OntoDev Suite
open source, modular libraries and tools
for ontology developmentand scientific data integration
ROBOT
Automate Ontologies
The flagship of the OntoDev Suite is ROBOT, a library and command-line tool for automating a wide range of common ontology development and application tasks, such as importing, converting, extracting, merging, reasoning, querying, template-based term building, quality control, and release processes.
ROBOTDROID
Accessible Automation
ROBOT and the other OntoDev tools are often used together with a workflow execution tool such as GNU Make, and a version control system such as a GitHub repository. DROID makes these powerful tools approachable to a wider audience by both hosting the tools and providing a simple web interface with a curated set of functionality, customized for each project.
DROIDTables
FAIR and Square
Most scientific ontology and data integration projects make use of spreadsheets at some point, but this can undercut the use of version control systems, which work best with text files. COGS and AXLE make it easy to synchronize Google Sheets and Excel (respectively) with tab- or comma-separated value files (TSV or CSV) in a version control system. VALVE is a table validation tool that also uses tables to configure the validation rules. By combining VALVE with COGS and AXLE you can see your data and your validation rules side-by-side, highlight and filter cells that fail validation, and see validation messages and suggested fixes as comments on those cells. These tools are often used together to build and validate ROBOT templates that define ontology terms, but they work with any sort of tabular data.
COGS AXLE VALVERDF/OWL
Linking Open Data
In addition to spreadsheets, many scientific projects also use relational atabases and the Structured Query Language (SQL). It's often useful to include scientific ontologies and scientific data in the same SQL database. OntoDev's RDFTab and LDTab tools convert RDF/OWL into and SQL tables, and Gizmos is a Python library for extracting, exporting, searching, and browsing ontologies via SQL.
RDFTab LDTab GizmosODK
Ontology Development Kit
Many of the OntoDev tools are included in the Ontology Development Kit (ODK), which provides a portable Docker image with various tools installed and configured, and also helps standardize the organization and workflows for OBO projects.
ODKOBO
Open Ontologies
The Open Biological and Biomedical Ontologies community has adopted and invested in ROBOT as a common toolset for their ontology development workflows and quality control infrastructure.
OBO