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).
Cell Biology
Final Report Abstract
Human pluripotent stem cells (hPSCs) are cells that have the ability to differentiate into almost any type of cell in the body. There are two main types of hPSCs: embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs). In contrast to hESCs, HiPSCs are generated by reprogramming adult cells, such as skin cells, to become pluripotent. PSC lines are currently used in a number of research applications, including clinical trials, drug testing, and disease modelling. In clinical trials, hPSCs can be used to develop new treatments for a range of diseases, including genetic disorders and degenerative diseases. HPSCs are also used in drug testing to identify potential new treatments for a variety of diseases. In addition, pluripotent stem cells are used to model diseases, allowing researchers to study the causes of a wide range of diseases. Stem cell research has made significant progress in recent decades. This has also led to a steady increase in the number of available cell lines with a wide variety of characteristics. The human pluripotent stem cell registry (hPSCreg®) is a registry where scientists from all over the world can register their hiPSC lines. There are now more than 9000 lines registered in hPSCreg, including more than 4700 with extensively annotated records, including information on donors, consent, manufacturing and quality characteristics of the cells. The European Bank for induced pluripotent stem cell lines (EBiSC) is a centralised, not-for-profit hiPSC bank providing researchers across academia and industry with access to scalable, cost-efficient and consistent, high quality hiPSC lines and derived products for new medicines development. More than 950 lines are now available on EBiSC. Both hPSCreg® and EBiSC provide users with very detailed information about the hiPSC lines registered and available there. The biggest problem, however, is also making these datasets searchable to help scientists find the hiPSC lines they need for their research. This prevents the need for costly regeneration of new lines and increases scientific reproducibility. In this project, we annotated the data available in hPSCreg and implemented several semantic search options to allow stem cell researcher to make complex queries and identify available hiPSCs appropriate for specific research tasks. This includes, among others, a search for similar lines that may be more readily available or have well-documented consents, or the ability to ask complex queries involving, for example, the role of genetically modified genes in specific metabolic processes that may be relevant to disease.
