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BibGlimpse: the case for a light-weight reprint manager in distributed literature research.

Tüchler T, Velez G, Graf A, Kreil DP - BMC Bioinformatics (2008)

Bottom Line: Features like drop-to-file, SVM based automated retrieval of PubMed bibliography for PDF reprints, and annotation support make BibGlimpse an efficient, light-weight reprint manager that facilitates distributed literature research for work groups.BibGlimpse offers scientists a tool that enhances their own literature management.Moreover, it may be used to create content enriched, annotated text corpora for research in text-mining.

View Article: PubMed Central - HTML - PubMed

Affiliation: Chair of Bioinformatics, Boku University, Vienna, Austria. thomas.tuechler@boku.ac.at

ABSTRACT

Background: While text-mining and distributed annotation systems both aim at capturing knowledge and presenting it in a standardized form, there have been few attempts to investigate potential synergies between these two fields. For instance, distributed annotation would be very well suited for providing topic focussed, expert knowledge enriched text corpora. A key limitation for this approach is the availability of literature annotation systems that can be routinely used by groups of collaborating researchers on a day to day basis, not distracting from the main focus of their work.

Results: For this purpose, we have designed BibGlimpse. Features like drop-to-file, SVM based automated retrieval of PubMed bibliography for PDF reprints, and annotation support make BibGlimpse an efficient, light-weight reprint manager that facilitates distributed literature research for work groups. Building on an established open search engine, full-text search and structured queries are supported, while at the same time making shared collections of annotated reprints accessible to literature classification and text-mining tools.

Conclusion: BibGlimpse offers scientists a tool that enhances their own literature management. Moreover, it may be used to create content enriched, annotated text corpora for research in text-mining.

Show MeSH
BibGlimpse scheme. The figure schematically illustrates how BibGlimpse incorporates automated Medline retrieval into the Webglimpse search environment. Saved PDFs are automatically matched with a Medline record and indexed. For integration with external tools, all data are directly available in flatfile format.
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Figure 1: BibGlimpse scheme. The figure schematically illustrates how BibGlimpse incorporates automated Medline retrieval into the Webglimpse search environment. Saved PDFs are automatically matched with a Medline record and indexed. For integration with external tools, all data are directly available in flatfile format.

Mentions: A defining design requirement for BibGlimpse was that users can file a new PDF reprint by simply saving or copying it to disk, or by uploading it online without being prompted to fill in any forms. The lightweight filesystem-based approach also means that users can easily import an entire collection of reprints using just a single command or 'drag and drop' operation for copying the directories of their PDF files. Users can of course also manually edit or add bibliographic records, personal annotation, and supplement files. Medline, BibTeX, and RIS formats are supported. When a Medline or RIS format record is available but not a BibTeX record, the system automatically creates one. Extending standard Webglimpse functionality (cf. Figure 1), the index is updated in the background to cover the bibliographic record, any user annotation, and the extracted full-text of an article.


BibGlimpse: the case for a light-weight reprint manager in distributed literature research.

Tüchler T, Velez G, Graf A, Kreil DP - BMC Bioinformatics (2008)

BibGlimpse scheme. The figure schematically illustrates how BibGlimpse incorporates automated Medline retrieval into the Webglimpse search environment. Saved PDFs are automatically matched with a Medline record and indexed. For integration with external tools, all data are directly available in flatfile format.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2571996&req=5

Figure 1: BibGlimpse scheme. The figure schematically illustrates how BibGlimpse incorporates automated Medline retrieval into the Webglimpse search environment. Saved PDFs are automatically matched with a Medline record and indexed. For integration with external tools, all data are directly available in flatfile format.
Mentions: A defining design requirement for BibGlimpse was that users can file a new PDF reprint by simply saving or copying it to disk, or by uploading it online without being prompted to fill in any forms. The lightweight filesystem-based approach also means that users can easily import an entire collection of reprints using just a single command or 'drag and drop' operation for copying the directories of their PDF files. Users can of course also manually edit or add bibliographic records, personal annotation, and supplement files. Medline, BibTeX, and RIS formats are supported. When a Medline or RIS format record is available but not a BibTeX record, the system automatically creates one. Extending standard Webglimpse functionality (cf. Figure 1), the index is updated in the background to cover the bibliographic record, any user annotation, and the extracted full-text of an article.

Bottom Line: Features like drop-to-file, SVM based automated retrieval of PubMed bibliography for PDF reprints, and annotation support make BibGlimpse an efficient, light-weight reprint manager that facilitates distributed literature research for work groups.BibGlimpse offers scientists a tool that enhances their own literature management.Moreover, it may be used to create content enriched, annotated text corpora for research in text-mining.

View Article: PubMed Central - HTML - PubMed

Affiliation: Chair of Bioinformatics, Boku University, Vienna, Austria. thomas.tuechler@boku.ac.at

ABSTRACT

Background: While text-mining and distributed annotation systems both aim at capturing knowledge and presenting it in a standardized form, there have been few attempts to investigate potential synergies between these two fields. For instance, distributed annotation would be very well suited for providing topic focussed, expert knowledge enriched text corpora. A key limitation for this approach is the availability of literature annotation systems that can be routinely used by groups of collaborating researchers on a day to day basis, not distracting from the main focus of their work.

Results: For this purpose, we have designed BibGlimpse. Features like drop-to-file, SVM based automated retrieval of PubMed bibliography for PDF reprints, and annotation support make BibGlimpse an efficient, light-weight reprint manager that facilitates distributed literature research for work groups. Building on an established open search engine, full-text search and structured queries are supported, while at the same time making shared collections of annotated reprints accessible to literature classification and text-mining tools.

Conclusion: BibGlimpse offers scientists a tool that enhances their own literature management. Moreover, it may be used to create content enriched, annotated text corpora for research in text-mining.

Show MeSH