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. 2011 Apr 15;2011:bar013.
doi: 10.1093/database/bar013. Print 2011.

Allie: A Database and a Search Service of Abbreviations and Long Forms

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Allie: A Database and a Search Service of Abbreviations and Long Forms

Yasunori Yamamoto et al. Database (Oxford). .
Free PMC article

Abstract

Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader's expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly. Database URL: The Allie service is available at http://allie.dbcls.jp/.

Figures

Figure 1.
Figure 1.
A part of a bipartite graph used in Allie. GENA gives the concept ID ‘C0812425-T034’ to ‘S-phase fractions’, ‘S-phase fraction’, ‘mitotic index’ and ‘mitotic indices’. Allie changes the ID to one that corresponds to each cluster using connected components of the graph.
Figure 2.
Figure 2.
Images of Allie’s outputs. (A) Hit cluster-list page for the abbreviation ‘SPF’. By clicking links in the ‘Co-occurring Abbreviation’ or the ‘PubMed/MEDLINE Info.’ cells, the user can access these corresponding pages (A to B or A to C, respectively). (B) Co-occurring abbreviation page. Here, the user is provided with all the co-occurring abbreviations, and by clicking one of the listed abbreviations, one can access the hit cluster-list page. (C) PubMed/MEDLINE Information page. Here, the user is provided with all publication years, titles, and co-occurring abbreviations that appear in the titles or abstracts with the pair. Each title is anchor text that links to the corresponding PubMed page. By clicking one of the co-occurring abbreviations, the user can access the hit cluster-list page (C to D). (D) Hit cluster-list page for the abbreviation ‘BVD’.
Figure 2.
Figure 2.
Images of Allie’s outputs. (A) Hit cluster-list page for the abbreviation ‘SPF’. By clicking links in the ‘Co-occurring Abbreviation’ or the ‘PubMed/MEDLINE Info.’ cells, the user can access these corresponding pages (A to B or A to C, respectively). (B) Co-occurring abbreviation page. Here, the user is provided with all the co-occurring abbreviations, and by clicking one of the listed abbreviations, one can access the hit cluster-list page. (C) PubMed/MEDLINE Information page. Here, the user is provided with all publication years, titles, and co-occurring abbreviations that appear in the titles or abstracts with the pair. Each title is anchor text that links to the corresponding PubMed page. By clicking one of the co-occurring abbreviations, the user can access the hit cluster-list page (C to D). (D) Hit cluster-list page for the abbreviation ‘BVD’.

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