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Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building

التفاصيل البيبلوغرافية
العنوان: Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building
المؤلفون: Cui, Hong, Xu, Dongfang, Chong, Steven S., Ramirez, Martin, Rodenhausen, Thomas, Macklin, James A., Ludäscher, Bertram, Morris, Robert A., Soto, Eduardo M., Koch, Nicolás Mongiardino
المصدر: Cui, Hong, Dongfang Xu, Steven S. Chong, Martin Ramirez, Thomas Rodenhausen, James A. Macklin, Bertram Ludäscher, Robert A. Morris, Eduardo M. Soto, and Nicolás Mongiardino Koch. 2016. “Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.” BMC Bioinformatics 17 (1): 471. doi:10.1186/s12859-016-1352-7. http://dx.doi.org/10.1186/s12859-016-1352-7Test.
بيانات النشر: BioMed Central, 2016.
سنة النشر: 2016
المجموعة: FAS Scholarly Articles
مصطلحات موضوعية: Information extraction, Text mining, Natural language processing, Taxonomic morphological descriptions, Phenotypic characters, Phenotypic traits, Evaluation, Spiders, ETC, Explorer of Taxon Concepts
الوصف: Background: Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. Results: From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. Conclusions: ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1352-7) contains supplementary material, which is available to authorized users.
نوع الوثيقة: Journal Article
اللغة: English
تدمد: 1471-2105
العلاقة: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114841/pdfTest/; BMC Bioinformatics
DOI: 10.1186/s12859-016-1352-7
الوصول الحر: http://nrs.harvard.edu/urn-3:HUL.InstRepos:29626194Test
حقوق: open
URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAATest
رقم الانضمام: edshld.1.29626194
قاعدة البيانات: Digital Access to Scholarship at Harvard (DASH)
الوصف
تدمد:14712105
DOI:10.1186/s12859-016-1352-7