Package Bio :: Package Phylo :: Module _cdao_owl
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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   
   9  cdao_namespaces = { 
  10      'cdao': 'http://purl.obolibrary.org/obo/cdao.owl#', 
  11      'obo': 'http://purl.obolibrary.org/obo/', 
  12  } 
  13   
  14   
15 -def resolve_uri(s, namespaces=cdao_namespaces, cdao_to_obo=True, xml_style=False):
16 """Converts prefixed URIs to full URIs. 17 18 Optionally, converts CDAO named identifiers to OBO numeric identifiers. 19 """ 20 21 if cdao_to_obo and s.startswith('cdao:'): 22 return resolve_uri('obo:%s' % cdao_elements[s[5:]], namespaces, cdao_to_obo) 23 24 for prefix in namespaces: 25 if xml_style: 26 s = s.replace(prefix + ':', '{%s}' % namespaces[prefix]) 27 else: 28 s = s.replace(prefix + ':', namespaces[prefix]) 29 30 return s
31 32 33 cdao_owl = '''<?xml version="1.0"?> 34 35 36 <!DOCTYPE rdf:RDF [ 37 <!ENTITY owl "http://www.w3.org/2002/07/owl#" > 38 <!ENTITY obo "http://purl.obolibrary.org/obo/" > 39 <!ENTITY dc "http://purl.org/dc/elements/1.1/" > 40 <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > 41 <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > 42 <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > 43 ]> 44 45 46 <rdf:RDF xmlns="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#" 47 xml:base="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl" 48 xmlns:dc="http://purl.org/dc/elements/1.1/" 49 xmlns:obo="http://purl.obolibrary.org/obo/" 50 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 51 xmlns:owl="http://www.w3.org/2002/07/owl#" 52 xmlns:xsd="http://www.w3.org/2001/XMLSchema#" 53 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> 54 <owl:Ontology rdf:about="&obo;cdao.owl"> 55 <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> 56 <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> 57 <dc:creator xml:lang="en">CDAO Team</dc:creator> 58 <dc:title xml:lang="en">Comparative Data Analysis Ontology</dc:title> 59 <dc:subject xml:lang="en">comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics</dc:subject> 60 <dc:rights rdf:resource="http://creativecommons.org/publicdomain/zero/1.0/"/> 61 <owl:versionIRI rdf:resource="&obo;cdao/2012-06-06/cdao.owl"/> 62 <owl:imports rdf:resource="&obo;iao/ontology-metadata.owl"/> 63 </owl:Ontology> 64 65 66 67 <!-- 68 /////////////////////////////////////////////////////////////////////////////////////// 69 // 70 // Annotation properties 71 // 72 /////////////////////////////////////////////////////////////////////////////////////// 73 --> 74 75 <owl:AnnotationProperty rdf:about="&dc;creator"/> 76 <owl:AnnotationProperty rdf:about="&dc;subject"/> 77 <owl:AnnotationProperty rdf:about="&dc;description"/> 78 <owl:AnnotationProperty rdf:about="&dc;coverage"/> 79 <owl:AnnotationProperty rdf:about="&dc;language"/> 80 <owl:AnnotationProperty rdf:about="&dc;identifier"/> 81 <owl:AnnotationProperty rdf:about="&dc;date"/> 82 <owl:AnnotationProperty rdf:about="&dc;source"/> 83 <owl:AnnotationProperty rdf:about="&dc;title"/> 84 <owl:AnnotationProperty rdf:about="&dc;rights"/> 85 86 87 88 89 90 91 <!-- 92 /////////////////////////////////////////////////////////////////////////////////////// 93 // 94 // Object Properties 95 // 96 /////////////////////////////////////////////////////////////////////////////////////// 97 --> 98 99 100 101 102 <!-- http://purl.obolibrary.org/obo/CDAO_0000142 --> 103 104 <owl:ObjectProperty rdf:about="&obo;CDAO_0000142"> 105 <rdfs:label rdf:datatype="&xsd;string">has_Character</rdfs:label> 106 <dc:description rdf:datatype="&xsd;string">This property associates a character data matrix with a character (a column) represented in the matrix.</dc:description> 107 <rdfs:domain rdf:resource="&obo;CDAO_0000056"/> 108 <rdfs:range rdf:resource="&obo;CDAO_0000071"/> 109 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 110 </owl:ObjectProperty> 111 112 113 114 <!-- http://purl.obolibrary.org/obo/CDAO_0000143 --> 115 116 <owl:ObjectProperty rdf:about="&obo;CDAO_0000143"> 117 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Edge_as_Child</rdfs:label> 118 <dc:description>The property links a Node to the Edge it belongs to in the child position.</dc:description> 119 <rdfs:range rdf:resource="&obo;CDAO_0000139"/> 120 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 121 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000146"/> 122 <owl:inverseOf rdf:resource="&obo;CDAO_0000209"/> 123 </owl:ObjectProperty> 124 125 126 127 <!-- http://purl.obolibrary.org/obo/CDAO_0000144 --> 128 129 <owl:ObjectProperty rdf:about="&obo;CDAO_0000144"> 130 <rdf:type rdf:resource="&owl;TransitiveProperty"/> 131 <rdfs:label rdf:datatype="&xsd;string">has_Ancestor</rdfs:label> 132 <dc:description>The property links a node to any of the other nodes that are its ancestors in a rooted tree.</dc:description> 133 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 134 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 135 <owl:inverseOf rdf:resource="&obo;CDAO_0000174"/> 136 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 137 </owl:ObjectProperty> 138 139 140 141 <!-- http://purl.obolibrary.org/obo/CDAO_0000145 --> 142 143 <owl:ObjectProperty rdf:about="&obo;CDAO_0000145"> 144 <rdfs:label rdf:datatype="&xsd;string">has_Nucleotide_State</rdfs:label> 145 <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> 146 <rdfs:domain rdf:resource="&obo;CDAO_0000002"/> 147 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 148 <rdfs:range> 149 <owl:Class> 150 <owl:unionOf rdf:parseType="Collection"> 151 <rdf:Description rdf:about="&obo;CDAO_0000015"/> 152 <rdf:Description rdf:about="&obo;CDAO_0000133"/> 153 </owl:unionOf> 154 </owl:Class> 155 </rdfs:range> 156 </owl:ObjectProperty> 157 158 159 160 <!-- http://purl.obolibrary.org/obo/CDAO_0000146 --> 161 162 <owl:ObjectProperty rdf:about="&obo;CDAO_0000146"> 163 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Edge</rdfs:label> 164 <dc:description>The property links a Node to one of the edges that are incident on such node.</dc:description> 165 <rdfs:range rdf:resource="&obo;CDAO_0000099"/> 166 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 167 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 168 </owl:ObjectProperty> 169 170 171 172 <!-- http://purl.obolibrary.org/obo/CDAO_0000147 --> 173 174 <owl:ObjectProperty rdf:about="&obo;CDAO_0000147"> 175 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Character_State_Data_Matrix</rdfs:label> 176 <rdfs:range rdf:resource="&obo;CDAO_0000056"/> 177 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 178 <rdfs:domain> 179 <owl:Class> 180 <owl:unionOf rdf:parseType="Collection"> 181 <rdf:Description rdf:about="&obo;CDAO_0000071"/> 182 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 183 </owl:unionOf> 184 </owl:Class> 185 </rdfs:domain> 186 </owl:ObjectProperty> 187 188 189 190 <!-- http://purl.obolibrary.org/obo/CDAO_0000148 --> 191 192 <owl:ObjectProperty rdf:about="&obo;CDAO_0000148"> 193 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 194 <rdfs:label rdf:datatype="&xsd;string">has_Root</rdfs:label> 195 <dc:description>The property links a rooted tree to the specific node that represents the unique root of the tree.</dc:description> 196 <rdfs:domain rdf:resource="&obo;CDAO_0000012"/> 197 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 198 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 199 </owl:ObjectProperty> 200 201 202 203 <!-- http://purl.obolibrary.org/obo/CDAO_0000149 --> 204 205 <owl:ObjectProperty rdf:about="&obo;CDAO_0000149"> 206 <rdfs:label rdf:datatype="&xsd;string">has_Child</rdfs:label> 207 <dc:description>The property links a node to a node that is an immediate descendant in the tree.</dc:description> 208 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 209 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 210 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000174"/> 211 <owl:inverseOf rdf:resource="&obo;CDAO_0000179"/> 212 <owl:propertyChainAxiom rdf:parseType="Collection"> 213 <rdf:Description rdf:about="&obo;CDAO_0000177"/> 214 <rdf:Description rdf:about="&obo;CDAO_0000209"/> 215 </owl:propertyChainAxiom> 216 </owl:ObjectProperty> 217 218 219 220 <!-- http://purl.obolibrary.org/obo/CDAO_0000150 --> 221 222 <owl:ObjectProperty rdf:about="&obo;CDAO_0000150"> 223 <rdfs:label rdf:datatype="&xsd;string">has_First_Coordinate_Item</rdfs:label> 224 <dc:description rdf:datatype="&xsd;string">The property that relates a coordinate list to the first item in the list.</dc:description> 225 <rdfs:domain rdf:resource="&obo;CDAO_0000092"/> 226 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 227 <rdfs:range> 228 <owl:Class> 229 <owl:unionOf rdf:parseType="Collection"> 230 <rdf:Description rdf:about="&obo;CDAO_0000003"/> 231 <rdf:Description rdf:about="&obo;CDAO_0000095"/> 232 </owl:unionOf> 233 </owl:Class> 234 </rdfs:range> 235 </owl:ObjectProperty> 236 237 238 239 <!-- http://purl.obolibrary.org/obo/CDAO_0000151 --> 240 241 <owl:ObjectProperty rdf:about="&obo;CDAO_0000151"> 242 <rdfs:label rdf:datatype="&xsd;string">has_Coordinate</rdfs:label> 243 <rdfs:range rdf:resource="&obo;CDAO_0000022"/> 244 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 245 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 246 </owl:ObjectProperty> 247 248 249 250 <!-- http://purl.obolibrary.org/obo/CDAO_0000152 --> 251 252 <owl:ObjectProperty rdf:about="&obo;CDAO_0000152"> 253 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 254 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Continuous_Character</rdfs:label> 255 <rdfs:domain rdf:resource="&obo;CDAO_0000019"/> 256 <rdfs:range rdf:resource="&obo;CDAO_0000068"/> 257 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 258 </owl:ObjectProperty> 259 260 261 262 <!-- http://purl.obolibrary.org/obo/CDAO_0000153 --> 263 264 <owl:ObjectProperty rdf:about="&obo;CDAO_0000153"> 265 <rdfs:label rdf:datatype="&xsd;string">has_Datum</rdfs:label> 266 <dc:description rdf:datatype="&xsd;string">This property relates a character to a state datum for the character.</dc:description> 267 <rdfs:range rdf:resource="&obo;CDAO_0000098"/> 268 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 269 <rdfs:domain> 270 <owl:Class> 271 <owl:unionOf rdf:parseType="Collection"> 272 <rdf:Description rdf:about="&obo;CDAO_0000071"/> 273 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 274 </owl:unionOf> 275 </owl:Class> 276 </rdfs:domain> 277 </owl:ObjectProperty> 278 279 280 281 <!-- http://purl.obolibrary.org/obo/CDAO_0000154 --> 282 283 <owl:ObjectProperty rdf:about="&obo;CDAO_0000154"> 284 <rdfs:label rdf:datatype="&xsd;string">has_Standard_Datum</rdfs:label> 285 <rdfs:range rdf:resource="&obo;CDAO_0000008"/> 286 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000183"/> 287 <rdfs:domain> 288 <owl:Class> 289 <owl:unionOf rdf:parseType="Collection"> 290 <rdf:Description rdf:about="&obo;CDAO_0000075"/> 291 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 292 </owl:unionOf> 293 </owl:Class> 294 </rdfs:domain> 295 </owl:ObjectProperty> 296 297 298 299 <!-- http://purl.obolibrary.org/obo/CDAO_0000155 --> 300 301 <owl:ObjectProperty rdf:about="&obo;CDAO_0000155"> 302 <rdfs:label rdf:datatype="&xsd;string">subtree_of</rdfs:label> 303 <dc:description>This property links two networks where the latter is a substructure of the former</dc:description> 304 <rdfs:range rdf:resource="&obo;CDAO_0000006"/> 305 <rdfs:domain rdf:resource="&obo;CDAO_0000006"/> 306 </owl:ObjectProperty> 307 308 309 310 <!-- http://purl.obolibrary.org/obo/CDAO_0000156 --> 311 312 <owl:ObjectProperty rdf:about="&obo;CDAO_0000156"> 313 <rdfs:label rdf:datatype="&xsd;string">has_Amino_Acid_State</rdfs:label> 314 <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> 315 <rdfs:domain rdf:resource="&obo;CDAO_0000112"/> 316 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 317 <rdfs:range> 318 <owl:Class> 319 <owl:unionOf rdf:parseType="Collection"> 320 <rdf:Description rdf:about="&obo;CDAO_0000015"/> 321 <rdf:Description rdf:about="&obo;CDAO_0000076"/> 322 </owl:unionOf> 323 </owl:Class> 324 </rdfs:range> 325 </owl:ObjectProperty> 326 327 328 329 <!-- http://purl.obolibrary.org/obo/CDAO_0000157 --> 330 331 <owl:ObjectProperty rdf:about="&obo;CDAO_0000157"> 332 <rdfs:label rdf:datatype="&xsd;string">is_annotation_of</rdfs:label> 333 <rdfs:domain rdf:resource="&obo;CDAO_0000040"/> 334 <rdfs:range rdf:resource="&owl;Thing"/> 335 </owl:ObjectProperty> 336 337 338 339 <!-- http://purl.obolibrary.org/obo/CDAO_0000158 --> 340 341 <owl:ObjectProperty rdf:about="&obo;CDAO_0000158"> 342 <rdfs:label rdf:datatype="&xsd;string">has_RNA_Datum</rdfs:label> 343 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000206"/> 344 </owl:ObjectProperty> 345 346 347 348 <!-- http://purl.obolibrary.org/obo/CDAO_0000159 --> 349 350 <owl:ObjectProperty rdf:about="&obo;CDAO_0000159"> 351 <rdfs:label rdf:datatype="&xsd;string">has_Left_State</rdfs:label> 352 <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> 353 <rdfs:range rdf:resource="&obo;CDAO_0000091"/> 354 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 355 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 356 </owl:ObjectProperty> 357 358 359 360 <!-- http://purl.obolibrary.org/obo/CDAO_0000160 --> 361 362 <owl:ObjectProperty rdf:about="&obo;CDAO_0000160"> 363 <rdfs:label rdf:datatype="&xsd;string">precedes</rdfs:label> 364 </owl:ObjectProperty> 365 366 367 368 <!-- http://purl.obolibrary.org/obo/CDAO_0000161 --> 369 370 <owl:ObjectProperty rdf:about="&obo;CDAO_0000161"> 371 <rdfs:label rdf:datatype="&xsd;string">exclude</rdfs:label> 372 </owl:ObjectProperty> 373 374 375 376 <!-- http://purl.obolibrary.org/obo/CDAO_0000162 --> 377 378 <owl:ObjectProperty rdf:about="&obo;CDAO_0000162"> 379 <rdfs:label rdf:datatype="&xsd;string">has_Node</rdfs:label> 380 <dc:description>Property that associates to each Edge the Nodes it connects.</dc:description> 381 <rdfs:domain rdf:resource="&obo;CDAO_0000099"/> 382 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 383 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 384 </owl:ObjectProperty> 385 386 387 388 <!-- http://purl.obolibrary.org/obo/CDAO_0000163 --> 389 390 <owl:ObjectProperty rdf:about="&obo;CDAO_0000163"> 391 <rdfs:label rdf:datatype="&xsd;string">nca_node_of</rdfs:label> 392 <rdfs:range rdf:resource="&obo;CDAO_0000059"/> 393 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 394 </owl:ObjectProperty> 395 396 397 398 <!-- http://purl.obolibrary.org/obo/CDAO_0000164 --> 399 400 <owl:ObjectProperty rdf:about="&obo;CDAO_0000164"> 401 <rdfs:label rdf:datatype="&xsd;string">has_External_Reference</rdfs:label> 402 <rdfs:comment rdf:datatype="&rdfs;Literal">Associates a TU to some external taxonomy reference.</rdfs:comment> 403 <rdfs:domain rdf:resource="&obo;CDAO_0000138"/> 404 <rdfs:range rdf:resource="&owl;Thing"/> 405 </owl:ObjectProperty> 406 407 408 409 <!-- http://purl.obolibrary.org/obo/CDAO_0000165 --> 410 411 <owl:ObjectProperty rdf:about="&obo;CDAO_0000165"> 412 <rdfs:label rdf:datatype="&xsd;string">has_Coordinate_System</rdfs:label> 413 <dc:description rdf:datatype="&xsd;string">This property links a coordinate to the coordinate system it references.</dc:description> 414 <rdfs:domain rdf:resource="&obo;CDAO_0000022"/> 415 <rdfs:range rdf:resource="&obo;CDAO_0000104"/> 416 </owl:ObjectProperty> 417 418 419 420 <!-- http://purl.obolibrary.org/obo/CDAO_0000166 --> 421 422 <owl:ObjectProperty rdf:about="&obo;CDAO_0000166"> 423 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 424 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Nucleotide_Character</rdfs:label> 425 <rdfs:domain rdf:resource="&obo;CDAO_0000002"/> 426 <rdfs:range rdf:resource="&obo;CDAO_0000094"/> 427 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 428 </owl:ObjectProperty> 429 430 431 432 <!-- http://purl.obolibrary.org/obo/CDAO_0000167 --> 433 434 <owl:ObjectProperty rdf:about="&obo;CDAO_0000167"> 435 <rdf:type rdf:resource="&owl;SymmetricProperty"/> 436 <rdfs:label rdf:datatype="&xsd;string">connects_to</rdfs:label> 437 <owl:inverseOf rdf:resource="&obo;CDAO_0000167"/> 438 </owl:ObjectProperty> 439 440 441 442 <!-- http://purl.obolibrary.org/obo/CDAO_0000168 --> 443 444 <owl:ObjectProperty rdf:about="&obo;CDAO_0000168"> 445 <rdfs:label rdf:datatype="&xsd;string">has_Amino_Acid_Datum</rdfs:label> 446 <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> 447 <rdfs:range rdf:resource="&obo;CDAO_0000112"/> 448 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000206"/> 449 <rdfs:domain> 450 <owl:Class> 451 <owl:unionOf rdf:parseType="Collection"> 452 <rdf:Description rdf:about="&obo;CDAO_0000131"/> 453 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 454 </owl:unionOf> 455 </owl:Class> 456 </rdfs:domain> 457 </owl:ObjectProperty> 458 459 460 461 <!-- http://purl.obolibrary.org/obo/CDAO_0000169 --> 462 463 <owl:ObjectProperty rdf:about="&obo;CDAO_0000169"> 464 <rdfs:label rdf:datatype="&xsd;string">hereditary_change_of</rdfs:label> 465 <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> 466 <rdfs:range rdf:resource="&obo;CDAO_0000071"/> 467 </owl:ObjectProperty> 468 469 470 471 <!-- http://purl.obolibrary.org/obo/CDAO_0000170 --> 472 473 <owl:ObjectProperty rdf:about="&obo;CDAO_0000170"> 474 <rdfs:label rdf:datatype="&xsd;string">has_Compound_Datum</rdfs:label> 475 <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> 476 <rdfs:range rdf:resource="&obo;CDAO_0000136"/> 477 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000183"/> 478 <rdfs:domain> 479 <owl:Class> 480 <owl:unionOf rdf:parseType="Collection"> 481 <rdf:Description rdf:about="&obo;CDAO_0000078"/> 482 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 483 </owl:unionOf> 484 </owl:Class> 485 </rdfs:domain> 486 </owl:ObjectProperty> 487 488 489 490 <!-- http://purl.obolibrary.org/obo/CDAO_0000171 --> 491 492 <owl:ObjectProperty rdf:about="&obo;CDAO_0000171"> 493 <rdfs:label rdf:datatype="&xsd;string">has_Descendants</rdfs:label> 494 <rdfs:range rdf:resource="&obo;CDAO_0000059"/> 495 <rdfs:domain rdf:resource="&obo;CDAO_0000080"/> 496 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 497 </owl:ObjectProperty> 498 499 500 501 <!-- http://purl.obolibrary.org/obo/CDAO_0000172 --> 502 503 <owl:ObjectProperty rdf:about="&obo;CDAO_0000172"> 504 <rdfs:label rdf:datatype="&xsd;string">reconciliation_of</rdfs:label> 505 <rdfs:domain rdf:resource="&obo;CDAO_0000030"/> 506 <rdfs:range rdf:resource="&obo;CDAO_0000110"/> 507 </owl:ObjectProperty> 508 509 510 511 <!-- http://purl.obolibrary.org/obo/CDAO_0000173 --> 512 513 <owl:ObjectProperty rdf:about="&obo;CDAO_0000173"> 514 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 515 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Amino_Acid_Character</rdfs:label> 516 <rdfs:domain rdf:resource="&obo;CDAO_0000112"/> 517 <rdfs:range rdf:resource="&obo;CDAO_0000131"/> 518 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 519 </owl:ObjectProperty> 520 521 522 523 <!-- http://purl.obolibrary.org/obo/CDAO_0000174 --> 524 525 <owl:ObjectProperty rdf:about="&obo;CDAO_0000174"> 526 <rdf:type rdf:resource="&owl;TransitiveProperty"/> 527 <rdfs:label rdf:datatype="&xsd;string">has_Descendant</rdfs:label> 528 <dc:description>A property that links a node to any of its descendants in a rooted tree.</dc:description> 529 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 530 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 531 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 532 </owl:ObjectProperty> 533 534 535 536 <!-- http://purl.obolibrary.org/obo/CDAO_0000175 --> 537 538 <owl:ObjectProperty rdf:about="&obo;CDAO_0000175"> 539 <rdfs:label rdf:datatype="&xsd;string">has_Continuous_State</rdfs:label> 540 <dc:description rdf:datatype="&xsd;string">This property associates a character-state instance with a state value on a continuous numeric scale.</dc:description> 541 <rdfs:domain rdf:resource="&obo;CDAO_0000019"/> 542 <rdfs:range rdf:resource="&obo;CDAO_0000031"/> 543 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 544 </owl:ObjectProperty> 545 546 547 548 <!-- http://purl.obolibrary.org/obo/CDAO_0000176 --> 549 550 <owl:ObjectProperty rdf:about="&obo;CDAO_0000176"> 551 <rdfs:label rdf:datatype="&xsd;string">has_Type</rdfs:label> 552 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 553 </owl:ObjectProperty> 554 555 556 557 <!-- http://purl.obolibrary.org/obo/CDAO_0000177 --> 558 559 <owl:ObjectProperty rdf:about="&obo;CDAO_0000177"> 560 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Edge_as_Parent</rdfs:label> 561 <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> 562 <rdfs:range rdf:resource="&obo;CDAO_0000139"/> 563 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 564 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000146"/> 565 <owl:inverseOf rdf:resource="&obo;CDAO_0000201"/> 566 </owl:ObjectProperty> 567 568 569 570 <!-- http://purl.obolibrary.org/obo/CDAO_0000178 --> 571 572 <owl:ObjectProperty rdf:about="&obo;CDAO_0000178"> 573 <rdfs:label rdf:datatype="&xsd;string">has</rdfs:label> 574 <dc:description>Generic &#39;has&#39; property.</dc:description> 575 </owl:ObjectProperty> 576 577 578 579 <!-- http://purl.obolibrary.org/obo/CDAO_0000179 --> 580 581 <owl:ObjectProperty rdf:about="&obo;CDAO_0000179"> 582 <rdfs:label rdf:datatype="&xsd;string">has_Parent</rdfs:label> 583 <dc:description>The property that links a node to its unique parent in a rooted tree.</dc:description> 584 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 585 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 586 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000144"/> 587 <owl:propertyChainAxiom rdf:parseType="Collection"> 588 <rdf:Description rdf:about="&obo;CDAO_0000143"/> 589 <rdf:Description rdf:about="&obo;CDAO_0000201"/> 590 </owl:propertyChainAxiom> 591 </owl:ObjectProperty> 592 593 594 595 <!-- http://purl.obolibrary.org/obo/CDAO_0000180 --> 596 597 <owl:ObjectProperty rdf:about="&obo;CDAO_0000180"> 598 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Compound_Character</rdfs:label> 599 <rdfs:range rdf:resource="&obo;CDAO_0000078"/> 600 <rdfs:domain rdf:resource="&obo;CDAO_0000136"/> 601 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000205"/> 602 </owl:ObjectProperty> 603 604 605 606 <!-- http://purl.obolibrary.org/obo/CDAO_0000181 --> 607 608 <owl:ObjectProperty rdf:about="&obo;CDAO_0000181"> 609 <rdfs:label rdf:datatype="&xsd;string">homologous_to</rdfs:label> 610 <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> 611 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 612 <rdfs:range rdf:resource="&obo;CDAO_0000098"/> 613 </owl:ObjectProperty> 614 615 616 617 <!-- http://purl.obolibrary.org/obo/CDAO_0000182 --> 618 619 <owl:ObjectProperty rdf:about="&obo;CDAO_0000182"> 620 <rdfs:label rdf:datatype="&xsd;string">has_Change_Component</rdfs:label> 621 <dc:description rdf:datatype="&xsd;string">This property relates a transformation to the components that compose it.</dc:description> 622 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 623 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 624 </owl:ObjectProperty> 625 626 627 628 <!-- http://purl.obolibrary.org/obo/CDAO_0000183 --> 629 630 <owl:ObjectProperty rdf:about="&obo;CDAO_0000183"> 631 <rdfs:label rdf:datatype="&xsd;string">has_Categorical_Datum</rdfs:label> 632 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000153"/> 633 </owl:ObjectProperty> 634 635 636 637 <!-- http://purl.obolibrary.org/obo/CDAO_0000184 --> 638 639 <owl:ObjectProperty rdf:about="&obo;CDAO_0000184"> 640 <rdfs:label rdf:datatype="&xsd;string">has_State</rdfs:label> 641 <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> 642 <rdfs:range rdf:resource="&obo;CDAO_0000091"/> 643 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 644 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 645 </owl:ObjectProperty> 646 647 648 649 <!-- http://purl.obolibrary.org/obo/CDAO_0000185 --> 650 651 <owl:ObjectProperty rdf:about="&obo;CDAO_0000185"> 652 <rdfs:label rdf:datatype="&xsd;string">has_Left_Node</rdfs:label> 653 <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> 654 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 655 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 656 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 657 </owl:ObjectProperty> 658 659 660 661 <!-- http://purl.obolibrary.org/obo/CDAO_0000186 --> 662 663 <owl:ObjectProperty rdf:about="&obo;CDAO_0000186"> 664 <rdfs:label rdf:datatype="&xsd;string">has_Right_State</rdfs:label> 665 <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> 666 <rdfs:range rdf:resource="&obo;CDAO_0000091"/> 667 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 668 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 669 </owl:ObjectProperty> 670 671 672 673 <!-- http://purl.obolibrary.org/obo/CDAO_0000187 --> 674 675 <owl:ObjectProperty rdf:about="&obo;CDAO_0000187"> 676 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 677 <rdfs:label rdf:datatype="&xsd;string">represents_TU</rdfs:label> 678 <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> 679 <rdfs:range rdf:resource="&obo;CDAO_0000138"/> 680 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 681 </owl:ObjectProperty> 682 683 684 685 <!-- http://purl.obolibrary.org/obo/CDAO_0000188 --> 686 687 <owl:ObjectProperty rdf:about="&obo;CDAO_0000188"> 688 <rdfs:label rdf:datatype="&xsd;string">exclude_Node</rdfs:label> 689 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 690 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000161"/> 691 </owl:ObjectProperty> 692 693 694 695 <!-- http://purl.obolibrary.org/obo/CDAO_0000189 --> 696 697 <owl:ObjectProperty rdf:about="&obo;CDAO_0000189"> 698 <rdfs:label rdf:datatype="&xsd;string">has_Compound_State</rdfs:label> 699 <dc:description rdf:datatype="&xsd;string">This property associates a compound character-state instance with its compound state value.</dc:description> 700 <rdfs:domain rdf:resource="&obo;CDAO_0000136"/> 701 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000184"/> 702 <rdfs:range> 703 <owl:Class> 704 <owl:unionOf rdf:parseType="Collection"> 705 <rdf:Description rdf:about="&obo;CDAO_0000015"/> 706 <rdf:Description rdf:about="&obo;CDAO_0000055"/> 707 </owl:unionOf> 708 </owl:Class> 709 </rdfs:range> 710 </owl:ObjectProperty> 711 712 713 714 <!-- http://purl.obolibrary.org/obo/CDAO_0000190 --> 715 716 <owl:ObjectProperty rdf:about="&obo;CDAO_0000190"> 717 <rdfs:label rdf:datatype="&xsd;string">belongs_to</rdfs:label> 718 <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> 719 <owl:equivalentProperty rdf:resource="&obo;CDAO_0000194"/> 720 <rdfs:range rdf:resource="&owl;Thing"/> 721 <rdfs:domain rdf:resource="&owl;Thing"/> 722 </owl:ObjectProperty> 723 724 725 726 <!-- http://purl.obolibrary.org/obo/CDAO_0000191 --> 727 728 <owl:ObjectProperty rdf:about="&obo;CDAO_0000191"> 729 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 730 <rdfs:label rdf:datatype="&xsd;string">belongs_to_TU</rdfs:label> 731 <dc:description rdf:datatype="&xsd;string">This property relates a character-state datum to its TU.</dc:description> 732 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 733 <rdfs:range rdf:resource="&obo;CDAO_0000138"/> 734 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 735 </owl:ObjectProperty> 736 737 738 739 <!-- http://purl.obolibrary.org/obo/CDAO_0000192 --> 740 741 <owl:ObjectProperty rdf:about="&obo;CDAO_0000192"> 742 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Network</rdfs:label> 743 <rdfs:range rdf:resource="&obo;CDAO_0000006"/> 744 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 745 <rdfs:domain> 746 <owl:Class> 747 <owl:unionOf rdf:parseType="Collection"> 748 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 749 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 750 </owl:unionOf> 751 </owl:Class> 752 </rdfs:domain> 753 </owl:ObjectProperty> 754 755 756 757 <!-- http://purl.obolibrary.org/obo/CDAO_0000193 --> 758 759 <owl:ObjectProperty rdf:about="&obo;CDAO_0000193"> 760 <rdfs:label rdf:datatype="&xsd;string">has_Annotation</rdfs:label> 761 <rdfs:range rdf:resource="&obo;CDAO_0000040"/> 762 <owl:inverseOf rdf:resource="&obo;CDAO_0000157"/> 763 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 764 <rdfs:domain rdf:resource="&owl;Thing"/> 765 </owl:ObjectProperty> 766 767 768 769 <!-- http://purl.obolibrary.org/obo/CDAO_0000194 --> 770 771 <owl:ObjectProperty rdf:about="&obo;CDAO_0000194"> 772 <rdfs:label rdf:datatype="&xsd;string">part_of</rdfs:label> 773 <owl:inverseOf rdf:resource="&obo;CDAO_0000178"/> 774 </owl:ObjectProperty> 775 776 777 778 <!-- http://purl.obolibrary.org/obo/CDAO_0000195 --> 779 780 <owl:ObjectProperty rdf:about="&obo;CDAO_0000195"> 781 <rdfs:label rdf:datatype="&xsd;string">has_Nucleotide_Datum</rdfs:label> 782 <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> 783 <rdfs:range rdf:resource="&obo;CDAO_0000002"/> 784 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000206"/> 785 <rdfs:domain> 786 <owl:Class> 787 <owl:unionOf rdf:parseType="Collection"> 788 <rdf:Description rdf:about="&obo;CDAO_0000094"/> 789 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 790 </owl:unionOf> 791 </owl:Class> 792 </rdfs:domain> 793 </owl:ObjectProperty> 794 795 796 797 <!-- http://purl.obolibrary.org/obo/CDAO_0000196 --> 798 799 <owl:ObjectProperty rdf:about="&obo;CDAO_0000196"> 800 <rdfs:label rdf:datatype="&xsd;string">represented_by_Node</rdfs:label> 801 <dc:description rdf:datatype="&xsd;string">This property relates a TU to a node that represents it in a network.</dc:description> 802 <rdfs:domain rdf:resource="&obo;CDAO_0000138"/> 803 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 804 <owl:inverseOf rdf:resource="&obo;CDAO_0000187"/> 805 </owl:ObjectProperty> 806 807 808 809 <!-- http://purl.obolibrary.org/obo/CDAO_0000197 --> 810 811 <owl:ObjectProperty rdf:about="&obo;CDAO_0000197"> 812 <rdfs:label rdf:datatype="&xsd;string">has_Remaining_Coordinate_List</rdfs:label> 813 <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> 814 <rdfs:range rdf:resource="&obo;CDAO_0000092"/> 815 <rdfs:domain rdf:resource="&obo;CDAO_0000092"/> 816 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 817 </owl:ObjectProperty> 818 819 820 821 <!-- http://purl.obolibrary.org/obo/CDAO_0000198 --> 822 823 <owl:ObjectProperty rdf:about="&obo;CDAO_0000198"> 824 <rdfs:label rdf:datatype="&xsd;string">has_Element</rdfs:label> 825 <rdfs:domain rdf:resource="&obo;CDAO_0000118"/> 826 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 827 </owl:ObjectProperty> 828 829 830 831 <!-- http://purl.obolibrary.org/obo/CDAO_0000199 --> 832 833 <owl:ObjectProperty rdf:about="&obo;CDAO_0000199"> 834 <rdfs:label rdf:datatype="&xsd;string">exclude_Subtree</rdfs:label> 835 <rdfs:range rdf:resource="&obo;CDAO_0000070"/> 836 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000161"/> 837 </owl:ObjectProperty> 838 839 840 841 <!-- http://purl.obolibrary.org/obo/CDAO_0000200 --> 842 843 <owl:ObjectProperty rdf:about="&obo;CDAO_0000200"> 844 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Tree</rdfs:label> 845 <rdfs:range rdf:resource="&obo;CDAO_0000110"/> 846 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 847 <rdfs:domain> 848 <owl:Class> 849 <owl:unionOf rdf:parseType="Collection"> 850 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 851 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 852 </owl:unionOf> 853 </owl:Class> 854 </rdfs:domain> 855 </owl:ObjectProperty> 856 857 858 859 <!-- http://purl.obolibrary.org/obo/CDAO_0000201 --> 860 861 <owl:ObjectProperty rdf:about="&obo;CDAO_0000201"> 862 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 863 <rdfs:label rdf:datatype="&xsd;string">has_Parent_Node</rdfs:label> 864 <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> 865 <rdfs:domain rdf:resource="&obo;CDAO_0000139"/> 866 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 867 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000162"/> 868 </owl:ObjectProperty> 869 870 871 872 <!-- http://purl.obolibrary.org/obo/CDAO_0000202 --> 873 874 <owl:ObjectProperty rdf:about="&obo;CDAO_0000202"> 875 <rdfs:label rdf:datatype="&xsd;string">has_Lineage_node</rdfs:label> 876 <rdfs:domain rdf:resource="&obo;CDAO_0000004"/> 877 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 878 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 879 </owl:ObjectProperty> 880 881 882 883 <!-- http://purl.obolibrary.org/obo/CDAO_0000203 --> 884 885 <owl:ObjectProperty rdf:about="&obo;CDAO_0000203"> 886 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Tree_as_Root</rdfs:label> 887 <rdfs:range rdf:resource="&obo;CDAO_0000110"/> 888 <rdfs:domain rdf:resource="&obo;CDAO_0000140"/> 889 <owl:inverseOf rdf:resource="&obo;CDAO_0000148"/> 890 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 891 </owl:ObjectProperty> 892 893 894 895 <!-- http://purl.obolibrary.org/obo/CDAO_0000204 --> 896 897 <owl:ObjectProperty rdf:about="&obo;CDAO_0000204"> 898 <rdfs:label rdf:datatype="&xsd;string">has_Hereditary_Change</rdfs:label> 899 <rdfs:range rdf:resource="&obo;CDAO_0000097"/> 900 <rdfs:domain rdf:resource="&obo;CDAO_0000099"/> 901 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 902 </owl:ObjectProperty> 903 904 905 906 <!-- http://purl.obolibrary.org/obo/CDAO_0000205 --> 907 908 <owl:ObjectProperty rdf:about="&obo;CDAO_0000205"> 909 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 910 <rdfs:label rdf:datatype="&xsd;string">belongs_to_Character</rdfs:label> 911 <rdfs:range rdf:resource="&obo;CDAO_0000071"/> 912 <rdfs:domain rdf:resource="&obo;CDAO_0000098"/> 913 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000190"/> 914 </owl:ObjectProperty> 915 916 917 918 <!-- http://purl.obolibrary.org/obo/CDAO_0000206 --> 919 920 <owl:ObjectProperty rdf:about="&obo;CDAO_0000206"> 921 <rdfs:label rdf:datatype="&xsd;string">has_Molecular_Datum</rdfs:label> 922 <rdfs:range rdf:resource="&obo;CDAO_0000050"/> 923 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000183"/> 924 <rdfs:domain> 925 <owl:Class> 926 <owl:unionOf rdf:parseType="Collection"> 927 <rdf:Description rdf:about="&obo;CDAO_0000115"/> 928 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 929 </owl:unionOf> 930 </owl:Class> 931 </rdfs:domain> 932 </owl:ObjectProperty> 933 934 935 936 <!-- http://purl.obolibrary.org/obo/CDAO_0000207 --> 937 938 <owl:ObjectProperty rdf:about="&obo;CDAO_0000207"> 939 <rdfs:label rdf:datatype="&xsd;string">has_Continuous_Datum</rdfs:label> 940 <dc:description rdf:datatype="&xsd;string">This property relates a continuous character to a state datum for the character.</dc:description> 941 <rdfs:range rdf:resource="&obo;CDAO_0000019"/> 942 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000153"/> 943 <rdfs:domain> 944 <owl:Class> 945 <owl:unionOf rdf:parseType="Collection"> 946 <rdf:Description rdf:about="&obo;CDAO_0000068"/> 947 <rdf:Description rdf:about="&obo;CDAO_0000138"/> 948 </owl:unionOf> 949 </owl:Class> 950 </rdfs:domain> 951 </owl:ObjectProperty> 952 953 954 955 <!-- http://purl.obolibrary.org/obo/CDAO_0000208 --> 956 957 <owl:ObjectProperty rdf:about="&obo;CDAO_0000208"> 958 <rdfs:label rdf:datatype="&xsd;string">has_TU</rdfs:label> 959 <dc:description rdf:datatype="&xsd;string">This property associates a character data matrix with a TU (a row) represented in the matrix.</dc:description> 960 <rdfs:domain rdf:resource="&obo;CDAO_0000056"/> 961 <rdfs:range rdf:resource="&obo;CDAO_0000138"/> 962 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000178"/> 963 </owl:ObjectProperty> 964 965 966 967 <!-- http://purl.obolibrary.org/obo/CDAO_0000209 --> 968 969 <owl:ObjectProperty rdf:about="&obo;CDAO_0000209"> 970 <rdf:type rdf:resource="&owl;FunctionalProperty"/> 971 <rdfs:label rdf:datatype="&xsd;string">has_Child_Node</rdfs:label> 972 <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> 973 <rdfs:domain rdf:resource="&obo;CDAO_0000139"/> 974 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 975 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000162"/> 976 </owl:ObjectProperty> 977 978 979 980 <!-- http://purl.obolibrary.org/obo/CDAO_0000210 --> 981 982 <owl:ObjectProperty rdf:about="&obo;CDAO_0000210"> 983 <rdfs:label rdf:datatype="&xsd;string">has_Right_Node</rdfs:label> 984 <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> 985 <rdfs:domain rdf:resource="&obo;CDAO_0000097"/> 986 <rdfs:range rdf:resource="&obo;CDAO_0000140"/> 987 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000182"/> 988 </owl:ObjectProperty> 989 990 991 992 <!-- 993 /////////////////////////////////////////////////////////////////////////////////////// 994 // 995 // Data properties 996 // 997 /////////////////////////////////////////////////////////////////////////////////////// 998 --> 999 1000 1001 1002 1003 <!-- http://purl.obolibrary.org/obo/CDAO_0000211 --> 1004 1005 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000211"> 1006 <rdfs:label rdf:datatype="&xsd;string">has_Precision</rdfs:label> 1007 <rdfs:range rdf:resource="&xsd;float"/> 1008 </owl:DatatypeProperty> 1009 1010 1011 1012 <!-- http://purl.obolibrary.org/obo/CDAO_0000212 --> 1013 1014 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000212"> 1015 <rdfs:label rdf:datatype="&xsd;string">has_Point_Coordinate_Value</rdfs:label> 1016 <rdfs:domain rdf:resource="&obo;CDAO_0000003"/> 1017 <rdfs:range rdf:resource="&xsd;integer"/> 1018 </owl:DatatypeProperty> 1019 1020 1021 1022 <!-- http://purl.obolibrary.org/obo/CDAO_0000213 --> 1023 1024 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000213"> 1025 <rdfs:label rdf:datatype="&xsd;string">has_Int_Value</rdfs:label> 1026 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000215"/> 1027 <rdfs:range rdf:resource="&xsd;int"/> 1028 </owl:DatatypeProperty> 1029 1030 1031 1032 <!-- http://purl.obolibrary.org/obo/CDAO_0000214 --> 1033 1034 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000214"> 1035 <rdfs:label rdf:datatype="&xsd;string">has_Support_Value</rdfs:label> 1036 <rdfs:range rdf:resource="&xsd;float"/> 1037 </owl:DatatypeProperty> 1038 1039 1040 1041 <!-- http://purl.obolibrary.org/obo/CDAO_0000215 --> 1042 1043 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000215"> 1044 <rdfs:label rdf:datatype="&xsd;string">has_Value</rdfs:label> 1045 </owl:DatatypeProperty> 1046 1047 1048 1049 <!-- http://purl.obolibrary.org/obo/CDAO_0000216 --> 1050 1051 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000216"> 1052 <rdfs:label rdf:datatype="&xsd;string">has_Uncertainty_Factor</rdfs:label> 1053 <rdfs:range rdf:resource="&xsd;float"/> 1054 </owl:DatatypeProperty> 1055 1056 1057 1058 <!-- http://purl.obolibrary.org/obo/CDAO_0000217 --> 1059 1060 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000217"> 1061 <rdfs:label rdf:datatype="&xsd;string">has_Range_End_Value</rdfs:label> 1062 <rdfs:domain rdf:resource="&obo;CDAO_0000095"/> 1063 <rdfs:range rdf:resource="&xsd;integer"/> 1064 </owl:DatatypeProperty> 1065 1066 1067 1068 <!-- http://purl.obolibrary.org/obo/CDAO_0000218 --> 1069 1070 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000218"> 1071 <rdfs:label rdf:datatype="&xsd;string">has_Float_Value</rdfs:label> 1072 <rdfs:subPropertyOf rdf:resource="&obo;CDAO_0000215"/> 1073 <rdfs:range rdf:resource="&xsd;float"/> 1074 </owl:DatatypeProperty> 1075 1076 1077 1078 <!-- http://purl.obolibrary.org/obo/CDAO_0000219 --> 1079 1080 <owl:DatatypeProperty rdf:about="&obo;CDAO_0000219"> 1081 <rdfs:label rdf:datatype="&xsd;string">has_Range_Start_Value</rdfs:label> 1082 <rdfs:domain rdf:resource="&obo;CDAO_0000095"/> 1083 <rdfs:range rdf:resource="&xsd;integer"/> 1084 </owl:DatatypeProperty> 1085 1086 1087 1088 <!-- 1089 /////////////////////////////////////////////////////////////////////////////////////// 1090 // 1091 // Classes 1092 // 1093 /////////////////////////////////////////////////////////////////////////////////////// 1094 --> 1095 1096 1097 1098 1099 <!-- http://purl.obolibrary.org/obo/CDAO_0000002 --> 1100 1101 <owl:Class rdf:about="&obo;CDAO_0000002"> 1102 <rdfs:label rdf:datatype="&xsd;string">DesoxiRibonucleotideResidueStateDatum</rdfs:label> 1103 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000050"/> 1104 </owl:Class> 1105 1106 1107 1108 <!-- http://purl.obolibrary.org/obo/CDAO_0000003 --> 1109 1110 <owl:Class rdf:about="&obo;CDAO_0000003"> 1111 <rdfs:label rdf:datatype="&xsd;string">CoordinatePoint</rdfs:label> 1112 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000022"/> 1113 </owl:Class> 1114 1115 1116 1117 <!-- http://purl.obolibrary.org/obo/CDAO_0000004 --> 1118 1119 <owl:Class rdf:about="&obo;CDAO_0000004"> 1120 <rdfs:label rdf:datatype="&xsd;string">Lineage</rdfs:label> 1121 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 1122 <rdfs:subClassOf> 1123 <owl:Restriction> 1124 <owl:onProperty rdf:resource="&obo;CDAO_0000202"/> 1125 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1126 </owl:Restriction> 1127 </rdfs:subClassOf> 1128 </owl:Class> 1129 1130 1131 1132 <!-- http://purl.obolibrary.org/obo/CDAO_0000005 --> 1133 1134 <owl:Class rdf:about="&obo;CDAO_0000005"> 1135 <rdfs:label rdf:datatype="&xsd;string">Phylo4Tree</rdfs:label> 1136 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1137 </owl:Class> 1138 1139 1140 1141 <!-- http://purl.obolibrary.org/obo/CDAO_0000006 --> 1142 1143 <owl:Class rdf:about="&obo;CDAO_0000006"> 1144 <rdfs:label rdf:datatype="&xsd;string">Network</rdfs:label> 1145 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1146 <rdfs:subClassOf> 1147 <owl:Restriction> 1148 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 1149 <owl:allValuesFrom> 1150 <owl:Class> 1151 <owl:unionOf rdf:parseType="Collection"> 1152 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 1153 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 1154 </owl:unionOf> 1155 </owl:Class> 1156 </owl:allValuesFrom> 1157 </owl:Restriction> 1158 </rdfs:subClassOf> 1159 </owl:Class> 1160 1161 1162 1163 <!-- http://purl.obolibrary.org/obo/CDAO_0000007 --> 1164 1165 <owl:Class rdf:about="&obo;CDAO_0000007"> 1166 <rdfs:label rdf:datatype="&xsd;string">ModelDescription</rdfs:label> 1167 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1168 <dc:description>Description of a model of transformations.</dc:description> 1169 <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> 1170 </owl:Class> 1171 1172 1173 1174 <!-- http://purl.obolibrary.org/obo/CDAO_0000008 --> 1175 1176 <owl:Class rdf:about="&obo;CDAO_0000008"> 1177 <rdfs:label rdf:datatype="&xsd;string">StandardStateDatum</rdfs:label> 1178 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000089"/> 1179 </owl:Class> 1180 1181 1182 1183 <!-- http://purl.obolibrary.org/obo/CDAO_0000009 --> 1184 1185 <owl:Class rdf:about="&obo;CDAO_0000009"> 1186 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharacterLengthType</rdfs:label> 1187 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 1188 </owl:Class> 1189 1190 1191 1192 <!-- http://purl.obolibrary.org/obo/CDAO_0000010 --> 1193 1194 <owl:Class rdf:about="&obo;CDAO_0000010"> 1195 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharBayesianLengthType</rdfs:label> 1196 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 1197 </owl:Class> 1198 1199 1200 1201 <!-- http://purl.obolibrary.org/obo/CDAO_0000011 --> 1202 1203 <owl:Class rdf:about="&obo;CDAO_0000011"> 1204 <rdfs:label rdf:datatype="&xsd;string">NEXUSTreeBlock</rdfs:label> 1205 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1206 </owl:Class> 1207 1208 1209 1210 <!-- http://purl.obolibrary.org/obo/CDAO_0000012 --> 1211 1212 <owl:Class rdf:about="&obo;CDAO_0000012"> 1213 <rdfs:label rdf:datatype="&xsd;string">RootedTree</rdfs:label> 1214 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1215 <rdfs:subClassOf> 1216 <owl:Restriction> 1217 <owl:onProperty rdf:resource="&obo;CDAO_0000155"/> 1218 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000012"/> 1219 </owl:Restriction> 1220 </rdfs:subClassOf> 1221 <rdfs:subClassOf> 1222 <owl:Restriction> 1223 <owl:onProperty rdf:resource="&obo;CDAO_0000148"/> 1224 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 1225 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1226 </owl:Restriction> 1227 </rdfs:subClassOf> 1228 <rdfs:subClassOf> 1229 <owl:Restriction> 1230 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 1231 <owl:allValuesFrom> 1232 <owl:Class> 1233 <owl:unionOf rdf:parseType="Collection"> 1234 <rdf:Description rdf:about="&obo;CDAO_0000139"/> 1235 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 1236 </owl:unionOf> 1237 </owl:Class> 1238 </owl:allValuesFrom> 1239 </owl:Restriction> 1240 </rdfs:subClassOf> 1241 <owl:disjointWith rdf:resource="&obo;CDAO_0000088"/> 1242 </owl:Class> 1243 1244 1245 1246 <!-- http://purl.obolibrary.org/obo/CDAO_0000013 --> 1247 1248 <owl:Class rdf:about="&obo;CDAO_0000013"> 1249 <rdfs:label rdf:datatype="&xsd;string">Kimura2Parameters</rdfs:label> 1250 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000020"/> 1251 </owl:Class> 1252 1253 1254 1255 <!-- http://purl.obolibrary.org/obo/CDAO_0000014 --> 1256 1257 <owl:Class rdf:about="&obo;CDAO_0000014"> 1258 <rdfs:label rdf:datatype="&xsd;string">TreeProcedure</rdfs:label> 1259 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000044"/> 1260 </owl:Class> 1261 1262 1263 1264 <!-- http://purl.obolibrary.org/obo/CDAO_0000015 --> 1265 1266 <owl:Class rdf:about="&obo;CDAO_0000015"> 1267 <rdfs:label rdf:datatype="&xsd;string">Generic_State</rdfs:label> 1268 <owl:equivalentClass> 1269 <owl:Class> 1270 <owl:oneOf rdf:parseType="Collection"> 1271 <rdf:Description rdf:about="&obo;CDAO_0000222"/> 1272 <rdf:Description rdf:about="&obo;CDAO_0000221"/> 1273 <rdf:Description rdf:about="&obo;CDAO_0000223"/> 1274 </owl:oneOf> 1275 </owl:Class> 1276 </owl:equivalentClass> 1277 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1278 <rdfs:comment>This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.</rdfs:comment> 1279 <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> 1280 </owl:Class> 1281 1282 1283 1284 <!-- http://purl.obolibrary.org/obo/CDAO_0000016 --> 1285 1286 <owl:Class rdf:about="&obo;CDAO_0000016"> 1287 <rdfs:label rdf:datatype="&xsd;string">UnrootedSubtree</rdfs:label> 1288 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000070"/> 1289 </owl:Class> 1290 1291 1292 1293 <!-- http://purl.obolibrary.org/obo/CDAO_0000017 --> 1294 1295 <owl:Class rdf:about="&obo;CDAO_0000017"> 1296 <rdfs:label rdf:datatype="&xsd;string">UnresolvedTree</rdfs:label> 1297 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1298 </owl:Class> 1299 1300 1301 1302 <!-- http://purl.obolibrary.org/obo/CDAO_0000018 --> 1303 1304 <owl:Class rdf:about="&obo;CDAO_0000018"> 1305 <rdfs:label rdf:datatype="&xsd;string">BifurcatingTree</rdfs:label> 1306 <owl:equivalentClass rdf:resource="&obo;CDAO_0000130"/> 1307 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1308 </owl:Class> 1309 1310 1311 1312 <!-- http://purl.obolibrary.org/obo/CDAO_0000019 --> 1313 1314 <owl:Class rdf:about="&obo;CDAO_0000019"> 1315 <rdfs:label rdf:datatype="&xsd;string">ContinuousStateDatum</rdfs:label> 1316 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000098"/> 1317 </owl:Class> 1318 1319 1320 1321 <!-- http://purl.obolibrary.org/obo/CDAO_0000020 --> 1322 1323 <owl:Class rdf:about="&obo;CDAO_0000020"> 1324 <rdfs:label rdf:datatype="&xsd;string">SubstitutionModel</rdfs:label> 1325 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000007"/> 1326 </owl:Class> 1327 1328 1329 1330 <!-- http://purl.obolibrary.org/obo/CDAO_0000021 --> 1331 1332 <owl:Class rdf:about="&obo;CDAO_0000021"> 1333 <rdfs:label rdf:datatype="&xsd;string">JukesKantor</rdfs:label> 1334 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000020"/> 1335 </owl:Class> 1336 1337 1338 1339 <!-- http://purl.obolibrary.org/obo/CDAO_0000022 --> 1340 1341 <owl:Class rdf:about="&obo;CDAO_0000022"> 1342 <rdfs:label rdf:datatype="&xsd;string">DatumCoordinate</rdfs:label> 1343 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1344 <rdfs:subClassOf> 1345 <owl:Restriction> 1346 <owl:onProperty rdf:resource="&obo;CDAO_0000165"/> 1347 <owl:onClass rdf:resource="&obo;CDAO_0000104"/> 1348 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1349 </owl:Restriction> 1350 </rdfs:subClassOf> 1351 <dc:description>A positional coordinate giving the source of a character state, used for molecular sequences.</dc:description> 1352 <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> 1353 </owl:Class> 1354 1355 1356 1357 <!-- http://purl.obolibrary.org/obo/CDAO_0000023 --> 1358 1359 <owl:Class rdf:about="&obo;CDAO_0000023"> 1360 <rdfs:label rdf:datatype="&xsd;string">UnresolvedRootedTree</rdfs:label> 1361 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 1362 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000017"/> 1363 </owl:Class> 1364 1365 1366 1367 <!-- http://purl.obolibrary.org/obo/CDAO_0000024 --> 1368 1369 <owl:Class rdf:about="&obo;CDAO_0000024"> 1370 <rdfs:label rdf:datatype="&xsd;string">Branch</rdfs:label> 1371 <owl:equivalentClass rdf:resource="&obo;CDAO_0000099"/> 1372 <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> 1373 </owl:Class> 1374 1375 1376 1377 <!-- http://purl.obolibrary.org/obo/CDAO_0000025 --> 1378 1379 <owl:Class rdf:about="&obo;CDAO_0000025"> 1380 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDataMatrixAnnotation</rdfs:label> 1381 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1382 <dc:description>Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.</dc:description> 1383 </owl:Class> 1384 1385 1386 1387 <!-- http://purl.obolibrary.org/obo/CDAO_0000026 --> 1388 1389 <owl:Class rdf:about="&obo;CDAO_0000026"> 1390 <rdfs:label rdf:datatype="&xsd;string">AncestralNode</rdfs:label> 1391 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000140"/> 1392 <rdfs:subClassOf> 1393 <owl:Restriction> 1394 <owl:onProperty rdf:resource="&obo;CDAO_0000174"/> 1395 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1396 </owl:Restriction> 1397 </rdfs:subClassOf> 1398 <rdfs:subClassOf> 1399 <owl:Restriction> 1400 <owl:onProperty rdf:resource="&obo;CDAO_0000194"/> 1401 <owl:onClass rdf:resource="&obo;CDAO_0000012"/> 1402 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 1403 </owl:Restriction> 1404 </rdfs:subClassOf> 1405 </owl:Class> 1406 1407 1408 1409 <!-- http://purl.obolibrary.org/obo/CDAO_0000027 --> 1410 1411 <owl:Class rdf:about="&obo;CDAO_0000027"> 1412 <rdfs:label rdf:datatype="&xsd;string">UnresolvedUnrootedTree</rdfs:label> 1413 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000017"/> 1414 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000088"/> 1415 </owl:Class> 1416 1417 1418 1419 <!-- http://purl.obolibrary.org/obo/CDAO_0000029 --> 1420 1421 <owl:Class rdf:about="&obo;CDAO_0000029"> 1422 <rdfs:label rdf:datatype="&xsd;string">UncertainStateDomain</rdfs:label> 1423 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1424 <rdfs:subClassOf> 1425 <owl:Restriction> 1426 <owl:onProperty rdf:resource="&obo;CDAO_0000216"/> 1427 <owl:someValuesFrom rdf:resource="&xsd;float"/> 1428 </owl:Restriction> 1429 </rdfs:subClassOf> 1430 </owl:Class> 1431 1432 1433 1434 <!-- http://purl.obolibrary.org/obo/CDAO_0000030 --> 1435 1436 <owl:Class rdf:about="&obo;CDAO_0000030"> 1437 <rdfs:label rdf:datatype="&xsd;string">ReconcileTree</rdfs:label> 1438 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1439 <rdfs:subClassOf> 1440 <owl:Restriction> 1441 <owl:onProperty rdf:resource="&obo;CDAO_0000172"/> 1442 <owl:onClass rdf:resource="&obo;CDAO_0000110"/> 1443 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:minQualifiedCardinality> 1444 </owl:Restriction> 1445 </rdfs:subClassOf> 1446 </owl:Class> 1447 1448 1449 1450 <!-- http://purl.obolibrary.org/obo/CDAO_0000031 --> 1451 1452 <owl:Class rdf:about="&obo;CDAO_0000031"> 1453 <rdfs:label rdf:datatype="&xsd;string">Continuous</rdfs:label> 1454 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1455 <rdfs:subClassOf> 1456 <owl:Restriction> 1457 <owl:onProperty rdf:resource="&obo;CDAO_0000215"/> 1458 <owl:cardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:cardinality> 1459 </owl:Restriction> 1460 </rdfs:subClassOf> 1461 <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> 1462 </owl:Class> 1463 1464 1465 1466 <!-- http://purl.obolibrary.org/obo/CDAO_0000032 --> 1467 1468 <owl:Class rdf:about="&obo;CDAO_0000032"> 1469 <rdfs:label rdf:datatype="&xsd;string">AlignmentProcedure</rdfs:label> 1470 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000025"/> 1471 </owl:Class> 1472 1473 1474 1475 <!-- http://purl.obolibrary.org/obo/CDAO_0000033 --> 1476 1477 <owl:Class rdf:about="&obo;CDAO_0000033"> 1478 <rdfs:label rdf:datatype="&xsd;string">Dichotomy</rdfs:label> 1479 <owl:equivalentClass rdf:resource="&obo;CDAO_0000124"/> 1480 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 1481 <owl:disjointWith rdf:resource="&obo;CDAO_0000042"/> 1482 </owl:Class> 1483 1484 1485 1486 <!-- http://purl.obolibrary.org/obo/CDAO_0000034 --> 1487 1488 <owl:Class rdf:about="&obo;CDAO_0000034"> 1489 <rdfs:label rdf:datatype="&xsd;string">Molecular</rdfs:label> 1490 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1491 </owl:Class> 1492 1493 1494 1495 <!-- http://purl.obolibrary.org/obo/CDAO_0000035 --> 1496 1497 <owl:Class rdf:about="&obo;CDAO_0000035"> 1498 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharParsimonyLengthType</rdfs:label> 1499 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 1500 </owl:Class> 1501 1502 1503 1504 <!-- http://purl.obolibrary.org/obo/CDAO_0000039 --> 1505 1506 <owl:Class rdf:about="&obo;CDAO_0000039"> 1507 <rdfs:label rdf:datatype="&xsd;string">Categorical</rdfs:label> 1508 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1509 </owl:Class> 1510 1511 1512 1513 <!-- http://purl.obolibrary.org/obo/CDAO_0000040 --> 1514 1515 <owl:Class rdf:about="&obo;CDAO_0000040"> 1516 <rdfs:label rdf:datatype="&xsd;string">CDAOAnnotation</rdfs:label> 1517 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1518 <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> 1519 <dc:description>The base class of annotations in CDAO.</dc:description> 1520 </owl:Class> 1521 1522 1523 1524 <!-- http://purl.obolibrary.org/obo/CDAO_0000041 --> 1525 1526 <owl:Class rdf:about="&obo;CDAO_0000041"> 1527 <rdfs:label rdf:datatype="&xsd;string">originationEvent</rdfs:label> 1528 <rdfs:subClassOf> 1529 <owl:Restriction> 1530 <owl:onProperty rdf:resource="&obo;CDAO_0000190"/> 1531 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000097"/> 1532 </owl:Restriction> 1533 </rdfs:subClassOf> 1534 </owl:Class> 1535 1536 1537 1538 <!-- http://purl.obolibrary.org/obo/CDAO_0000042 --> 1539 1540 <owl:Class rdf:about="&obo;CDAO_0000042"> 1541 <rdfs:label rdf:datatype="&xsd;string">Polytomy</rdfs:label> 1542 <owl:equivalentClass> 1543 <owl:Restriction> 1544 <owl:onProperty rdf:resource="&obo;CDAO_0000177"/> 1545 <owl:minCardinality rdf:datatype="&xsd;nonNegativeInteger">3</owl:minCardinality> 1546 </owl:Restriction> 1547 </owl:equivalentClass> 1548 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 1549 <owl:disjointWith rdf:resource="&obo;CDAO_0000124"/> 1550 </owl:Class> 1551 1552 1553 1554 <!-- http://purl.obolibrary.org/obo/CDAO_0000043 --> 1555 1556 <owl:Class rdf:about="&obo;CDAO_0000043"> 1557 <rdfs:label rdf:datatype="&xsd;string">PolymorphicStateDomain</rdfs:label> 1558 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000091"/> 1559 <rdfs:subClassOf> 1560 <owl:Restriction> 1561 <owl:onProperty rdf:resource="&obo;CDAO_0000216"/> 1562 <owl:hasValue rdf:datatype="&xsd;float">1.0</owl:hasValue> 1563 </owl:Restriction> 1564 </rdfs:subClassOf> 1565 </owl:Class> 1566 1567 1568 1569 <!-- http://purl.obolibrary.org/obo/CDAO_0000044 --> 1570 1571 <owl:Class rdf:about="&obo;CDAO_0000044"> 1572 <rdfs:label rdf:datatype="&xsd;string">TreeAnnotation</rdfs:label> 1573 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1574 <rdfs:subClassOf> 1575 <owl:Restriction> 1576 <owl:onProperty rdf:resource="&obo;CDAO_0000157"/> 1577 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000110"/> 1578 </owl:Restriction> 1579 </rdfs:subClassOf> 1580 </owl:Class> 1581 1582 1583 1584 <!-- http://purl.obolibrary.org/obo/CDAO_0000045 --> 1585 1586 <owl:Class rdf:about="&obo;CDAO_0000045"> 1587 <rdfs:label rdf:datatype="&xsd;string">Standard</rdfs:label> 1588 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1589 </owl:Class> 1590 1591 1592 1593 <!-- http://purl.obolibrary.org/obo/CDAO_0000046 --> 1594 1595 <owl:Class rdf:about="&obo;CDAO_0000046"> 1596 <rdfs:label rdf:datatype="&xsd;string">EdgeLength</rdfs:label> 1597 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000101"/> 1598 <rdfs:subClassOf> 1599 <owl:Restriction> 1600 <owl:onProperty rdf:resource="&obo;CDAO_0000176"/> 1601 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000063"/> 1602 </owl:Restriction> 1603 </rdfs:subClassOf> 1604 <rdfs:subClassOf> 1605 <owl:Restriction> 1606 <owl:onProperty rdf:resource="&obo;CDAO_0000215"/> 1607 <owl:someValuesFrom rdf:resource="&rdfs;Literal"/> 1608 </owl:Restriction> 1609 </rdfs:subClassOf> 1610 <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> 1611 <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> 1612 </owl:Class> 1613 1614 1615 1616 <!-- http://purl.obolibrary.org/obo/CDAO_0000047 --> 1617 1618 <owl:Class rdf:about="&obo;CDAO_0000047"> 1619 <rdfs:label rdf:datatype="&xsd;string">RibonucleotideResidue</rdfs:label> 1620 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000034"/> 1621 </owl:Class> 1622 1623 1624 1625 <!-- http://purl.obolibrary.org/obo/CDAO_0000048 --> 1626 1627 <owl:Class rdf:about="&obo;CDAO_0000048"> 1628 <rdfs:label rdf:datatype="&xsd;string">Clade</rdfs:label> 1629 <owl:equivalentClass rdf:resource="&obo;CDAO_0000129"/> 1630 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1631 </owl:Class> 1632 1633 1634 1635 <!-- http://purl.obolibrary.org/obo/CDAO_0000049 --> 1636 1637 <owl:Class rdf:about="&obo;CDAO_0000049"> 1638 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharParsimonyLengthType</rdfs:label> 1639 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 1640 </owl:Class> 1641 1642 1643 1644 <!-- http://purl.obolibrary.org/obo/CDAO_0000050 --> 1645 1646 <owl:Class rdf:about="&obo;CDAO_0000050"> 1647 <rdfs:label rdf:datatype="&xsd;string">MolecularStateDatum</rdfs:label> 1648 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000089"/> 1649 </owl:Class> 1650 1651 1652 1653 <!-- http://purl.obolibrary.org/obo/CDAO_0000051 --> 1654 1655 <owl:Class rdf:about="&obo;CDAO_0000051"> 1656 <rdfs:label rdf:datatype="&xsd;string">PolyphyleticGroup</rdfs:label> 1657 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 1658 <rdfs:subClassOf> 1659 <owl:Restriction> 1660 <owl:onProperty rdf:resource="&obo;CDAO_0000188"/> 1661 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1662 </owl:Restriction> 1663 </rdfs:subClassOf> 1664 <owl:disjointWith rdf:resource="&obo;CDAO_0000127"/> 1665 </owl:Class> 1666 1667 1668 1669 <!-- http://purl.obolibrary.org/obo/CDAO_0000052 --> 1670 1671 <owl:Class rdf:about="&obo;CDAO_0000052"> 1672 <rdfs:label rdf:datatype="&xsd;string">NexusDataBlock</rdfs:label> 1673 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 1674 </owl:Class> 1675 1676 1677 1678 <!-- http://purl.obolibrary.org/obo/CDAO_0000053 --> 1679 1680 <owl:Class rdf:about="&obo;CDAO_0000053"> 1681 <rdfs:label rdf:datatype="&xsd;string">BranchingNode</rdfs:label> 1682 <owl:equivalentClass> 1683 <owl:Restriction> 1684 <owl:onProperty rdf:resource="&obo;CDAO_0000177"/> 1685 <owl:minCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:minCardinality> 1686 </owl:Restriction> 1687 </owl:equivalentClass> 1688 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 1689 </owl:Class> 1690 1691 1692 1693 <!-- http://purl.obolibrary.org/obo/CDAO_0000055 --> 1694 1695 <owl:Class rdf:about="&obo;CDAO_0000055"> 1696 <rdfs:label rdf:datatype="&xsd;string">Compound</rdfs:label> 1697 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000039"/> 1698 </owl:Class> 1699 1700 1701 1702 <!-- http://purl.obolibrary.org/obo/CDAO_0000056 --> 1703 1704 <owl:Class rdf:about="&obo;CDAO_0000056"> 1705 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDataMatrix</rdfs:label> 1706 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1707 <rdfs:subClassOf> 1708 <owl:Restriction> 1709 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 1710 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000025"/> 1711 </owl:Restriction> 1712 </rdfs:subClassOf> 1713 <rdfs:subClassOf> 1714 <owl:Restriction> 1715 <owl:onProperty rdf:resource="&obo;CDAO_0000208"/> 1716 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000138"/> 1717 </owl:Restriction> 1718 </rdfs:subClassOf> 1719 <rdfs:subClassOf> 1720 <owl:Restriction> 1721 <owl:onProperty rdf:resource="&obo;CDAO_0000142"/> 1722 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000071"/> 1723 </owl:Restriction> 1724 </rdfs:subClassOf> 1725 <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> 1726 </owl:Class> 1727 1728 1729 1730 <!-- http://purl.obolibrary.org/obo/CDAO_0000057 --> 1731 1732 <owl:Class rdf:about="&obo;CDAO_0000057"> 1733 <rdfs:label rdf:datatype="&xsd;string">RibonucleotideResidueStateDatum</rdfs:label> 1734 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000050"/> 1735 </owl:Class> 1736 1737 1738 1739 <!-- http://purl.obolibrary.org/obo/CDAO_0000058 --> 1740 1741 <owl:Class rdf:about="&obo;CDAO_0000058"> 1742 <rdfs:label rdf:datatype="&xsd;string">TimeCalibratedLengthType</rdfs:label> 1743 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 1744 </owl:Class> 1745 1746 1747 1748 <!-- http://purl.obolibrary.org/obo/CDAO_0000059 --> 1749 1750 <owl:Class rdf:about="&obo;CDAO_0000059"> 1751 <rdfs:label rdf:datatype="&xsd;string">SetOfNodes</rdfs:label> 1752 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000118"/> 1753 <rdfs:subClassOf> 1754 <owl:Restriction> 1755 <owl:onProperty rdf:resource="&obo;CDAO_0000198"/> 1756 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000140"/> 1757 </owl:Restriction> 1758 </rdfs:subClassOf> 1759 </owl:Class> 1760 1761 1762 1763 <!-- http://purl.obolibrary.org/obo/CDAO_0000060 --> 1764 1765 <owl:Class rdf:about="&obo;CDAO_0000060"> 1766 <rdfs:label rdf:datatype="&xsd;string">MRCANode</rdfs:label> 1767 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000080"/> 1768 <rdfs:subClassOf> 1769 <owl:Restriction> 1770 <owl:onProperty rdf:resource="&obo;CDAO_0000163"/> 1771 <owl:onClass rdf:resource="&obo;CDAO_0000118"/> 1772 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 1773 </owl:Restriction> 1774 </rdfs:subClassOf> 1775 </owl:Class> 1776 1777 1778 1779 <!-- http://purl.obolibrary.org/obo/CDAO_0000061 --> 1780 1781 <owl:Class rdf:about="&obo;CDAO_0000061"> 1782 <rdfs:label rdf:datatype="&xsd;string">FASTADataMatrix</rdfs:label> 1783 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 1784 </owl:Class> 1785 1786 1787 1788 <!-- http://purl.obolibrary.org/obo/CDAO_0000062 --> 1789 1790 <owl:Class rdf:about="&obo;CDAO_0000062"> 1791 <rdfs:label rdf:datatype="&xsd;string">evolutionaryTransition</rdfs:label> 1792 <owl:equivalentClass rdf:resource="&obo;CDAO_0000065"/> 1793 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000097"/> 1794 <rdfs:subClassOf> 1795 <owl:Restriction> 1796 <owl:onProperty rdf:resource="&obo;CDAO_0000159"/> 1797 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 1798 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1799 </owl:Restriction> 1800 </rdfs:subClassOf> 1801 <rdfs:subClassOf> 1802 <owl:Restriction> 1803 <owl:onProperty rdf:resource="&obo;CDAO_0000186"/> 1804 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 1805 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1806 </owl:Restriction> 1807 </rdfs:subClassOf> 1808 <rdfs:subClassOf> 1809 <owl:Restriction> 1810 <owl:onProperty rdf:resource="&obo;CDAO_0000169"/> 1811 <owl:onClass rdf:resource="&obo;CDAO_0000071"/> 1812 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 1813 </owl:Restriction> 1814 </rdfs:subClassOf> 1815 </owl:Class> 1816 1817 1818 1819 <!-- http://purl.obolibrary.org/obo/CDAO_0000063 --> 1820 1821 <owl:Class rdf:about="&obo;CDAO_0000063"> 1822 <rdfs:label rdf:datatype="&xsd;string">EdgeLengthType</rdfs:label> 1823 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 1824 </owl:Class> 1825 1826 1827 1828 <!-- http://purl.obolibrary.org/obo/CDAO_0000064 --> 1829 1830 <owl:Class rdf:about="&obo;CDAO_0000064"> 1831 <rdfs:label rdf:datatype="&xsd;string">cladogeneticChange</rdfs:label> 1832 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000097"/> 1833 </owl:Class> 1834 1835 1836 1837 <!-- http://purl.obolibrary.org/obo/CDAO_0000065 --> 1838 1839 <owl:Class rdf:about="&obo;CDAO_0000065"> 1840 <rdfs:label rdf:datatype="&xsd;string">anageneticChange</rdfs:label> 1841 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000097"/> 1842 </owl:Class> 1843 1844 1845 1846 <!-- http://purl.obolibrary.org/obo/CDAO_0000066 --> 1847 1848 <owl:Class rdf:about="&obo;CDAO_0000066"> 1849 <rdfs:label rdf:datatype="&xsd;string">TUAnnotation</rdfs:label> 1850 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 1851 </owl:Class> 1852 1853 1854 1855 <!-- http://purl.obolibrary.org/obo/CDAO_0000067 --> 1856 1857 <owl:Class rdf:about="&obo;CDAO_0000067"> 1858 <rdfs:label rdf:datatype="&xsd;string">PhyloTree</rdfs:label> 1859 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1860 </owl:Class> 1861 1862 1863 1864 <!-- http://purl.obolibrary.org/obo/CDAO_0000068 --> 1865 1866 <owl:Class rdf:about="&obo;CDAO_0000068"> 1867 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharacter</rdfs:label> 1868 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000071"/> 1869 <rdfs:subClassOf> 1870 <owl:Restriction> 1871 <owl:onProperty rdf:resource="&obo;CDAO_0000207"/> 1872 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000019"/> 1873 </owl:Restriction> 1874 </rdfs:subClassOf> 1875 <rdfs:subClassOf> 1876 <owl:Restriction> 1877 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 1878 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000019"/> 1879 </owl:Restriction> 1880 </rdfs:subClassOf> 1881 </owl:Class> 1882 1883 1884 1885 <!-- http://purl.obolibrary.org/obo/CDAO_0000069 --> 1886 1887 <owl:Class rdf:about="&obo;CDAO_0000069"> 1888 <rdfs:label rdf:datatype="&xsd;string">PHYLIPTree</rdfs:label> 1889 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 1890 </owl:Class> 1891 1892 1893 1894 <!-- http://purl.obolibrary.org/obo/CDAO_0000070 --> 1895 1896 <owl:Class rdf:about="&obo;CDAO_0000070"> 1897 <rdfs:label rdf:datatype="&xsd;string">Subtree</rdfs:label> 1898 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1899 <rdfs:subClassOf> 1900 <owl:Restriction> 1901 <owl:onProperty rdf:resource="&obo;CDAO_0000155"/> 1902 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000110"/> 1903 </owl:Restriction> 1904 </rdfs:subClassOf> 1905 </owl:Class> 1906 1907 1908 1909 <!-- http://purl.obolibrary.org/obo/CDAO_0000071 --> 1910 1911 <owl:Class rdf:about="&obo;CDAO_0000071"> 1912 <rdfs:label rdf:datatype="&xsd;string">Character</rdfs:label> 1913 <rdfs:subClassOf> 1914 <owl:Restriction> 1915 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 1916 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000098"/> 1917 </owl:Restriction> 1918 </rdfs:subClassOf> 1919 <rdfs:comment rdf:datatype="&xsd;string">Traits shown to be relevant for phylogenetic classification</rdfs:comment> 1920 </owl:Class> 1921 1922 1923 1924 <!-- http://purl.obolibrary.org/obo/CDAO_0000072 --> 1925 1926 <owl:Class rdf:about="&obo;CDAO_0000072"> 1927 <rdfs:label rdf:datatype="&xsd;string">GalledTree</rdfs:label> 1928 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 1929 </owl:Class> 1930 1931 1932 1933 <!-- http://purl.obolibrary.org/obo/CDAO_0000073 --> 1934 1935 <owl:Class rdf:about="&obo;CDAO_0000073"> 1936 <rdfs:label rdf:datatype="&xsd;string">SpeciesTree</rdfs:label> 1937 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 1938 </owl:Class> 1939 1940 1941 1942 <!-- http://purl.obolibrary.org/obo/CDAO_0000074 --> 1943 1944 <owl:Class rdf:about="&obo;CDAO_0000074"> 1945 <rdfs:label rdf:datatype="&xsd;string">TreeFormat</rdfs:label> 1946 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000044"/> 1947 </owl:Class> 1948 1949 1950 1951 <!-- http://purl.obolibrary.org/obo/CDAO_0000075 --> 1952 1953 <owl:Class rdf:about="&obo;CDAO_0000075"> 1954 <rdfs:label rdf:datatype="&xsd;string">StandardCharacter</rdfs:label> 1955 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000111"/> 1956 </owl:Class> 1957 1958 1959 1960 <!-- http://purl.obolibrary.org/obo/CDAO_0000076 --> 1961 1962 <owl:Class rdf:about="&obo;CDAO_0000076"> 1963 <rdfs:label rdf:datatype="&xsd;string">AminoAcidResidue</rdfs:label> 1964 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000034"/> 1965 <dc:description>This class will be declared equivalent ot the amino acid class description imported</dc:description> 1966 </owl:Class> 1967 1968 1969 1970 <!-- http://purl.obolibrary.org/obo/CDAO_0000077 --> 1971 1972 <owl:Class rdf:about="&obo;CDAO_0000077"> 1973 <rdfs:label rdf:datatype="&xsd;string">geneDuplication</rdfs:label> 1974 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000064"/> 1975 </owl:Class> 1976 1977 1978 1979 <!-- http://purl.obolibrary.org/obo/CDAO_0000078 --> 1980 1981 <owl:Class rdf:about="&obo;CDAO_0000078"> 1982 <rdfs:label rdf:datatype="&xsd;string">CompoundCharacter</rdfs:label> 1983 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000111"/> 1984 <rdfs:subClassOf> 1985 <owl:Restriction> 1986 <owl:onProperty rdf:resource="&obo;CDAO_0000170"/> 1987 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000136"/> 1988 </owl:Restriction> 1989 </rdfs:subClassOf> 1990 <rdfs:subClassOf> 1991 <owl:Restriction> 1992 <owl:onProperty rdf:resource="&obo;CDAO_0000142"/> 1993 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000071"/> 1994 </owl:Restriction> 1995 </rdfs:subClassOf> 1996 <rdfs:subClassOf> 1997 <owl:Restriction> 1998 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 1999 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000136"/> 2000 </owl:Restriction> 2001 </rdfs:subClassOf> 2002 <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> 2003 </owl:Class> 2004 2005 2006 2007 <!-- http://purl.obolibrary.org/obo/CDAO_0000079 --> 2008 2009 <owl:Class rdf:about="&obo;CDAO_0000079"> 2010 <rdfs:label rdf:datatype="&xsd;string">SIMMAPTree</rdfs:label> 2011 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 2012 </owl:Class> 2013 2014 2015 2016 <!-- http://purl.obolibrary.org/obo/CDAO_0000080 --> 2017 2018 <owl:Class rdf:about="&obo;CDAO_0000080"> 2019 <rdfs:label rdf:datatype="&xsd;string">CommonAncestralNode</rdfs:label> 2020 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 2021 <rdfs:subClassOf> 2022 <owl:Class> 2023 <owl:unionOf rdf:parseType="Collection"> 2024 <rdf:Description rdf:about="&obo;CDAO_0000053"/> 2025 <owl:Restriction> 2026 <owl:onProperty rdf:resource="&obo;CDAO_0000174"/> 2027 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000053"/> 2028 </owl:Restriction> 2029 </owl:unionOf> 2030 </owl:Class> 2031 </rdfs:subClassOf> 2032 </owl:Class> 2033 2034 2035 2036 <!-- http://purl.obolibrary.org/obo/CDAO_0000081 --> 2037 2038 <owl:Class rdf:about="&obo;CDAO_0000081"> 2039 <rdfs:label rdf:datatype="&xsd;string">NewickTree</rdfs:label> 2040 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000074"/> 2041 </owl:Class> 2042 2043 2044 2045 <!-- http://purl.obolibrary.org/obo/CDAO_0000082 --> 2046 2047 <owl:Class rdf:about="&obo;CDAO_0000082"> 2048 <rdfs:label rdf:datatype="&xsd;string">TimeProportionalLengthType</rdfs:label> 2049 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 2050 </owl:Class> 2051 2052 2053 2054 <!-- http://purl.obolibrary.org/obo/CDAO_0000083 --> 2055 2056 <owl:Class rdf:about="&obo;CDAO_0000083"> 2057 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharDistanceLengthType</rdfs:label> 2058 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 2059 </owl:Class> 2060 2061 2062 2063 <!-- http://purl.obolibrary.org/obo/CDAO_0000084 --> 2064 2065 <owl:Class rdf:about="&obo;CDAO_0000084"> 2066 <rdfs:label rdf:datatype="&xsd;string">StarTree</rdfs:label> 2067 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 2068 <rdfs:subClassOf> 2069 <owl:Restriction> 2070 <owl:onProperty rdf:resource="&obo;CDAO_0000149"/> 2071 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000108"/> 2072 </owl:Restriction> 2073 </rdfs:subClassOf> 2074 </owl:Class> 2075 2076 2077 2078 <!-- http://purl.obolibrary.org/obo/CDAO_0000085 --> 2079 2080 <owl:Class rdf:about="&obo;CDAO_0000085"> 2081 <rdfs:label rdf:datatype="&xsd;string">FullyResolvedUnrootedTree</rdfs:label> 2082 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000018"/> 2083 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000088"/> 2084 </owl:Class> 2085 2086 2087 2088 <!-- http://purl.obolibrary.org/obo/CDAO_0000086 --> 2089 2090 <owl:Class rdf:about="&obo;CDAO_0000086"> 2091 <rdfs:label rdf:datatype="&xsd;string">ParaphyleticGroup</rdfs:label> 2092 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000127"/> 2093 <rdfs:subClassOf> 2094 <owl:Restriction> 2095 <owl:onProperty rdf:resource="&obo;CDAO_0000199"/> 2096 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000070"/> 2097 </owl:Restriction> 2098 </rdfs:subClassOf> 2099 <owl:disjointWith rdf:resource="&obo;CDAO_0000129"/> 2100 </owl:Class> 2101 2102 2103 2104 <!-- http://purl.obolibrary.org/obo/CDAO_0000087 --> 2105 2106 <owl:Class rdf:about="&obo;CDAO_0000087"> 2107 <rdfs:label rdf:datatype="&xsd;string">geneticEvent</rdfs:label> 2108 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000041"/> 2109 </owl:Class> 2110 2111 2112 2113 <!-- http://purl.obolibrary.org/obo/CDAO_0000088 --> 2114 2115 <owl:Class rdf:about="&obo;CDAO_0000088"> 2116 <rdfs:label rdf:datatype="&xsd;string">UnrootedTree</rdfs:label> 2117 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 2118 </owl:Class> 2119 2120 2121 2122 <!-- http://purl.obolibrary.org/obo/CDAO_0000089 --> 2123 2124 <owl:Class rdf:about="&obo;CDAO_0000089"> 2125 <rdfs:label rdf:datatype="&xsd;string">CategoricalStateDatum</rdfs:label> 2126 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000098"/> 2127 </owl:Class> 2128 2129 2130 2131 <!-- http://purl.obolibrary.org/obo/CDAO_0000090 --> 2132 2133 <owl:Class rdf:about="&obo;CDAO_0000090"> 2134 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharLikelihoodLengthType</rdfs:label> 2135 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 2136 </owl:Class> 2137 2138 2139 2140 <!-- http://purl.obolibrary.org/obo/CDAO_0000091 --> 2141 2142 <owl:Class rdf:about="&obo;CDAO_0000091"> 2143 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDomain</rdfs:label> 2144 <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> 2145 </owl:Class> 2146 2147 2148 2149 <!-- http://purl.obolibrary.org/obo/CDAO_0000092 --> 2150 2151 <owl:Class rdf:about="&obo;CDAO_0000092"> 2152 <rdfs:label rdf:datatype="&xsd;string">CoordinateList</rdfs:label> 2153 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000022"/> 2154 </owl:Class> 2155 2156 2157 2158 <!-- http://purl.obolibrary.org/obo/CDAO_0000093 --> 2159 2160 <owl:Class rdf:about="&obo;CDAO_0000093"> 2161 <rdfs:label rdf:datatype="&xsd;string">GammaDistribution</rdfs:label> 2162 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000020"/> 2163 </owl:Class> 2164 2165 2166 2167 <!-- http://purl.obolibrary.org/obo/CDAO_0000094 --> 2168 2169 <owl:Class rdf:about="&obo;CDAO_0000094"> 2170 <rdfs:label rdf:datatype="&xsd;string">DesoxiRibonucleotideResidueCharacter</rdfs:label> 2171 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000115"/> 2172 <rdfs:subClassOf> 2173 <owl:Restriction> 2174 <owl:onProperty rdf:resource="&obo;CDAO_0000195"/> 2175 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000002"/> 2176 </owl:Restriction> 2177 </rdfs:subClassOf> 2178 <rdfs:subClassOf> 2179 <owl:Restriction> 2180 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 2181 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000002"/> 2182 </owl:Restriction> 2183 </rdfs:subClassOf> 2184 </owl:Class> 2185 2186 2187 2188 <!-- http://purl.obolibrary.org/obo/CDAO_0000095 --> 2189 2190 <owl:Class rdf:about="&obo;CDAO_0000095"> 2191 <rdfs:label rdf:datatype="&xsd;string">CoordinateRange</rdfs:label> 2192 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000022"/> 2193 </owl:Class> 2194 2195 2196 2197 <!-- http://purl.obolibrary.org/obo/CDAO_0000096 --> 2198 2199 <owl:Class rdf:about="&obo;CDAO_0000096"> 2200 <rdfs:label rdf:datatype="&xsd;string">ReticulateEvolution</rdfs:label> 2201 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 2202 </owl:Class> 2203 2204 2205 2206 <!-- http://purl.obolibrary.org/obo/CDAO_0000097 --> 2207 2208 <owl:Class rdf:about="&obo;CDAO_0000097"> 2209 <rdfs:label rdf:datatype="&xsd;string">hereditaryChange</rdfs:label> 2210 <rdfs:subClassOf> 2211 <owl:Restriction> 2212 <owl:onProperty rdf:resource="&obo;CDAO_0000186"/> 2213 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 2214 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2215 </owl:Restriction> 2216 </rdfs:subClassOf> 2217 <rdfs:subClassOf> 2218 <owl:Restriction> 2219 <owl:onProperty rdf:resource="&obo;CDAO_0000159"/> 2220 <owl:onClass rdf:resource="&obo;CDAO_0000091"/> 2221 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2222 </owl:Restriction> 2223 </rdfs:subClassOf> 2224 <rdfs:subClassOf> 2225 <owl:Restriction> 2226 <owl:onProperty rdf:resource="&obo;CDAO_0000169"/> 2227 <owl:onClass rdf:resource="&obo;CDAO_0000071"/> 2228 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2229 </owl:Restriction> 2230 </rdfs:subClassOf> 2231 </owl:Class> 2232 2233 2234 2235 <!-- http://purl.obolibrary.org/obo/CDAO_0000098 --> 2236 2237 <owl:Class rdf:about="&obo;CDAO_0000098"> 2238 <rdfs:label rdf:datatype="&xsd;string">CharacterStateDatum</rdfs:label> 2239 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2240 <rdfs:subClassOf> 2241 <owl:Restriction> 2242 <owl:onProperty rdf:resource="&obo;CDAO_0000205"/> 2243 <owl:onClass rdf:resource="&obo;CDAO_0000071"/> 2244 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2245 </owl:Restriction> 2246 </rdfs:subClassOf> 2247 <rdfs:subClassOf> 2248 <owl:Restriction> 2249 <owl:onProperty rdf:resource="&obo;CDAO_0000191"/> 2250 <owl:onClass rdf:resource="&obo;CDAO_0000138"/> 2251 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2252 </owl:Restriction> 2253 </rdfs:subClassOf> 2254 <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> 2255 </owl:Class> 2256 2257 2258 2259 <!-- http://purl.obolibrary.org/obo/CDAO_0000099 --> 2260 2261 <owl:Class rdf:about="&obo;CDAO_0000099"> 2262 <rdfs:label rdf:datatype="&xsd;string">Edge</rdfs:label> 2263 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2264 <rdfs:subClassOf> 2265 <owl:Restriction> 2266 <owl:onProperty rdf:resource="&obo;CDAO_0000193"/> 2267 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000101"/> 2268 </owl:Restriction> 2269 </rdfs:subClassOf> 2270 <rdfs:subClassOf> 2271 <owl:Restriction> 2272 <owl:onProperty rdf:resource="&obo;CDAO_0000162"/> 2273 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 2274 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:qualifiedCardinality> 2275 </owl:Restriction> 2276 </rdfs:subClassOf> 2277 <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> 2278 </owl:Class> 2279 2280 2281 2282 <!-- http://purl.obolibrary.org/obo/CDAO_0000100 --> 2283 2284 <owl:Class rdf:about="&obo;CDAO_0000100"> 2285 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharacterLengthType</rdfs:label> 2286 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 2287 </owl:Class> 2288 2289 2290 2291 <!-- http://purl.obolibrary.org/obo/CDAO_0000101 --> 2292 2293 <owl:Class rdf:about="&obo;CDAO_0000101"> 2294 <rdfs:label rdf:datatype="&xsd;string">EdgeAnnotation</rdfs:label> 2295 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000040"/> 2296 </owl:Class> 2297 2298 2299 2300 <!-- http://purl.obolibrary.org/obo/CDAO_0000102 --> 2301 2302 <owl:Class rdf:about="&obo;CDAO_0000102"> 2303 <rdfs:label rdf:datatype="&xsd;string">FullyResolvedRootedTree</rdfs:label> 2304 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 2305 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000018"/> 2306 <rdfs:subClassOf> 2307 <owl:Restriction> 2308 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 2309 <owl:allValuesFrom> 2310 <owl:Class> 2311 <owl:unionOf rdf:parseType="Collection"> 2312 <rdf:Description rdf:about="&obo;CDAO_0000033"/> 2313 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 2314 <rdf:Description rdf:about="&obo;CDAO_0000108"/> 2315 </owl:unionOf> 2316 </owl:Class> 2317 </owl:allValuesFrom> 2318 </owl:Restriction> 2319 </rdfs:subClassOf> 2320 </owl:Class> 2321 2322 2323 2324 <!-- http://purl.obolibrary.org/obo/CDAO_0000103 --> 2325 2326 <owl:Class rdf:about="&obo;CDAO_0000103"> 2327 <rdfs:label rdf:datatype="&xsd;string">GrafenLengthType</rdfs:label> 2328 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000063"/> 2329 </owl:Class> 2330 2331 2332 2333 <!-- http://purl.obolibrary.org/obo/CDAO_0000104 --> 2334 2335 <owl:Class rdf:about="&obo;CDAO_0000104"> 2336 <rdfs:label rdf:datatype="&xsd;string">CoordinateSystem</rdfs:label> 2337 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2338 <dc:description>A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.</dc:description> 2339 </owl:Class> 2340 2341 2342 2343 <!-- http://purl.obolibrary.org/obo/CDAO_0000105 --> 2344 2345 <owl:Class rdf:about="&obo;CDAO_0000105"> 2346 <rdfs:label rdf:datatype="&xsd;string">GenBankDataMatrix</rdfs:label> 2347 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 2348 </owl:Class> 2349 2350 2351 2352 <!-- http://purl.obolibrary.org/obo/CDAO_0000107 --> 2353 2354 <owl:Class rdf:about="&obo;CDAO_0000107"> 2355 <rdfs:label rdf:datatype="&xsd;string">DataMatrixFormat</rdfs:label> 2356 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000025"/> 2357 </owl:Class> 2358 2359 2360 2361 <!-- http://purl.obolibrary.org/obo/CDAO_0000108 --> 2362 2363 <owl:Class rdf:about="&obo;CDAO_0000108"> 2364 <rdfs:label rdf:datatype="&xsd;string">TerminalNode</rdfs:label> 2365 <owl:equivalentClass> 2366 <owl:Class> 2367 <owl:intersectionOf rdf:parseType="Collection"> 2368 <rdf:Description rdf:about="&obo;CDAO_0000140"/> 2369 <owl:Restriction> 2370 <owl:onProperty rdf:resource="&obo;CDAO_0000149"/> 2371 <owl:allValuesFrom> 2372 <owl:Class> 2373 <owl:complementOf rdf:resource="&obo;CDAO_0000140"/> 2374 </owl:Class> 2375 </owl:allValuesFrom> 2376 </owl:Restriction> 2377 </owl:intersectionOf> 2378 </owl:Class> 2379 </owl:equivalentClass> 2380 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000140"/> 2381 </owl:Class> 2382 2383 2384 2385 <!-- http://purl.obolibrary.org/obo/CDAO_0000109 --> 2386 2387 <owl:Class rdf:about="&obo;CDAO_0000109"> 2388 <rdfs:label rdf:datatype="&xsd;string">RibonucleotideResidueCharacter</rdfs:label> 2389 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000115"/> 2390 <rdfs:subClassOf> 2391 <owl:Restriction> 2392 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 2393 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000057"/> 2394 </owl:Restriction> 2395 </rdfs:subClassOf> 2396 </owl:Class> 2397 2398 2399 2400 <!-- http://purl.obolibrary.org/obo/CDAO_0000110 --> 2401 2402 <owl:Class rdf:about="&obo;CDAO_0000110"> 2403 <rdfs:label rdf:datatype="&xsd;string">Tree</rdfs:label> 2404 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 2405 </owl:Class> 2406 2407 2408 2409 <!-- http://purl.obolibrary.org/obo/CDAO_0000111 --> 2410 2411 <owl:Class rdf:about="&obo;CDAO_0000111"> 2412 <rdfs:label rdf:datatype="&xsd;string">CategoricalCharacter</rdfs:label> 2413 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000071"/> 2414 </owl:Class> 2415 2416 2417 2418 <!-- http://purl.obolibrary.org/obo/CDAO_0000112 --> 2419 2420 <owl:Class rdf:about="&obo;CDAO_0000112"> 2421 <rdfs:label rdf:datatype="&xsd;string">AminoAcidResidueStateDatum</rdfs:label> 2422 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000050"/> 2423 </owl:Class> 2424 2425 2426 2427 <!-- http://purl.obolibrary.org/obo/CDAO_0000113 --> 2428 2429 <owl:Class rdf:about="&obo;CDAO_0000113"> 2430 <rdfs:label rdf:datatype="&xsd;string">PHYLIPDataMatrix</rdfs:label> 2431 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000107"/> 2432 </owl:Class> 2433 2434 2435 2436 <!-- http://purl.obolibrary.org/obo/CDAO_0000114 --> 2437 2438 <owl:Class rdf:about="&obo;CDAO_0000114"> 2439 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharLikelihoodLengthType</rdfs:label> 2440 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 2441 </owl:Class> 2442 2443 2444 2445 <!-- http://purl.obolibrary.org/obo/CDAO_0000115 --> 2446 2447 <owl:Class rdf:about="&obo;CDAO_0000115"> 2448 <rdfs:label rdf:datatype="&xsd;string">MolecularCharacter</rdfs:label> 2449 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000111"/> 2450 </owl:Class> 2451 2452 2453 2454 <!-- http://purl.obolibrary.org/obo/CDAO_0000116 --> 2455 2456 <owl:Class rdf:about="&obo;CDAO_0000116"> 2457 <rdfs:label rdf:datatype="&xsd;string">hereditaryPersistance</rdfs:label> 2458 <rdfs:subClassOf> 2459 <owl:Restriction> 2460 <owl:onProperty rdf:resource="&obo;CDAO_0000190"/> 2461 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000097"/> 2462 </owl:Restriction> 2463 </rdfs:subClassOf> 2464 </owl:Class> 2465 2466 2467 2468 <!-- http://purl.obolibrary.org/obo/CDAO_0000117 --> 2469 2470 <owl:Class rdf:about="&obo;CDAO_0000117"> 2471 <rdfs:label rdf:datatype="&xsd;string">SetOfCharacters</rdfs:label> 2472 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000118"/> 2473 </owl:Class> 2474 2475 2476 2477 <!-- http://purl.obolibrary.org/obo/CDAO_0000118 --> 2478 2479 <owl:Class rdf:about="&obo;CDAO_0000118"> 2480 <rdfs:label rdf:datatype="&xsd;string">SetOfThings</rdfs:label> 2481 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2482 <rdfs:subClassOf> 2483 <owl:Restriction> 2484 <owl:onProperty rdf:resource="&obo;CDAO_0000198"/> 2485 <owl:allValuesFrom> 2486 <owl:Class> 2487 <owl:unionOf rdf:parseType="Collection"> 2488 <rdf:Description rdf:about="&obo;CDAO_0000071"/> 2489 <rdf:Description rdf:about="&obo;CDAO_0000117"/> 2490 </owl:unionOf> 2491 </owl:Class> 2492 </owl:allValuesFrom> 2493 </owl:Restriction> 2494 </rdfs:subClassOf> 2495 <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> 2496 </owl:Class> 2497 2498 2499 2500 <!-- http://purl.obolibrary.org/obo/CDAO_0000120 --> 2501 2502 <owl:Class rdf:about="&obo;CDAO_0000120"> 2503 <rdfs:label rdf:datatype="&xsd;string">Sequence</rdfs:label> 2504 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2505 <rdfs:subClassOf> 2506 <owl:Restriction> 2507 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 2508 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000098"/> 2509 </owl:Restriction> 2510 </rdfs:subClassOf> 2511 <rdfs:subClassOf> 2512 <owl:Restriction> 2513 <owl:onProperty rdf:resource="&obo;CDAO_0000178"/> 2514 <owl:allValuesFrom> 2515 <owl:Restriction> 2516 <owl:onProperty rdf:resource="&obo;CDAO_0000151"/> 2517 <owl:onClass rdf:resource="&obo;CDAO_0000022"/> 2518 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 2519 </owl:Restriction> 2520 </owl:allValuesFrom> 2521 </owl:Restriction> 2522 </rdfs:subClassOf> 2523 <dc:description>A set of ordered states, typically the residues in a macromolecular sequence.</dc:description> 2524 </owl:Class> 2525 2526 2527 2528 <!-- http://purl.obolibrary.org/obo/CDAO_0000121 --> 2529 2530 <owl:Class rdf:about="&obo;CDAO_0000121"> 2531 <rdfs:label rdf:datatype="&xsd;string">speciation</rdfs:label> 2532 <owl:equivalentClass rdf:resource="&obo;CDAO_0000122"/> 2533 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000064"/> 2534 </owl:Class> 2535 2536 2537 2538 <!-- http://purl.obolibrary.org/obo/CDAO_0000122 --> 2539 2540 <owl:Class rdf:about="&obo;CDAO_0000122"> 2541 <rdfs:label rdf:datatype="&xsd;string">cladogenesis</rdfs:label> 2542 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000064"/> 2543 </owl:Class> 2544 2545 2546 2547 <!-- http://purl.obolibrary.org/obo/CDAO_0000124 --> 2548 2549 <owl:Class rdf:about="&obo;CDAO_0000124"> 2550 <rdfs:label rdf:datatype="&xsd;string">Bifurcation</rdfs:label> 2551 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000026"/> 2552 <rdfs:subClassOf> 2553 <owl:Restriction> 2554 <owl:onProperty rdf:resource="&obo;CDAO_0000177"/> 2555 <owl:cardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:cardinality> 2556 </owl:Restriction> 2557 </rdfs:subClassOf> 2558 </owl:Class> 2559 2560 2561 2562 <!-- http://purl.obolibrary.org/obo/CDAO_0000125 --> 2563 2564 <owl:Class rdf:about="&obo;CDAO_0000125"> 2565 <rdfs:label rdf:datatype="&xsd;string">DiscreteCharBayesianLengthType</rdfs:label> 2566 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000100"/> 2567 </owl:Class> 2568 2569 2570 2571 <!-- http://purl.obolibrary.org/obo/CDAO_0000126 --> 2572 2573 <owl:Class rdf:about="&obo;CDAO_0000126"> 2574 <rdfs:label rdf:datatype="&xsd;string">TaxonomicLink</rdfs:label> 2575 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000066"/> 2576 <dc:description>Link to an externally defined taxonomic hierarchy.</dc:description> 2577 </owl:Class> 2578 2579 2580 2581 <!-- http://purl.obolibrary.org/obo/CDAO_0000127 --> 2582 2583 <owl:Class rdf:about="&obo;CDAO_0000127"> 2584 <rdfs:label rdf:datatype="&xsd;string">MonophyleticGroup</rdfs:label> 2585 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000006"/> 2586 </owl:Class> 2587 2588 2589 2590 <!-- http://purl.obolibrary.org/obo/CDAO_0000128 --> 2591 2592 <owl:Class rdf:about="&obo;CDAO_0000128"> 2593 <rdfs:label rdf:datatype="&xsd;string">molecularRecombination</rdfs:label> 2594 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000132"/> 2595 </owl:Class> 2596 2597 2598 2599 <!-- http://purl.obolibrary.org/obo/CDAO_0000129 --> 2600 2601 <owl:Class rdf:about="&obo;CDAO_0000129"> 2602 <rdfs:label rdf:datatype="&xsd;string">HolophyleticGroup</rdfs:label> 2603 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000127"/> 2604 </owl:Class> 2605 2606 2607 2608 <!-- http://purl.obolibrary.org/obo/CDAO_0000130 --> 2609 2610 <owl:Class rdf:about="&obo;CDAO_0000130"> 2611 <rdfs:label rdf:datatype="&xsd;string">FullyResolvedTree</rdfs:label> 2612 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000110"/> 2613 </owl:Class> 2614 2615 2616 2617 <!-- http://purl.obolibrary.org/obo/CDAO_0000131 --> 2618 2619 <owl:Class rdf:about="&obo;CDAO_0000131"> 2620 <rdfs:label rdf:datatype="&xsd;string">AminoAcidResidueCharacter</rdfs:label> 2621 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000115"/> 2622 <rdfs:subClassOf> 2623 <owl:Restriction> 2624 <owl:onProperty rdf:resource="&obo;CDAO_0000168"/> 2625 <owl:someValuesFrom rdf:resource="&obo;CDAO_0000112"/> 2626 </owl:Restriction> 2627 </rdfs:subClassOf> 2628 <rdfs:subClassOf> 2629 <owl:Restriction> 2630 <owl:onProperty rdf:resource="&obo;CDAO_0000153"/> 2631 <owl:allValuesFrom rdf:resource="&obo;CDAO_0000112"/> 2632 </owl:Restriction> 2633 </rdfs:subClassOf> 2634 </owl:Class> 2635 2636 2637 2638 <!-- http://purl.obolibrary.org/obo/CDAO_0000132 --> 2639 2640 <owl:Class rdf:about="&obo;CDAO_0000132"> 2641 <rdfs:label rdf:datatype="&xsd;string">recombination</rdfs:label> 2642 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000087"/> 2643 </owl:Class> 2644 2645 2646 2647 <!-- http://purl.obolibrary.org/obo/CDAO_0000133 --> 2648 2649 <owl:Class rdf:about="&obo;CDAO_0000133"> 2650 <rdfs:label rdf:datatype="&xsd;string">DesoxiRibonucleotideResidue</rdfs:label> 2651 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000034"/> 2652 </owl:Class> 2653 2654 2655 2656 <!-- http://purl.obolibrary.org/obo/CDAO_0000134 --> 2657 2658 <owl:Class rdf:about="&obo;CDAO_0000134"> 2659 <rdfs:label rdf:datatype="&xsd;string">RootedSubtree</rdfs:label> 2660 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000012"/> 2661 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000070"/> 2662 </owl:Class> 2663 2664 2665 2666 <!-- http://purl.obolibrary.org/obo/CDAO_0000136 --> 2667 2668 <owl:Class rdf:about="&obo;CDAO_0000136"> 2669 <rdfs:label rdf:datatype="&xsd;string">CompoundStateDatum</rdfs:label> 2670 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000089"/> 2671 </owl:Class> 2672 2673 2674 2675 <!-- http://purl.obolibrary.org/obo/CDAO_0000137 --> 2676 2677 <owl:Class rdf:about="&obo;CDAO_0000137"> 2678 <rdfs:label rdf:datatype="&xsd;string">GapCost</rdfs:label> 2679 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000007"/> 2680 </owl:Class> 2681 2682 2683 2684 <!-- http://purl.obolibrary.org/obo/CDAO_0000138 --> 2685 2686 <owl:Class rdf:about="&obo;CDAO_0000138"> 2687 <rdfs:label rdf:datatype="&xsd;string">TU</rdfs:label> 2688 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2689 <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> 2690 </owl:Class> 2691 2692 2693 2694 <!-- http://purl.obolibrary.org/obo/CDAO_0000139 --> 2695 2696 <owl:Class rdf:about="&obo;CDAO_0000139"> 2697 <rdfs:label rdf:datatype="&xsd;string">DirectedEdge</rdfs:label> 2698 <owl:equivalentClass> 2699 <owl:Class> 2700 <owl:intersectionOf rdf:parseType="Collection"> 2701 <rdf:Description rdf:about="&obo;CDAO_0000099"/> 2702 <owl:Restriction> 2703 <owl:onProperty rdf:resource="&obo;CDAO_0000201"/> 2704 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 2705 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2706 </owl:Restriction> 2707 <owl:Restriction> 2708 <owl:onProperty rdf:resource="&obo;CDAO_0000209"/> 2709 <owl:onClass rdf:resource="&obo;CDAO_0000140"/> 2710 <owl:qualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:qualifiedCardinality> 2711 </owl:Restriction> 2712 </owl:intersectionOf> 2713 </owl:Class> 2714 </owl:equivalentClass> 2715 <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> 2716 </owl:Class> 2717 2718 2719 2720 <!-- http://purl.obolibrary.org/obo/CDAO_0000140 --> 2721 2722 <owl:Class rdf:about="&obo;CDAO_0000140"> 2723 <rdfs:label rdf:datatype="&xsd;string">Node</rdfs:label> 2724 <rdfs:subClassOf rdf:resource="&owl;Thing"/> 2725 <rdfs:subClassOf> 2726 <owl:Restriction> 2727 <owl:onProperty rdf:resource="&obo;CDAO_0000143"/> 2728 <owl:onClass rdf:resource="&obo;CDAO_0000139"/> 2729 <owl:maxQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:maxQualifiedCardinality> 2730 </owl:Restriction> 2731 </rdfs:subClassOf> 2732 <rdfs:subClassOf> 2733 <owl:Restriction> 2734 <owl:onProperty rdf:resource="&obo;CDAO_0000194"/> 2735 <owl:onClass rdf:resource="&obo;CDAO_0000006"/> 2736 <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">1</owl:minQualifiedCardinality> 2737 </owl:Restriction> 2738 </rdfs:subClassOf> 2739 </owl:Class> 2740 2741 2742 2743 <!-- http://purl.obolibrary.org/obo/CDAO_0000141 --> 2744 2745 <owl:Class rdf:about="&obo;CDAO_0000141"> 2746 <rdfs:label rdf:datatype="&xsd;string">ContinuousCharDistanceLengthType</rdfs:label> 2747 <rdfs:subClassOf rdf:resource="&obo;CDAO_0000009"/> 2748 </owl:Class> 2749 2750 2751 2752 <!-- 2753 /////////////////////////////////////////////////////////////////////////////////////// 2754 // 2755 // Individuals 2756 // 2757 /////////////////////////////////////////////////////////////////////////////////////// 2758 --> 2759 2760 2761 2762 2763 <!-- http://purl.obolibrary.org/obo/CDAO_0000220 --> 2764 2765 <owl:Thing rdf:about="&obo;CDAO_0000220"> 2766 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2767 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2768 <rdfs:label rdf:datatype="&xsd;string">dA</rdfs:label> 2769 </owl:Thing> 2770 2771 2772 2773 <!-- http://purl.obolibrary.org/obo/CDAO_0000221 --> 2774 2775 <owl:Thing rdf:about="&obo;CDAO_0000221"> 2776 <rdf:type rdf:resource="&obo;CDAO_0000015"/> 2777 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2778 <rdfs:label rdf:datatype="&xsd;string">absent</rdfs:label> 2779 </owl:Thing> 2780 2781 2782 2783 <!-- http://purl.obolibrary.org/obo/CDAO_0000222 --> 2784 2785 <owl:Thing rdf:about="&obo;CDAO_0000222"> 2786 <rdf:type rdf:resource="&obo;CDAO_0000015"/> 2787 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2788 <rdfs:label rdf:datatype="&xsd;string">unknown</rdfs:label> 2789 </owl:Thing> 2790 2791 2792 2793 <!-- http://purl.obolibrary.org/obo/CDAO_0000223 --> 2794 2795 <owl:Thing rdf:about="&obo;CDAO_0000223"> 2796 <rdf:type rdf:resource="&obo;CDAO_0000015"/> 2797 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2798 <rdfs:label rdf:datatype="&xsd;string">gap</rdfs:label> 2799 </owl:Thing> 2800 2801 2802 2803 <!-- http://purl.obolibrary.org/obo/CDAO_0000224 --> 2804 2805 <owl:Thing rdf:about="&obo;CDAO_0000224"> 2806 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2807 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2808 <rdfs:label rdf:datatype="&xsd;string">dG</rdfs:label> 2809 </owl:Thing> 2810 2811 2812 2813 <!-- http://purl.obolibrary.org/obo/CDAO_0000225 --> 2814 2815 <owl:Thing rdf:about="&obo;CDAO_0000225"> 2816 <rdf:type rdf:resource="&obo;CDAO_0000057"/> 2817 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2818 <rdfs:label rdf:datatype="&xsd;string">rU</rdfs:label> 2819 </owl:Thing> 2820 2821 2822 2823 <!-- http://purl.obolibrary.org/obo/CDAO_0000226 --> 2824 2825 <owl:Thing rdf:about="&obo;CDAO_0000226"> 2826 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2827 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2828 <rdfs:label rdf:datatype="&xsd;string">dC</rdfs:label> 2829 </owl:Thing> 2830 2831 2832 2833 <!-- http://purl.obolibrary.org/obo/CDAO_0000227 --> 2834 2835 <owl:Thing rdf:about="&obo;CDAO_0000227"> 2836 <rdf:type rdf:resource="&obo;CDAO_0000133"/> 2837 <rdf:type rdf:resource="&owl;NamedIndividual"/> 2838 <rdfs:label rdf:datatype="&xsd;string">dT</rdfs:label> 2839 </owl:Thing> 2840 2841 2842 2843 <!-- 2844 /////////////////////////////////////////////////////////////////////////////////////// 2845 // 2846 // General axioms 2847 // 2848 /////////////////////////////////////////////////////////////////////////////////////// 2849 --> 2850 2851 <rdf:Description> 2852 <rdf:type rdf:resource="&owl;AllDisjointClasses"/> 2853 <owl:members rdf:parseType="Collection"> 2854 <rdf:Description rdf:about="&obo;CDAO_0000068"/> 2855 <rdf:Description rdf:about="&obo;CDAO_0000094"/> 2856 <rdf:Description rdf:about="&obo;CDAO_0000131"/> 2857 </owl:members> 2858 </rdf:Description> 2859 <rdf:Description> 2860 <rdf:type rdf:resource="&owl;AllDisjointClasses"/> 2861 <owl:members rdf:parseType="Collection"> 2862 <rdf:Description rdf:about="&obo;CDAO_0000002"/> 2863 <rdf:Description rdf:about="&obo;CDAO_0000019"/> 2864 <rdf:Description rdf:about="&obo;CDAO_0000112"/> 2865 </owl:members> 2866 </rdf:Description> 2867 </rdf:RDF> 2868 2869 2870 2871 <!-- Generated by the OWL API (version 3.2.3.1824) http://owlapi.sourceforge.net --> 2872 2873 ''' 2874 2875 cdao_elements = {} 2876 2877 root = ET.fromstring(cdao_owl) 2878 for node_type in 'ObjectProperty', 'Class', 'DatatypeProperty': 2879 for element in root.findall('{http://www.w3.org/2002/07/owl#}%s' % node_type): 2880 obo = element.attrib[ 2881 '{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about'].split('/')[-1] 2882 cdao = element.find( 2883 '{http://www.w3.org/2000/01/rdf-schema#}label').text 2884 cdao_elements[cdao] = obo 2885