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Volume 11
Journal of Proteomics & Bioinformatics Open Access
Computational Biology 2018
September 05-06, 2018
September 05-06, 2018 Tokyo, Japan
International Conference on
Computational Biology and Bioinformatics
J Proteomics Bioinform 2018, Volume 11
DOI: 10.4172/0974-276X-C1-113
ETC: A toolkit for converting phenotype descriptions into computable data
Hong Cui
1
, Thomas Rodenhausen
1
, Bertram Ludäscher
2
, James Macklin
3
and Nico Franz
4
1
University of Arizona, USA
2
University of Illinois at Urbana-Champaign, USA
3
Agriculture and Agri-Food, Canada
4
Arizona State University, USA
T
he explorer of taxon concepts project has produced a web application that consists a set of five tools unlocking phenotype
data from text narratives often found as taxonomic descriptions or character descriptions. Aside from the tools described
below, the site supports division of labor by allowing users share their tasks. Text capture tool parses textual taxonomic
descriptions and marks up anatomical entities and characters. The tool is powered by CharaParser and MicroPIE (for microbial
taxonomic descriptions). Ontology building tool enables experts without ontology knowledge to organize a set of phenotypic
terms (e.g. those discovered by using is a part of or synonym relationships. Resulting ontology can be used in the other tools to
improve data quality. Matrix generation tool takes the output and assembles a raw taxon-character matrix for the user to edit
and refine, with or without ontology. Key generation tool employs a novel algorithm that directly takes a taxon-character matrix
with polymorphic characters as input and computes the information entropy scores for each character. The result is a multi-
access key that order the characters based on their discrimination power within the pool of the taxa. Taxonomy comparison
tool supports the task of taxon concept analysis by supporting both expert asserted RCC-5 (congruent, narrower/broader than,
disjoint and overlap) relationships among taxa, as well as providing character data related to the taxa in question to aid expert
decisions. These five tools can be used to construct several pipelines that generate a taxon-by-character matrix, create a multi-
access identification tool or facilitate taxon concept comparisons. A related software application, matrix converter is public
available for users to convert a raw matrix to a scored matrix for phylogenetic analysis.
hongcui@email.arizona.edu