BP_BIBLIO(1p)

📦 version 1.70, in debian trixie, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 BP_BIBLIO 💖

okay bestie, buckle up 🎀 this is bp_biblio from the 1p manual — User Contributed Perl Documentation, the whole vibe. It's a bioperl client for accessing and querying a bibliographic repository, and honestly it ate. Let me walk you through every single thing because we do not skip. 🦋

✨ VERSION ✨

version 1.70 — she's been through some things and she's thriving 💅

🎀 SYNOPSIS 🎀

Usage:

bp_biblio [vh]
bp_biblio [bcFgOpq]         [-l <URL>]
bp_biblio [abcdDeFknmOpqrs] [-l <URL>] -i <collection-ID>
bp_biblio [abcdDeFknmOpqrs] [-l <URL>] - -find <keywords> \
       [-attrs <attrs>]...
bp_biblio [Vq]              [-l <URL>]
bp_biblio [FOq]             [-f <filename>]

🌸 DESCRIPTION 🌸

So bp_biblio is a client that shows you how to use the Bio::Biblio module — which is, like, the module for accessing and querying a bibliographic repository. ✨

It also shows off Bio::Biblio::IO::medlinexml and Bio::Biblio::IO::medline2ref, which convert XML MEDLINE citations into a simple hash table and into full Perl objects. Iconic of them honestly. 🫶

It has so many options because it's trying to cover as many methods as possible. And because of that, it can also be used as a fully functional command-line client for querying a repository and retrieving citations from it. Periodt. 🔥

✨ OPTIONS ✨

💅 What service to contact:

🎀 What query collection to use:

Some options don't need you to specify a collection. Some do. Not me making you read the fine print 🙈

  • -i <collection_id> — the collection ID. You get this from a previous invocation by specifying the argument -p (that's the print ID one, we'll get there 💖)
  • -find <keywords> [-attrs <attrs>] — create a collection from citations containing the given keywords — either in all the default attributes, or only in the attributes you name.

You can repeat it! For example:

-find brazma -attrs authors -find -study

(the repetitions refine previous results 🔍)

Both <keywords> and <attrs> may be comma-delimited multi-values.

Heads up: -find must be separated from the rest of the options by -.
Also heads up: this script is a bit stupid regarding quoted keywords, or keywords containing commas... TBD better. She's trying her best 😭
  • What XML format is used for citations:
    • -Fm — MEDLINE (this is the default, bestie)
    • -Fp — PubMed

👑 What to do (with the query collection):

  • -g <id> — get citation <id>
  • -c — get count (a number of citations)
  • -p — print collection ID (which you may use in the next invocation as an -i argument); it also implies -k, sneaky
  • -b — print citations in a non-XML format (TBD)

Other options can be used only on a sub-collection — which you can get directly by specifying the -i argument, or indirectly by specifying one or more queries with -find arguments:

  • -d — get all citation IDs
  • -n — get next citation
  • -m [<how_many>] — get how_many more
  • -r — reset iteration to the first citation in the collection (now you can use -n or -m again 🔁)
  • -a — get all citations — as an array
  • -s — as -a but get it as one string
  • -e — check if given collection exists and has more citations
  • -k — keep the resulting collection persistent (this only makes sense when collection IDs are being printed, otherwise you would not know how to contact the persistent collection next time 💀)
  • -D — destroy given collection (makes sense together with -i)

Options specifying output format of the results:

  • -Ox — output in XML format (the default)
  • -Oo — output as Biblio objects
  • -Or — output as a raw hashtable

The options above can also be used for converting an XML MEDLINE local file without using any SOAP connection at all:

  • -f <filename> — an XML file to be read and converted

Options dealing with controlled vocabularies:

  • -Vn — get all vocabulary names
  • -Vv::<name> — get all values from vocabulary <name>
  • -Va::<name> — get everything from vocabulary <name>
  • -Vd::<name>::<value> — get description of <value> from vocabulary <name>
  • -Ve::<name>::<value> — return 1 if <value> exists in vocabulary <name>

And the remaining options, the little guys 🥺:

  • -h — get help
  • -v — get version
  • -q — be quiet (less verbose)

🌈 EXAMPLES 🌈

bp_biblio - -find Java -attrs abstract -find perl

Several separate invocations sharing the same query collection:

bp_biblio -p -q - -find Brazma,Robinson > b.tmp
bp_biblio -i `cat b.tmp` -d
MEDLINE2005/10693778
MEDLINE2005/10977099
MEDLINE2005/11726920
MEDLINE2005/12225585
MEDLINE2005/12227734
bp_biblio -i `cat b.tmp` -g 10693778
<MedlineCitation Status="Completed">
 ...
</MedlineCitation>

bp_biblio -i `cat b.tmp` -e
Exists: 1       Has next: 1

bp_biblio -i `cat b.tmp` -D
Destroyed OK.

bp_biblio -i `cat b.tmp` -e
Exists: 0       Has next: 0

Access to controlled vocabularies:

bp_biblio -Vn
MEDLINE2005/JournalArticle/properties
MEDLINENEW/resource_types
MEDLINE2005/resource_types
MEDLINE2005/Person/properties
MEDLINE2005/*/publication_type
MEDLINENEW/JournalArticle/properties
repository_subsets
MEDLINE2005/*/citation_subset

bp_biblio -Vv::MEDLINE2005/JournalArticle/properties
AllText
ID
PMID
ISSN
...

Converting local XML MEDLINE file:

bp_biblio -g 10693778 > a_file.xml
bp_biblio -f a_file.xml -Oo   ... to Perl objects
bp_biblio -f a_file.xml -Or   ... as a raw hash

🦋 ENVIRONMENT VARIABLES 🦋

HTTPPROXY = <HTTP proxy server>

Use this if you run this script on a machine which needs to access remote HTTP targets via a proxy server. Like, if you're behind the firewall bestie, this is your girl 💜 For example:

export HTTPPROXY=http://128.243.220.41:3128
bp_biblio -c

🕰️ HISTORY 🕰️

Written February 2002. Updated July 2005. A vintage. An heirloom. 🎀

💌 FEEDBACK 💌

💬 Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated, fr fr 🫶

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and responsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. The more deets the better, bestie 🙏

🐛 Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

✍️ Authors

Martin Senger <martin.senger@gmail.com>

This software is Copyright (c) by 2002 European Bioinformatics Institute and released under the license of the same terms as the perl 5 programming language system itself.

okay that's the whole page, no notes 💅 this was perl v5.36.0, dated 2023-02-14, and you just read BP_BIBLIO(1p) — go query something iconic, bestie 🌟👑💖

📦 where this page comes from