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 mod‐
23 ules 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
35 provided as a WebService
36 (default: http://www.ebi.ac.uk/openbqs/services/MedlineSRS)
37 What query collection to use:
39 Some options do not need to specify a collection, some do.
41 -i <collection_id> ... the collection ID can be obtained in a
43 previous invocation by specifying argument
44 '-p' (print ID)
45 -find <keywords> [-attrs <attrs>]
46 ... create a collection from citations
47 containing given keywords - either in all
48 default attributes, or only in the given
49 attributes;
50 it is possible to repeat it, for example:
52 -find brazma -attrs authors -find -study
53 (the repetitions refine previous results)
54 both <keywords> and <attrs> may be
55 comma-delimited multi-values;
56 note that '-find' must be separated from
57 the rest of options by '-';
58 note that this script is a bit stupid
60 regarding quoted keywords, or keywords
61 containing commans... TBD better
62 what XML format is used for citations:
64 -Fm ... MEDLINE (default)
65 -Fp ... PubMed
66 What to do (with the query collection):
68 -g <id> ... get citation <id>
70 -c ... get count (a number of citations)
71 -p ... print collection ID (which may be used in the next
72 invocation as an '-i' argument); it implies also '-k'
73 -b ... print citations in a non-XML format (TBD)
74 Other options can be used only on a sub-collection - which can be
76 obtained directly by specifying '-i' argument, or indirectly by speci‐
77 fying one or more queries by '-find' arguments:
78 -d ... get all citation IDs
80 -n ... get next citation
81 -m [<how_many>] ... get 'how_many' more
82 -r ... reset iteration to the first citation in the collection
83 (now you can use '-n' or '-m' again)
84 -a ... get all citations - as an array
85 -s ... as '-a' but get it as one string
86 -e ... check if given collection exists and has more citations
87 -k ... keep resulting collection persistent (makes sense only
88 when collection IDs are being printed otherwise you
89 would not know how to contact the persistent collection
90 next time)
91 -D ... destroy given collection (makes sense together with '-i')
92 Options specifying output format of the results:
94 -Ox ... output in XML format (default)
96 -Oo ... output as Biblio objects
97 -Or ... output as a raw hashtable
98 The options above can be used also for converting an XML MEDLINE
100 local file without using any SOAP connection at all;
101 -f <filename> ... an XML file to be read and converted
103 Options dealing with controlled vocabularies:
105 -Vn ... get all vocabulary names
107 -Vv::<name> ... get all values from vocabulary <name>
108 -Va::<name> ... get everything from vocabulary <name>
109 -Vd::<name>::<value> ... get description of <value>
110 from vocabulary <name>
111 -Ve::<name>::<value> ... return 1 if <value> exists
112 in vocabulary <name>
113 And the remaining options:
115 -h ... get help
117 -v ... get version
118 -q ... be quiet (less verbose)
119
121 biblio.PLS - -find Java -attrs abstract -find perl
122 Several separate invocations sharing the same query collection:
124 biblio.PLS -p -q - -find Brazma,Robinson > b.tmp
126 biblio.PLS -i `cat b.tmp` -d
127 MEDLINE2005/10693778
128 MEDLINE2005/10977099
129 MEDLINE2005/11726920
130 MEDLINE2005/12225585
131 MEDLINE2005/12227734
132 biblio.PLS -i `cat b.tmp` -g 10693778
133 <MedlineCitation Status="Completed">
134 ...
135 </MedlineCitation>
136 biblio.PLS -i `cat b.tmp` -e
138 Exists: 1 Has next: 1
139 biblio.PLS -i `cat b.tmp` -D
141 Destroyed OK.
142 biblio.PLS -i `cat b.tmp` -e
144 Exists: 0 Has next: 0
145 Access to controlled vocabularies:
147 biblio.PLS -Vn
149 MEDLINE2005/JournalArticle/properties
150 MEDLINENEW/resource_types
151 MEDLINE2005/resource_types
152 MEDLINE2005/Person/properties
153 MEDLINE2005/*/publication_type
154 MEDLINENEW/JournalArticle/properties
155 repository_subsets
156 MEDLINE2005/*/citation_subset
157 biblio.PLS -Vv::MEDLINE2005/JournalArticle/properties
159 AllText
160 ID
161 PMID
162 ISSN
163 ...
164 Converting local XML MEDLINE file:
166 biblio.PLS -g 10693778 > a_file.xml
168 biblio.PLS -f a_file.xml -Oo ... to Perl objects
169 biblio.PLS -f a_file.xml -Or ... as a raw hash
170
172 HTTPPROXY = <HTTP proxy server>
173 Use this if you use this script on a machine which needs to access
175 remote HTTP targets via a proxy server. For example:
176 export HTTPPROXY=http://128.243.220.41:3128
178 biblio.PLS -c
179
181 Mailing Lists
182 User feedback is an integral part of the evolution of this and other
184 Bioperl modules. Send your comments and suggestions preferably to the
185 Bioperl mailing list. Your participation is much appreciated.
186 bioperl-l@bioperl.org - General discussion
188 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
189 Reporting Bugs
191 Report bugs to the Bioperl bug trackingi system to help us keep track
193 of the bugs and their resolution. Bug reports can be submitted via the
194 web:
195 http://bugzilla.open-bio.org/
197
199 Email martin.senger@gmail.com
200
202 Written February 2002 Updated July 2005
203perl v5.8.8 2007-05-07 BP_BIBLIO(1)