NAME¶
Boulder::Omim - 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.
The tags returned by the parsing operation are taken from the names shown in the
network Entrez interface to Omim.
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;
SEE ALSO¶
Boulder, Boulder::Blast, Boulder::Genbank
AUTHOR¶
Lincoln Stein <lstein@cshl.org>. Luca I.G. Toldo
<luca.toldo@merck.de>
Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of
warranty.