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Paynter R, Bañez LL, Berliner E, et al. EPC Methods: An Exploration of the Use of Text-Mining Software in Systematic Reviews [Internet]. Rockville (MD): Agency for Healthcare Research and Quality (US); 2016 Apr.

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EPC Methods: An Exploration of the Use of Text-Mining Software in Systematic Reviews [Internet].

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Appendix ETools Catalog

Table E-1Tools evaluation table

Name
Acronym
URL		Availabilitya
Cost		Web BasedbPlatformDeveloperMultiuserbKIbLit Review a Citation(s)Publication(s)aSR SupportaDeploy Statusa,bTech LevelaFeaturesaHelpbRegistrationa,bComments
Abstrackr

http://abstrackr​.cebm​.brown.edu/account/login		FR

0		1NABrown University111452IE10NDND1ND
Anne O'tate

http://arrowsmith​.psych​.uic.edu/cgi-bin/arrowsmith_uic​/AnneOTate.cgi		FR

0		1NADepartment of Psychiatry and Psychiatric Institute, University of Illinois at Chicago0016
34
64		64TR
FI		10IR
DCL
ATM
TSM		ND0ND
AntCont

http://www​.laurenceanthony​.net/software/antconc/		FR

0		0MULTILaurence AnthonyUC1NDNDTR
FI		11ATM
DCL		1NDRequires installation
AQ21 machine learning software

http://www​.mli.gmu.edu/software		FR

0		0MULTIJanusz WojtusiakUC065NDND1NDND10Requires installation
Aquad

http://www​.aquad.de/en/		FR

0		0MULTIGunter L. HuberUC0NDNDND1NDNDNDNDRequires installation
askMEDLINE

http://askmedline​.nlm​.nih.gov/ask/ask.php		FR

0		1NANational Library of Medicine001666TR
FI		10NLP
IR		NDNDND
Automated Sequence Annotation Pipeline (ASAP)

http:​//bioinformatics​.fccc.edu/software/OpenSource​/ASAP/ASAP.shtml		FR

0		0MULTIFox Chase Cancer CenterUC05467IE12DCL
NLP		10ND
BioIE

http://www​.bioinf.manchester​.ac.uk/dbbrowser/bioie/		FR

0		1NAThe University of Manchester, Bioinformatics00ND68TR
FI		10NDND0ND
BioTextQuestFR

0		1NAUniversity of Crete003469TR
FI		10DCL
NLP
VIZ		ND0Web site cannot be displayed
carrott2

http://project​.carrot2​.org/download-workbench-win32-64bit​.html		FR

0		0MULTIDavid Weiss and Stanislaw Osinksi0170
34		NDDCT1NDND1NDRequires installation
Cassandre

http://cassandra​.apache.org/		FR

0		0MULTIApache Software FoundationND0NDNDNDND2NDNDNDProbably out of scope
Chilibot

http://www​.chilibot.net/		FR

0		1NAUniversity of Tennessee Health Science Center001671TR
FI		10NLP
IR
VIZ
ATM		10ND
Coding Analysis Toolkit (CAT)

http://cat​.ucsur.pitt.edu/		FR

0		0MULTIQualitative Data Analysis Program, University of Pittsburgh00NDNDIE
EX		12DCL
IEX		1NDRequires installation
Computer Aided Textual Markup & Analysis (CATMA)

http://www​.catma.de/		FR

0		1NAUniversity of HamburgND0NDNDNDNDNDND11Literary analysis
Concordance

http://www​.concordancesoftware.co.uk/		FRT

0		0MULTIR. J. C. Watt0037
36		NDNDNDNDNDNDNDRequires installation
CoPub

http://services​.nbic.nl/copub/portal/		FR

0		1NAComputational Drug Discovery Group of Radboud University Nijmegen Medical Centre001672TR
FI		10NLPND0ND
COREMINE medical

http://www​.coremine.com/medical/#search		FR

0		1NAPubGene AS0016NDTR
FI		10NLP
ATM
IR
VIZ		10ND
Dbpedia

http://wiki​.dbpedia.org/		FR

0		0MULTIDbpedia00ND73NDNDNDNDNDNDRequires installation
EndNote

http://endnote​.com/		CP

varies		1MULTIThomas-Reuters114646ND1NDNDNDNDND
EPPI-Reviewer 4 (EPPI)

http://eppi​.ioe.ac.uk/cms/Default​.aspx?tabid=1913		FRT

UC		1NAEvidence for Policy and Practice Information and Coordinating Centre, UCL Institute of Education, University of London1114NDIE
EX		11ATM
DCT
DCL		11ND
ETBLAST

http://etest​.vbi.vt.edu/etblast3/		FR

0		1NAVirginia Bioinformatics Institute001674TR
FI		10NLP1l0ND
ExaCT

Not found		ND

ND		NDNDNDND0ND75EXNDNDNDNDNDND
FACTA+

http://www​.nactem.ac.uk/facta/		FR

0		1NANational Centre for Text Mining, School of Computer Science, The University of Manchester001676TR
FI
EX		10NLP
IR
IEX		10ND
FreeQDA

https://github​.com/produnis​/FreeQDA/downloads		FR

0		0NDND00NDNDNDNDNDNDNDNDRequires installation
GAPScreener

http://www​.hugenavigator​.net/HuGENavigator​/HNDescription/opensource_GAP.htm		FR

0		0MULTIWei Yu, National Office of Public Health Genomics, Centers for Disease Control and PreventionUC1ND77TR
FI
IE		12IEXNDNDRequires installation; human genome epidemiology network
GATE

https://gate​.ac.uk/		FR

0		0MULTIUniversity of SheffieldUC17860TR
FI
IE		12TCL1NDRequires installation
Gopubmed

http://www​.gopubmed.org/web/gopubmed/		FR

0		1NATransinsight GmbH0116
34
35		79TR
FI		10NLP11ND
Hierarchical Cluster Explorer (HCE)

http://www​.cs.umd.edu/hcil/hce/		FR

0		0WINHuman-Computer Interaction Lab, University of MarylandUC07880NDNDNDNDNDNDRequires installation
HubMed

http://git​.macropus.org/hubmed/		FR

0		1NAND00ND81TR
FI		10NLP10
HuGENet

http://www​.hugenavigator​.net/HuGENavigator​/HNDescription/opensource_GAP.htm		FR

0		1NANDND1NDNDNDNDNDNDNDNDND
Idealist

Unavailable		ND

ND		NDNDNDND036NDNDNDNDNDNDNDBlackwell bibliographic software
KH Coder

http://khc​.sourceforge.net/en/		FR

0		0MULTIKoichi HiguchiUC0ND82NDNDNDNDNDNDRequires installation
Konstanz Information Miner (KNIME)

https://www​.knime.org/		FR

0		0NAKNIMEUC0NDNDNDNDNDNDND1Requires installation
LEXIMANCER

http://info​.leximancer.com/		FRT

varies		1NALeximancer1041NDNDNDNDNDNDNDRequires installation
libSVM

http://ntucsu​.csie.ntu​.edu.tw/∼cjlin/libsvm/		FR

0		0MULTIChih-Chung Chang and Chih-Jen LinUC040NDIE12DCLNDNDRequires installation
Lingo3G

http://carrotsearch​.com/lingo3g-overview		FRT

varies		0MULTICarrotUC183NDNDNDNDTCL
VIZ		NDNDRequires installation
LingPipe

http://alias-i​.com/lingpipe/		FR

0		0WINAlias-iUC084NDEX12IEX1NDRequires installation
linguamatics (I2E)

http://www​.linguamatics​.com/welcome/software/I2E.html		CP

varies		1NALinguamaticsUC0ND85NDNDNDNLPNDNDTrial includes subset of data
Machine Learning for Language Toolkit (MALLET)

http://mallet​.cs.umass.edu/		FR

0		0MULTIAndrew McCallum, University of MassachusettsUC0NDNDND12NLP
DCL
IEX		1NDRequires installation
MEDIE

http://www​.nactem.ac.uk/medie/		FR

0		1NATsujii Laboratory001686TR
FI		10NLP
IR
ATM		0NDND
Medline Ranker

http://cbdm-01​.zdv.uni-mainz​.de/∼jfontain​/cms/?page_id=4		FR

0		1NAComputational Biology and Data Mining group, Miguel Andrade-Navarro, Johannes Gutenberg University Mainz0016
34		NDTR
FI		10ATM
TCL		1NDND
medsum

http://webtools​.mf.uni-lj​.si/public/medsum.html		FR

0		NDNDNDND03487NDNDNDNDNDNDND
MeSHY

http://tools​.bat.infspire.org/meshy/		FR

0		1NABioinformatics Analysis Team008788TR
FI		11IR
TCL		NDNDND
MetaMap

http://metamap​.nlm.nih.gov/		FR

0		0NDAlan Aronson, National Library of MedicineND038
64		89NDNDNDND1NDOut of scope
Meva

http://www​.med-ai.com/meva/		FR

0		1NDInstitute for Medical Statistics and Epidemiology, Technical University of Munich00ND90TR
FI		11ATM
TCL		1NDND
Mscanner

http://mscanner​.stanford.edu/		FR

0		1NAGraham Poulter004391TR
FI		10DCL
IR		1NDND
MyMiner

http://myminer​.armi.monash.edu.au/		FR

0		1NAAustralian Regenerative Medicine Institute, Monash University00NA92TR
FI		11TCA1NDND
NLM Medical Text Indexer (MTI)

http://ii​.nlm.nih.gov/MTI/		FR

0		NDNDNDND0ND93TR
FI		NDNDNLPNDNDND
Nvivo

http://www​.nvivo10.com/en/whats-new.html		CP

varies		0MULTIQSRUC015NDND11TCA1NDRequires installation
OpenNLP

https://opennlp​.apache.org/		FR

0		0MULTIApache Software FoundationUC054NDIE11TCANDNDND
Perceptron classifier

http://reference​.wolfram​.com/applications​/neuralnetworks/NeuralNetworkTheory/2​.4.0.html		NA

NA		NANANANA194NDNDNA2NDNANDClassifier algorithm
PICO

http://pubmedhh​.nlm.nih​.gov/nlmd/pico/piconew.php		FR

0		1NANational Library of Medicine0016NDTR
FI		10IRNDNDND
Pimiento

http://erabaki​.ehu.es/jjga/pimiento/		FR

0		0MULTIJuan Jose Garcia AdevaUC01495ND12DCT
TSM		NDNDRequires installation
PPIinterFinder

http://www​.biominingbu​.org/ppinterfinder/about.html		FR

0		1NAData Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University00NDNDNDNDNDNDNDNDProtein-protein interactions
Projection Explorer (PEx)

http://infoserver​.lcad​.icmc.usp.br/infovis2/PEx		FR

0		0MULTIFernando Vieira Paulovich, University of Sao PauloUC096NDTRUC2VIZNDNDND
PubCrawler

http://pubcrawler​.gen.tcd.ie/		FR

0		1NAKen Wolfe Lab, Genetics Department Trinity College001697TR
FI		10IR11ND
PubGet

http://pubget​.com/		FR

0		1NANDND016NDNDNDNDNDNDNDND
PubMatrix

http://pubmatrix​.grc.nia.nih.gov/		FR

0		1NANational Institute of Health0016
34		98TR
FI		11IRND1Registered but unable to login
PubNet

http://pubnet​.gersteinlab.org/		FR

0		1NAGerstein Lab, Department of Molecular Biophysics and Biochemistry, Yale University001699TR
FI		11IR
VIZ		1NDND
PubReMiner

http://hgserver2​.amc​.nl/cgi-bin/miner/miner2.cgi		FR

0		1NAJan Koster, Academic Medical Center0142NDTR
FI		10TCL
IR		1NDStandalone for searching
PubViz

https://github​.com/aha01/PubViz/		FR

0		0MULTIMatthias Fabi, Andrea Haberson, San Rasul, Elisabeth Schnaitt, Paul Theisen0016NDTR
FI		11VIZ1NDRequires installation
QCAmap

http://www​.qualitative-content-analysis​.aau.at/software/		FR

0		1NAPhilipp Mayring, Thomas Fenzl00NDNDNDNDNDND1yesQualitative content analysis
QDA Miner

http:​//provalisresearch​.com/products/qualitative-data-analysis-software/		FR

0		0WINProvalis Research10NDNDND11NDNDNDQualitative content analysis
Qiqqa

http://www​.qiqqa.com/Download		FR

0		1WIN
ADR		ND00ND82TR
FI
EX		11DCL
CLA		1NDPremium features with paid subscription
Quetzal

https://www​.quetzal-search​.info/loginpage		FRT

varies		1NAQuertle LLCUC016100TR
FI
EX		11IR
DCL		ND1Key concepts available with paid subscription; previously Quertle
r Simple Learner with Iterative Pruning to Produce Error Reduction (SLIPPER)ND

ND		NDNDNDND094101NDNDNDNDNDNDRule learning algorithm
RapidMiner

https://rapidminer​.com/		CP

varies		1NARapidMinerUC014NDND11NDNDNDRequires installation
Rayyan

http://rayyan​.qcri.org/		FR

0		1NAQCRI10NDNDIE10NDND1ND
RCT Tagger

http://arrowsmith​.psych​.uic.edu/cgi-bin/arrowsmith_uic​/RCT_Tagger.cgi		FR

0		1NACohen et al.0056102FI
IE		10DCLND0ND
Reflect

http://reflect​.embl.de/		FR

0		1NAEuropean Molecular Biology Laboratory001653ND10NDNDNDGene and protein tagging tool
RobotReviewer

http://vortext​.systems/robotreviewer		FR

0		1MULTINDUC053NDEX11IEXNDNDWeb version for testing; requires installation
RQDA

http://rqda​.r-forge.r-project.org/		FR

0		0MULTINDUC0ND103NDNDNDNDNDNDRequires installation; qualitative content analysis
Semantic Medline

http://skr3​.nlm.nih.gov/SemMed/index​.html		FR

0		1MULTIFiszman, Marcelo00ND104ND10NLP11Requires registration; extract semantic predication
SIDER 2

http://sideeffects​.embl.de/drugs/4158/		FR

0		1NAMichael Kuhn, Structural and Computational Biology Unit, European Molecular Biology LaboratoryND0NDNDND10IEXND1ND
SimStat

http:​//provalisresearch​.com/products/simstat/		CP

varies		0MULTIProvalis ResearchUC1NDNDND12NDNDNDRequires installation; qualitative and quantitative statistical package
Site Content Analyzer

http://www​.cleverstat​.com/en/sca-website-analysis-software-index.htm		OTH

79		0WINCleverStatUC078NDNDUCUCUC1NDRequires installation; website content parser
SLRTOOL

http://slrtool​.org/v0		FR

0		1NAND10105NDND01UC01ND
SPSS

http://www-01​.ibm.com​/software/analytics/spss/		CP

varies		0MULTIIBMUC036106ND11ND1NDRequires installation
State of the Art through systematic review (StArt)

http://lapes​.dc.ufscar​.br/tools/start_tool		FR

0		0MULTILaboratory of Research on Software Engineering, Computing Department of the Federal University of São CarlosUC0107
78
105		NDFI
EX		12IEX
TCL		1NDRequires installation
STRING

http://string-db​.org/		FR

0		1NASwiss Institute of Bioinformatics0016108NDNDNDND1NDProtein-protein interactions
Systematic Literature unified Review Program (SLuRp)

https:​//codefeedback​.cs.herts.ac.uk/SLuRp/		FR

0		0MULTIDavid Bowes, Science and Technology Research Institute University of Hertfordshire1078
105		109FI
IE
EX		12IEXNDNDND
Systematic review supported by visual analytics (REVIS)

http://ccsl​.icmc.usp​.br/pt-br/projects/revis		FR

0		0UCUniversity of Sao PauloUC01447ND1NDVIZNDNDRequires installation
TerMine

http://www​.nactem.ac​.uk/software/termine/		FR

0		1NASophia Ananiadou, National Centre for Text MiningUC140NDIE11ATM1NDWeb version for demonstration; register for batch service
Text Analysis Markup System (TAMS)

http://tamsys​.sourceforge.net/		FR

0		0MACMatthew WeinsteinUC0ND110ND12TCL1NDRequires installation; qualitative content analysis
Text Mining Infrastructure in R (tm in R)

http://tm​.r-forge.r-project.org/		FR

0		0MULTINDND132NDND12DTMNDNDND
Textpresso

http://www​.textpresso.org/about.html		FR

0		NDNDNDND034NDNDNDNDTCANDNDBiological literature; entity recognition
TinySVM

http://chasen​.org/∼taku​/software/TinySVM/		FR

0		0MULTINDUC070NDFI
IE
EX		12NDNDNDLearning algorithms
Ultimate Research Assistant

http://www​.ultimate-research-assistant​.com​/GenerateResearchReport.asp		ND

ND		NDNDNDND03454NDNDNDNDNDNDND
Unstructured Information Management Application Framework (UIMA)

http://uima​.apache.org/		FR

0		0WINIBM; currently at Apache Software FoundationUC054NDND12DCL
NLP		0NDRequires validation workstation; out of scope
VOSviewer

http://www​.vosviewer.com/Home		FR

0		0MULTICentre for Science and Technology Studies, Leiden UniversityND1111NDNDND1VIZ
TCL		NDNDND
Voyant Tools

http://voyant-tools​.org/		FR

0		1NAStefan Sinclair and Geoffrey Rockwell01NDNDND1NDVIZ
TCL		0NDND
Weka

http://www​.cs.waikato.ac.nz/ml/weka/		FR

0		0MULTIUniversity of WaikatoND0112113NDNDNDNDNDNDMachine learning
Whatizit

https://www​.ebi.ac.uk​/webservices/whatizit/info.jsf		FR

0		1NAEuropean Bioinformatics Institute001646TR
FI		10TCLNDNDND
WordStat

http://www​.stata.com​/news/wordstat-for-stata/		CP

varies		0MULTIProvalis ResearchND146NDNDNDNDNDNDNDND
xPDF

http://www​.foolabs.com/xpdf/home.html		FR

0		0MULTIFoolabs0053114NDND0TRVNDNDPDF to text utility; not relevant
XplorMed

http://xplormed​.ogic.ca/		FR

0		1NACarolina Perez-Iratxeta, Peer Bork, and Miguel A. Andrade0016NDTR
FI		10TCL
IR		1NDND

Notes:

a

See Table E-2 for explanation of fields and answer codes.

b

“0”= No; “1”=Yes.

ATM = automatic term recognition; CP = commercial product; DCL = document classification; DCT = document clustering; DTM = document term matrix; EX = data extraction or synthesis; FI = searching collecting, retrieving literature or data; FR = free; FRT = free trial; IE = screening or eligibility assessment; IEX = information extraction; IR = information retrieval; MULTI = multiple; NA = not applicable; ND = no data; NLP = national language processing; OTH = other; TCA = text categorization; TCL = text cluster; TR = topic refinement; TSM = text summarization; TRV = text retrieval; UC = unclear; VIZ = visualization

Note: Fourteen tools were reviewed but not included in the table of characteristics. The tool name, URL, and reason for exclusion:

AggregatorNot foundCannot locate; possibly forthcoming; not publicly available
Ali Babahttp://alibaba​.informatik.hu-berlin.de/Retired
ClusterMedhttp://compbio​.dfci.harvard​.edu/compbio/tools/clustermedRetired; appears that it is no longer supported or functional
ConceptLinkhttp://project​.cis.drexel​.edu/conceptlinkUnavailable; cannot access URL
KNALIJhttp://knalij​.comUnavailable; cannot access URL
LibreQDANot foundCannot locate
Literature and Genetic Electronic Resource and Cataloguehttp://ligercat​.ubio.org/Unavailable; cannot access URL
MiSearchhttp://misearch​.ncibi.org/Not working; site indicates “down for maintenance”
PubFocushttp://www​.pubfocus.com/Not working; site available but not functional
PubhubNot foundCannot locate
Semantic Features In Texthttp://sent​.dacya.ucm.es./Unavailable; cannot access URL
SpaNot foundCannot locate
SYstematic Review Information Automated CollectionNot foundCannot locate; possibly not publicly available
Weft QDAhttp://www​.pressure.to/qda/Retired; site indicates “(Jun 2014) Since Weft QDA was developed, free (but not open source) versions of some commercial software have emerged (e.g., QDA Miner Lite).”

Table E-2. Evaluation components and choices.

Table E-2

Evaluation components and choices.

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