1Boulder::Omim(3)      User Contributed Perl Documentation     Boulder::Omim(3)
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NAME

6       Boulder::Omim - Fetch Omim data records as parsed Boulder Stones
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SYNOPSIS

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
17         # 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

DESCRIPTION

26       Boulder::Omim provides retrieval and parsing services for OMIM records
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28       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
34       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:
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39       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
46       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
49   Boulder::Omim methods
50       This section lists the public methods that the Boulder::Omim class
51       makes available.
52
53       new()
54              # Local fetch via File
55              $om=new Boulder::Omim(-accessor  =>  'File',
56                                       -param     =>  '/data/omim/omim.txt');
57
58           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
62           new() takes the following arguments:
63
64                   -accessor       Name of the accessor to use
65                   -param          Parameters to pass to the accessor
66
67           Specify the accessor to use with the -accessor argument.  If not
68           specified, it defaults to File.
69
70           -param is an accessor-specific argument.  The possibilities is:
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72           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
76       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.
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82       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.
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OUTPUT TAGS

89       The tags returned by the parsing operation are taken from the names
90       shown in the network Entrez interface to Omim.
91
92   Top-Level Tags
93       These are tags that appear at the top level of the parsed Omim entry.
94
95       Identifier
96           The Omim identifier of this entry.  Identifier is a single-value
97           tag.
98
99           Example:
100
101                 my $identifierNo = $s->Identifier;
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103       Title
104           The Omim title for this entry.
105
106           Example:
107                 my $titledef=$s->Title;
108
109       Text The Text of this Omim entry
110           Example:
111                 my $thetext=$s->Text;
112
113       Mini The text condensed version, also called "Mini" in Entrez interface
114           Example:
115                 my $themini=$s->Mini;
116
117       SeeAlso References to other relevant work.
118           Example:
119                 my $thereviews=$s->Reviews;
120
121       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
128       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=$s->Contributors;
133
134       History This field contains the edit history of this record, with an
135       identifier and a date in which minor changes had been performed on the
136       record.
137           Example:
138                 my @theHistory=$s->History;
139
140       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

SEE ALSO

148       Boulder, Boulder::Blast, Boulder::Genbank
149

AUTHOR

151       Lincoln Stein <lstein@cshl.org>.  Luca I.G. Toldo <luca.toldo@merck.de>
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153       Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo
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155       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.
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161perl v5.30.1                      2020-01-29                  Boulder::Omim(3)
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