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WoS
WoS2Pajek
networks from
Web of Science
version 0.7
Vladimir Batagelj
FMF, matematika
University of Ljubljana
Manual
Ljubljana, August 2009 / December 2007
version: 24. Aug 2009 / 04 : 25
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Index
1 Searching on the Web of Science . . . . . . . . . . . . . . . . . . . . . . . . . . 1
4 Using the Advanced Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
8 The list of citing articles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
11 Structure of a WoS record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
12 Names of works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
14 Program WoS2Pajek . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
25 Types on DC le . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
26 Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
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Searching on the Web of Science
The Web of Science WoS
(ISI/Thomson) allows us to save
on a le the records correspond-
ing to our queries.
For example, using General
search with a query "social
network
*
" we get 6936 hits
(27. December 2007).
Trying to save them we are in-
formed that we can save at once at
most 500 records. We have to save
the records by parts on separate
les. At the end we concatenate
all these les into a single le.
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Saving the records
At the bottom of the page in the Output Records select Records and enter the interval bounds
firstRec to lastRec on record numbers that you want to save.
Select Full Record + Cited Reference.
Select also - as Plain Text and click on the Save button.
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. . . Saving the records
In a new window the export
process starts . . . it takes some
time . . . wait until done. Select
Save it to disk and click
OK. When the le-chooser ap-
pears determine the le on which
the records are saved.
Clicking on the Back to Results
button you return back to the re-
sults window.
Repeat these steps until all the
records are saved on les.
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Using the Advanced Search
At the computer with access to
Web of Science (at Uni-LJ you
can use the IZUM and select the
option ISI Web of Knowledge
(Web of Science) - na stre zniku
Thomson Reuters).
Once on the WoS we select the
folder Advanced Search and en-
ter our query for example:
TS=(centrali
*
AND
(network
*
OR graph))
If necessary we can set also the
time bounds (WoS allows only up
to 100000 hits in a query).
We obtain the information about
the number of hits at the bottom
of the page.
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Get the list of hits and save selected on le
To get the list of hits we click to
their number (blue 3,199 in our
case).
At the bottom of this page we can
request that some of the hits are
saved to the le. For longer lists
we have to do this by parts - WoS
allows only 500 hits to be saved at
once.
To save selected hits we proceed as follows:
* step 1: determine the range of hits to be saved (1-500, 501-1000, 1001-1500, ...);
* step 2: select Full Record and plus Cited Reference;
* step 3: select Save to Plain Text.
Finally we click on the Save button.
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... saving
A new page Processing Records
appears. We have to wait until
the selected records are processed
and written to the le. In the win-
dow that appears we select the op-
tion Save to Disk and click OK.
In a new window that appears we
select the directory and enter the
name of the le on which the se-
lected hits are saved, for example
Centrali004.txt.
Finally we click on the Save but-
ton.
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... saving
To return back to the saving of selected hits we click on Back to Results.
We repeat the procedure described in this subsection until all the hits are saved.
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The list of citing articles
We return to the top of the page
with list of hits - see the picture
in the subsection Get the list of
hits. In the upper right corner we
click on the option Create Cita-
tion Report. We obtain a new
page with histograms.
To obtain the list of citing articles
we click on the option View Cit-
ing Articles.
To save them we repeat the proce-
dure described in subsection Save
the selected hits to le.
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Additional records
At WoS we enter the advanced
search and for an entry from the
list, for example
97
"FELSENST J(1985)39:783"
we enter a query
au=(FELSENST
*
J
*
) and
py=1985
In the list of hits at the bottom of
the page click the blue number of
hits to obtain the list of their basic
descriptions.
Using the information about the volume and the rst page, 39 and 783 in our example, identify
the corresponding work (if it exists), check the box in front of it and then click the button Add
to Marked List at the beginning of the list. After addition of the work to the Marked list the
red check mark will appear in front of the work (see picture). Repeat the described procedure
for other entries.
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. . . Additional records
When the list of hits becomes to
long click the Select All button in
its Delete Sets column and after it
the Delete button. The list of hits
will empty.
To save the works from the
Marked List click on Marked List
at the top of the page. In the new
window select all options in Step
1 and in Step 2 select the Plain
Text option in front of Save to
File button and click on this but-
ton.
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Structure of a WoS record
PT J
AU KOSMELJ, K
BATAGELJ, V
TI CROSS-SECTIONAL APPROACH FOR CLUSTERING TIME-VARYING DATA
SO JOURNAL OF CLASSIFICATION
DT Article
CR
*
UN, 1979, STAT YB
*
UN, 1981, STAT YB
*
UN, 1982, STAT YB
ANDERBERG MR, 1973, CLUSTER ANAL APPLICA
BATAGELJ V, 1981, CLUSE CLUSTERING PRO
BATAGELJ V, 1988, 2ND M YUG SECT CLASS
BATAGELJ V, 1988, CLASSIFICATION RELAT, P67
GORDON AD, 1981, CLASSIFICATION
KOSMELJ K, 1983, REV STAT APPL, V31, P5
KOSMELJ K, 1986, J MATH SOCIOL, V12, P315
TC 7
SN 0176-4268
J9 J CLASSIF
JI J. Classif.
PY 1990
VL 7
IS 1
BP 99
EP 109
SC Mathematics, Interdisciplinary Applications; Psychology, ...
UT ISI:A1990DE57600006
ER
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Names of works
The usual ISI name of a work (eld CR)
LEFKOVITCH LP, 1985, THEOR APPL GENET, V70, P585
has the following structure
AU + , + PY + , + SO[:20] + , V + VL + , P + BP
All its elements are in upper case.
In WoS the same work can have different ISI names. To improve the precission
the program WoS2Pajek supports also short names (similar to the names used in
HISTCITE output). They have the format:
LastNm[:8] + + FirstNm[0] + ( + PY + ) + VL + : + BP
For example: LEFKOVIT L(1985)70:585
From the last names with prexes VAN, DE, . . . the space is deleted.
Unusual names start with character
*
or $.
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. . . Names of works
In the CR eld other forms of ISI names and several errors and inconsistencies can
be found:
NEWMAN MEJ, 2004, PHYS REV E 2, V69, ARTN 066133
PALLA G, 2005, NATURE, V435, P814, DOI 10.1038/nature03607
PAPIN JA, 2004, TRENDS BIOCHEM SCI, V29, P641, DOI
10.1016/j.tibs.2004.10.001
DOLCINI MM, 2005, J ADOLESCENT HEALTH, V36, UNSP 267.E6-15
EVANS JD, 2001, GENOME BIOL, V2, UNSP RESEARCH0001
NEWMAN MEJ, 2001, IN PRESS COMPLEX NETUNSP 215239
GRANOVET.MS, 1973, AM J SOCIOL, V78, P1360
GRANOVETTER M, 1983, SOCIOLOGICAL THEORY, V1, P203
BORGATTI SP, 2002, UGINET WINDOWS SOFTW
BORGATTI S, 1999, UCINET V USERS GUIDE
CANTANZARO M, 2005, PHYS REV E, V71, UNSP 027103
CANTAZARO M, 2005, PHYS REV E, V71, UNSP 056104
CATANZARO M, 2005, PHYS REV E 2, V71, ARTN 056104
BRICKER PD, 1968, OCT M PSYCH SOC ST L : BRICKER
We decided to treat in short names the ARTN and UNSP values as BP values. We
also remove the DOI parts. There are also irregular names in AU eld:
AU BENSON, , C
KULHAVY, , W
AU SCHONEMA.PH
The user can correct the typing errors and nonuniformities on the WoS le.
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Program WoS2Pajek
For converting WoS le into networks in Pajeks format a program
WoS2Pajek was developed (in Python). It produces the following les:
citation network: works works;
authorship (two-mode) network: works authors, for works without
complete description only the rst author is known;
keywords (two-mode) network: works keywords, only for works
with complete description;
journals (two-mode) network: works journals, eld J9;
partition of works by the publication year;
partition of works complete description (1) / ISI name only (0);
vector number of pages, PG or EP BP +1.
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Program WoS2Pajek
The keywords are obtained from the elds TI (title), ID, DE and AB
(abstract). From the text the stopwords are removed and a list of words is
produced. The words are lemmatized using MontyLingua package.
In future versions aditional networks can be derived: works discipline,
works countries, . . .
In version 0.7 a GUI support (based on Tkinter) for specifying the program
parameters was implemented.
Program WoS2Pajek can be run as an executable program by double-
clicking on its icon see slide 21.
The source code can be executed in different ways using the Python
interpreter. See slides 19, 22 and 23.
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Program WoS2Pajek
The current version of WoS2Pajek requires 7 parameters to be given by the user:
MontyLingua directory: path to the directory in which the MontyLingua
package is installed (put it also in the PATH env-variable);
project directory: where the output les are saved;
WoS le;
maxnum estimate of the number of all vertices (number of records + number
of cited Works) 30 number of records;
step prints info about each k*step record as a trace; step = 0 no trace.
use ISI name / short name;
make a clean WoS le without duplicates;
boolean list [ DE, ID, TI, AB ] specifying which elds are sources of keywords.
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Program WoS2Pajek details
To use WoS2Pajek program you need to install at your computer:
Python, version 2.5
download WoS2Pajek 0.7 (latest ver-
sion)
MontyLingua package
Copy the MontyLingua package
into directory Python25\Lib\
site-packages\montylingua-2.1\
add to the environment variable
MONTYLINGUA (or PATH) the path
to MontyLingua (see the picture):
Control Panel/ System/
Advanced System Settings/
Environment Variables/ New
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. . . Program WoS2Pajek details
WoS2Pajek expects in the subdirectory resources (of directory in which it is
located) the les StopWords.dat and Pajek.ico;
run Python and use the commands similar to the following:
>>> import sys; wdir = rc:\users\Batagelj\work\Python\WoS
>>> sys.path.append(wdir)
>>> MLdir = rc:\Python25\Lib\site-packages\MontyLingua-2.1\Python
>>> sys.path.append(MLdir)
>>> import WoS2Pajek
A dialog box will appear in which we specify required parameters and press the RUN button.
WoS2Pajek 0.6 works nicely also on 64-bit machines with python-2.5.4.amd64.
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Running WoS2Pajek 0.7 / from Python interpreter
>>> import sys; wdir = rc:\users\Batagelj\work\Python\WoS; sys.path.append(wdir)
>>> MLdir = rc:\Python25\Lib\site-packages\MontyLingua-2.1\Python
>>> sys.path.append(MLdir)
>>> import WoS2Pajek
Module Wos2Pajek imported.
***
WoS2Pajek - 0.7
by V. Batagelj, August 23, 2009 / March 23, 2007
WoS2Pajek parameters
WoS dir: c:\users\Batagelj\work\Python\WoS
ML dir: c:\Python25\Lib\site-packages\MontyLingua-2.1\Python
Proj dir: C:/Users/Batagelj/work/Python/WoS/batagelj
WoS file: C:/Users/Batagelj/work/Python/WoS/batagelj/batagelj.WoS
MaxNum : 1000
step : 10
ISI name: False
clean : True
keywords: [True, True, False, False]
******
MontyLingua v.2.1
******
*****
by [email protected]
*****
Lemmatiser OK!
Custom Lexicon Found! Now Loading!
Fast Lexicon Found! Now Loading!
Lexicon OK!
LexicalRuleParser OK!
ContextualRuleParser OK!
Commonsense OK!
Semantic Interpreter OK!
Loading Morph Dictionary!
*********************************
***
WoS2Pajek - 0.7
by V. Batagelj, August 23, 2009 / March 23, 2007
started: Mon Aug 24 03:19:29 2009
10 : DOREIAN_P(2000)17:3 - 2009-08-24 03:19:29.614000
20 : BATAGELJ_V(1994)11:93 - 2009-08-24 03:19:30.134000
30 : BATAGELJ_V(1984)52:113 - 2009-08-24 03:19:30.426000
36 : BATAGELJ_V(1975)18:216 - 2009-08-24 03:19:30.640000
>>> End of processing of WoS file
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. . . Running WoS2Pajek 0.7 / from Python interpreter
number of works = 371
number of authors = 230
number of journals = 102
number of keywords = 82
number of records = 36
number of duplicates = 0
clean WoS data: clean.WoS
***
FILES:
year of publication partition: C:/Users/Batagelj/work/Python/WoS/batagelj\Year.clu
described / cited only partition: C:/Users/Batagelj/work/Python/WoS/batagelj\DC.clu
number of pages vector: C:/Users/Batagelj/work/Python/WoS/batagelj\NP.vec
citation network: C:/Users/Batagelj/work/Python/WoS/batagelj\Cite.net
works X journals network: C:/Users/Batagelj/work/Python/WoS/batagelj\WJ.net
works X keywords network: C:/Users/Batagelj/work/Python/WoS/batagelj\WK.net
works X authors network: C:/Users/Batagelj/work/Python/WoS/batagelj\WA.net
finished: Mon Aug 24 03:19:30 2009
time used: 0:00:01.770000
***
To rerun, type:
reload(WoS2Pajek)
<module WoS2Pajek from c:\users\Batagelj\work\Python\WoS\WoS2Pajek.py>
>>>
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Running WoS2Pajek / Python by double-clicking it
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Running WoS2Pajek / Python from Dos window
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Running WoS2Pajek / Python from Dos window using
parameters
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Types on DC le
When we combine partial les with saved records from WoS into a single
le required by the programWoS2Pajek we can include into this le some
additional lines: Comments have the form
**
comment
Besides this we can specify diffent types of input records using the lines of
the form
*
T n
where n is a type number (1, 2, . . . ). Since the same record can appear in
different parts of the le its class is determined as the set of all corresponding
types transformed in integer. For example: {3, 1} 5.
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Analyses
The saved records from WoS can still contain some inconsistencies:
different names for the same person;
same name for different persons;
duplicated entries;
. . .
Some of them are detected as results of the analyses. The simplest way
to deal with them is to correct them in the saved WoS le and rerun the
creation of Pajeks les and analyses.
To improve the quality of the data some tools for detecting (possible)
inconsistencies could be developed.
Check (in Pajek) the obtained networks for multiple lines and remove
them, if they exist. Remove also the loops from the citation network.
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Preparing the citation network
Using on PRcite.net the commands
Info/Network/General
Net/Transform/Remove/Loops
Net/Transform/Remove lines/Single line
we get the information about the number of loops and multiple lines,
remove loops, and replace multiple lines with single lines. The obtained
network we save (Options - Save coordinates [OFF]) to le
PRciteR.net. For further analysis the citation network has to be
acyclic has no nontrivial strong component. To identify nontrivial strong
component and extract them use the commands:
Net/Components/Strong [2]
Operations/Extract from Network/Partition [1-
*
]
Operations/Transform/Remove Lines/Between Clusters
Save the obtained network to le PRstrong.net.
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. . . Preparing the citation network
To transform the network PRciteR.net into acyclic network using the
preprint transformation use the program Preprint
import Preprint;
Preprint.run(wdir,PR,PRciteR.net,PRstrong.net)
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. . . Analyses: network boundary problem
Networks obtained from the WoS le using the programWoS2Pajek are in
the raw form. We still have to resolve in some way the network boundary
problem. The rst option is to limit the network to the works with complete
descriptions records from the WoS le. We can get a richer network if
we decide to include also some referenced (only) works that are referenced
often at least k times; we delete vertices for which it holds
(0 < indeg(v) < k) (outdeg(v) = 0)
Net/Partition/Degree/Input
Partition/Binarize [1-(k-1)]
Net/Partition/Degree/Output
Partition/Binarize [0]
[select partition 1]
[select partition 2]
Partitions/Min(V1,V2)
Operations/Extract from Network/Partition [0]
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. . . Analyses: collaboration network
OLSON_J
FRIEZE_I
WALL_S
ZDANIUK_B
FERLIGOJ_A
KOGOVSEK_T
HORVAT_J
SARLIJA_N
JAROSOVA_E
PAUKNERO_D
LUU_L
KOVACS_M
MILUSKA_J
ORGOCKA_A
EROKHINA_L
MITINA_O
POPOVA_L
PETKEVIC_N
PEJIC-BA_M
KUBUSOVA_S
MAKOVEC_M
RENER_T
BATAGELJ_V
ZAVERSNI_M
DOREIAN_P
BREN_M
TELPUCHO_N
BONEVA_B
HLEBEC_V
SARIS_W
BRANDES_U
COENDERS_G
PAHOR_M
PRASNIKA_J
WHITE_D
KOROBANO_J
SUKHAREV_N
MORINAGA_Y
MRVAR_A
JORDAN_V
PISANSKI_T
KERZIC_D
BLAZIC_B
JERMANBL_B
KORENJAK_S
KLAVZAR_S
FABICPET_I
POMPEKIR_V
SIMOESPE_J
KOSMELJ_K
RAJKOVIC_V
BOHANEC_M
RAVNIHAR_B
SPLICHAL_S
Pajek
Let us denote the citation network with Ci ,
and the authorship network with WA. Then
Co = WA
T
WA is the collaboration
network
[Read xyzWA.net]
Net/Transform/2-mode to 1-mode
/Columns
Net/Components/Weak [2]
Operations/Extract from Network
/Partition [1-
*
]
Net/Transform/Remove/Loops
and Ca = WA
T
Ci WA is a network
of citations between authors. [3]
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. . . Analyses: Bibliographic Coupling and Co-Citation
In WoS2Pajek the citation relation means uCiv ucitesv. Therefore the bibliographic
coupling network biCo can be determined as
biCo = Ci Ci
T
[Read xyzCite.net]
Net/Transform/1-mode to 2-mode
Net/Transform/2-mode to 1-mode/Rows
Net/Components/Weak [2]
Operations/Extract from Network/Partition [1-
*
]
and the co-citation network coCi can be determined as
coCi = Ci
T
Ci
Since the network can be quite large we rst eliminate the only-cited works.
[Read xyzCite.net]
Net/Partitions/Degree/Output
Operations/Extract from Network/Partition [1-
*
]
Net/Transform/1-mode to 2-mode
Net/Transform/2-mode to 1-mode/Columns
Net/Components/Weak [2]
Operations/Extract from Network/Partition [1-
*
]
In the analysis of the obtained networks the comparability of units could/should be considered
[1].
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. . . Analyses: other derived networks
The weights w(a, p) in the author citation network
ACi = WA
T
Ci
counts the number of times author a cited work p.
[Read xyzWA.net]
Net/Transform/Transpose/2-mode
[Read xyzCite.net]
Nets/Multiply First
*
Second
Net/Components/Weak [2]
Operations/Extract from Network/Partition [1-
*
]
Let b(A) denotes the binarized version of A. The author co-citation network can be obtained
as
ACo = b(ACi) b(ACi)
T
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. . . Analyses: temporal network
We can also transform the citation network into temporal network using the partition of works
by publication year:
[Read xyzCite.net]
[Read xyzYear.clu]
Vector/Create Identity Vector
Vector/Transform/Multiply by [2008]
Vector/Make Partition/by Truncating
[select as partition 1: xyzYear]
[select as partition 2: obtained from vector]
Operations/Transform/Add/Time intervals determined by Partitions
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References
[1] Batagelj V., Mrvar A.: Density based approaches to network analysis Analysis of
Reuters terror news network. Workshop on Link Analysis for Detecting Complex
Behavior (LinkKDD2003, Washington, DC, USA) August 27, 2003.
http://www.cs.cmu.edu/ dunja/LinkKDD2003/papers/Batagelj.pdf
[2] Gareld E.: HISTCITE. http://www.histcite.com/;
HISTCITE/index; Social networks
[3] Kej zar N., Korenjak-

Cerne, Batagelj V.: Network Analysis of Works

on Clustering and Classication from Web of Science. Submit-
ted to Proceedings of IFCS09 (Dresden, Germany, March 2009).
http://pajek.imfm.si/lib/exe/fetch.php?media=dl:gfkl 305.pdf
[4] Kessler, M. M.: Bibliographic Coupling between Scientic Papers. American Documen-
tation, 14(1963)1, 10-25.
[5] Small H.: Co-citation In Scientic Literature New Measure Of Relationship Between
2 Documents. Journal Of The American Society For Information Science, 24(1973)4,
265-269.
[6] WoS2Pajek:
http://pajek.imfm.si/doku.php?id=wos2pajek
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[7] Web of Science WoS (ISI/Thomson):
http://portal.isiknowledge.com/portal.cgi
[8] Python: http://www.python.org/
[9] Py2Exe: http://www.py2exe.org/
[10] MontyLingua package: http://web.media.mit.edu/hugo/montylingua/
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