1Boulder::Omim(3) User Contributed Perl Documentation Boulder::Omim(3)
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6 Boulder::Omim - Fetch Omim data records as parsed Boulder Stones
7
9 # parse a file of Omim records
10 $om = new Boulder::Omim(-accessor=>'File',
11 -param => '/data/omim/omim.txt');
12 while (my $s = $om->get) {
13 print $s->Identifier;
14 print $s->Text;
15 }
16 # parse flatfile records yourself
18 open (OM,"/data/omim/omim.txt");
19 local $/ = "*RECORD*";
20 while (<OM>) {
21 my $s = Boulder::Omim->parse($_);
22 # etc.
23 }
24
26 Boulder::Omim provides retrieval and parsing services for OMIM records
27 Boulder::Omim provides retrieval and parsing services for NCBI Omim
29 records. It returns Omim entries in Stone format, allowing easy access
30 to the various fields and values. Boulder::Omim is a descendent of
31 Boulder::Stream, and provides a stream-like interface to a series of
32 Stone objects.
33 Access to Omim is provided by one accessors, which give access to
35 local Omim database. When you create a new Boulder::Omim stream, you
36 provide the accessors, along with accessor-specific parameters that
37 control what entries to fetch. The accessors is:
38 File
40 This provides access to local Omim entries by reading from a flat
41 file (typically omim.txt file downloadable from NCBI's Ftp site).
42 The stream will return a Stone corresponding to each of the entries
43 in the file, starting from the top of the file and working downward.
44 The parameter is the path to the local file.
45 It is also possible to parse a single Omim entry from a text string
47 stored in a scalar variable, returning a Stone object.
48 Boulder::Omim methods
50 This section lists the public methods that the Boulder::Omim class
52 makes available.
53 new()
55 # Local fetch via File
56 $om=new Boulder::Omim(-accessor => 'File',
57 -param => '/data/omim/omim.txt');
58 The new() method creates a new Boulder::Omim stream on the accessor
60 provided. The only possible accessors is File. If successful, the
61 method returns the stream object. Otherwise it returns undef.
62 new() takes the following arguments:
64 -accessor Name of the accessor to use
66 -param Parameters to pass to the accessor
67 Specify the accessor to use with the -accessor argument. If not
69 specified, it defaults to File.
70 -param is an accessor-specific argument. The possibilities is:
72 For File, the -param argument must point to a string-valued scalar,
74 which will be interpreted as the path to the file to read Omim
75 entries from.
76 get()
78 The get() method is inherited from Boulder::Stream, and simply
79 returns the next parsed Omim Stone, or undef if there is nothing
80 more to fetch. It has the same semantics as the parent class,
81 including the ability to restrict access to certain top-level tags.
82 put()
84 The put() method is inherited from the parent Boulder::Stream
85 class, and will write the passed Stone to standard output in Boul‐
86 der format. This means that it is currently not possible to write
87 a Boulder::Omim object back into Omim flatfile form.
88
90 The tags returned by the parsing operation are taken from the names
91 shown in the network Entrez interface to Omim.
92 Top-Level Tags
94 These are tags that appear at the top level of the parsed Omim entry.
96 Identifier
98 The Omim identifier of this entry. Identifier is a single-value
99 tag.
100 Example:
102 my $identifierNo = $s->Identifier;
104 Title
106 The Omim title for this entry.
107 Example:
109 my $titledef=$s->Title;
110 Text The Text of this Omim entry
112 Example:
113 my $thetext=$s->Text;
114 Mini The text condensed version, also called "Mini" in Entrez interface
116 Example:
117 my $themini=$s->Mini;
118 SeeAlso References to other relevant work.
120 Example:
121 my $thereviews=$s->Reviews;
122 CreationDate This field contains the name of the person who originated
124 the initial entry in OMIM and the date it appeared in the database. The
125 entry may have been subsequently added to, edited, or totally rewritten
126 by others, and their attribution is listed in the CONTRIBUTORS field.
127 Example:
128 my $theCreation=$s->CreationDate;
129 Contributors This field contains a list, in chronological order, of the
131 persons who have contributed significantly to the content of the MIM
132 entry. The name is followed by "updated", "edited" or "re-created".
133 Example:
134 my @theContributors=$s->Contributors;
135 History This field contains the edit history of this record, with an
137 identifier and a date in which minor changes had been performed on the
138 record.
139 Example:
140 my @theHistory=$s->History;
141 References The references cited in the entry. Example: my @theRefer‐
143 ences=$s->References;
144 ClinicalSynopsis The content of the Clinical Synopsis data field. Exam‐
145 ple: my @theClinicalSynopsis=$s->ClinicalSynopsis;
146 AllelicVariants The Allelic Variants Example: my @theAllelicVari‐
147 ants=$s->AllelicVariants;
148
150 Boulder, Boulder::Blast, Boulder::Genbank
151
153 Lincoln Stein <lstein@cshl.org>. Luca I.G. Toldo <luca.toldo@merck.de>
154 Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo
156 This library is free software; you can redistribute it and/or modify it
158 under the same terms as Perl itself. See DISCLAIMER.txt for dis‐
159 claimers of warranty.
160perl v5.8.8 2000-06-08 Boulder::Omim(3)