl.obolibrary.org/obo/CDAO_0000128 --> 2587 2588 <owl:Class rdf:about="&obo;CDAO_0000128"> 2589 <rdfs:label rdf:datatype="&xsd;string">molecularRecombination</rdfs:label> 2590 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000132"/> 2591 </owl:Class> 2592 2593 2594 2595 <!-- http://purl.obolibrary.org/obo/CDAO_0000129 --> 2596 2597 <owl:Class rdf:about="&obo;CDAO_0000129"> 2598 <rdfs:label rdf:datatype="&xsd;string">HolophyleticGroup</rdfs:label> 2599 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000127"/> 2600 </owl:Class> 2601 2602 2603 2604 <!-- http://purl.obolibrary.org/obo/CDAO_0000130 --> 2605 2606 <owl:Class rdf:about="&obo;CDAO_0000130"> 2607 <rdfs:label rdf:datatype="&xsd;string">FullyResolvedTree</rdfs:label> 2608 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 2609 </owl:Class> 2610 2611 2612 2613 <!-- http://purl.obolibrary.org/obo/CDAO_0000131 --> 2614 2615 <owl:Class rdf:about="&obo;CDAO_0000131"> 2616 <rdfs:label rdf:datatype="&xsd;string">AminoAcidResidueCharacter</rdfs:label> 2617 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000115"/> 2618 <rdfs:subClassOf> 2619 <owl:Restriction> 2620 <owl:onProperty rdf:resource="&obo;CDAO_0000168"/> 2621 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000112"/> 2622 </owl:Restriction> 2623 </rdfs:subClassOf> 2624 <rdfs:subClassOf> 2625 <owl:Restriction> 2626 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 2627 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000112"/> 2628 </owl:Restriction> 2629 </rdfs:subClassOf> 2630 </owl:Class> 2631 2632 2633 2634 <!-- http://purl.obolibrary.org/obo/CDAO_0000132 --> 2635 2636 <owl:Class rdf:about="&obo;CDAO_0000132"> 2637 <rdfs:label rdf:datatype="&xsd;string">recombination</rdfs:label> 2638 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000087"/> 2639 </owl:Class> 2640 2641 2642 2643 <!-- http://purl.obolibrary.org/obo/CDAO_0000133 --> 2644 2645 <owl:Class rdf:about="&obo;CDAO_0000133"> 2646 <rdfs:label rdf:datatype="&xsd;string">DesoxiRibonucleotideResidue</rdfs:label> 2647 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000034"/> 2648 </owl:Class> 2649 2650 2651 2652 <!-- http://purl.obolibrary.org/obo/CDAO_0000134 --> 2653 2654 <owl:Class rdf:about="&obo;CDAO_0000134"> 2655 <rdfs:label rdf:datatype="&xsd;string">RootedSubtree</rdfs:label> 2656 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 2657 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000070"/> 2658 </owl:Class> 2659 2660 2661 2662 <!-- http://purl.obolibrary.org/obo/CDAO_0000136 --> 2663 2664 <owl:Class rdf:about="&obo;CDAO_0000136"> 2665 <rdfs:label rdf:datatype="&xsd;string">CompoundStateDatum</rdfs:label> 2666 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000089"/> 2667 </owl:Class> 2668 2669 2670 2671 <!-- http://purl.obolibrary.org/obo/CDAO_0000137 --> 2672 2673 <owl:Class rdf:about="&obo;CDAO_0000137"> 2674 <rdfs:label rdf:datatype="&xsd;string">GapCost</rdfs:label> 2675 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000007"/> 2676 </owl:Class> 2677 2678 2679 2680 <!-- http://purl.obolibrary.org/obo/CDAO_0000138 --> 2681 2682 <owl:Class rdf:about="&obo;CDAO_0000138"> 2683 <rdfs:label rdf:datatype="&xsd;string">TU</rdfs:label> 2684 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2685 <dc:description>A unit of analysis that may be tied to a node in a tree and to a row in a character matrix. It subsumes the traditional concepts of &#39;OTU&#39; and &#39;HTU&#39;.</dc:description> 2686 </owl:Class> 2687 2688 2689 2690 <!-- http://purl.obolibrary.org/obo/CDAO_0000139 --> 2691 2692 <owl:Class rdf:about="&obo;CDAO_0000139"> 2693 <rdfs:label rdf:datatype="&xsd;string">DirectedEdge</rdfs:label> 2694 <owl:equivalentClass> 2695 <owl:Class> 2696 <owl:intersectionOf rdf:parseType="Collection"> 2697 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 2698 <owl:Restriction> 2699 <owl:onProperty rdf:resource="&obo;CDAO_0000201"/> 2700 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 2701 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2702 </owl:Restriction> 2703 <owl:Restriction> 2704 <owl:onProperty rdf:resource="&obo;CDAO_0000209"/> 2705 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 2706 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2707 </owl:Restriction> 2708 </owl:intersectionOf> 2709 </owl:Class> 2710 </owl:equivalentClass> 2711 <dc:description>A directed edge. Rooted trees have directed edges. The direction is specified by way of the parent and child relationships of nodes that the edge connects.</dc:description> 2712 </owl:Class> 2713 2714 2715 2716 <!-- http://purl.obolibrary.org/obo/CDAO_0000140 --> 2717 2718 <owl:Class rdf:about="&obo;CDAO_0000140"> 2719 <rdfs:label rdf:datatype="&xsd;string">Node</rdfs:label> 2720 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2721 <rdfs:subClassOf> 2722 <owl:Restriction> 2723 <owl:onProperty rdf:resource="&obo;CDAO_0000143"/> 2724 <owl:onClass rdf:resource="&obo;CDAO_0000139"/> 2725 <owl:maxQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:maxQualifiedCardinality> 2726 </owl:Restriction> 2727 </rdfs:subClassOf> 2728 <rdfs:subClassOf> 2729 <owl:Restriction> 2730 <owl:onProperty rdf:resource="&obo;CDAO_0000194"/> 2731 <owl:onClass rdf:resource="&obo;CDAO_0000006"/> 2732 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 2733 </owl:Restriction> 2734 </rdfs:subClassOf> 2735 </owl:Class> 2736 2737 2738 2739 <!-- http://purl.obolibrary.org/obo/CDAO_0000141 --> 2740 2741 <owl:Class rdf:about="&obo;CDAO_0000141"> 2742 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharDistanceLengthType</rdfs:label> 2743 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 2744 </owl:Class> 2745 2746 2747 2748 <!-- 2749 /////////////////////////////////////////////////////////////////////////////////////// 2750 // 2751 // Individuals 2752 // 2753 /////////////////////////////////////////////////////////////////////////////////////// 2754 --> 2755 2756 2757 2758 2759 <!-- http://purl.obolibrary.org/obo/CDAO_0000220 --> 2760 2761 <owl:Thing rdf:about="&obo;CDAO_0000220"> 2762 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2763 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2764 <rdfs:label rdf:datatype="&xsd;string">dA</rdfs:label> 2765 </owl:Thing> 2766 2767 2768 2769 <!-- http://purl.obolibrary.org/obo/CDAO_0000221 --> 2770 2771 <owl:Thing rdf:about="&obo;CDAO_0000221"> 2772 <rdf:type rdf:resource="&obo;CDAO_0000015"/> 2773 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2774 <rdfs:label rdf:datatype="&xsd;string">absent</rdfs:label> 2775 </owl:Thing> 2776 2777 2778 2779 <!-- http://purl.obolibrary.org/obo/CDAO_0000222 --> 2780 2781 <owl:Thing rdf:about="&obo;CDAO_0000222"> 2782 <rdf:type rdf:resource="&obo;CDAO_0000015"/> 2783 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2784 <rdfs:label rdf:datatype="&xsd;string">unknown</rdfs:label> 2785 </owl:Thing> 2786 2787 2788 2789 <!-- http://purl.obolibrary.org/obo/CDAO_0000223 --> 2790 2791 <owl:Thing rdf:about="&obo;CDAO_0000223"> 2792 <rdf:type rdf:resource="&obo;CDAO_0000015"/> 2793 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2794 <rdfs:label rdf:datatype="&xsd;string">gap</rdfs:label> 2795 </owl:Thing> 2796 2797 2798 2799 <!-- http://purl.obolibrary.org/obo/CDAO_0000224 --> 2800 2801 <owl:Thing rdf:about="&obo;CDAO_0000224"> 2802 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2803 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2804 <rdfs:label rdf:datatype="&xsd;string">dG</rdfs:label> 2805 </owl:Thing> 2806 2807 2808 2809 <!-- http://purl.obolibrary.org/obo/CDAO_0000225 --> 2810 2811 <owl:Thing rdf:about="&obo;CDAO_0000225"> 2812 <rdf:type rdf:resource="&obo;CDAO_0000057"/> 2813 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2814 <rdfs:label rdf:datatype="&xsd;string">rU</rdfs:label> 2815 </owl:Thing> 2816 2817 2818 2819 <!-- http://purl.obolibrary.org/obo/CDAO_0000226 --> 2820 2821 <owl:Thing rdf:about="&obo;CDAO_0000226"> 2822 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2823 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2824 <rdfs:label rdf:datatype="&xsd;string">dC</rdfs:label> 2825 </owl:Thing> 2826 2827 2828 2829 <!-- http://purl.obolibrary.org/obo/CDAO_0000227 --> 2830 2831 <owl:Thing rdf:about="&obo;CDAO_0000227"> 2832 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2833 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2834 <rdfs:label rdf:datatype="&xsd;string">dT</rdfs:label> 2835 </owl:Thing> 2836 2837 2838 2839 <!-- 2840 /////////////////////////////////////////////////////////////////////////////////////// 2841 // 2842 // General axioms 2843 // 2844 /////////////////////////////////////////////////////////////////////////////////////// 2845 --> 2846 2847 <rdf:Description> 2848 <rdf:type rdf:resource="&owl;AllDisjointClasses"/> 2849 <owl:members rdf:parseType="Collection"> 2850 <rdf:Description rdf:about="&obo;CDAO_0000068"/> 2851 <rdf:Description rdf:about="&obo;CDAO_0000094"/> 2852 <rdf:Description rdf:about="&obo;CDAO_0000131"/> 2853 </owl:members> 2854 </rdf:Description> 2855 <rdf:Description> 2856 <rdf:type rdf:resource="&owl;AllDisjointClasses"/> 2857 <owl:members rdf:parseType="Collection"> 2858 <rdf:Description rdf:about="&obo;CDAO_0000002"/> 2859 <rdf:Description rdf:about="&obo;CDAO_0000019"/> 2860 <rdf:Description rdf:about="&obo;CDAO_0000112"/> 2861 </owl:members> 2862 </rdf:Description> 2863 </rdf:RDF> 2864 2865 2866 2867 <!-- Generated by the OWL API (version 3.2.3.1824) http://owlapi.sourceforge.net --> 2868 2869 ''' 2870 2871 cdao_elements = {} 2872 2873 root = ET.fromstring(cdao_owl) 2874 for node_type in 'ObjectProperty', 'Class', 'DatatypeProperty': 2875 for element in root.findall('{http://www.w3.org/2002/07/owl#}%s' % node_type): 2876 obo = element.attrib['{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about'].split('/')[-1] 2877 cdao = element.find('{http://www.w3.org/2000/01/rdf-schema#}label').text 2878 cdao_elements[cdao] = obo 2879