Bio::Biblio::IO medline2ref
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Biblio::IO::medline2ref - A converter of a raw hash to MEDLINE citations
Package variables
No package variables defined.
Included modules
Bio::Biblio::MedlineBook
Bio::Biblio::MedlineJournal
Bio::Biblio::Organisation
Bio::Biblio::Person
Bio::Biblio::Provider
Inherit
Bio::Root::Root
Synopsis
 # to be written
Description
 # to be written
Methods
new
No description
Code
_load_instance
No description
Code
convert
No description
Code
_new_instance
No description
Code
_convert_date
No description
Code
_convert_personal_name
No description
Code
_convert_journal_article
No description
Code
_convert_book_article
No description
Code
_convert_article
No description
Code
_convert_providers
No description
Code
Methods description
None available.
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    my $class = ref ($caller) || $caller;

    # object creation and blessing    
my ($self) = $class->SUPER::new (@args); # make a hashtable from @args
my %param = @args; @param { map { lc $_ } keys %param } = values %param; # lowercase keys
# copy all @args into this object (overwriting what may already be
# there) - changing '-key' into '_key', and making keys lowercase
my $new_key; foreach my $key (keys %param) { ($new_key = $key) =~ s/^-/_/; $self->{ lc $new_key } = $param { $key }; } # done
return $self; } # ---------------------------------------------------------------------
#
# Here is the core...
#
# ---------------------------------------------------------------------
}
_load_instancedescriptionprevnextTop
sub _load_instance {
    my ($self, $source) = @_;

    #
# MEDLINE has only JournalArticles and BookArticles
# but we may create a general Ref if there is no attribute 'article'
#
my $result; my $article = $$source{'article'}; if (defined $article) { if (defined $$article{'journal'}) { $result = $self->_new_instance ('Bio::Biblio::MedlineJournalArticle'); $result->type ('JournalArticle'); } elsif (defined $$article{'book'}) { $result = $self->_new_instance ('Bio::Biblio::MedlineBookArticle'); $result->type ('BookArticle'); } else { $result->type ('MedlineArticle'); } } $result = $self->_new_instance ('Bio::Biblio::Ref') unless defined $result; return $result;
}
convertdescriptionprevnextTop
sub convert {
   my ($self, $source) = @_;
   my $result = $self->_load_instance ($source);

   if (defined $result->type) {
       if ($result->type eq 'JournalArticle') {
	   &_convert_journal_article ($result, $source);
       } elsif ($result->type eq 'BookArticle') {
	   &_convert_book_article ($result, $source);
       } elsif ($result->type eq 'Article') {
	   &_convert_article ($result, $source);
       }
   }

   #
# now do the attributes which are the same for all resource types
#
# ...identification is now by MedlineID but the trend is to replace
# it by PMID (I have heard) theefore we keep both also separately
# from the 'identifier'
if (defined $$source{'medlineID'}) { $result->identifier ($$source{'medlineID'}); } else { $result->identifier ($$source{'PMID'}); } $result->pmid ($$source{'PMID'}) if defined $$source{'PMID'}; $result->medline_id ($$source{'medlineID'}) if defined $$source{'medlineID'}; # ...few others
$result->citation_owner ($$source{'owner'}) if defined $$source{'owner'}; $result->status ($$source{'status'}) if defined $$source{'status'}; $result->number_of_references ($$source{'numberOfReferences'}) if defined $$source{'numberOfReferences'}; # ...entry status of the citation in the repository
my $date; if (defined $$source{'dateRevised'}) { $result->last_modified_date (&_convert_date ($$source{'dateRevised'})); $date = &_convert_date ($$source{'dateCreated'}); $result->date_created ($date) if defined $date; $date = &_convert_date ($$source{'dateCompleted'}); $result->date_completed ($date) if defined $date; } elsif (defined $$source{'dateCompleted'}) { $result->last_modified_date (&_convert_date ($$source{'dateCompleted'})); $date = &_convert_date ($$source{'dateCreated'}); $result->date_created ($date) if defined $date; } elsif (defined $$source{'dateCreated'}) { $result->last_modified_date (&_convert_date ($$source{'dateCreated'})); } # ...put citation subsets in a comma-separated string
if (defined $$source{'citationSubsets'}) { $result->repository_subset (join (',', @{ $$source{'citationSubsets'} })); } # ...MEDLINE's Comments & Corrections will be arrays of hashes
if (defined $$source{'commentsCorrections'}) { my $corr = $$source{'commentsCorrections'}; $result->comment_ons ($$corr{'commentOns'}) if defined $$corr{'commentOns'}; $result->comment_ins ($$corr{'commentIns'}) if defined $$corr{'commentIns'}; $result->erratum_ins ($$corr{'erratumIns'}) if defined $$corr{'erratumIns'}; $result->erratum_fors ($$corr{'erratumFors'}) if defined $$corr{'erratumFors'}; $result->original_report_ins ($$corr{'originalReportIns'}) if defined $$corr{'originalReportIns'}; $result->republished_froms ($$corr{'republishedFroms'}) if defined $$corr{'republishedFroms'}; $result->republished_ins ($$corr{'republishedIns'}) if defined $$corr{'republishedIns'}; $result->retraction_ofs ($$corr{'retractionOfs'}) if defined $$corr{'retractionOfs'}; $result->retraction_ins ($$corr{'retractionIns'}) if defined $$corr{'retractionIns'}; $result->summary_for_patients_ins ($$corr{'summaryForPatientsIns'}) if defined $$corr{'summaryForPatientsIns'}; $result->update_ins ($$corr{'updateIns'}) if defined $$corr{'updateIns'}; $result->update_ofs ($$corr{'updateOfs'}) if defined $$corr{'updateOfs'}; } # ...MEDLINE's GeneSymbols are put in a comma-separated string
if (defined $$source{'geneSymbols'}) { $result->gene_symbols (join (',', @{ $$source{'geneSymbols'} })); } # ...MEDLINE's GeneralNotes into an array of hashtables, each one
# having keys for the 'owner' and the 'note'
$result->general_notes ($$source{'generalNotes'}) if defined $$source{'generalNotes'}; # ...MEDLINE's PersonalNameSubjects into contributors (TBD: is that correct?)
if (defined $$source{'personalNameSubjects'}) { my @contributors; foreach my $person ( @{ $$source{'personalNameSubjects'} } ) { push (@contributors, &_convert_personal_name ($person)); } $result->contributors (\@contributors); } # ...MEDLINE's OtherAbstract into an array of hashtables, each one
# having keys for the 'type', 'AbstractText' and the 'copyright'
$result->other_abstracts ($$source{'otherAbstracts'}) if defined $$source{'otherAbstracts'}; # if (defined $$source{'otherAbstracts'}) {
# my @other_abstracts = ();
# foreach my $oa ( @{ $$source{'otherAbstracts'} } ) {
# if (defined $$oa{'abstractText'}) {
# my $abstract = $$oa{'abstractText'};
# delete $$oa{'abstractText'};
# $$oa{'abstract'} = $$abstract{'abstractText'};
# $$oa{'rights'} = $$abstract{'copyrightInformation'} if defined $$abstract{'copyrightInformation'};
# push (@other_abstracts, $oa);
# }
# }
# $result->other_abstracts (\@other_abstracts);
# }
# ...MEDLINE's OtherIDs into an array of hashtables, each one
# having keys for the 'id', and 'source'
$result->other_ids ($$source{'otherIDs'}) if defined $$source{'otherIDs'}; # ...MEDLINE's Chemicals - store them as an array of hashtables
# (each one for each Chemical)
$result->chemicals ($$source{'chemicals'}) if defined $$source{'chemicals'}; # MeshHeadings are put on two places:
# - a complete information in a property called "MeshHeadings", and
# - only descriptors in the hashtable "subject_headings", together
# with the word "MeSH" in "subject_headings_source"
if (defined $$source{'meshHeadings'}) { $result->mesh_headings ($$source{'meshHeadings'}); my %subject_headings; foreach my $mesh ( @{ $$source{'meshHeadings'} } ) { $subject_headings{ $$mesh{'descriptorName'} } = 1 if defined $$mesh{'descriptorName'}; } if (%subject_headings) { $result->subject_headings (\%subject_headings); $result->subject_headings_source ('Mesh'); } } # ...MEDLINE's keyword lists are merger all together (this may not
# be good idea - but again the keywords are better accessible
# -TBD?)
if (defined $$source{'keywordLists'}) { my %keywords; foreach my $keywords ( @{ $$source{'keywordLists'} } ) { if ($$keywords{'keywords'}) { foreach my $keyword ( @{ $$keywords{'keywords'} } ) { $keywords{$keyword} = 1; } } } $result->keywords (\%keywords) if %keywords; } # Done!
return $result; } # load a module (given as a real module name, e.g. 'Bio::Biblio::MedlineJournalArticle'),
# call new() method on it, and return the instance returned by the new() method
}
_new_instancedescriptionprevnextTop
sub _new_instance {
    my ($self, $module) = @_;
    my ($filename);
    ($filename = $module . '.pm') =~ s|\:\:|/|g;
    eval { require $filename; };
    $self->throw ("Loading error when trying '$filename'. $@\n") if $@;
    return $module->new;
}

#
# see OpenBQS specification (http://www.ebi.ac.uk/~senger/openbqs/) how
# a date should be coded;
# TBD: this can be improved - checking is missing, timezones,
# converting to UTC...
# Also note that this routine does not convert 'medline_date' - it
# is stored in a separate attribute without ant conversion.
#
}
_convert_datedescriptionprevnextTop
sub _convert_date {
    my ($date) = @_;
    return unless
	exists $$date{'year'} or
	    exists $$date{'month'} or
		exists $$date{'day'} or
		    exists $$date{'hour'} or
			exists $$date{'minute'} or
			    exists $$date{'second'};


    my $converted = (exists $$date{'year'} ? $$date{'year'} : '0000');

    if (exists $$date{'month'}) {
	$converted .= '-' . $$date{'month'};
    } elsif (exists $$date{'day'}) {
	$converted .= '-00';
    }

    if (exists $$date{'day'}) {
	$converted .= '-' . $$date{'day'};
    } elsif (exists $$date{'hour'}) {
	$converted .= '-00';
    }

    if (exists $$date{'hour'}) {
	$converted .= 'T' . $$date{'hour'} .
	    ':' . (exists $$date{'minute'} ? $$date{'minute'} : '00') .
		':' . (exists $$date{'second'} ? $$date{'second'} : '00') . 'Z';
    }
    return $converted;
}

# $person is a hash with persons attributes - we need to create and
# return a Bio::Biblio::Person object
}
_convert_personal_namedescriptionprevnextTop
sub _convert_personal_name {
    my ($person) = @_;
    foreach my $key (keys %$person) {
	$$person{"_$key"} = $$person{$key};
	delete $$person{$key};
    }
    Bio::Biblio::Person->new(%$person);
}

#
# takes journal article related attributes from $article and convert
# them into $result and at the end call _convert_article (which is
# shared with book article)
#
}
_convert_journal_articledescriptionprevnextTop
sub _convert_journal_article {
    my ($result, $source) = @_;
    my $article = $$source{'article'};

    # create and populate both a Journal and a resulting Article objects
my $from_journal = $$article{'journal'}; my $journal = Bio::Biblio::MedlineJournal->new(); $journal->name ($$from_journal{'title'}) if defined $$from_journal{'title'}; $journal->issn ($$from_journal{'iSSN'}) if defined $$from_journal{'iSSN'}; $journal->abbreviation ($$from_journal{'iSOAbbreviation'}) if defined $$from_journal{'iSOAbbreviation'}; $journal->coden ($$from_journal{'coden'}) if defined $$from_journal{'coden'}; if (defined $$from_journal{'journalIssue'}) { my $issue = $$from_journal{'journalIssue'}; $result->volume ($$issue{'volume'}) if defined $$issue{'volume'}; $result->issue ($$issue{'issue'}) if defined $$issue{'issue'}; if (defined $$issue{'pubDate'}) { my $pub_date = $$issue{'pubDate'}; my $converted = &_convert_date ($pub_date); $result->date ($converted) if defined $converted; # Some parts of a MEDLINE date are stored just as properties
# because they have almost non-parseable format :-).
$result->medline_date ($$pub_date{'medlineDate'}) if defined $$pub_date{'medlineDate'}; $result->season ($$pub_date{'season'}) if defined $$pub_date{'season'}; } } # ...some attributes are in journalInfo (which is outside of the article)
my $journal_info = $$source{'journalInfo'}; if (defined $journal_info) { $journal->country ($$journal_info{'country'}) if defined $$journal_info{'country'}; $journal->medline_ta ($$journal_info{'medlineTA'}) if defined $$journal_info{'medlineTA'}; $journal->medline_code ($$journal_info{'medlineCode'}) if defined $$journal_info{'medlineCode'}; $journal->nlm_unique_id ($$journal_info{'nlmUniqueID'}) if defined $$journal_info{'nlmUniqueID'}; } $result->journal ($journal); &_convert_article ($result, $source); } #
# takes book article related attributes from $article and convert
# them into $result and at the end call _convert_article (which is
# shared with journal article)
#
}
_convert_book_articledescriptionprevnextTop
sub _convert_book_article {
    my ($result, $source) = @_;
    my $article = $$source{'article'};

    # create and populate both book and resulting article objects
my $from_book = $$article{'book'}; my $book = Bio::Biblio::MedlineBook->new(); $book->title ($$from_book{'title'}) if defined $$from_book{'title'}; $book->volume ($$from_book{'volume'}) if defined $$from_book{'volume'}; $book->series ($$from_book{'collectionTitle'}) if defined $$from_book{'collectionTitle'}; if (defined $$from_book{'pubDate'}) { my $pub_date = $$from_book{'pubDate'}; my $converted = &_convert_date ($pub_date); $result->pub_date ($converted) if defined $converted; # Some parts of a MEDLINE date are stored just as properties
# because they have almost non-parseable format :-).
$result->medline_date ($$pub_date{'medlineDate'}) if defined $$pub_date{'medlineDate'}; $result->season ($$pub_date{'season'}) if defined $$pub_date{'season'}; } if (defined $$from_book{'publisher'}) { my $publisher = Bio::Biblio::Organisation->new(); $publisher->name ($$from_book{'publisher'}); $book->publisher ($publisher); } my @authors = &_convert_providers ($$from_book{'authors'}); $book->authors (\@authors) if @authors; $result->book ($book); &_convert_article ($result, $source); } #
# takes from $source article related attributes and convert them into
# $article (these attributes are the same both for journal and book
# articles
#
}
_convert_articledescriptionprevnextTop
sub _convert_article {
    my ($article, $source) = @_;
    my $from_article = $$source{'article'};

    $article->title ($$from_article{'articleTitle'}) if defined $$from_article{'articleTitle'};
    $article->affiliation ($$from_article{'affiliation'}) if defined $$from_article{'affiliation'};
    $article->vernacular_title ($$from_article{'vernacularTitle'}) if defined $$from_article{'vernacularTitle'};
    $article->date_of_electronic_publication
	($$from_article{'dateOfElectronicPublication'}) if defined $$from_article{'dateOfElectronicPublication'};

    if (defined $$from_article{'pagination'}) {
	my $pagination = $$from_article{'pagination'};
	$article->first_page ($$pagination{'startPage'}) if defined $$pagination{'startPage'};
	$article->last_page ($$pagination{'endPage'}) if defined $$pagination{'endPage'};
	$article->medline_page ($$pagination{'medlinePgn'}) if defined $$pagination{'medlinePgn'};
    }

    if (defined $$from_article{'abstract'}) {
	my $abstract = $$from_article{'abstract'};
	$article->abstract ($$abstract{'abstractText'}) if defined $$abstract{'abstractText'};
	$article->abstract_type ('text/plain');
	$article->rights ($$abstract{'copyrightInformation'}) if defined $$abstract{'copyrightInformation'};
    }

    if (defined $$from_article{'languages'}) {
	my $languages = $$from_article{'languages'};  # ref-array
if ( @{ $languages } > 0) { $article->language ( $$languages[0] ); } if ( @{ $languages } > 1) { $article->other_languages (join (',', @{ $languages })); } } my @authors = &_convert_providers ($$from_article{'authors'}); if (@authors) { $article->authors (\@authors); $article->author_list_complete ($$from_article{'authorListComplete'}) if defined $$from_article{'authorListComplete'}; } # references to database entries are prefixed with database name
# (separated by a slash)
use Bio::Annotation::DBLink; if (defined $$from_article{'dataBanks'}) { my $databanks = $$from_article{'dataBanks'}; # a ref-array
my @references; foreach my $bank ( @{ $databanks } ) { my $db_name = $$bank{'dataBankName'}; if (defined $$bank{'accessionNumbers'}) { foreach my $accn ( @{ $$bank{'accessionNumbers'} } ) { my $dblink = Bio::Annotation::DBLink->new(-primary_id => $accn); $dblink->database ($db_name); # it does not matter if it is undef
push (@references, $dblink); } } } if (@references) { $article->cross_references (\@references); $article->cross_references_list_complete ($$from_article{'dataBankListComplete'}) if defined $$from_article{'dataBankListComplete'}; } } # grants are stored in an array of hashtables (each of the
# hashtables has keys agency, grantID and acronym)
$article->grants ($$from_article{'grants'}) if defined $$from_article{'grants'}; $article->grant_list_complete ($$from_article{'grantListComplete'}) if defined $$from_article{'grandListComplete'}; } #
# takes a ref-array of providers - they can be persons or
# organisations, and returns an array of converted providers
#
}
_convert_providersdescriptionprevnextTop
sub _convert_providers {
    my ($providers) = @_;
    return () unless defined $providers;

    my @results;
    foreach my $provider ( @{ $providers } ) {
	if (defined $$provider{'personalName'}) {
	    my $converted = &_convert_personal_name ($$provider{'personalName'});
	    push (@results, $converted) if defined $converted;
	} elsif (defined $$provider{'collectiveName'}) {
	    push (@results, Bio::Biblio::Organisation->new(-name => $$provider{'collectiveName'}));
	} else {
            Bio::Biblio::Provider->new();
	}
    }
    return () unless @results;
    return @results;
}

1;
__END__
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Martin Senger (senger@ebi.ac.uk)
COPYRIGHTTop
Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop
Here is the rest of the object methods. Internal methods are preceded
with an underscore _.