Ontology of Prokaryotic Phenotypic and Metabolic Characters

An ontology of prokaryotic phenotypic and metabolic characters

Ontology information

Ontology ID: micro
Version: MicrO (An Ontology of Prokaryotic Phenotypic and Metabolic Characters). Version 1.5.1 released 6/14/2018. Includes terms and term synonyms extracted from > 3000 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 (University of Southern Maine). Descriptions and links to MicroPIE can be found at http://avatol.org/ngp/nlp/overview-2/. https://github.com/biosemantics/micropie2 The most current version of MicrO can be downloaded from https://github.com/carrineblank/MicrO.
Number of terms: 17286
Last loaded: Wed Aug 25 20:06:40 BST 2021


Lead Creator: 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).


Many 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 and term definitions. 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.