CSO Validator

CSO validator is an ontology-based validation tool that guides creating high-quality biological pathways in CSO (Cell System Ontology).

In a typical curation process, biological information resources are collected from literature, background knowledge, and other databases. To create and evaluate pathway models, the information is organized into the building blocks in pathway databases. After creating the pathways models, the domain experts validate the created pathways and the curators update them based on appropriate feedback. This validation and update are an iterative procedure to obtain the desired pathway. To reduce the repetitions and time and effort during curation, we have developed a rule-based validation tool.

CSO validator uses the Systems Biology application XiP that is a flexible, editable and modular environment with a user-friendly interface that does not require previous programming skills to run, construct and edit workflows.


Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, and Satoru Miyano, CSO validator: Improving manual curation workow for biological pathways, Bioinformatics, 27(17):2471-2472, 2011