A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.
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DOI：
10.3233/jad-200206
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发表时间：
2020
期刊：
影响因子：
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通讯作者：
IMEx Consortium, UniProt Consortium
中科院分区：
文献类型：
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作者：
Breuza L;Arighi CN;Argoud-Puy G;Casals-Casas C;Estreicher A;Famiglietti ML;Georghiou G;Gos A;Gruaz-Gumowski N;Hinz U;Hyka-Nouspikel N;Kramarz B;Lovering RC;Lussi Y;Magrane M;Masson P;Perfetto L;Poux S;Rodriguez-Lopez M;Stoeckert C;Sundaram S;Wang LS;Wu E;Orchard S;IMEx Consortium, UniProt Consortium
对患者来源的临床样本生成的数据进行分析和解释依赖于对高质量生物信息学资源的访问。这些由专家策展人维护和更新，从自由文本期刊文章中描述的非结构化生物数据中提取知识，并将其转换为更结构化，计算可访问的形式。这使得分析，如功能富集的基因/蛋白质组使用基因本体论，并使数据的搜索更富有成效的管理问题，如基因/蛋白质名称同义词，标识符映射和数据质量。对关键的公共领域资源进行协调的注释更新，以更好地支持阿尔茨海默病研究。我们已经系统地确定了对疾病过程至关重要的靶蛋白，部分是通过从临床研究界获得知情的输入。来自954篇论文的数据已被添加到UniProtKB，Gene Ontology和International Molecular Exchange Consortium（IMEx）数据库中，UniProtKB中更新了299种人类蛋白质和279种直系同源物。将745个二元相互作用添加到IMEx人类分子相互作用数据集。这代表了在一些生物医学数据库中与阿尔茨海默病相关的专家策划数据的显著增强。UniProtKB中的相关蛋白质条目已更新，同时在基因本体中也进行了更新。IMEx Consortium数据集中的分子相互作用网络得到了显著扩展，并创建了一组参考蛋白质复合物。所有描述的资源都是开源的，可供研究界免费使用，我们提供了研究人员如何利用这些数据的例子。
The analysis and interpretation of data generated from patient-derived clinical samples relies on access to high-quality bioinformatics resources. These are maintained and updated by expert curators extracting knowledge from unstructured biological data described in free-text journal articles and converting this into more structured, computationally-accessible forms. This enables analyses such as functional enrichment of sets of genes/proteins using the Gene Ontology, and makes the searching of data more productive by managing issues such as gene/protein name synonyms, identifier mapping, and data quality. To undertake a coordinated annotation update of key public-domain resources to better support Alzheimer’s disease research. We have systematically identified target proteins critical to disease process, in part by accessing informed input from the clinical research community. Data from 954 papers have been added to the UniProtKB, Gene Ontology, and the International Molecular Exchange Consortium (IMEx) databases, with 299 human proteins and 279 orthologs updated in UniProtKB. 745 binary interactions were added to the IMEx human molecular interaction dataset. This represents a significant enhancement in the expert curated data pertinent to Alzheimer’s disease available in a number of biomedical databases. Relevant protein entries have been updated in UniProtKB and concomitantly in the Gene Ontology. Molecular interaction networks have been significantly extended in the IMEx Consortium dataset and a set of reference protein complexes created. All the resources described are open-source and freely available to the research community and we provide examples of how these data could be exploited by researchers.