isi = Ruby Scripts and Libraries for ISI Export Format

What is isi?

“isi” is a package of Ruby libraries and scripts for ISI Export Format. “isi2bibtex” converts ISI Export Format to BibTeX Format. “isi2html” generates a list of articles in an HTML file. The package also includes “isi2kakenhi” and “isi2tohoku”.

(Thomson Reuters Web of Science webofknowledge.com provides their bibliographic information in ISI Export Format. You can get the tagged Marked List in Web of Science by clicking the [SAVE TO FILE] button.)

Where is the homepage of isi?

isi-rb.rubyforge.org/

Where can I download isi?

Go to rubyforge.org/projects/isi-rb or rubygems.org/gems/isi .

How can I install isi?

There are three different ways to install isi.

I. Conservative way; use setup.rb

isi-X.Y.Z.tgz package can be installed as:

$ tar zxf isi-X.Y.Z.tgz
$ cd isi-X.Y.Z
$ su
# ruby setup.rb

Note that the text-format and text-hyphen libraries rubyforge.org/projects/text-format is required.

II. RubyGems users can take an easy way

There is an easy way, if you are a RubyGems user:

$ su
# gem install isi

If you do not have the text-format and text-hyphen libraries, gem will download and install the libraries automatically.

III. Simple way; just copy isi.rb and journaltitleabbreviation.rb

Just copy lib/isi.rb (isi-X.Y.Z.rb) and lib/journaltitleabbreviation.rb (journaltitleabbreviation-X.Y.Z.rb) into your working directory which contains your saved “Marked List”, e.g. savedrecs.txt.

 $ cp lib/isi.rb lib/journaltitleabbreviation.rb ~/your/working/directory/
($ cp isi-X.Y.Z.rb ~/your/working/directory/isi.rb)
 $ cp lib/journaltitleabbreviation.rb ~/your/working/directory/
($ cp journaltitleabbreviation-X.Y.Z.rb ~/your/working/directory/journaltitleabbreviation.rb)
 $ cd ~/your/working/directory/
 $ ruby isi.rb savedrecs1.txt savedrecs2.txt
 $ ruby isi.rb < savedrecs.txt > savedrecs.bib

Last two lines are examples of usage for this installation way.

Note that the text-format and text-hyphen libraries rubyforge.org/projects/text-format is required.

How can I use it?

Save the marked records to an output file in ISI Web of Science

Mark the articles in ISI Web of Science. Then, view and save the marked records to an output file (savedrecs.txt). I recommend to check “Author(s)”, “Title”, “Source”, “abstract*”, “keywords”, “times cited” and “source abbreviation” as the fields to include in the output file.

Here are some examples

$ isi2bibtex savedrecs.txt
$ isi2bibtex savedrecs1.txt savedrecs2.txt > savedrecs.bib
$ isi2bibtex < savedrecs.txt > savedrecs.bib
$ cat savedrecs.txt | isi2bibtex > savedrecs.bib

Some other useful executables

For KakenhiLaTeX osksn2.hep.sci.osaka-u.ac.jp/~taku/kakenhiLaTeX/

$ isi2kakenhi --help
$ isi2kakenhi --name-regexp='(H\. Yukawa|Hideki Yukawa)' savedrecs.txt > papers.tex

For the database of “Academic Research Staff at Tohoku University” db.tohoku.ac.jp/whois/TunvTopE.html

$ isi2tohoku --help
$ isi2tohoku --id 12345678 --name 'Example Name' savedrecs.txt

To convert ISI Export Format to HTML

$ isi2html --help
$ isi2html --full-name='Hideki Yukawa' --name-regexp='(H\. Yukawa|Hideki Yukawa)' savedrecs.txt > index.html

You can use isi as a library.

Here is an example:

#!/usr/bin/env ruby
##
require 'rubygems'   # You may not need this line.
require 'isi'

class ISI_record
  def to_title_author
    "#{@hash['TI']} - #{and_separated_authors}\n"
  end
end

while rec = ARGF.read_an_ISI_record
  print rec.to_title_author
end

Copying

isi is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. You can copy, modify and redistribute isi, but only under the conditions described in the GNU General Public License (the “GPL”). For more detail, see COPYING.

Thanks to contributor(s)!

Marcin Dulak

Who is the author?

NISHIMATSU Takeshi t-nissieatimr.tohoku.ac.jp

Why did he write it?

Because he do not like the output format of the Perl version.

Is there a Perl version?

Yes. You can find the Perl version by Jonathan Swinton, Ben Bolker, Anthony Stone, John J. Lee in CTAN www.ctan.org/tex-archive/biblio/bibtex/utils/isi2bibtex .

I do not like the output format of isi2bibtex, neither!

The output format is defined in the source code WYSIWYGly. So you can easily change the output format by yourself.

How can I get the latest source tree of isi?

You can checkout the latest source tree of isi anonymously from RubyForge with svn(1) command:

$ svn checkout svn://rubyforge.org/var/svn/isi-rb/isi

Meanings of tags in ISI Export Format

file-unique tags

FN: File type. The file starts with 'FN ISI Export Format' or 'FN Thomson Reuters Web of Knowledge'
VR: Version number of ISI export file format
EF: End of file

normal tags

AB: Abstract
AF: Authors Full (AU Foo, BAR -> AF Foo, B. A. R.; AU Nishimatsu, T -> AF Nishimatsu Takeshi)
AP: Article number of new APS journals (in ISI Web of Knowledge, 2008-)
AR: Article number of new APS journals
AU: Authors
BE: Editors of Proceedings ???
BN: ISBN
BP: Beginning page
C1: Research addresses
CA: Group authors
CL: Conference location
CR: Cited references
CT: Conference title
CY: Conference Date
DE: Original keywords
DI: DOI
DT: Document type
ED: Editors
EM: E-mail address
EP: Ending page
ER: end of a record
FN: File name
FU: Funding agency and grant number
FX: Funding text
GA: IDS number (ISI original)
HO: Conference host
ID: New keywords given by ISI
IS: issue
J9: 29-character journal title abbreviation
JI: ISO journal title abbreviation
LA: Language
NR: Cited reference count
PD: Publication date e.g. "JUN 8" or "JUL"
PA: Publisher Address
PG: the number of pages
PI: Publisher city
PN: Part number
PT: Publication type (e.g., book, journal, book in series)
PU: Publisher
PY: Publication year
RID: Researcher ID
RP: Reprint address
SE: Book series title
SI: Special issue
SN: ISSN
SO: journal title, in full
SP: Conference Sponsors
SU: Supplement
TC: Times cited
TI: Title
UT: ISI unique article identifier
VL: Volume
WC: Research field
WP: Publisher web address
Z9: Total times cited ???

isi original tags

UR: URL

Known bugs

* none.

TODO

* In lib/isi.rb, combine
  ISI_record#and_separated_authors() and
  ISI_record#comma_and_separated_authors() into
  ISI_record#separated_authors().
* Write papers, not tools for writing papers.
* tests/isi_test.rb
* Move output formats from lib/isi.rb to isi2html, isi2tohoku and isi2kakenhi.
  Leave that for isi2bibtex in lib/isi.rb.
* We do not need journaltitleabbreviation.rb any more.
* Daemon for Linux. Automatic ~/Desktop/savedrecs.txt -> savedrecs.bib
  using inotify().

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