THE CANCER EPITOPE DATABASE AND ANALYSIS RESOURCE

癌症表位数据库和分析资源

• 批准号: 10842172
• 负责人: Bjoern Peters
• 金额: $ 36.6万
• 依托单位: LA JOLLA INSTITUTE FOR IMMUNOLOGY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-18 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10842172
• 关键词: Abbreviations; Adopted; Algorithms; Artificial Intelligence; Award; Catalogs; Code; Communities; Consumption; Data; Data Reporting; Data Set; Data Sources; Databases; Deposition; Epitopes; Extensible Markup Language; Feedback; Funding; Future; Goals; Journals; Knowledge Extraction; Language; Letters; Link; Literature; Location; Machine Learning; Malignant Neoplasms; Manuals; Manuscripts; Methods; Modeling; Molecular Target; Outcome; Performance; Policies; Provider; PubMed; Readability; Readiness; Records; Resources; Science; Specific qualifier value; Standardization; System; Testing; Text; Time; Training; United States National Institutes of Health; Validation; Work; Writing; access restrictions; adaptive immune response; data resource; data standards; high standard; improved; journal article; knowledgebase; neoplastic cell; spelling; text searching; timeline; web site

Project Summary The primary goal of our proposal is to improve the AI/ML-readiness of data in the Cancer Epitope Database and Analysis Resource (CEDAR). CEDAR provides a catalog of manually curated information from journal articles that describe the specific molecular targets of adaptive immune responses - also called `epitopes' - in tumor cells. Like many other curated resources in the biomedical domain, CEDAR tracks the provenance of the statements it captures by identifying the journal article (which is straightforward by its PubMed record) and the specific part of the article where the curated data is contained. We here propose to make the data location field in CEDAR accessible for AI/ML approaches, that will allow the comparison of information extracted by algorithms from a free text article to the curated data in CEDAR. Specifically, we will: 1) Standardize how `data location' in a manuscript is captured in CEDAR. 2) Programmatically link data locations to parts of journal articles in PubMed Central (PMC). Completing these Aims will make the CEDAR data more valuable for large language models (LLM) and related AI applications. Moreover, the approaches and code developed will be applicable to the many other biomedical knowledgebases that curate data from the literature and capture its specific location.

项目摘要 我们建议的主要目的是改善癌症表位数据库中数据的AI/ML准备就绪，并 分析资源（Cedar）。雪松提供了期刊文章中手动策划信息的目录 描述了自适应免疫反应的特定分子靶标 - 也称为肿瘤中的“表位” 细胞。像生物医学领域中的许多其他策划资源一样，雪松跟踪了 它通过识别期刊文章（PubMed记录很简单）和 包含精选数据的文章的特定部分。我们在这里建议将数据位置字段进行 在可用于AI/ML方法的Cedar中，将允许比较算法提取的信息 从自由文本文章到Cedar的策划数据。具体来说，我们将：1）标准化如何“数据位置” 手稿在雪松中被捕获。 2）将数据位置链接到PubMed中期刊文章的一部分 中央（PMC）。完成这些目标将使雪松数据对于大语言模型更有价值 （LLM）和相关的AI应用程序。此外，开发的方法和代码将适用于许多 其他生物医学知识库从文献中策划数据并捕获其特定位置。

项目成果

IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community.

IEDB 和 CEDAR：为全球科学界服务的两个兄弟数据库。

• DOI: 10.1007/978-1-0716-3239-0_9
• 发表时间: 2023
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Blazeska,Nina;Kosaloglu-Yalcin,Zeynep;Vita,Randi;Peters,Bjoern;Sette,Alessandro
• 通讯作者: Sette,Alessandro

Estimating tissue-specific peptide abundance from public RNA-Seq data.

• DOI: 10.3389/fgene.2023.1082168
• 发表时间: 2023
• 期刊: FRONTIERS IN GENETICS
• 影响因子: 3.7
• 作者: Frentzen, Angela;Greenbaum, Jason A.;Kim, Haeuk;Peters, Bjoern;Kosaloglu-Yalcin, Zeynep
• 通讯作者: Kosaloglu-Yalcin, Zeynep

The role of antigen expression in shaping the repertoire of HLA presented ligands.

• DOI: 10.1016/j.isci.2022.104975
• 发表时间: 2022-09-16
• 期刊: ISCIENCE
• 影响因子: 5.8
• 作者: Alvarez, Heli M. Garcia;Kosaloglu-Yalcin, Zeynep;Peters, Bjoern;Nielsen, Morten
• 通讯作者: Nielsen, Morten

Evaluating the Bioenergetics Health Index Ratio in Leigh Syndrome Fibroblasts to Understand Disease Severity.

• DOI: 10.3390/ijms221910344
• 发表时间: 2021-09-26
• 期刊: International journal of molecular sciences
• 影响因子: 5.6
• 作者: Bakare AB;Dean J;Chen Q;Thorat V;Huang Y;LaFramboise T;Lesnefsky EJ;Iyer S
• 通讯作者: Iyer S

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.

• DOI: 10.1186/s12859-023-05606-4
• 发表时间: 2023-12-18
• 期刊: BMC bioinformatics
• 影响因子: 3