integration of citation tools in the virtual research environment (vre)

7/29/2019 Integration of Citation Tools in the Virtual Research Environment (VRE)

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Integration of Citation Tools

in the Virtual Research

Environment (VRE)COMPILED BY

Keegan Fisher & Frans Labuschagne

13 July 2011


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FINAL REPORT - 13 July 2011

PROJECT TITLE

Enhancing the existing virtual research environment (VRE) by evaluating open source citation tools

and identifying a suitable application to be integrated with the VRE.

COMPILED BY

Keegan Fisher & Frans Labuschagne

July 2011

A) PROBLEM STATMENT

This project was devised to give the information science students insight into the use of

collaboration tools within a virtual research environment (VRE). Students will be required to

investigate the usability of a citation tool to be selected for the VRE. Students will then be

required to gain hands-on experience in the VRE. Once they have a good understanding of

the possibilities they will be required to investigate the integration between the selected

citation tool and Alfresco the document management system.(Rakobela 2011)

B) INTRODUCTION

The VRE that is currently being developed by the CSIRIS has a core focus on offering a

digital workspace to various researchers involved in food security, human and animal health

around Southern Africa, including Malawi, Mozambique, South Africa, Tanzania and

Namibia.(Virtual Research Environment 2011)

This report will discuss the feasibility of possible integration of a citation tool to be used

within this digital workspace. In order to reach our conclusion we have looked at three

separate citation tools, the discovery and overall structure of VRE with Alfresco as an

integrated document management system and finally propose a solution.

C) DISCOVERY OF CITATION TOOLS

In order for us to conduct our analysis and discovery of the suggested citation tools, such as

RefWorks, Zotero and Mendeley, we were provided with a template containing a list of

various aspects and features to help conduct our analysis.

RefWorks-A proprietary, web based citation tool used by researchers to build a database of

references for creating a bibliographic list and in-text citation in a user friendly and speedy

way. RefWorks requires a plug-in known as Write-N-Cite for use with Microsoft

Word.(RefWorks 2011)

Zotero A browser plug-in built for use with Mozilla Firefox which is a free-ware citation tool

used by researches to build a database of references for creating a bibliographic list and in-

text citations.(Zotero 2011)

Mendeley A free, open source web based and stand alone citation tool for use by

researchers and academics that can help them organize their research and collaborate with

others online.(Mendeley 2011)

We have summarised our analysis of the three abovementioned citation tools in a

comparison table bellow highlighting their various differences and similarities adapted from

Mendeley.com 2011.


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Compare Products

Basic software package (includes all featur

Free web storage space (online backup of

Offline Storage

Premium software package (additional sto

Availability of product support

Availability of training

Software UpdatesReference/Document Management

Built in quality control measures, e.g. auth

Linking to full text items (e.g. URL)

Organization of PDFs and other document

Citation Plug-ins for Word

Citation Plug-ins for Open Office

Annotations/Highlighting in PDFs in the Ci

Cross-platform synching across desktop, w

Ability to create customised citation or ou

Number citation styles available

Duplicate elimination

Knowledge Discovery

Free and open database approaching 100

Personalized paper recommendations

Readership statistics & community tags

Open API/Third party apps

Full text search across all your papers

Search across external databases

CollaborationAbility to export citations to other formats

Ability to import citations from other form

Private groups

Public groups

Social network

Collaboration newsfeed

General Technology

Web application

Stand Alone Desktop application

Compatibility with all modern web browse

Compatibility with Mac/Win/Linux

Mobile & iPad

Product feedback forum

Library systems integration/EZProxy Supp

Metadata Extraction Technology

Extraction of DOIs (Digital Object Identifie

Extraction of PubmedIDs and ArxivIDs fro

Extraction of embedded metadata from P

Extraction of citation details from PDFs wi

Extraction of metadata from webpages

Extracting metadata from subscription dat

Mendeley

es listed below) Free

our papers) 1GB

rage space & features) $4.99-9.99/mo

or format

tation Tool

eb and mobile devices

put style

1180

illion documents

ats

rs

rt

s) from PDFs

PDFs

Fs

hout embedded metadata

abases (e.g. Science Direct)

3

Zotero RefWorks

Free $100

100MB NA

$1.67-20.00/mo NA

1581 3011


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D) DISCOVERY OF VRE & ALFRESCO

This specific VRE of the CSIRIS is being developed on a platform known as Chisimba; a

freeware development platform designed by the University of the Western Cape and is under

development by 16 higher education institutions around Africa. (Virtual Research

Environment 2011)

During the process of discovering the VRE platform, we looked at various factors such as

the overall user experience, program functionality and features as well as potential issuessurrounding the VRE platform.

Below is a visual representation of the current VRE system and the proposed integration of a

citation tool into the VRE.

Figure 1: Current method and integration of citation tool

Currently, components such as news, calendar, and announcement features which normally forms

part of a Content Management System (CMS), functions as individual components within the VRE

and are not interconnected. The same can be said for the collaboration tools, such as Wikis, Blogs

and Forums.


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The current Document Management System (DMS) in use by the VRE is known as Alfresco. This is a

standalone server based application embedded into the VRE web page, allowing for the effective

management of group projects and its documents. Alfresco is a very advanced DMS which offers

limitless functionality and features.

The purpose of this project was to investigate and select a citation tool for integration (Red bordered

box in Figure 1) into the VRE which will be discussed in the next section.

E) INTEGRATION OF CITATION TOOL INTO THE VRE

With the discovery and analysis of the various citation tools, keeping the current operation of the

VRE and Alfresco DMS in mind, we have established that instead of incorporating an independent

citation tool into the VRE, forcing the user to use the selected tool, rather allow the user to make his

own individual decision on which citation tool he would like to use. It is suggested that the three

citation tools that we have analysed be made available on the VRE for the user.

Taking into consideration that the citation tools are used outside of the VRE environment, due to the

fact that documents are typically typed in either MS Word or Open Office and references are

collected independently, the citation tools also require plug-ins to operate in the respective text

editing programs. It is suggested that when a document is created using a citation tool and uploaded

into the DMS by peers, the reference library that the creator used is also uploaded into the DMS

should the group functionality of the selected citation tool not be in use or when the group

members use their own individually selected citation tool. This should be established on creation of

a group within the VRE.

If a document was created with a different citation tool than what the potential reviewer is using,

and should the reviewer find it necessary to edit citations, they are then able to download the

citation tool and library used to create this document, for editing. This is therefore solved by the fact

that users can import and export their reference libraries to and from the DMS.

We found that with the resources available to the CSIRIS it will be a difficult task to fully integrate a

citation tool into the VRE, which also lead us to a proposed future options.

F) PROPOSED FUTURE OPTIONS

After taking into consideration on how VRE functions, we discovered that Alfresco Share offers all

the functionality required by the VRE in one package, in a more effective and user friendly way,

which will make the operating of a VRE platform more useful and easy to maintain.

This will allow for various tools such as news, announcements, calendar and other tools to be

interlinked and interoperable, whereas the current operation of the existing VRE does not allow for

this.

Below is a diagram of our proposed solution depicting a restructured version the VRE system,

depending on funds and resources available. It should be kept in mind that the future functionality

of such a system is ever changing in todays technological environment and by using Alfresco Share it

will make it possible to positively adapt to these future changes.


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Figure 2: Proposed future method of integration of Alfresco Share, VRE and citation tools

From Figure 2 it can be deduced that the VRE platform should only be used as a user interface, with

Alfresco Share feeding the CMS information to the VRE interface on an interactive basis. This means

that the database of information is kept on Alfresco Share rather than on the VRE platform.

Alfresco Share not only provides a CMS but also Collaboration Tools as well as a DMS, which are all


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interoperable, therefore combining all the needs and functionalities of the current VRE in a more

streamlined way.

The VRE interface should also offer access to tools that are not available on Alfresco Share such as

ChemDoodle and JChem, etc. .

Another proposed solution, which can be introduced, is that an online text editing software be

developed and incorporated into the VRE. This would have to be developed from scratch, and only

then can a custom citation tool also be developed and incorporated into this newly created onlinetext editor. This is due to the fact that the individual citation tools which we have discussed above

do not have plug-ins developed for custom online text editors; this would have to be developed as

well, and can become an extremely costly development. At the moment this option is not advisable

due to internet stability, available ICT infrastructure, various platforms, and funds required to

develop such an integrated system.

G) CONCLUSION

In conclusion, taking into consideration the limited budget presented for the development of the

VRE platform. The incorporation of Alfresco Share for the redesign and re-structuring of the VRE

would most likely be the best method to follow in order to ensure the proper functioning and use of

such a system in the future. The effective design of a VRE platform will also contribute and

encourage potential researchers, students and mentors to make use of such a system which should

be addressed in a separate case study.

H) BIBLIOGRAPHY

MENDELEY, 2011-last update, Mendeley Citation Tool. Available: http://www.mendeley.com/

[07/15, 2011].

RAKOBELA, B., 2011. Enhancing the exisiting Virtual Research Environment (VRE) by evaluating opensource citation tools and identifying a suitable application to integrate with the VRE. Project

Guidelines edn. CSIR: .

REFWORKS, 2011-last update, RefWorks Citation Tool. Available: http://www.refworks.com [07/15,

2011].

VIRTUAL RESEARCH ENVIRONMENT, 2011-last update, VRE - Virtual Research Environment.

Available: http://chisimba.bi.up.ac.za/vre/ [07/15, 2011].

ZOTERO, 2011-last update, Zotero Citation Tool. Available: http://www.zotero.org/ [07/15, 2011].

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