Bibliography Tools in the Context of WWW and LATEX
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Wright State University CORE Scholar Browse all Theses and Dissertations Theses and Dissertations 2007 Bibliography Tools in the Context of WWW and LATEX Munushree Thummala Wright State University Follow this and additional works at: https://corescholar.libraries.wright.edu/etd_all Part of the Computer Engineering Commons Repository Citation Thummala, Munushree, "Bibliography Tools in the Context of WWW and LATEX" (2007). Browse all Theses and Dissertations. 222. https://corescholar.libraries.wright.edu/etd_all/222 This Thesis is brought to you for free and open access by the Theses and Dissertations at CORE Scholar. It has been accepted for inclusion in Browse all Theses and Dissertations by an authorized administrator of CORE Scholar. For more information, please contact [email protected]. Bibliography Tools in the Context of WWW and LATEX A thesis submitted in partial ful¯llment of the requirements for the degree of Master of Science in Computer Engineering By MUNUSHREE THUMMALA B.Tech., Sri Venkateswara University, 1999 2007 Wright State University Dayton, Ohio 45435-0001 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES November 13, 2007 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY Munushree Thummala ENTITLED Bibliography Tools in the Context of WWW and LaTeX BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science in Computer Engineering. Prabhaker Mateti, Ph. D. Thesis Director Thomas Sudkamp, Ph. D. Department Chair Committee on Final Examination Prabhaker Mateti, Ph. D. Thomas Hartrum, Ph. D. T. K. Prasad, Ph. D. Joseph F. Thomas, Jr., Ph. D. Dean, School of Graduate Studies ABSTRACT Thummala, Munushree. M.S.C.E Department of Computer Science and Engineering, Wright State University, 2007. Bibliography Tools in the Context of WWW and LATEX Preparation of academic papers involves not only the creative processes but also the more me- chanical tasks such as adjusting the form and style to suit the demands of the publishing journal or conference. Among several packages that help in these rather tedious mechanical tasks, the TEX + LATEX + BibTEX combination is extremely popular. This thesis is about tools that help in the nec- essary task of citing related work accurately. It focuses on three aspects of this larger bibliography frame work: (i) a survey of existing bibliography formats and tools, (ii) a database view of BibTEX ¯les and functionality that ensues, and (iii) processing references given as free style pieces of text. Numerous tools that ease the citation task have been developed in the last ¯ve years. The thesis reviews thoroughly the 65 open source, and freeware tools, and somewhat less thoroughly the 18 commercial tools because of limitations of trial ware. These tools range from small stand-alone utilities of a couple of thousand lines of code to large suites of tools that evolved out of the research work of teams over a few years. Their functionality includes the collection of references and searching the various on-line bibliographies for full details and prepare them for inclusion in the references section typically found at the end of papers. We identify a few voids in functionality, especially dealing with free style references, and contribute new tools. The second focus of the thesis is on the maintenance of bibliographies by individuals. In this context, we contribute several new tools: (i) LoadBibTeX stores bibliographic entries as a MySQL- database of BibTEX ¯elds as tables as opposed to storing them as plain text .bib ¯les. (ii) BibSearch allows authors to search the database of BibTEX entries based on multiple keywords that can be matched in multiple ¯elds and the resulting output may be saved as a standard .bib ¯le. (iii) Normalization is a feature incorporated into the above tools to bring about normalization of equiv- alent BibTEX entries. (iv) Duplicate discovery as a feature of LoadBibTeX detects duplicates in a bibliography database in a reliable way. The third focus of the thesis is on the extraction and conversion of references from free style plain text into bibliographic entries expressed in the formal syntax of BibTEX. Often an author collects references as a ¯le of copied-and-pasted pieces of text. We developed a tool that converts iii such clippings in free style text to bibliographic entries in BibTEX format. Being free style, author names, titles of papers, names of journals and conferences, page numbers, etc. may not appear in a guaranteed order. Recognition of these ¯elds is driven by heuristics. Our tool provides feedback to the authors with (i) a con¯dence number indicating the correctness of the recognition of a ¯eld, and (ii) a colorized HTML version of the input free style text indicating the results of the translation. An extension of this tool extracts the references section of papers published as PDF and translates them into BibTEX entries. We developed an API as a Java package to allow other developers to incorporate the free style to BibTEX conversion functionality into their applications. As an example, we integrate into Aigaion, a highly e®ective web-based bibliographic tool, both translating free style references, and extracting references from PDF ¯les. iv Contents 1 Introduction 1 1.1 Citations, References, and Bibliographies . 1 1.2 Searching the Web for Bibliographic Entries . 2 1.3 BibTEX ........................................... 2 1.3.1 Contents of a BibTEX File . 3 1.3.2 Running BibTEX.................................. 4 1.3.3 Citation Styles of BibTEX............................. 4 1.4 Contributions of the Thesis . 5 1.4.1 Survey of Bibliographic Tools . 5 1.4.2 Bibliographic Databases . 5 1.4.3 Free Style Text to BibTEX Translation . 6 1.5 BibTEX Usage in This Thesis . 7 1.6 Organization of the Thesis . 7 2 Evaluation of Bibliography Tools 8 2.1 Functionality of Bibliographic Tools . 8 2.1.1 Create and Maintain Bibliographic Entries . 9 2.1.2 Search On-Line Resources . 9 2.1.3 Preparing Citations and References . 9 2.1.4 Organizing Ideas and References . 9 2.1.5 Conversion Between Various Formats . 10 2.2 Evaluation Method . 10 2.3 Summary Table of Tool Evaluations . 10 2.4 Aigaion . 13 2.5 BibSonomy . 19 2.6 Zotero . 23 v 2.7 JabRef . 26 2.8 Web Browser Based Tools . 29 2.8.1 Basilic . 29 2.8.2 BibAdmin . 30 2.8.3 BibORB . 30 2.8.4 Bibnet . 31 2.8.5 CiteULike . 31 2.8.6 Document Archive . 33 2.8.7 Document Database . 34 2.8.8 Google Scholar . 35 2.8.9 PubsOnline . 36 2.8.10 smArticle . 36 2.8.11 WIKINDX . 37 2.9 Desktop/Small Scale Tools . 38 2.9.1 B3 . 39 2.9.2 BibCursed . 40 2.9.3 BibDB . 42 2.9.4 BibDesk . 44 2.9.5 BibEdit . 45 2.9.6 Bibi . 46 2.9.7 Bib-it . 46 2.9.8 Biblioexpress . 47 2.9.9 Bibster . 49 2.9.10 BibtexDbMgr . 50 2.9.11 BibTool . 50 2.9.12 BibTexMng . 52 2.9.13 Citavi/LiteRat . 52 2.9.14 Da®odil . 53 2.9.15 Easybib . 55 2.9.16 Ebib . 56 2.9.17 BibTEX mode for Emacs . 57 2.9.18 gBib . 58 2.9.19 KBibTeX . 58 2.9.20 Patmus . 59 vi 2.9.21 Open O±ce Bibliography Database . 59 2.9.22 Papyrus . 60 2.9.23 Pybliographic . 62 2.9.24 RefTEX ....................................... 63 2.9.25 Synapsen . 63 2.9.26 Tellico . 64 2.9.27 Tkbibtex . 65 2.10 Commercial Tools . 65 2.10.1 askSam . 66 2.10.2 Bibliographix . 66 2.10.3 Bookends, Reference Miner . 67 2.10.4 Citation . 68 2.10.5 CiteIt . 69 2.10.6 EndNote . 70 2.10.7 Refbase . 71 2.10.8 Reference Manager . 72 2.10.9 Referencer . 73 2.10.10 RefViz . ..