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).

开发基于本体的人类多能干细胞搜索方法以及细胞系、出版物和研究项目的推荐工具（OsemPSC）。

• 批准号: 425872946
• 负责人: Professor Dr. Andreas Kurtz
• 金额: --
• 依托单位: Berlin-Brandenburger Centrum für Regenerative Therapien (BCRT)
• 依托单位国家: 德国
• 项目类别: Research data and software (Scientific Library Services and Information Systems)
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2022-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/425872946?language=en
• 关键词: Development; ontology; based; search; method

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.

胚胎干细胞(ES细胞)或诱导多能干细胞(IPS细胞)可以分化为人体所有类型的细胞)，并代表供体的基因型(ES细胞的胚胎，IPS系的体细胞)。因此，多能干细胞(PS细胞)可用于疾病和组织的体外建模、药物试验和再生医学。已经建立了大型细胞库和登记处，为各种疾病提供表型和遗传型代表性的PS细胞，这些疾病已经以标准化的方式衍生和表征。对于用户识别合适的PS细胞，关于供体、细胞和已经进行的应用的信息是必不可少的。这些信息以不同的数据类型编码，并分布在不同的数据库、单元库和登记处。随着数据的海量和多样性的增加，用户识别相关数据和高质量的PS线变得越来越困难。此外，不可能以有意义的方式将来自不同登记册和数据库的数据联系起来。这不仅是对资源的浪费和用户的问题，也是科学重现性和透明度面临的越来越大的风险。为了以有意义的方式将现有数据资源中的PSC数据联系起来并加以限定，必须开发新的方法和工具。在提出的项目中，我想开发并实现一个基于本体的搜索算法，通过识别数据的含义并将其用于搜索来解决从不同数据源搜索细胞系的问题。在此基础上，将开发一个建议自动完成的工具，以自动向用户推荐感兴趣的单元格系列、出版物和研究项目。为了实现这一目标，将实施一个本体，其中包含关于线条的所有相关信息，并将它们与其他本体相链接，例如关于疾病、表型、组织和细胞类型的本体。这还实现了不同数据源的链接。人类多能干细胞登记处(HPSCreg)是PS细胞的一个公共国际数据库，将作为研究、实施、用户互动和可持续性的基础。在这个项目中开发的工具应该以模块化的方式实施，以允许与其他细胞库(如EBiSC(欧洲诱导多能干细胞银行)或其他平台)的互操作性。