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dc.contributor.author
Cui, Hong
dc.contributor.author
Xu, Dongfang
dc.contributor.author
Chong, Steven S.
dc.contributor.author
Ramirez, Martin Javier
dc.contributor.author
Rodenhausen, Thomas
dc.contributor.author
Macklin, James A.
dc.contributor.author
Ludäscher, Bertram
dc.contributor.author
Morris, Robert A.
dc.contributor.author
Soto, Eduardo Maria
dc.contributor.author
Mongiardino Koch, Nicolás
dc.date.available
2018-06-21T18:59:35Z
dc.date.issued
2016-11
dc.identifier.citation
Cui, Hong; Xu, Dongfang; Chong, Steven S.; Ramirez, Martin Javier; Rodenhausen, Thomas; et al.; Introducing explorer of taxon concepts with a case study on spider measurement matrix building; BioMed Central; Bmc Bioinformatics; 17; 1; 11-2016; 2-22
dc.identifier.issn
1471-2105
dc.identifier.uri
http://hdl.handle.net/11336/49580
dc.description.abstract
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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
BioMed Central
dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
Etc
dc.subject
Evaluation
dc.subject
Explorer of Taxon Concepts
dc.subject
Information Extraction
dc.subject
Natural Language Processing
dc.subject
Phenotypic Characters
dc.subject
Phenotypic Traits
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Spiders
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Taxonomic Morphological Descriptions
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Text Mining
dc.subject.classification
Ciencias de la Computación
dc.subject.classification
Ciencias de la Computación e Información
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
dc.title
Introducing explorer of taxon concepts with a case study on spider measurement matrix building
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2018-05-30T15:13:29Z
dc.journal.volume
17
dc.journal.number
1
dc.journal.pagination
2-22
dc.journal.pais
Reino Unido
dc.journal.ciudad
Londres
dc.description.fil
Fil: Cui, Hong. University of Arizona; Estados Unidos
dc.description.fil
Fil: Xu, Dongfang. University of Arizona; Estados Unidos
dc.description.fil
Fil: Chong, Steven S.. University of Arizona; Estados Unidos
dc.description.fil
Fil: Ramirez, Martin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Argentina
dc.description.fil
Fil: Rodenhausen, Thomas. University of Arizona; Estados Unidos
dc.description.fil
Fil: Macklin, James A.. Agriculture and Agri-Food Canada; Canadá
dc.description.fil
Fil: Ludäscher, Bertram. University of Illinois. Urbana - Champaign; Estados Unidos
dc.description.fil
Fil: Morris, Robert A.. University of Massachussets; Estados Unidos. Harvard University; Estados Unidos
dc.description.fil
Fil: Soto, Eduardo Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina. University of Yale; Estados Unidos
dc.description.fil
Fil: Mongiardino Koch, Nicolás. University of Yale; Estados Unidos
dc.journal.title
Bmc Bioinformatics
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1352-7
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1186/s12859-016-1352-7
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