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 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.

Semantic Publication of Agricultural Scientific Literature Using Property Graphs

“…This annotator uses more than 100 ontologies covering domains like agricultural research, animal science, ecology, nutrition or farming, among others, including ontologies such as Global Agricultural Concept Scheme (gacs) [32], Thesaurus for Animal Physiology and Livestock systems (TriPhase) [33], Environment Ontology (envo) [34], FoodOn [35] or AgroRDF [36]. These ontologies were obtained through the AgroPortal REST API and, when possible, converted to RDF/XML format with the ROBOT tool [37] in order to insert them into the knowledge graph.…”

DBpedia Archivo: A Web-Scale Interface for Ontology Archiving Under Consumer-Oriented Aspects

“…ROBOT [8] deserves a special mention as a highly automatized and configurable evaluator. The idea here is that sub-communities for certain domains (e.g.…”

The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research

“…Once terms were validated during the general online discussion meeting (or internal review), curators added their annotations from the spreadsheet into the WebProtege project (recording in the spreadsheet which terms had been added). Thereafter, ROBOT, an open source tool for automating ontology development workflows and tasks [18], was used to compile the complete ontology release files, which are Web Ontology Language (OWL) and Open Biomedical Ontology (OBO) formats.…”