CSO validator: improving manual curation workflow for biological pathways

Abstract

Summary: Manual curation and validation of large-scale biological pathways are required to obtain high-quality pathway databases. In a typical curation process, model validation and model update based on appropriate feedback are repeated and requires considerable cooperation of scientists. We have developed a CSO (Cell System Ontology) validator to reduce the repetition and time during the curation process. This tool assists in quickly obtaining agreement among curators and domain experts and in providing a consistent and accurate pathway database.

Availability: The tool is available on http://csovalidator.csml.org.

Contact: masao@hgc.jp.

Fig. 1.

(a) an example model to validate; (b) the validation window to guide correction; (c) the validated model, visualized on CIO. The table in (b) shows four warnings in the model. The highlighted part in (a) is a DNA binding process which is listed because there is no DNA as its input entity. Therefore, the validation window suggests that one entity from two should be changed into DNA. In the setting value pane, the recommended value is DNA and two candidate entities are listed below because the corresponding process has two input entities. In (c), the validated model shows the main changes: (i) one entity type is changed into DNA, (ii) the product of DNA binding is a complex, not a protein, and (iii) the connector is changed to represent the input entity, not an enzyme.