Journal:ROBOT: A Tool for Automating Ontology Workflows
| Full article title | ROBOT: A Tool for Automating Ontology Workflows |
|---|---|
| Journal | BMC Bioinformatics |
| Author(s) | Jackson, Rebecca C.; Balhoff, James, P.; Douglass, Eric; Harris, Nomi L.; Mungall, Christopher J.; Overton, James A. |
| Author affiliation(s) | Knocean, Inc.; University of North Carolina; Lawrence Berkeley National Laboratory |
| Primary contact | Email: via SpringerLink |
| Year published | 2019 |
| Volume and issue | 20 |
| Page(s) | 407 |
| DOI | 10.1186/s12859-019-3002-3 |
| ISSN | 1471-2105 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://link.springer.com/article/10.1186/s12859-019-3002-3 |
| Download | https://link.springer.com/content/pdf/10.1186/s12859-019-3002-3.pdf (PDF) |
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This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed. |
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 (application programming interface) 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 they can spend more time focusing on development tasks. It also helps guarantee 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.
Keywords: ontology development, automation, ontology release, reasoning, workflows, quality control, import management
Background
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This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. We also added PMCID and DOI when they were missing from the original reference.
