| Index: trunk/extensions/Wikidata/php-tools/SwissProtImport.php |
| — | — | @@ -53,6 +53,8 @@ |
| 54 | 54 | |
| 55 | 55 | function importEntriesFromXMLFile($fileHandle, $umlsCollectionId, $goCollection, $hugoCollection, $EC2GoMeaningIdMapping, $keyword2GoMeaningIdMapping, ProgressBar $progressBar) { |
| 56 | 56 | $languageId = 85; |
| | 57 | + bootstrapCollection("concept mapping", $languageId, "MAPP"); |
| | 58 | + |
| 57 | 59 | $collectionId = bootstrapCollection("Swiss-Prot", $languageId, ""); |
| 58 | 60 | $classCollectionId = bootstrapCollection("Swiss-Prot classes", $languageId, "CLAS"); |
| 59 | 61 | $relationTypeCollectionId = bootstrapCollection("Swiss-Prot relation types", $languageId, "RELT"); |
| — | — | @@ -189,238 +191,98 @@ |
| 190 | 192 | protected $progressBar; |
| 191 | 193 | |
| 192 | 194 | protected function bootstrapDefinedMeaning($spelling, $definition = null) { |
| 193 | | - if (!isset( $definition ) ){ |
| | 195 | + if (!isset($definition)) |
| 194 | 196 | $definition = $spelling; |
| 195 | | - } |
| | 197 | + |
| 196 | 198 | $expression = $this->getOrCreateExpression($spelling); |
| 197 | 199 | $definedMeaningId = createNewDefinedMeaning($expression->id, $this->languageId, $definition); |
| 198 | 200 | |
| 199 | 201 | return $definedMeaningId; |
| 200 | 202 | } |
| 201 | 203 | |
| | 204 | + protected function bootstrapConcept($conceptId, $spelling, $classId = 0) { |
| | 205 | + if ($conceptId == 0) |
| | 206 | + $conceptId = $this->bootstrapDefinedMeaning($spelling); |
| | 207 | + |
| | 208 | + if ($classId != 0) |
| | 209 | + addClassMembership($conceptId, $classId); |
| | 210 | + |
| | 211 | + return $conceptId; |
| | 212 | + } |
| | 213 | + |
| 202 | 214 | protected function bootstrapConceptIds() { |
| 203 | | - if ($this->proteinConceptId == 0) |
| 204 | | - $this->proteinConceptId = $this->bootstrapDefinedMeaning("amino acid, peptide, or protein"); |
| | 215 | + $this->proteinConceptId = $this->bootstrapConcept($this->proteinConceptId, "protein"); |
| | 216 | + $this->proteinFragmentConceptId = $this->bootstrapConcept($this->proteinFragmentConceptId, "protein fragment"); |
| | 217 | + $this->organismSpecificProteinConceptId = $this->bootstrapConcept($this->organismSpecificProteinConceptId, "organism specific protein"); |
| | 218 | + $this->organismSpecificGeneConceptId = $this->bootstrapConcept($this->organismSpecificGeneConceptId, "organism specific gene"); |
| | 219 | + $this->geneConceptId = $this->bootstrapConcept($this->geneConceptId, "gene or genome"); |
| | 220 | + $this->organismConceptId = $this->bootstrapConcept($this->organismConceptId, "organism"); |
| | 221 | + $this->functionalDomainConceptId = $this->bootstrapConcept($this->functionalDomainConceptId, "functional domain"); |
| | 222 | + $this->proteinComponentConceptId = $this->bootstrapConcept($this->proteinComponentConceptId, "protein component"); |
| | 223 | + $this->biologicalProcessConceptId = $this->bootstrapConcept($this->biologicalProcessConceptId, "biological process"); |
| | 224 | + $this->molecularFunctionConceptId = $this->bootstrapConcept($this->molecularFunctionConceptId, "molecular function"); |
| | 225 | + $this->cellularComponentConceptId = $this->bootstrapConcept($this->cellularComponentConceptId, "cellular component"); |
| | 226 | +// $this->keywordConceptId = $this->bootstrapConcept($this->keywordConceptId, "keyword"); |
| | 227 | + $this->enzymeCommissionNumberConceptId = $this->bootstrapConcept($this->enzymeCommissionNumberConceptId, "enzyme commission number"); |
| 205 | 228 | |
| 206 | | - if ($this->proteinFragmentConceptId == 0) |
| 207 | | - $this->proteinFragmentConceptId = $this->bootstrapDefinedMeaning("protein fragment"); |
| | 229 | + $this->textAttributeConceptId = $this->bootstrapConcept($this->textAttributeConceptId, "text attribute"); // TODO: Is this one necessary? |
| 208 | 230 | |
| 209 | | - if ($this->organismSpecificProteinConceptId == 0) |
| 210 | | - $this->organismSpecificProteinConceptId = $this->bootstrapDefinedMeaning("organism specific protein"); |
| 211 | | - |
| 212 | | - if ($this->organismSpecificGeneConceptId == 0) |
| 213 | | - $this->organismSpecificGeneConceptId = $this->bootstrapDefinedMeaning("organism specific gene"); |
| 214 | | - |
| 215 | | - if ($this->geneConceptId == 0) |
| 216 | | - $this->geneConceptId = $this->bootstrapDefinedMeaning("gene or genome"); |
| 217 | | - |
| 218 | | - if ($this->organismConceptId == 0) |
| 219 | | - $this->organismConceptId = $this->bootstrapDefinedMeaning("organism"); |
| 220 | | - |
| 221 | | - if ($this->functionalDomainConceptId == 0) |
| 222 | | - $this->functionalDomainConceptId = $this->bootstrapDefinedMeaning("functional domain"); |
| 223 | | - |
| 224 | | - if ($this->proteinComponentConceptId == 0) |
| 225 | | - $this->proteinComponentConceptId = $this->bootstrapDefinedMeaning("protein component"); |
| 226 | | - |
| 227 | | - if ($this->biologicalProcessConceptId == 0) |
| 228 | | - $this->biologicalProcessConceptId = $this->bootstrapDefinedMeaning("biological process"); |
| 229 | | - |
| 230 | | - if ($this->molecularFunctionConceptId == 0) |
| 231 | | - $this->molecularFunctionConceptId = $this->bootstrapDefinedMeaning("molecular function"); |
| 232 | | - |
| 233 | | - if ($this->cellularComponentConceptId == 0) |
| 234 | | - $this->cellularComponentConceptId = $this->bootstrapDefinedMeaning("cellular component"); |
| 235 | | - |
| 236 | | -// if ($this->keywordConceptId == 0) |
| 237 | | -// $this->keywordConceptId = $this->bootstrapDefinedMeaning("keyword"); |
| 238 | | - |
| 239 | | - if ($this->enzymeCommissionNumberConceptId == 0) |
| 240 | | - $this->enzymeCommissionNumberConceptId = $this->bootstrapDefinedMeaning("enzyme commission number"); |
| 241 | | - |
| 242 | | - if ($this->textAttributeConceptId == 0) |
| 243 | | - $this->textAttributeConceptId = $this->bootstrapDefinedMeaning("text attribute"); |
| 244 | | - |
| 245 | 231 | // create root class for all defined meaning comment types |
| 246 | | - if ($this->textAttributeClassId == 0) |
| 247 | | - $this->textAttributeClassId = $this->bootstrapDefinedMeaning("text attribute class"); |
| | 232 | + $this->textAttributeClassId = $this->bootstrapConcept($this->textAttributeClassId, "text attribute class"); // TODO: Is this one necessary? |
| 248 | 233 | |
| 249 | 234 | // create top class for semantic comment types and link it to the root class |
| 250 | | - if ($this->semanticGroupId == 0) |
| 251 | | - $this->semanticGroupId = $this->bootstrapDefinedMeaning("Semantic Group"); |
| 252 | | - addClassMemberShip($this->semanticGroupId, $this->textAttributeClassId); |
| | 235 | + $this->semanticGroupId = $this->bootstrapConcept($this->semanticGroupId, "Semantic Group", $this->textAttributeClassId); |
| 253 | 236 | |
| 254 | 237 | // define a different comment type aspects and link them with the comment top class |
| 255 | | - if ($this->localizationAspectId == 0) |
| 256 | | - $this->localizationAspectId = $this->bootstrapDefinedMeaning("Localization aspects"); |
| 257 | | - addClassMemberShip($this->localizationAspectId, $this->semanticGroupId); |
| | 238 | + $this->localizationAspectId = $this->bootstrapConcept($this->localizationAspectId, "Localization aspects", $this->semanticGroupId); |
| | 239 | + $this->functionalAspectId = $this->bootstrapConcept($this->functionalAspectId, "Functional aspects", $this->semanticGroupId); |
| | 240 | + $this->structuralAspectId = $this->bootstrapConcept($this->structuralAspectId, "Structural aspects", $this->semanticGroupId); |
| | 241 | + $this->pharmaceuticalAspectId = $this->bootstrapConcept($this->pharmaceuticalAspectId, "Pharmaceutical aspects", $this->semanticGroupId); |
| | 242 | + $this->externalInformationId = $this->bootstrapConcept($this->externalInformationId, "External information", $this->semanticGroupId); |
| | 243 | + $this->otherAspectId = $this->bootstrapConcept($this->otherAspectId, "Other aspects", $this->semanticGroupId); |
| | 244 | + $this->functionallyRelatedId = $this->bootstrapConcept($this->functionallyRelatedId, "Functionally related", $this->semanticGroupId); |
| | 245 | + $this->spatiallyRelatedId = $this->bootstrapConcept($this->spatiallyRelatedId, "Spatially related", $this->semanticGroupId); |
| | 246 | + $this->physicallyRelatedId = $this->bootstrapConcept($this->physicallyRelatedId, "Physically related", $this->semanticGroupId); |
| | 247 | + $this->temporallyRelatedId = $this->bootstrapConcept($this->temporallyRelatedId, "Temporally related", $this->semanticGroupId); |
| | 248 | + $this->terminologicallyRelatedId = $this->bootstrapConcept($this->terminologicallyRelatedId, "Terminologically related", $this->semanticGroupId); |
| | 249 | + $this->conceptuallyRelatedId = $this->bootstrapConcept($this->conceptuallyRelatedId, "Conceptually related", $this->semanticGroupId); |
| 258 | 250 | |
| 259 | | - if ($this->functionalAspectId == 0) |
| 260 | | - $this->functionalAspectId = $this->bootstrapDefinedMeaning("Functional aspects"); |
| 261 | | - addClassMemberShip($this->functionalAspectId, $this->semanticGroupId); |
| 262 | | - |
| 263 | | - if ($this->structuralAspectId == 0) |
| 264 | | - $this->structuralAspectId = $this->bootstrapDefinedMeaning("Structural aspects"); |
| 265 | | - addClassMemberShip($this->structuralAspectId, $this->semanticGroupId); |
| 266 | | - |
| 267 | | - if ($this->pharmaceuticalAspectId == 0) |
| 268 | | - $this->pharmaceuticalAspectId = $this->bootstrapDefinedMeaning("Pharmaceutical aspects"); |
| 269 | | - addClassMemberShip($this->pharmaceuticalAspectId, $this->semanticGroupId); |
| 270 | | - |
| 271 | | - if ($this->externalInformationId == 0) |
| 272 | | - $this->externalInformationId = $this->bootstrapDefinedMeaning("External information"); |
| 273 | | - addClassMemberShip($this->externalInformationId, $this->semanticGroupId); |
| 274 | | - |
| 275 | | - if ($this->otherAspectId == 0) |
| 276 | | - $this->otherAspectId = $this->bootstrapDefinedMeaning("Other aspects"); |
| 277 | | - addClassMemberShip($this->otherAspectId, $this->semanticGroupId); |
| 278 | | - |
| 279 | | - if ($this->functionallyRelatedId == 0) |
| 280 | | - $this->functionallyRelatedId = $this->bootstrapDefinedMeaning("Functionally related"); |
| 281 | | - addClassMemberShip($this->functionallyRelatedId, $this->semanticGroupId); |
| 282 | | - |
| 283 | | - if ($this->spatiallyRelatedId == 0) |
| 284 | | - $this->spatiallyRelatedId = $this->bootstrapDefinedMeaning("Spatially related"); |
| 285 | | - addClassMemberShip($this->spatiallyRelatedId, $this->semanticGroupId); |
| 286 | | - |
| 287 | | - if ($this->physicallyRelatedId == 0) |
| 288 | | - $this->physicallyRelatedId = $this->bootstrapDefinedMeaning("Physically related"); |
| 289 | | - addClassMemberShip($this->physicallyRelatedId, $this->semanticGroupId); |
| 290 | | - |
| 291 | | - if ($this->temporallyRelatedId == 0) |
| 292 | | - $this->temporallyRelatedId = $this->bootstrapDefinedMeaning("Temporally related"); |
| 293 | | - addClassMemberShip($this->temporallyRelatedId, $this->semanticGroupId); |
| 294 | | - |
| 295 | | - if ($this->terminologicallyRelatedId == 0) |
| 296 | | - $this->terminologicallyRelatedId = $this->bootstrapDefinedMeaning("Terminologically related"); |
| 297 | | - addClassMemberShip($this->terminologicallyRelatedId, $this->semanticGroupId); |
| 298 | | - |
| 299 | | - if ($this->conceptuallyRelatedId == 0) |
| 300 | | - $this->conceptuallyRelatedId = $this->bootstrapDefinedMeaning("Conceptually related"); |
| 301 | | - addClassMemberShip($this->conceptuallyRelatedId, $this->semanticGroupId); |
| | 251 | + // some relations and their super class |
| | 252 | + $this->activityConceptId = $this->bootstrapConcept($this->activityConceptId, "performs", $this->functionallyRelatedId); |
| | 253 | + $this->containsConceptId = $this->bootstrapConcept($this->containsConceptId, "contains", $this->functionallyRelatedId); |
| | 254 | + $this->includesConceptId = $this->bootstrapConcept($this->includesConceptId, "consists of", $this->physicallyRelatedId); |
| 302 | 255 | |
| 303 | | - // some relation and there supper class |
| 304 | | - if ($this->activityConceptId == 0) |
| 305 | | - $this->activityConceptId = $this->bootstrapDefinedMeaning("performs"); |
| 306 | | - addClassMemberShip($this->activityConceptId, $this->functionallyRelatedId); |
| 307 | | - |
| 308 | | - if ($this->containsConceptId == 0) |
| 309 | | - $this->containsConceptId = $this->bootstrapDefinedMeaning("contains"); |
| 310 | | - addClassMemberShip($this->containsConceptId, $this->functionallyRelatedId); |
| | 256 | + // assign each comment type to one type aspect (later perhaps to multiple aspects) |
| | 257 | + $this->subcellularLocationId = $this->bootstrapConcept($this->subcellularLocationId, "subcellular location", $this->localizationAspectId); |
| | 258 | + $this->tissueSpecificityId = $this->bootstrapConcept($this->tissueSpecificityId, "tissue specificity", $this->localizationAspectId); |
| | 259 | + $this->catalyticActivityId = $this->bootstrapConcept($this->catalyticActivityId, "catalytic activity", $this->functionalAspectId); |
| | 260 | + $this->cofactorId = $this->bootstrapConcept($this->cofactorId, "cofactor", $this->functionalAspectId); |
| | 261 | + $this->functionId = $this->bootstrapConcept($this->functionId, "function", $this->functionalAspectId); |
| | 262 | + $this->diseaseId = $this->bootstrapConcept($this->diseaseId, "disease", $this->functionalAspectId); |
| | 263 | + $this->enzymeRegulationId = $this->bootstrapConcept($this->enzymeRegulationId, "enzyme regulation", $this->functionalAspectId); |
| | 264 | + $this->inductionId = $this->bootstrapConcept($this->inductionId, "induction", $this->functionalAspectId); |
| | 265 | + $this->interactionId = $this->bootstrapConcept($this->interactionId, "interaction", $this->functionalAspectId); |
| | 266 | + $this->pathwayId = $this->bootstrapConcept($this->pathwayId, "pathway", $this->functionalAspectId); |
| | 267 | + $this->rnaEditingId = $this->bootstrapConcept($this->rnaEditingId, "RNA editing", $this->functionalAspectId); |
| 311 | 268 | |
| 312 | | - if ($this->includesConceptId == 0) |
| 313 | | - $this->includesConceptId = $this->bootstrapDefinedMeaning("consists of"); |
| 314 | | - addClassMemberShip($this->includesConceptId, $this->physicallyRelatedId); |
| | 269 | + $this->alternativeProductsId = $this->bootstrapConcept($this->alternativeProductsId, "alternative products", $this->structuralAspectId); |
| | 270 | + $this->domainId = $this->bootstrapConcept($this->domainId, "domain", $this->structuralAspectId); |
| | 271 | + $this->ptmId = $this->bootstrapConcept($this->ptmId, "PTM", $this->structuralAspectId); |
| | 272 | + $this->polymorphismId = $this->bootstrapConcept($this->polymorphismId, "polymorphism", $this->structuralAspectId); |
| | 273 | + $this->similarityId = $this->bootstrapConcept($this->similarityId, "similarity", $this->structuralAspectId); |
| | 274 | + $this->massSpectrometryId = $this->bootstrapConcept($this->massSpectrometryId, "mass spectometry", $this->structuralAspectId); |
| | 275 | + $this->subunitId = $this->bootstrapConcept($this->subunitId, "subunit", $this->structuralAspectId); |
| 315 | 276 | |
| 316 | | - // assign each comment type to one type aspect (later perhaps to multiple aspects) |
| 317 | | - if ($this->subcellularLocationId == 0){ |
| 318 | | - $this->subcellularLocationId = $this->bootstrapDefinedMeaning("SUBCELLULAR LOCATION"); |
| 319 | | - addClassMemberShip($this->subcellularLocationId, $this->localizationAspectId); |
| 320 | | - } |
| 321 | | - if ($this->tissueSpecificityId == 0){ |
| 322 | | - $this->tissueSpecificityId = $this->bootstrapDefinedMeaning("TISSUE SPECIFICITY"); |
| 323 | | - addClassMemberShip($this->tissueSpecificityId, $this->localizationAspectId); |
| 324 | | - } |
| 325 | | - if ($this->catalyticActivityId == 0){ |
| 326 | | - $this->catalyticActivityId = $this->bootstrapDefinedMeaning("CATALYTIC ACTIVITY"); |
| 327 | | - addClassMemberShip($this->catalyticActivityId, $this->functionalAspectId); |
| 328 | | - } |
| 329 | | - if ($this->cofactorId == 0){ |
| 330 | | - $this->cofactorId = $this->bootstrapDefinedMeaning("COFACTOR"); |
| 331 | | - addClassMemberShip($this->cofactorId, $this->functionalAspectId); |
| 332 | | - } |
| 333 | | - if ($this->functionId == 0){ |
| 334 | | - $this->functionId = $this->bootstrapDefinedMeaning("FUNCTION"); |
| 335 | | - addClassMemberShip($this->functionId, $this->functionalAspectId); |
| 336 | | - } |
| 337 | | - if ($this->diseaseId == 0){ |
| 338 | | - $this->diseaseId = $this->bootstrapDefinedMeaning("DISEASE"); |
| 339 | | - addClassMemberShip($this->diseaseId, $this->functionalAspectId); |
| 340 | | - } |
| 341 | | - if ($this->enzymeRegulationId == 0){ |
| 342 | | - $this->enzymeRegulationId = $this->bootstrapDefinedMeaning("ENZYME REGULATION"); |
| 343 | | - addClassMemberShip($this->enzymeRegulationId, $this->functionalAspectId); |
| 344 | | - } |
| 345 | | - if ($this->inductionId == 0){ |
| 346 | | - $this->inductionId = $this->bootstrapDefinedMeaning("INDUCTION"); |
| 347 | | - addClassMemberShip($this->inductionId, $this->functionalAspectId); |
| 348 | | - } |
| 349 | | - if ($this->interactionId == 0){ |
| 350 | | - $this->interactionId = $this->bootstrapDefinedMeaning("INTERACTION"); |
| 351 | | - addClassMemberShip($this->interactionId, $this->functionalAspectId); |
| 352 | | - } |
| 353 | | - if ($this->pathwayId == 0){ |
| 354 | | - $this->pathwayId = $this->bootstrapDefinedMeaning("PATHWAY"); |
| 355 | | - addClassMemberShip($this->pathwayId, $this->functionalAspectId); |
| 356 | | - } |
| 357 | | - if ($this->rnaEditingId == 0){ |
| 358 | | - $this->rnaEditingId = $this->bootstrapDefinedMeaning("RNA EDITING"); |
| 359 | | - addClassMemberShip($this->rnaEditingId, $this->functionalAspectId); |
| 360 | | - } |
| 361 | | - if ($this->alternativeProductsId == 0){ |
| 362 | | - $this->alternativeProductsId = $this->bootstrapDefinedMeaning("ALTERNATIVE PRODUCTS"); |
| 363 | | - addClassMemberShip($this->alternativeProductsId, $this->structuralAspectId); |
| 364 | | - } |
| 365 | | - if ($this->domainId == 0){ |
| 366 | | - $this->domainId = $this->bootstrapDefinedMeaning("DOMAIN"); |
| 367 | | - addClassMemberShip($this->domainId, $this->structuralAspectId); |
| 368 | | - } |
| 369 | | - if ($this->ptmId == 0){ |
| 370 | | - $this->ptmId = $this->bootstrapDefinedMeaning("PTM"); |
| 371 | | - addClassMemberShip($this->ptmId, $this->structuralAspectId); |
| 372 | | - } |
| 373 | | - if ($this->polymorphismId == 0){ |
| 374 | | - $this->polymorphismId = $this->bootstrapDefinedMeaning("POLYMORPHISM"); |
| 375 | | - addClassMemberShip($this->polymorphismId, $this->structuralAspectId); |
| 376 | | - } |
| 377 | | - if ($this->similarityId == 0){ |
| 378 | | - $this->similarityId = $this->bootstrapDefinedMeaning("SIMILARITY"); |
| 379 | | - addClassMemberShip($this->similarityId, $this->structuralAspectId); |
| 380 | | - } |
| 381 | | - if ($this->massSpectrometryId == 0){ |
| 382 | | - $this->massSpectrometryId = $this->bootstrapDefinedMeaning("MASS SPECTROMETRY"); |
| 383 | | - addClassMemberShip($this->massSpectrometryId, $this->structuralAspectId); |
| 384 | | - } |
| 385 | | - if ($this->subunitId == 0){ |
| 386 | | - $this->subunitId = $this->bootstrapDefinedMeaning("SUBUNIT"); |
| 387 | | - addClassMemberShip($this->subunitId, $this->structuralAspectId); |
| 388 | | - } |
| 389 | | - if ($this->allergenId == 0){ |
| 390 | | - $this->allergenId = $this->bootstrapDefinedMeaning("ALLERGEN"); |
| 391 | | - addClassMemberShip($this->allergenId, $this->pharmaceuticalAspectId); |
| 392 | | - } |
| 393 | | - if ($this->pharmaceuticalId == 0){ |
| 394 | | - $this->pharmaceuticalId = $this->bootstrapDefinedMeaning("PHARMACEUTICAL"); |
| 395 | | - addClassMemberShip($this->pharmaceuticalId, $this->pharmaceuticalAspectId); |
| 396 | | - } |
| 397 | | - if ($this->biotechnologyId == 0){ |
| 398 | | - $this->biotechnologyId = $this->bootstrapDefinedMeaning("BIOTECHNOLOGY"); |
| 399 | | - addClassMemberShip($this->biotechnologyId, $this->pharmaceuticalAspectId); |
| 400 | | - } |
| 401 | | - if ($this->toxicDoseId == 0){ |
| 402 | | - $this->toxicDoseId = $this->bootstrapDefinedMeaning("TOXIC DOSE"); |
| 403 | | - addClassMemberShip($this->toxicDoseId, $this->pharmaceuticalAspectId); |
| 404 | | - } |
| 405 | | - if ($this->biophysicochemicalPropertiesId == 0){ |
| 406 | | - $this->biophysicochemicalPropertiesId = $this->bootstrapDefinedMeaning("BIOPHYSICOCHEMICAL PROPERTIES"); |
| 407 | | - addClassMemberShip($this->biophysicochemicalPropertiesId, $this->pharmaceuticalAspectId); |
| 408 | | - } |
| 409 | | - if ($this->onlineInformationId == 0){ |
| 410 | | - $this->onlineInformationId = $this->bootstrapDefinedMeaning("ONLINE INFORMATION"); |
| 411 | | - addClassMemberShip($this->onlineInformationId, $this->externalInformationId); |
| 412 | | - } |
| 413 | | - if ($this->developmentalStageId == 0){ |
| 414 | | - $this->developmentalStageId = $this->bootstrapDefinedMeaning("DEVELOPMENTAL STAGE"); |
| 415 | | - addClassMemberShip($this->developmentalStageId, $this->otherAspectId); |
| 416 | | - } |
| 417 | | - if ($this->miscellaneousId == 0){ |
| 418 | | - $this->miscellaneousId = $this->bootstrapDefinedMeaning("MISCELLANEOUS"); |
| 419 | | - addClassMemberShip($this->miscellaneousId, $this->otherAspectId); |
| 420 | | - } |
| 421 | | - if ($this->cautionId == 0){ |
| 422 | | - $this->cautionId = $this->bootstrapDefinedMeaning("CAUTION"); |
| 423 | | - addClassMemberShip($this->cautionId, $this->otherAspectId); |
| 424 | | - } |
| | 277 | + $this->allergenId = $this->bootstrapConcept($this->allergenId, "allergen", $this->pharmaceuticalAspectId); |
| | 278 | + $this->pharmaceuticalId = $this->bootstrapConcept($this->pharmaceuticalId, "pharmaceutical", $this->pharmaceuticalAspectId); |
| | 279 | + $this->biotechnologyId = $this->bootstrapConcept($this->biotechnologyId, "biotechnology", $this->pharmaceuticalAspectId); |
| | 280 | + $this->toxicDoseId = $this->bootstrapConcept($this->toxicDoseId, "toxic dose", $this->pharmaceuticalAspectId); |
| | 281 | + $this->biophysicochemicalPropertiesId = $this->bootstrapConcept($this->biophysicochemicalPropertiesId, "biophysicochemical properties", $this->pharmaceuticalAspectId); |
| | 282 | + |
| | 283 | + $this->onlineInformationId = $this->bootstrapConcept($this->onlineInformationId, "online information", $this->externalInformationId); |
| | 284 | + $this->developmentalStageId = $this->bootstrapConcept($this->developmentalStageId, "developmental stage", $this->otherAspectId); |
| | 285 | + $this->miscellaneousId = $this->bootstrapConcept($this->miscellaneousId, "miscellaneous", $this->otherAspectId); |
| | 286 | + $this->cautionId = $this->bootstrapConcept($this->cautionId, "caution", $this->otherAspectId); |
| 425 | 287 | } |
| 426 | 288 | |
| 427 | 289 | public function setProgressBar(ProgressBar $progressBar) { |