ROBOT: A Tool for Automating Ontology Workflows
Abstract
BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety ofmore »
- Authors:
-
[1];
- Knocean Inc., Toronto, ON (Canada)
- Univ. of North Carolina, Chapel Hill, NC (United States). Renaissance Computing Inst.
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1560605
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Bioinformatics
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2105
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; Ontology development; Automation; Ontology release; Reasoning; Workflows; Quality control; Import management
Citation Formats
Jackson, Rebecca C., Balhoff, James P., Douglass, Eric, Harris, Nomi L., Mungall, Christopher J., and Overton, James A. ROBOT: A Tool for Automating Ontology Workflows. United States: N. p., 2019.
Web. doi:10.1186/s12859-019-3002-3.
Jackson, Rebecca C., Balhoff, James P., Douglass, Eric, Harris, Nomi L., Mungall, Christopher J., & Overton, James A. ROBOT: A Tool for Automating Ontology Workflows. United States. doi:10.1186/s12859-019-3002-3.
Jackson, Rebecca C., Balhoff, James P., Douglass, Eric, Harris, Nomi L., Mungall, Christopher J., and Overton, James A. Mon .
"ROBOT: A Tool for Automating Ontology Workflows". United States. doi:10.1186/s12859-019-3002-3. https://www.osti.gov/servlets/purl/1560605.
@article{osti_1560605,
title = {ROBOT: A Tool for Automating Ontology Workflows},
author = {Jackson, Rebecca C. and Balhoff, James P. and Douglass, Eric and Harris, Nomi L. and Mungall, Christopher J. and Overton, James A.},
abstractNote = {BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. CONCLUSIONS:ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.},
doi = {10.1186/s12859-019-3002-3},
journal = {BMC Bioinformatics},
number = 1,
volume = 20,
place = {United States},
year = {2019},
month = {7}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Taking shortcuts with OWL using safe macros
journal, November 2010
- Mungall, Christopher; Ruttenberg, Alan; Osumi-Sutherland, David
- Nature Precedings
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
journal, January 2018
- He, Yongqun; Xiang, Zuoshuang; Zheng, Jie
- Journal of Biomedical Semantics, Vol. 9, Issue 1
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns
journal, January 2015
- Xiang, Zuoshuang; Zheng, Jie; Lin, Yu
- Journal of Biomedical Semantics, Vol. 6, Issue 1
Dead simple OWL design patterns
journal, June 2017
- Osumi-Sutherland, David; Courtot, Melanie; Balhoff, James P.
- Journal of Biomedical Semantics, Vol. 8, Issue 1
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
journal, November 2007
- Smith, Barry; Ashburner, Michael; Rosse, Cornelius
- Nature Biotechnology, Vol. 25, Issue 11
OntoPilot: New Software to Simplify and Accelerate Ontology Development and Deployment
journal, August 2017
- Stucky, Brian; Luc, Annie
- Proceedings of TDWG, Vol. 1
The Incredible ELK: From Polynomial Procedures to Efficient Reasoning with ℰ ℒ $\mathcal {E} \mathcal {L}$ Ontologies
journal, November 2013
- Kazakov, Yevgeny; Krötzsch, Markus; Simančík, František
- Journal of Automated Reasoning, Vol. 53, Issue 1
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment
journal, March 2015
- Hastings, Janna; Jeliazkova, Nina; Owen, Gareth
- Journal of Biomedical Semantics, Vol. 6, Issue 1
Modular Reuse of Ontologies: Theory and Practice
journal, January 2008
- Cuenca Grau, B.; Horrocks, I.; Kazakov, Y.
- Journal of Artificial Intelligence Research, Vol. 31
The Ontology Lookup Service: bigger and better
journal, May 2010
- Cote, R.; Reisinger, F.; Martens, L.
- Nucleic Acids Research, Vol. 38, Issue Web Server
Disease Ontology: improving and unifying disease annotations across species
journal, February 2018
- Bello, Susan M.; Shimoyama, Mary; Mitraka, Elvira
- Disease Models & Mechanisms, Vol. 11, Issue 3
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
journal, January 2013
- Hill, David P.; Adams, Nico; Bada, Mike
- BMC Genomics, Vol. 14, Issue 1
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
journal, November 2012
- Hastings, Janna; de Matos, Paula; Dekker, Adriano
- Nucleic Acids Research, Vol. 41, Issue D1
OntoFox: web-based support for ontology reuse
journal, June 2010
- Xiang, Zuoshuang; Courtot, Mélanie; Brinkman, Ryan R.
- BMC Research Notes, Vol. 3, Issue 1