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

Hong Cui, Dongfang Xu, Steven S. Chong, Martin Ramirez, Thomas Rodenhausen, James A. Macklin, Bertram Ludäscher, Robert A. Morris, Eduardo M. Soto, Nicolás Mongiardino Koch

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number471
JournalBMC bioinformatics
Volume17
Issue number1
DOIs
StatePublished - Nov 17 2016

Keywords

  • ETC
  • Evaluation
  • Explorer of Taxon Concepts
  • Information extraction
  • Natural language processing
  • Phenotypic characters
  • Phenotypic traits
  • Spiders
  • Taxonomic morphological descriptions
  • Text mining

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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