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Title: ROBOT: A Tool for Automating Ontology Workflows

Journal Article · · BMC Bioinformatics
ORCiD logo [1];  [2];  [3];  [3];  [3];  [1]
  1. Knocean Inc., Toronto, ON (Canada)
  2. Univ. of North Carolina, Chapel Hill, NC (United States). Renaissance Computing Inst.
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1560605
Journal Information:
BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 20; ISSN 1471-2105
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (23)

Taking shortcuts with OWL using safe macros journal November 2010
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment journal March 2015
OntoFox: web-based support for ontology reuse journal June 2010
Taking shortcuts with OWL using safe macros journal December 2011
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology journal January 2013
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns journal January 2015
MIREOT: the Minimum Information to Reference an External Ontology Term journal August 2009
OntoPilot: New Software to Simplify and Accelerate Ontology Development and Deployment journal August 2017
Modular Reuse of Ontologies: Theory and Practice journal January 2008
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 journal November 2012
Machine Understandable Policies and GDPR Compliance Checking journal July 2020
MIREOT: The minimum information to reference an external ontology term journal January 2011
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration journal November 2007
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability journal January 2018
MIREOT: the Minimum Information to Reference an External Ontology Term journal August 2009
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. journalarticle January 2013
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 journal November 2012
The Incredible ELK: From Polynomial Procedures to Efficient Reasoning with ℰ ℒ $\mathcal {E} \mathcal {L}$ Ontologies journal November 2013
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration journal November 2007
Dead simple OWL design patterns journal June 2017
Disease Ontology: improving and unifying disease annotations across species journal February 2018
The Ontology Lookup Service: bigger and better journal May 2010
The Ontology Lookup Service: bigger and better journal May 2010

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