Applying a conceptual modeling language developed over a decade ago, they depict complex biological systems both diagrammatically and textually in a formal yet intuitive way and at any desired level of detail
Technion researchers modeled the lifecycle of yeast mRNA, which transports genetic code from the nucleus to the ribosome for building proteins. Their novel method makes use of Object-Process Methodology (OPM), a holistic conceptual modeling paradigm that uses objects and processes as the only two building blocks of the universe. OPM, invented over fifteen years ago by Professor Dov Dori from the Faculty of Industrial Engineering and Management, is in advanced stages of becoming the first conceptual modeling language which is an ISO standard.
Recently, Professor Dori has teamed up with Mordechai Choder, a molecular biologist from the Bruce and Ruth Rappaport Faculty of Medicine. Jointly mentoring Ms. Judith Somekh, a PhD candidate about to complete her dissertation, they built a conceptual model consisting of hundreds of objects and processes at eight levels of detail that describes key aspects of the mRNA lifecycle, which is responsible for gene expression. “It’s like a gigantic puzzle with vast amounts of information that has accumulated over years of meticulous research by thousands of researchers”, explains Professor Dori. “The model we built allows for an overall conceptual view of this subsystem and for testing it via qualitative simulation of the model.”
The model is based on dozens of published studies made on many pieces of this “puzzle” that together form an overall picture of major parts of the mRNA lifecycle subsystem. The research paper was published in the open access journal PloS ONE. In the process of building the model, the team – professors Dori and Choder and Judith Somekh – found and classified knowledge gaps in the system. Identifying such gaps can assist scientists in pinpointing specific aspects such as unknown mechanism or substances whose resolution requires design and execution of “wet lab” experimentation to verify or refute conjectured facts, and update the model accordingly. While systems biology has been a subject of much research in recent year, this approach has opened conceptual model-based systems biology as a new research area within systems biology.