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
51 makes available.
52 new()
54 # Local fetch via File
55 $om=new Boulder::Omim(-accessor => 'File',
56 -param => '/data/omim/omim.txt');
57 The new() method creates a new Boulder::Omim stream on the accessor
59 provided. The only possible accessors is File. If successful, the
60 method returns the stream object. Otherwise it returns undef.
61 new() takes the following arguments:
63 -accessor Name of the accessor to use
65 -param Parameters to pass to the accessor
66 Specify the accessor to use with the -accessor argument. If not
68 specified, it defaults to File.
69 -param is an accessor-specific argument. The possibilities is:
71 For File, the -param argument must point to a string-valued scalar,
73 which will be interpreted as the path to the file to read Omim
74 entries from.
75 get()
77 The get() method is inherited from Boulder::Stream, and simply
78 returns the next parsed Omim Stone, or undef if there is nothing
79 more to fetch. It has the same semantics as the parent class,
80 including the ability to restrict access to certain top-level tags.
81 put()
83 The put() method is inherited from the parent Boulder::Stream
84 class, and will write the passed Stone to standard output in
85 Boulder format. This means that it is currently not possible to
86 write a Boulder::Omim object back into Omim flatfile form.
87
89 The tags returned by the parsing operation are taken from the names
90 shown in the network Entrez interface to Omim.
91 Top-Level Tags
93 These are tags that appear at the top level of the parsed Omim entry.
94 Identifier
96 The Omim identifier of this entry. Identifier is a single-value
97 tag.
98 Example:
100 my $identifierNo = $s->Identifier;
102 Title
104 The Omim title for this entry.
105 Example:
107 my $titledef=$s->Title;
108 Text The Text of this Omim entry
110 Example:
111 my $thetext=$s->Text;
112 Mini The text condensed version, also called "Mini" in Entrez interface
114 Example:
115 my $themini=$s->Mini;
116 SeeAlso References to other relevant work.
118 Example:
119 my $thereviews=$s->Reviews;
120 CreationDate This field contains the name of the person who originated
122 the initial entry in OMIM and the date it appeared in the database. The
123 entry may have been subsequently added to, edited, or totally rewritten
124 by others, and their attribution is listed in the CONTRIBUTORS field.
125 Example:
126 my $theCreation=$s->CreationDate;
127 Contributors This field contains a list, in chronological order, of the
129 persons who have contributed significantly to the content of the MIM
130 entry. The name is followed by "updated", "edited" or "re-created".
131 Example:
132 my @theContributors=$s->Contributors;
133 History This field contains the edit history of this record, with an
135 identifier and a date in which minor changes had been performed on the
136 record.
137 Example:
138 my @theHistory=$s->History;
139 References The references cited in the entry. Example: my
141 @theReferences=$s->References;
142 ClinicalSynopsis The content of the Clinical Synopsis data field.
143 Example: my @theClinicalSynopsis=$s->ClinicalSynopsis;
144 AllelicVariants The Allelic Variants Example: my
145 @theAllelicVariants=$s->AllelicVariants;
146
148 Boulder, Boulder::Blast, Boulder::Genbank
149
151 Lincoln Stein <lstein@cshl.org>. Luca I.G. Toldo <luca.toldo@merck.de>
152 Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo
154 This library is free software; you can redistribute it and/or modify it
156 under the same terms as Perl itself. See DISCLAIMER.txt for
157 disclaimers of warranty.
158perl v5.30.1 2020-01-29 Boulder::Omim(3)