public function add( IdStack $idPath, $record ) {
$objectId = $this->objectIdFetcher->fetch( $idPath->getKeyStack() );
$linkAttributeId = $this->determineAttributeId( $idPath, "URL", $record->linkAttribute );
$linkValue = $record->link;
$label = $linkValue->linkLabel;
$url = $linkValue->linkURL;
if ( $linkAttributeId != 0 && $url != "" ) {
addLinkAttributeValue( $objectId, $linkAttributeId, $this->validateURL( $url ), $label );
}
}
protected function addComments( SwissProtEntry $entry, $definedMeaningId, $proteinMeaningId, $organismSpeciesMeaningId ) {
foreach ( $entry->comments as $key => $comment ) {
$commentType = strtoupper( $comment->type );
$comment->text = trim( $comment->text );
// f.) Information in the attribute 'caution' is imported but it many times doesn’t
// make sense due to the fact it refers to References (in the SP entry) that are
// not shown in wikiproteins, therefore it should NOT be imported presently.
if ( $commentType == "CAUTION" )
continue; // ignore
// create definedMeaning for SP comment type
$attributeMeaningId = $this->getOrCreateAttributeMeaningId( $comment->type );
// initialize text value
$textValue = "";
$normalProcessing = true;
// link comments with the appropriate definedMeaning(defined by Chrisi and Erik)
// we have to create relation between comment and its aspect
// all comments have the relation 'has aspect'
switch ( $commentType ) {
// j.) the comments with the topic, SUBCELLULAR LOCATION and TISSUE SPECIFICITY
// need to be tagged with the attribute 'Localization Aspects'
case "SUBCELLULAR LOCATION":
case "TISSUE SPECIFICITY":
break;
// k.) the comments with the topic, CATALYTIC ACTIVITY, COFACTOR, FUNCTION, DISEASE,
// ENZYME REGULATION, INDUCTION, INTERACTION, PATHWAY, RNA EDITING, and
// DEVELOPMENTAL STAGE need to be tagged with the attribute 'Functional Aspects'
case "CATALYTIC ACTIVITY":
case "COFACTOR":
case "FUNCTION":
case "DISEASE":
case "ENZYME REGULATION":
case "INDUCTION":
case "INTERACTION":
case "PATHWAY":
case "RNA EDITING":
// add INTERACTION comment parameters
if ( $commentType == "INTERACTION" && count( $comment->children ) == 2 ) {
if ( $comment->children[0]->att_intactId == $comment->children[1]->att_intactId ) {
$textValue .= "with Self (accepted by Swiss-Prot);";
// build URL
$comment->url = "http://www.ebi.ac.uk/intact/search/do/search?binary=" .
$comment->children[0]->att_intactId . "," .
$comment->children[0]->att_intactId;
}
else {
if ( $comment->children[1]->label == "" )
$textValue .= "with -";
else
$textValue .= "with " . $comment->children[1]->label;
$textValue .= " (accepted by Swiss-Prot);";
$comment->url = "http://www.ebi.ac.uk/intact/search/do/search?binary=" .
$comment->children[0]->att_intactId . "," .
$comment->children[1]->att_intactId;
}
}
// ignore other parameters of INTERACTION comment
if ( $commentType == "INTERACTION" )
$comment->text = "";
break;
// l.) the comments with the topic, ALTERNATIVE PRODUCTS, DOMAIN, PTM,
// POLYMORPHISM, SIMILARITY, MASS SPECTROMETRY, and SUBUNIT need to be tagged
// with the attribute 'Structural Aspects'
case "ALTERNATIVE PRODUCTS":
foreach ( $comment->isoforms as $isoform ) {
$isoformId = $this->addIsoform( $entry, $definedMeaningId, $proteinMeaningId, $organismSpeciesMeaningId, $isoform );
addRelation( $definedMeaningId, $this->alternativeProductId, $isoformId );
}
break;
case "SIMILARITY":
if ( startsWith( $comment->text, "Belongs to the " ) ) {
$family = trim( substr( $comment->text, strlen( "Belongs to the " ) ) );
$familyId = $this->addSimilarityFamily( $family );
addRelation( $definedMeaningId, $this->conceptualPartOfId, $familyId );
$normalProcessing = false;
}
else if ( startsWith( $comment->text, "Contains " ) ) {
$domain = trim( substr( $comment->text, strlen( "Contains " ) ) );
while ( $domain[0] >= "0" && $domain[0] <= "9" )
$domain = substr( $domain, 1 );
$domain = trim( $domain );
$domainId = $this->addSimilarityFamily( $domain );
addRelation( $definedMeaningId, $this->consistsOfId, $domainId );
$normalProcessing = false;
}
break;
case "DOMAIN":
case "PTM":
case "POLYMORPHISM":
case "MASS SPECTROMETRY":
case "SUBUNIT":
// add mass SPECTROMETRY to text value
if ( $comment->mass != "" )
$textValue .= $comment->mass . " is the determined molecular weight; ";
// add method of MASS SPECTROMETRY to text value
if ( $comment->method != "" ) {
$textValue .= $comment->method . " is the ionization method; ";
}
// add error of MASS SPECTROMETRY to text value
if ( $comment->error != "" ) {
$textValue .= $comment->error . " is the accuracy or error range of the MW measurement; ";
}
// add position of MASS SPECTROMETRY to text value
if ( $commentType == "MASS SPECTROMETRY" && count( $comment->children ) > 0 )
$textValue .= $comment->children[0]->position . " is the part of the protein sequence entry that corresponds to the molecular weight;";
// ignore note of MASS SPECTROMETRY comment
if ( $commentType == "MASS SPECTROMETRY" )
$comment->text = "";
break;
// m.) the comments with the topic, ALLERGEN, PHARMACEUTICAL, BIOTECHNOLOGY,
// TOXIC DOSE, and BIOPHYSICOCHEMICAL PROPERTIES need to be tagged with the
// attribute 'Pharmaceutical Aspects'
case "ALLERGEN":
case "PHARMACEUTICAL":
case "BIOTECHNOLOGY":
case "TOXIC DOSE":
case "BIOPHYSICOCHEMICAL PROPERTIES":
if ( $commentType == "BIOPHYSICOCHEMICAL PROPERTIES" ) {
// add Kinetic parameters to text value
if ( count( $comment->children ) > 0 ) {
$textValue .= "Kinetic parameters:(";
if ( $comment->children[0]->km != "" )
$textValue .= "KM=" . $comment->children[0]->km . "; ";
if ( $comment->children[0]->vMax != "" )
$textValue .= "Vmax=" . $comment->children[0]->vMax;
$textValue .= "); ";
}
// add phDependence parameter
if ( $comment->phDependence != "" )
$textValue .= "pH dependence: " . $comment->phDependence . "; ";
// add temperatureDependence parameter
if ( $comment->temperatureDependence != "" )
$textValue .= "temperature dependence: " . $comment->temperatureDependence . ";";
}
break;
// o.) the comments with the topic, WEB RESOURCE or ONLINE INFORMATION needs to
// be tagged with the attribute 'External Information'
case "ONLINE INFORMATION":
// add comment name to text value
$label = "";
if ( $comment->name != "" )
$label .= $comment->name;
// add 'NOTE' child text to link label
if ( $comment->note != "" ) {
if ( $label != "" )
$label .= ", ";
$label .= $comment->note;
}
if ( $comment->text != "" ) {
$textValue = $comment->text;
if ( $comment->status != "" )
$textValue .= " (" . $comment->status . ")";
$idToAddLinkTo = addTextAttributeValue( $definedMeaningId, $attributeMeaningId, $textValue );
}
else
$idToAddLinkTo = $definedMeaningId;
addLinkAttributeValue( $idToAddLinkTo, $this->onlineInformationId, $comment->url, $label );
$normalProcessing = false;
break;
// n.) the comments with the topic, MISCELLANEOUS and CAUTION need to be tagged
// with the attribute 'Other Aspects'
case "DEVELOPMENTAL STAGE":
case "MISCELLANEOUS":
case "CAUTION":
default:
break;
}
if ( $normalProcessing ) {
// add comment text to text value
if ( $textValue != "" && ( $comment->text != "" || $comment->status != "" ) )
$textValue .= " TEXT=";
if ( $comment->text != "" )
$textValue .= $comment->text;
// add comment status to text value
if ( $comment->status != "" )
$textValue .= " (" . $comment->status . ")";
if ( $textValue != "" ) {
// add the comment fields as text attributes to the entry
$textAttributeValueId = addTextAttributeValue( $definedMeaningId, $attributeMeaningId, $textValue );
// add the comment URL as URL attribute to the entry and link URL attribute with text attribute
if ( $comment->url != "" )
addLinkAttributeValue( $textAttributeValueId, $this->onlineInformationId, $comment->url );
}
}
}
}
