tripal_chado.pub_importer_PMID.inc File Reference

Functions
	tripal_pub_remote_alter_form_PMID ($form, $form_state, $num_criteria=1)
	tripal_pub_remote_validate_form_PMID ($form, $form_state)
	tripal_pub_remote_search_PMID ($search_array, $num_to_retrieve, $page)
	tripal_pub_PMID_search_init ($search_str, $retmax)
	tripal_pub_PMID_fetch ($query_key, $web_env, $rettype='null', $retmod='null', $start=0, $limit=10, $args=[])
	tripal_pub_PMID_parse_pubxml ($pub_xml)
	tripal_pub_PMID_parse_medline_journal_info ($xml, &$pub)
	tripal_pub_PMID_parse_article ($xml, &$pub)
	tripal_pub_PMID_parse_publication_type ($xml, &$pub)
	tripal_pub_PMID_parse_abstract ($xml, &$pub)
	tripal_pub_PMID_parse_pagination ($xml, &$pub)
	tripal_pub_PMID_parse_journal ($xml, &$pub)
	tripal_pub_PMID_parse_journal_issue ($xml, &$pub)
	tripal_pub_PMID_parse_date ($xml, $element_name)
	tripal_pub_PMID_parse_authorlist ($xml, &$pub)
	tripal_pub_remote_search_get_language ($lang_abbr)

Detailed Description

This file provides support for importing and parsing of results from the NCBI PubMed database. The functions here are used by both the publication importer setup form and the publication importer.

Function Documentation

tripal_pub_PMID_fetch()

tripal_pub_PMID_fetch	(		$query_key,
			$web_env,
			$rettype = 'null',
			$retmod = 'null',
			$start = 0,
			$limit = 10,
			$args = []
	)

Retrieves from PubMed a set of publications from the previously initiated query.

Parameters

$query_key	The esearch QueryKey
$web_env	The esearch WebEnv
$rettype	The efetch return type
$retmod	The efetch return mode
$start	The start of the range to retrieve
$limit	The number of publications to retrieve
$args	Any additional arguments to add the efetch query URL

Returns

An array containing the total_records in the dataset, the search string and an array of the publications that were retrieved.

tripal_pub_PMID_parse_abstract()

tripal_pub_PMID_parse_abstract	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about the abstract

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_article()

tripal_pub_PMID_parse_article	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about an article.

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_authorlist()

tripal_pub_PMID_parse_authorlist	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about the author list for a publication

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_date()

tripal_pub_PMID_parse_date	(		$xml,
			$element_name
	)

Parses the section from the XML returned from PubMed that contains information regarding to dates

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_journal()

tripal_pub_PMID_parse_journal	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about a journal

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_journal_issue()

tripal_pub_PMID_parse_journal_issue	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about a journal issue

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_medline_journal_info()

tripal_pub_PMID_parse_medline_journal_info	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about the Journal

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_pagination()

tripal_pub_PMID_parse_pagination	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about pagination

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_publication_type()

tripal_pub_PMID_parse_publication_type	(		$xml,
		&	$pub
	)

Parses the section from the XML returned from PubMed that contains information about a publication

A full list of publication types can be found here: http://www.nlm.nih.gov/mesh/pubtypes.html.

The Tripal Pub ontology doesn't yet have terms for all of the publication types so we store the value in the 'publication_type' term.

Parameters

$xml	The XML to parse
$pub	The publication object to which additional details will be added

tripal_pub_PMID_parse_pubxml()

tripal_pub_PMID_parse_pubxml

(

$pub_xml

)

This function parses the XML containing details of a publication and converts it into an associative array of where keys are Tripal Pub ontology terms and the values are extracted from the XML. The XML should contain only a single publication record.

Information about the valid elements in the PubMed XML can be found here: https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html

Information about PubMed's citation format can be found here https://www.nlm.nih.gov/bsd/policy/cit_format.html

Parameters

$pub_xml

An XML string describing a single publication

Returns

An array describing the publication

tripal_pub_PMID_search_init()

tripal_pub_PMID_search_init	(		$search_str,
			$retmax
	)

Initailizes a PubMed Search using a given search string

Parameters

$search_str	The PubMed Search string
$retmax	The maximum number of records to return

Returns

An array containing the Count, WebEnv and QueryKey as return by PubMed's esearch utility

tripal_pub_remote_alter_form_PMID()

tripal_pub_remote_alter_form_PMID	(		$form,
			$form_state,
			$num_criteria = 1
	)

A hook for altering the publication importer form. It Changes the 'Abstract' filter to be 'Abstract/Title'.

Parameters

$form	The Drupal form array
$form_state	The form state array
$num_criteria	The number of criteria the user currently has added to the form

Returns

The form (drupal form api)

tripal_pub_remote_search_get_language()

tripal_pub_remote_search_get_language

(

$lang_abbr

)

Get the name of the language based on an abbreviation

Language abbreviations were obtained here: http://www.nlm.nih.gov/bsd/language_table.html

Parameters

$lang_abbr

The abbreviation of the language to return

Returns

The full name of the language

tripal_pub_remote_search_PMID()

tripal_pub_remote_search_PMID	(		$search_array,
			$num_to_retrieve,
			$page
	)

A hook for performing the search on the PubMed database.

Parameters

$search_array	An array containing the search criteria for the search
$num_to_retrieve	Indicates the maximum number of publications to retrieve from the remote database
$page	Indicates the page to retrieve. This corresponds to a paged table, where each page has $num_to_retrieve publications.

Returns

An array of publications.

tripal_pub_remote_validate_form_PMID()

tripal_pub_remote_validate_form_PMID	(		$form,
			$form_state
	)

A hook for providing additional validation of importer setup form.

Parameters

$form	The Drupal form array
$form_state	The form state array

Returns

The form (drupal form api)