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