function annotate($text) { parent::annotate($text, array(39933)); // 39933 = version-specific localOntologyId from http://rest.bioontology.org/obs/ontologies 1247 = virtualOntologyId foreach ($this->annotations as &$annotation) { $annotation['type'] = 'species'; } }
function annotate($text) { parent::annotate($text, array(42919)); // 42919 = version-specific localOntologyId from http://rest.bioontology.org/obs/ontologies foreach ($this->annotations as &$annotation) { $annotation['type'] = 'protein'; } }
function annotate($text) { parent::annotate($text, array(42878)); // 42878 = version-specific localOntologyId from http://rest.bioontology.org/obs/ontologies 1007 = virtualOntologyId foreach ($this->annotations as &$annotation) { $annotation['type'] = 'chemical'; } // TODO: lookup structures and calculate stdinchi + stdinchikey for each one }