Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques
Publication Date
April 24, 2017
Authors
Lisa M. Gandy, Jordan Gumm, Benjamin Fertig, Anne Thessen, et al
Volume
12
Issue
4
Pages
e0175860
DOI
https://dx.plos.org/10.1371/journal.pone.0175860
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0175860
Scopus
85017812665
Mendeley
http://www.mendeley.com/research/synthesizer-expediting-synthesis-studies-contextfree-data-information-retrieval-techniques
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Mendeley | Further Information

{"title"=>"Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques", "type"=>"journal", "authors"=>[{"first_name"=>"Lisa M.", "last_name"=>"Gandy", "scopus_author_id"=>"14009977700"}, {"first_name"=>"Jordan", "last_name"=>"Gumm", "scopus_author_id"=>"56720301700"}, {"first_name"=>"Benjamin", "last_name"=>"Fertig", "scopus_author_id"=>"26428144900"}, {"first_name"=>"Anne", "last_name"=>"Thessen", "scopus_author_id"=>"6506774324"}, {"first_name"=>"Michael J.", "last_name"=>"Kennish", "scopus_author_id"=>"7004237920"}, {"first_name"=>"Sameer", "last_name"=>"Chavan", "scopus_author_id"=>"56421613800"}, {"first_name"=>"Luigi", "last_name"=>"Marchionni", "scopus_author_id"=>"57200153628"}, {"first_name"=>"Xiaoxin", "last_name"=>"Xia", "scopus_author_id"=>"56421120300"}, {"first_name"=>"Shambhavi", "last_name"=>"Shankrit", "scopus_author_id"=>"57194070731"}, {"first_name"=>"Elana J.", "last_name"=>"Fertig", "scopus_author_id"=>"15768654400"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-85018585958", "pmid"=>"28437440", "doi"=>"10.1371/journal.pone.0175860", "isbn"=>"1111111111", "pui"=>"615593326", "sgr"=>"85018585958"}, "id"=>"e7ae1bf9-3378-3ef7-8993-c45221b6cfe1", "abstract"=>"Scientists have unprecedented access to a wide variety of high-quality datasets. These datasets, which are often independently curated, commonly use unstructured spreadsheets to store their data. Standardized annotations are essential to perform synthesis studies across investigators, but are often not used in practice. Therefore, accurately combining records in spreadsheets from differing studies requires tedious and error-prone human curation. These efforts result in a significant time and cost barrier to synthesis research. We propose an information retrieval inspired algorithm, Synthesize, that merges unstructured data automatically based on both column labels and values. Application of the Synthesize algorithm to cancer and ecological datasets had high accuracy (on the order of 85-100{%}). We further implement Synthesize in an open source web application, Synthesizer (https://github.com/lisagandy/synthesizer). The software accepts input as spreadsheets in comma separated value (CSV) format, visualizes the merged data, and outputs the results as a new spreadsheet. Synthesizer includes an easy to use graphical user interface, which enables the user to finish combining data and obtain perfect accuracy. Future work will allow detection of units to automatically merge continuous data and application of the algorithm to other data formats, including databases.", "link"=>"http://www.mendeley.com/research/synthesizer-expediting-synthesis-studies-contextfree-data-information-retrieval-techniques", "reader_count"=>14, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>3, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "group_count"=>0}

Scopus | Further Information

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