Development of an ontology-based search method for human pluripotent stem cells and of a recommendation tool for cell lines, publications and research projects (OsemPSC).

• Applicant: Professor Dr. Andreas Kurtz
• Subject Area: Data Management, Data-Intensive Systems, Computer Science Methods in Business Informatics ; Cell Biology
• Term: from 2019 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 425872946

Embryonic stem cells (ES - cells) or induced pluripotent stem cells (IPS - cells) can differentiate into all cell types of a human body) and represent the genotype of the donor (embryo for ES-cells, somatic cells for IPS-lines). Therefore, pluripotent stem cells (PS-cells) could be used for modelling diseases and tissues in vitro, testing drugs and for regenerative medicine. Large cell banks and registries have been established to provide phenotypic and genotypic representative PScells for a wide spectrum of diseases, which have been derived and characterised in a standardised way. For users to identify suitable PS cells, information about the donors, the cells and the already ensued application are essential. This information is encoded in different data types and distributed in different databanks, cell banks and registries. With the increasing mass and diversity of data it is getting more and more difficult for users to identify relevant data and PS-lines of high quality. It is furthermore impossible to link data from different registries and databases in a meaningful way. This not only is a waste of resources and a problem for users, it is also a increasing risk for scientific reproducibility and transparency. To link and qualify PSCdata from available data resources in a meaningful way, new methods and tools have to be developed. In the proposed project, I want to develop and implement an ontology-based search algorithm to solve the problem of searching for cell lines from different data sources by recognizing the meaning of the data and use it for searching. Based on this, a tool will be developed for proposing autocompletion to automatically recommend interesting cell lines, publications and research projects to the user. To reach this goal, an ontology will be implemented, containing all relevant information about the lines and linking them to other ontologies e.g. for diseases, phenotype, tissue and cell types. This also enables the linkage of different data sources. The human pluripotent stem cell registry (hPSCreg), a public international database for PS-cells will be used as basis for research, implementation, user interaction and sustainability. The tools developed in this project should be implemented in a modular way that allows interoperability with other cell banks like EBiSC (European Bank for induced pluripotent stem cells) or other platforms.

• DFG Programme: Research data and software (Scientific Library Services and Information Systems)
• International Connection: USA
• Co-Investigator: Dr. Stefanie Seltmann
• Cooperation Partner: Professor Dr. Yongqun He