document organism mappings

[bradfordcondon]

heres the XML parsing from the TaxonomyImporter class in core.

 if ($xml) {
      $taxon = $xml->Taxon;

      // Get the genus and species from the xml.
      $parent = (string) $taxon->ParentTaxId;
      $rank = (string) $taxon->Rank;
      $sci_name = (string) $taxon->ScientificName;
      //$this->logMessage(' - Importing @sci_name', array('@sci_name' => $sci_name));

      // If we don't have an organism record provided then see if there
      // is one provided by Chado, if not, the try to add one.
      if (!$organism) {
        $organism = $this->findOrganism($taxid, $sci_name);
        if (!$organism) {
          $organism = $this->addOrganism($sci_name, $rank);
          if (!$organism) {
            throw new Exception(t('Cannot add organism: @sci_name', array('@sci_name' => $sci_name)));
          }
        }
      }

      // Associate the Dbxref with the organism.
      $this->addDbxref($organism->organism_id, $taxid);

      // Get properties for this organism.
      $lineage = (string) $taxon->Lineage;
      $genetic_code = (string) $taxon->GeneticCode->GCId;
      $genetic_code_name = (string) $taxon->GeneticCode->GCName;
      $mito_genetic_code = (string) $taxon->MitoGeneticCode->MGCId;
      $mito_genetic_code_name = (string) $taxon->MitoGeneticCode->MGCName;
      $division = (string) $taxon->Division;

      // Add in the organism properties.
      $this->addProperty($organism->organism_id, 'division', $division);
      $this->addProperty($organism->organism_id, 'mitochondrial_genetic_code_name', $mito_genetic_code_name);
      $this->addProperty($organism->organism_id, 'mitochondrial_genetic_code', $mito_genetic_code);
      $this->addProperty($organism->organism_id, 'genetic_code_name', $genetic_code_name);
      $this->addProperty($organism->organism_id, 'lineage', $lineage);
      $this->addProperty($organism->organism_id, 'genetic_code', $genetic_code);

      $name_ranks = array();
      if ($taxon->OtherNames->children) {
        foreach ($taxon->OtherNames->children() as $child) {
          $type = $child->getName();
          $name = (string) $child;
          if (!array_key_exists($type, $name_ranks)) {
            $name_ranks[$type] = 0;
          }
          switch ($type) {
            case 'GenbankCommonName':
              $this->addProperty($organism->organism_id, 'genbank_common_name', $name, $name_ranks[$type]);
              break;
            case 'Synonym':
            case 'GenbankSynonym':
              $this->addProperty($organism->organism_id, 'synonym', $name, $name_ranks[$type]);
              break;
            case 'CommonName':
              // If we had to add the organism then include the commone name too.
              if ($adds_organism) {
                $organism->common_name = $name;
                $values = array('organism_id' => $organism->id);
                chado_update_record('organism', $values, $organism);
              }
            case 'Includes':
              $this->addProperty($organism->organism_id, 'other_name', $name, $name_ranks[$type]);
              break;
            case 'EquivalentName':
              $this->addProperty($organism->organism_id, 'equivalent_name', $name, $name_ranks[$type]);
              break;
            case 'Anamorph':
              $this->addProperty($organism->organism_id, 'anamorph', $name, $name_ranks[$type]);
              break;
            case 'Name':
              // skip the Name stanza
              break;
            default:
              print "NOTICE: Skipping unrecognzed name type: $type\n";
              // do nothing for unrecognized types
          }
          $name_ranks[$type]++;
        }
      }

[bradfordcondon]

OK I've sorted out the mappings. I see its all local terms for the organism properties... hmmm...