man Boulder::Omim (3): Fetch Omim data records as parsed Boulder Stones

SYNOPSIS

# parse a file of Omim records
$om = new Boulder::Omim(-accessor=>'File',
-param => '/data/omim/omim.txt');
while (my $s = $om->get) {
print $s->Identifier;
print $s->Text;
}
# parse flatfile records yourself
open (OM,"/data/omim/omim.txt");
local $/ = "*RECORD*";
while (<OM>) {
my $s = Boulder::Omim->parse($_);
# etc.
}

DESCRIPTION

Boulder::Omim provides retrieval and parsing services for OMIM records

Boulder::Omim provides retrieval and parsing services for NCBI Omim records. It returns Omim entries in Stone format, allowing easy access to the various fields and values. Boulder::Omim is a descendent of Boulder::Stream, and provides a stream-like interface to a series of Stone objects.

Access to Omim is provided by one accessors, which give access to local Omim database. When you create a new Boulder::Omim stream, you provide the accessors, along with accessor-specific parameters that control what entries to fetch. The accessors is:

File: This provides access to local Omim entries by reading from a flat file (typically omim.txt file downloadable from NCBI's Ftp site). The stream will return a Stone corresponding to each of the entries in the file, starting from the top of the file and working downward. The parameter is the path to the local file.

It is also possible to parse a single Omim entry from a text string stored in a scalar variable, returning a Stone object.

Boulder::Omim methods

This section lists the public methods that the Boulder::Omim class makes available.

new()

   # Local fetch via File
   $om=new Boulder::Omim(-accessor  =>  'File',
                            -param     =>  '/data/omim/omim.txt');

The new() method creates a new Boulder::Omim stream on the accessor provided. The only possible accessors is File. If successful, the method returns the stream object. Otherwise it returns undef.

new() takes the following arguments:

        -accessor       Name of the accessor to use
        -param          Parameters to pass to the accessor

Specify the accessor to use with the -accessor argument. If not specified, it defaults to File.

-param is an accessor-specific argument. The possibilities is:

For File, the -param argument must point to a string-valued scalar, which will be interpreted as the path to the file to read Omim entries from.

get()

The get() method is inherited from Boulder::Stream, and simply returns the next parsed Omim Stone, or undef if there is nothing more to fetch. It has the same semantics as the parent class, including the ability to restrict access to certain top-level tags.

put()

The put() method is inherited from the parent Boulder::Stream class, and will write the passed Stone to standard output in Boulder format. This means that it is currently not possible to write a Boulder::Omim object back into Omim flatfile form.

OUTPUT TAGS

The tags returned by the parsing operation are taken from the names shown in the network Entrez interface to Omim.

Top-Level Tags

These are tags that appear at the top level of the parsed Omim entry.

Identifier

The Omim identifier of this entry. Identifier is a single-value tag.

Example:

      my $identifierNo = $s->Identifier;

Title

The Omim title for this entry.

Example:
my $titledef=$s->Title;

Text The Text of this Omim entry

Example:
my $thetext=$s->Text;

Mini The text condensed version, also called "Mini" in Entrez interface

Example:
my $themini=$s->Mini;

SeeAlso References to other relevant work.

Example:
my $thereviews=$s->Reviews;

CreationDate This field contains the name of the person who originated the initial entry in OMIM and the date it appeared in the database. The entry may have been subsequently added to, edited, or totally rewritten by others, and their attribution is listed in the CONTRIBUTORS field.

Example:
my $theCreation=$s->CreationDate;

Contributors This field contains a list, in chronological order, of the persons who have contributed significantly to the content of the MIM entry. The name is followed by "updated", "edited" or "re-created".

Example:
my @theContributors=$s->Contributors;

History This field contains the edit history of this record, with an identifier and a date in which minor changes had been performed on the record.

Example:
my @theHistory=$s->History;

References The references cited in the entry. Example: my @theReferences=$s->References;

ClinicalSynopsis The content of the Clinical Synopsis data field. Example: my @theClinicalSynopsis=$s->ClinicalSynopsis;

AllelicVariants The Allelic Variants Example: my @theAllelicVariants=$s->AllelicVariants;

AUTHOR

Lincoln Stein <[email protected]>. Luca I.G. Toldo <[email protected]>