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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 impressions. The upper left panel shows results of a full-text query for 'HCT116'. A corresponding repository record is depicted on the right, where a domain expert captured relevant information in free-form annotation. Note that the short URLs can easily be sent to collaborating researchers. The lower-left panel demonstrates a structured query, searching only the bibliographic records for 'Brown', which avoids picking up this frequent term in the full-text, e.g., from the citations section.
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Figure 2: BibGlimpse impressions. The upper left panel shows results of a full-text query for 'HCT116'. A corresponding repository record is depicted on the right, where a domain expert captured relevant information in free-form annotation. Note that the short URLs can easily be sent to collaborating researchers. The lower-left panel demonstrates a structured query, searching only the bibliographic records for 'Brown', which avoids picking up this frequent term in the full-text, e.g., from the citations section.

Mentions: Freeing researchers from a need to look up or enter bibliographical records and giving them an opportunity of annotating their reprints together with full-text query capabilities not only raises acceptance of the system in day-to-day usage but has profound practical implications for knowledge discovery, sharing, and retrieval. We illustrate this with a few examples (Figure 2). Important information, such as the cell line types employed, is often not contained in the abstract but can be queried by full-text search (e.g., a query for cell line HCT116, Figure 2). Other information may even only be implicit in the full manuscript text but can be captured explicitly by user annotation (e.g., user annotation as 'p53 wildtype').


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 impressions. The upper left panel shows results of a full-text query for 'HCT116'. A corresponding repository record is depicted on the right, where a domain expert captured relevant information in free-form annotation. Note that the short URLs can easily be sent to collaborating researchers. The lower-left panel demonstrates a structured query, searching only the bibliographic records for 'Brown', which avoids picking up this frequent term in the full-text, e.g., from the citations section.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: BibGlimpse impressions. The upper left panel shows results of a full-text query for 'HCT116'. A corresponding repository record is depicted on the right, where a domain expert captured relevant information in free-form annotation. Note that the short URLs can easily be sent to collaborating researchers. The lower-left panel demonstrates a structured query, searching only the bibliographic records for 'Brown', which avoids picking up this frequent term in the full-text, e.g., from the citations section.
Mentions: Freeing researchers from a need to look up or enter bibliographical records and giving them an opportunity of annotating their reprints together with full-text query capabilities not only raises acceptance of the system in day-to-day usage but has profound practical implications for knowledge discovery, sharing, and retrieval. We illustrate this with a few examples (Figure 2). Important information, such as the cell line types employed, is often not contained in the abstract but can be queried by full-text search (e.g., a query for cell line HCT116, Figure 2). Other information may even only be implicit in the full manuscript text but can be captured explicitly by user annotation (e.g., user annotation as 'p53 wildtype').

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