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carrineblank / MicrO

A Microbial Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions
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bioinformatics-databases microbiology ontology phenomic prokaryotic-taxonomic-descriptions

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MicrO

An Ontology of Prokaryotic Phenotypic and Metabolic Characters, version 1.5.1b (released Jun 14, 2018) .

Created by Carrine E. Blank, University of Montana, fall 2013 through spring 2016. Co-contributors and advisors: Hong Cui (University of Arizona), Lisa Moore (University of Southern Maine), and Ramona Walls (University of Arizona).

Includes terms and term synonyms extracted from > 3,000 prokaryotic taxonomic descriptions, collected from a large number of taxonomic descriptions from Archaea, Cyanobacteria, Bacteroidetes, Firmicutes, and Mollicutes.

The ontology and the synonym lists were developed to facilitate the automated extraction of phenotypic data and character states from prokaryotic taxonomic descriptions using a natural language processing algorithm (MicroPIE). MicroPIE was developed by Hong Cui, Elvis Hsin-Hui Wu, and Jin Mao (University of Arizona) in collaboration with Carrine E. Blank (University of Montana) and Lisa R. Moore (Macquarie University).

Contains ~ 3,660 terms and term definitions, along with thousands of term synonyms. Constructed in OWL Protégé; following OBO Foundry principles. Imports over 13,600 terms from 20 other external ontologies, including Phenotype Quality (PATO), the Gene Ontology (GO), and Chemical Entities of Biological Interest (ChEBI) using import modules. Contains over 29,600 logical axioms connecting entities and processes across multiple ontologies to facilitate inference of higher-order phenotypic traits.

Please cite: Blank CE, Cui H, Moore LR, Walls RL. 2016. MicrO: An Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions, Journal of Biomedical Semantics 7:18. DOI:10.1186/s13326-016-0060-6. https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0060-6

Thanks to Chris Mungall (LBNL), Elvis Hsin-Hui Wu (University of Arizona), Gail Gasparich (Towson University), and Gordon Burleigh (University of Florida) for comments and/or assistance with ontology construction and compilation of taxonomic descriptions.Many thanks to Oliver He (University of Michigan) for technical assistance with OntoBee and OntoFox, and Gareth Owen (ChEBI project leader, head curator) and other curators at ChEBI for assistance in the incorporation of microbial-specific chemical terms and synonyms into ChEBI.Thanks also to the instructors (Melissa Haendel, Matt Yoder, Jim Baihoff) and students of the 2013 NESCent Ontologies for Evolutionary Biology workshop, and to Karen Cranston (NESCent director) and the support staff at NESCent.

This work was supported by a grant from the National Science Foundation Assembling the Tree of Life Program (DBI-1208534), and by a travel grant to attend the 2013 NESCent Ontologies for Evolutionary Biology workshop.

TO DOWLOAD

  1. Download the MicrO.owl file in the folder "MicrOandImportModules"

  2. Execute MicrO.owl using Protege v. 4.3 or Protege v. 5.0.0 (runs in beta 17).

  3. Once executed you can then run the reasoner.

  4. You must have a live internet connection when you open MicrO.owl in order to properly download and access all the ontology import modules.