SyBValS: a validation and error resolution service for biological pathway maps

Effective visualization of relational data is essential for thorough analysis, including in biological research. Annotating and depicting biological models in universally recognized formats is essential. Additionally, uncovering graph-theoretical characteristics within pathways and pinpointing specific paths or subgraphs within them are vital aspects of pathway data analysis. Standard formats such as SBGN impose stringent rules regarding the interaction among biological entities. However, many users tend to overlook or disregard these rules, resulting in the need to rectify them to ensure the validity of the map model. In response to this issue, we developed a web service called SyBValS. SyBValS begins by validating a pathway in SBGN process description format. Any encountered errors are documented along with relevant explanations and color-coded on an automatically laid out and generated map. If preferred, SyBValS can endeavor to rectify these errors whenever feasible, updating both the error list and the corresponding map image accordingly. SyBValS is open-source, available on GitHub, and distributed freely under the MIT license. Additionally, a sample deployment is accessible here for public use.