Boulder::Omim(3pm)

💖 Boulder::Omim — the manual, but make it make sense 💖

okay bestie, gather round, because this is the Boulder::Omim page from the User Contributed Perl Documentation, and it is genuinely iconic. It's a Perl module (a .3pm page, for the record) and it does exactly one thing extremely well: it fetches Omim data records as parsed Boulder Stones. Slay.

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✨ NAME ✨

Boulder::Omim — fetch Omim data records as parsed Boulder Stones 🧬💅

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✨ SYNOPSIS ✨

Two ways to do the thing, pick your fighter:

  # 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.
  }

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✨ DESCRIPTION ✨

Boulder::Omim provides retrieval and parsing services for OMIM records. (Yes, it says it twice in the original. It was THAT excited. Not me complaining — honestly, mood.)

Boulder::Omim provides retrieval and parsing services for NCBI Omim records. It returns Omim entries in Stone format, so all the various fields and values are just... right there for you to grab. Easy access, no cap. And fun fact: Boulder::Omim is a descendent of Boulder::Stream, and it gives you a stream-like interface to a series of Stone objects. ✨

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

• File — this one gives you access to local Omim entries by reading from a flat file (typically the omim.txt file you can download from NCBI's Ftp site 👀). The stream returns a Stone corresponding to each of the entries in the file, starting from the top of the file and working downward — very orderly, very demure. 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. So if you already have the goods, you're covered. 🫶

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✨ Boulder::Omim methods ✨

This section lists the public methods that the Boulder::Omim class makes available. The main characters, honestly.

🌸 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 accessor is File — that's it, that's the whole menu. If it works, 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 you don't specify it, it defaults to File. So if you're lazy (respectfully), it's already handled. 💅

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

• 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 it 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. Very much "you get what the parent gives you, plus vibes". 👑

🌸 put()

The put() method is inherited from the parent Boulder::Stream class, and it will write the passed Stone to standard output in Boulder format. Which means... yeah, it is currently not possible to write a Boulder::Omim object back into Omim flatfile form. It's giving one-way street. 🚧

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✨ OUTPUT TAGS ✨

The tags returned by the parsing operation are taken from the names shown in the network Entrez interface to Omim. So if the names look familiar, that's why — they're literally matching Entrez. 🧚

🌈 Top-Level Tags 🌈

These are the tags that appear at the top level of the parsed Omim entry. The whole squad:

• 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 the 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;

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✨ SEE ALSO ✨

Boulder, Boulder::Blast, Boulder::Genbank — the whole friend group. Go say hi. 🦋

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✨ 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.

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no warranty, bestie — read DISCLAIMER.txt, it's literally right there 💀

okay that's the whole page, you ate it, go parse some Omim records 🎀

perl v5.34.0 · 2022-06-08 · Boulder::Omim(3pm) — that's the version, the date, and the page, mwah 💋