1BP_BIBLIO(1) User Contributed Perl Documentation BP_BIBLIO(1)
2
6 biblio.PLS - bioperl client for accessing and querying a bibliographic
7 repository.
8
10 Usage:
11 biblio.PLS [vh]
13 biblio.PLS [bcFgOpq] [-l <URL>]
14 biblio.PLS [abcdDeFknmOpqrs] [-l <URL>] -i <collection-ID>
15 biblio.PLS [abcdDeFknmOpqrs] [-l <URL>] - -find <keywords> \
16 [-attrs <attrs>]...
17 biblio.PLS [Vq] [-l <URL>]
18 biblio.PLS [FOq] [-f <filename>]
19
21 A client showing how to use Bio::Biblio module, a module for accessing
22 and querying a bibliographic repository. It also shows how to use
23 modules Bio::Biblio::IO::medlinexml Bio::Biblio::IO::medline2ref which
24 converts XML MEDLINE citations into a simple hash table and into full
25 Perl objects.
26 It has many options in order to cover as many methods as possible.
28 Because of that, it can be also used as a fully functional command-line
29 client for querying repository and retrieving citations from it.
30
32 What service to contact:
33 -l <URL> ... a location where a Bibliographic Query service is
34 provided as a WebService
35 (default: http://www.ebi.ac.uk/openbqs/services/MedlineSRS)
36 What query collection to use:
38 Some options do not need to specify a collection, some do.
39 -i <collection_id> ... the collection ID can be obtained in a
41 previous invocation by specifying argument
42 '-p' (print ID)
43 -find <keywords> [-attrs <attrs>]
44 ... create a collection from citations
45 containing given keywords - either in all
46 default attributes, or only in the given
47 attributes;
48 it is possible to repeat it, for example:
50 -find brazma -attrs authors -find -study
51 (the repetitions refine previous results)
52 both <keywords> and <attrs> may be
53 comma-delimited multi-values;
54 note that '-find' must be separated from
55 the rest of options by '-';
56 note that this script is a bit stupid
58 regarding quoted keywords, or keywords
59 containing commans... TBD better
60 what XML format is used for citations:
62 -Fm ... MEDLINE (default)
63 -Fp ... PubMed
64 What to do (with the query collection):
66 -g <id> ... get citation <id>
67 -c ... get count (a number of citations)
68 -p ... print collection ID (which may be used in the next
69 invocation as an '-i' argument); it implies also '-k'
70 -b ... print citations in a non-XML format (TBD)
71 Other options can be used only on a sub-collection - which can be
73 obtained directly by specifying '-i' argument, or indirectly by
74 specifying one or more queries by '-find' arguments:
75 -d ... get all citation IDs
77 -n ... get next citation
78 -m [<how_many>] ... get 'how_many' more
79 -r ... reset iteration to the first citation in the collection
80 (now you can use '-n' or '-m' again)
81 -a ... get all citations - as an array
82 -s ... as '-a' but get it as one string
83 -e ... check if given collection exists and has more citations
84 -k ... keep resulting collection persistent (makes sense only
85 when collection IDs are being printed otherwise you
86 would not know how to contact the persistent collection
87 next time)
88 -D ... destroy given collection (makes sense together with '-i')
89 Options specifying output format of the results:
91 -Ox ... output in XML format (default)
93 -Oo ... output as Biblio objects
94 -Or ... output as a raw hashtable
95 The options above can be used also for converting an XML MEDLINE
97 local file without using any SOAP connection at all;
98 -f <filename> ... an XML file to be read and converted
100 Options dealing with controlled vocabularies:
102 -Vn ... get all vocabulary names
104 -Vv::<name> ... get all values from vocabulary <name>
105 -Va::<name> ... get everything from vocabulary <name>
106 -Vd::<name>::<value> ... get description of <value>
107 from vocabulary <name>
108 -Ve::<name>::<value> ... return 1 if <value> exists
109 in vocabulary <name>
110 And the remaining options:
112 -h ... get help
114 -v ... get version
115 -q ... be quiet (less verbose)
116
118 biblio.PLS - -find Java -attrs abstract -find perl
119 Several separate invocations sharing the same query collection:
121 biblio.PLS -p -q - -find Brazma,Robinson > b.tmp
123 biblio.PLS -i `cat b.tmp` -d
124 MEDLINE2005/10693778
125 MEDLINE2005/10977099
126 MEDLINE2005/11726920
127 MEDLINE2005/12225585
128 MEDLINE2005/12227734
129 biblio.PLS -i `cat b.tmp` -g 10693778
130 <MedlineCitation Status="Completed">
131 ...
132 </MedlineCitation>
133 biblio.PLS -i `cat b.tmp` -e
135 Exists: 1 Has next: 1
136 biblio.PLS -i `cat b.tmp` -D
138 Destroyed OK.
139 biblio.PLS -i `cat b.tmp` -e
141 Exists: 0 Has next: 0
142 Access to controlled vocabularies:
144 biblio.PLS -Vn
146 MEDLINE2005/JournalArticle/properties
147 MEDLINENEW/resource_types
148 MEDLINE2005/resource_types
149 MEDLINE2005/Person/properties
150 MEDLINE2005/*/publication_type
151 MEDLINENEW/JournalArticle/properties
152 repository_subsets
153 MEDLINE2005/*/citation_subset
154 biblio.PLS -Vv::MEDLINE2005/JournalArticle/properties
156 AllText
157 ID
158 PMID
159 ISSN
160 ...
161 Converting local XML MEDLINE file:
163 biblio.PLS -g 10693778 > a_file.xml
165 biblio.PLS -f a_file.xml -Oo ... to Perl objects
166 biblio.PLS -f a_file.xml -Or ... as a raw hash
167
169 HTTPPROXY = <HTTP proxy server>
170 Use this if you use this script on a machine which needs to access
172 remote HTTP targets via a proxy server. For example:
173 export HTTPPROXY=http://128.243.220.41:3128
175 biblio.PLS -c
176
178 Mailing Lists
179 User feedback is an integral part of the evolution of this and other
180 Bioperl modules. Send your comments and suggestions preferably to the
181 Bioperl mailing list. Your participation is much appreciated.
182 bioperl-l@bioperl.org - General discussion
184 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
185 Reporting Bugs
187 Report bugs to the Bioperl bug trackingi system to help us keep track
188 of the bugs and their resolution. Bug reports can be submitted via the
189 web:
190 http://bugzilla.open-bio.org/
192
194 Email martin.senger@gmail.com
195
197 Written February 2002 Updated July 2005
198perl v5.12.0 2010-04-29 BP_BIBLIO(1)