| Index: trunk/extensions/Wikidata/WP/SwissProtImport.php |
| — | — | @@ -113,15 +113,15 @@ |
| 114 | 114 | public $organismConceptId = 0; |
| 115 | 115 | public $functionalDomainConceptId = 0; |
| 116 | 116 | public $proteinComponentConceptId = 0; |
| 117 | | - public $referencedByConceptId = 0; |
| | 117 | +// public $referencedByConceptId = 0; |
| 118 | 118 | public $biologicalProcessConceptId = 0; |
| 119 | 119 | public $molecularFunctionConceptId = 0; |
| 120 | 120 | public $cellularComponentConceptId = 0; |
| 121 | | - public $keywordConceptId = 0; |
| | 121 | +// public $keywordConceptId = 0; |
| 122 | 122 | public $includesConceptId = 0; |
| 123 | | - public $includedInConceptId = 0; |
| | 123 | +// public $includedInConceptId = 0; |
| 124 | 124 | public $containsConceptId = 0; |
| 125 | | - public $containedInConceptId = 0; |
| | 125 | +// public $containedInConceptId = 0; |
| 126 | 126 | public $textAttributeConceptId = 0; |
| 127 | 127 | public $enzymeCommissionNumberConceptId = 0; |
| 128 | 128 | public $activityConceptId = 0; |
| — | — | @@ -158,8 +158,8 @@ |
| 159 | 159 | if ($this->proteinComponentConceptId == 0) |
| 160 | 160 | $this->proteinComponentConceptId = $this->bootstrapDefinedMeaning("protein component", "protein component"); |
| 161 | 161 | |
| 162 | | - if ($this->referencedByConceptId == 0) |
| 163 | | - $this->referencedByConceptId = $this->bootstrapDefinedMeaning("referenced by", "referenced by"); |
| | 162 | +// if ($this->referencedByConceptId == 0) |
| | 163 | +// $this->referencedByConceptId = $this->bootstrapDefinedMeaning("referenced by", "referenced by"); |
| 164 | 164 | |
| 165 | 165 | if ($this->biologicalProcessConceptId == 0) |
| 166 | 166 | $this->biologicalProcessConceptId = $this->bootstrapDefinedMeaning("biological process", "biological process"); |
| — | — | @@ -170,20 +170,20 @@ |
| 171 | 171 | if ($this->cellularComponentConceptId == 0) |
| 172 | 172 | $this->cellularComponentConceptId = $this->bootstrapDefinedMeaning("cellular component", "cellular component"); |
| 173 | 173 | |
| 174 | | - if ($this->keywordConceptId == 0) |
| 175 | | - $this->keywordConceptId = $this->bootstrapDefinedMeaning("keyword", "keyword"); |
| | 174 | +// if ($this->keywordConceptId == 0) |
| | 175 | +// $this->keywordConceptId = $this->bootstrapDefinedMeaning("keyword", "keyword"); |
| 176 | 176 | |
| 177 | 177 | if ($this->includesConceptId == 0) |
| 178 | 178 | $this->includesConceptId = $this->bootstrapDefinedMeaning("includes", "includes"); |
| 179 | 179 | |
| 180 | | - if ($this->includedInConceptId == 0) |
| 181 | | - $this->includedInConceptId = $this->bootstrapDefinedMeaning("included in", "included in"); |
| | 180 | +// if ($this->includedInConceptId == 0) |
| | 181 | +// $this->includedInConceptId = $this->bootstrapDefinedMeaning("included in", "included in"); |
| 182 | 182 | |
| 183 | 183 | if ($this->containsConceptId == 0) |
| 184 | 184 | $this->containsConceptId = $this->bootstrapDefinedMeaning("contains", "contains"); |
| 185 | 185 | |
| 186 | | - if ($this->containedInConceptId == 0) |
| 187 | | - $this->containedInConceptId = $this->bootstrapDefinedMeaning("contained in", "contained in"); |
| | 186 | +// if ($this->containedInConceptId == 0) |
| | 187 | +// $this->containedInConceptId = $this->bootstrapDefinedMeaning("contained in", "contained in"); |
| 188 | 188 | |
| 189 | 189 | if ($this->enzymeCommissionNumberConceptId == 0) |
| 190 | 190 | $this->enzymeCommissionNumberConceptId = $this->bootstrapDefinedMeaning("enzyme commission number", "enzyme commission number"); |
| — | — | @@ -212,7 +212,7 @@ |
| 213 | 213 | |
| 214 | 214 | // Add concepts to relation types |
| 215 | 215 | addDefinedMeaningToCollectionIfNotPresent($this->proteinConceptId, $this->relationTypeCollectionId, "protein"); |
| 216 | | - addDefinedMeaningToCollectionIfNotPresent($this->referencedByConceptId, $this->relationTypeCollectionId, "referenced by"); |
| | 216 | +// addDefinedMeaningToCollectionIfNotPresent($this->referencedByConceptId, $this->relationTypeCollectionId, "referenced by"); |
| 217 | 217 | addDefinedMeaningToCollectionIfNotPresent($this->geneConceptId, $this->relationTypeCollectionId, "gene"); |
| 218 | 218 | addDefinedMeaningToCollectionIfNotPresent($this->organismSpecificGeneConceptId, $this->relationTypeCollectionId, "organism specific gene"); |
| 219 | 219 | addDefinedMeaningToCollectionIfNotPresent($this->organismConceptId, $this->relationTypeCollectionId, "organism"); |
| — | — | @@ -220,11 +220,11 @@ |
| 221 | 221 | addDefinedMeaningToCollectionIfNotPresent($this->biologicalProcessConceptId, $this->relationTypeCollectionId, "biological process"); |
| 222 | 222 | addDefinedMeaningToCollectionIfNotPresent($this->molecularFunctionConceptId, $this->relationTypeCollectionId, "molecular function"); |
| 223 | 223 | addDefinedMeaningToCollectionIfNotPresent($this->cellularComponentConceptId, $this->relationTypeCollectionId, "cellular component"); |
| 224 | | - addDefinedMeaningToCollectionIfNotPresent($this->keywordConceptId, $this->relationTypeCollectionId, "keyword"); |
| | 224 | +// addDefinedMeaningToCollectionIfNotPresent($this->keywordConceptId, $this->relationTypeCollectionId, "keyword"); |
| 225 | 225 | addDefinedMeaningToCollectionIfNotPresent($this->includesConceptId, $this->relationTypeCollectionId, "includes"); |
| 226 | | - addDefinedMeaningToCollectionIfNotPresent($this->includedInConceptId, $this->relationTypeCollectionId, "included in"); |
| | 226 | +// addDefinedMeaningToCollectionIfNotPresent($this->includedInConceptId, $this->relationTypeCollectionId, "included in"); |
| 227 | 227 | addDefinedMeaningToCollectionIfNotPresent($this->containsConceptId, $this->relationTypeCollectionId, "contains"); |
| 228 | | - addDefinedMeaningToCollectionIfNotPresent($this->containedInConceptId, $this->relationTypeCollectionId, "contained in"); |
| | 228 | +// addDefinedMeaningToCollectionIfNotPresent($this->containedInConceptId, $this->relationTypeCollectionId, "contained in"); |
| 229 | 229 | } |
| 230 | 230 | |
| 231 | 231 | public function startElement($parser, $name, $attributes) { |
| — | — | @@ -473,7 +473,7 @@ |
| 474 | 474 | addSynonymOrTranslation($synonym, $this->languageId, $domainMeaningId, true); |
| 475 | 475 | |
| 476 | 476 | addRelation($definedMeaningId, $this->includesConceptId, $domainMeaningId); |
| 477 | | - addRelation($domainMeaningId, $this->includedInConceptId, $definedMeaningId); |
| | 477 | +// addRelation($domainMeaningId, $this->includedInConceptId, $definedMeaningId); |
| 478 | 478 | } |
| 479 | 479 | |
| 480 | 480 | // Add 'contained' proteins: |
| — | — | @@ -484,7 +484,7 @@ |
| 485 | 485 | addSynonymOrTranslation($synonym, $this->languageId, $componentMeaningId, true); |
| 486 | 486 | |
| 487 | 487 | addRelation($definedMeaningId, $this->containsConceptId, $componentMeaningId); |
| 488 | | - addRelation($componentMeaningId, $this->containedInConceptId, $definedMeaningId); |
| | 488 | +// addRelation($componentMeaningId, $this->containedInConceptId, $definedMeaningId); |
| 489 | 489 | } |
| 490 | 490 | |
| 491 | 491 | return $definedMeaningId; |