ncbi_utils.inc File Reference

Go to the source code of this file.

Functions
	tpps_ncbi_get_subkingdom ($organism)
	tpps_ncbi_get_taxon_id ($organism, $list=FALSE)
	tpps_ncbi_get_taxonomy ($organism, $rank)

Detailed Description

Defines EUtils functions for NCBI's EUtils API.

Definition in file ncbi_utils.inc.

Function Documentation

tpps_ncbi_get_subkingdom()

tpps_ncbi_get_subkingdom

(

$organism

)

Retrieves a subkingdom based on an organism name.

Parameters

string

$organism

The name of the organism.

Returns

mixed The name of the subkingdom or FALSE on failure.

Definition at line 53 of file ncbi_utils.inc.

                                             {
  $id = tpps_ncbi_get_taxon_id($organism);
  $fetch = new EFetch('taxonomy');
  $fetch->addParam('id', "$id");
  $response = $fetch->get()->xml();
  if (empty($response->Taxon->Lineage)) {
    drupal_set_message(t('Unable to load Lineage information from NCBI for organism: @org', array('@org' => $organism)));
    return FALSE;
  }

  $lineage = $response->Taxon->Lineage;
  if (preg_match('/(angiosperm|gymnosperm)/', $lineage, $matches)) {
    if (!empty($matches[1])) {
      return $matches[1];
    }
  }
  drupal_set_message(t('Unable to determine subkingdom from NCBI for organism: @org', array('@org' => $organism)));
  return FALSE;
}

tpps_ncbi_get_taxon_id()

tpps_ncbi_get_taxon_id	(		$organism,
			$list = FALSE
	)

Retrieves the NCBI Taxonomy Id of an organism based on its name.

Parameters

string

$organism

The name of the organism.

Returns

mixed The NCBI Taxonomy Id, or FALSE on failure.

Definition at line 82 of file ncbi_utils.inc.

                                                          {
  $formatted_org = implode('+', explode(' ', $organism));
  $search = new ESearch('taxonomy');
  $search->addParam('term', "{$formatted_org}[Scientific+Name]");

  $err_msg = 'Unable to load Taxon ID from NCBI for organism named: ' . $organism;
  try {
    $response = $search->get()->xml();
    if (empty($response->IdList->Id)) {
      drupal_set_message($err_msg);
      return FALSE;
    }
    if (!$list) {
      return $response->IdList->Id;
    }
    return $response->IdList;
  }
  catch (\Exception $e) {
    drupal_set_message($err_msg . ' EUtils Error: ' . $e->getMessage());
  }
}

tpps_ncbi_get_taxonomy()

tpps_ncbi_get_taxonomy	(		$organism,
			$rank
	)

Retrieves taxonomy information based on an organism name.

Parameters

string	$organism	The name of the organism.
string	$rank	The taxonomic rank (subkingdom, order, family, etc).

Returns

mixed The name of the family or FALSE on failure.

Definition at line 19 of file ncbi_utils.inc.

                                                  {
  // Subkingdom is a little different.
  if ($rank == 'subkingdom') {
    return tpps_ncbi_get_subkingdom($organism);
  }

  $id = tpps_ncbi_get_taxon_id($organism);
  $fetch = new EFetch('taxonomy');
  $fetch->addParam('id', "$id");
  $response = $fetch->get()->xml();
  if (empty($response->Taxon->LineageEx->Taxon)) {
    drupal_set_message(t('Unable to load Lineage information from NCBI for organism: @org', array('@org' => $organism)));
    return FALSE;
  }

  $lineage = $response->Taxon->LineageEx->Taxon;
  foreach ($lineage as $item) {
    if ($item->Rank == $rank) {
      return $item->ScientificName;
    }
  }
  drupal_set_message("Unable to determine $rank from NCBI for organism: $organism");
  return FALSE;
}