Advancing FAIRness and TRUST in the gEAR portal

在 gEAR 门户中促进公平和信任

• 批准号: 10408360
• 负责人: Ronna Hertzano
• 金额: $ 22.59万
• 依托单位: UNIVERSITY OF MARYLAND BALTIMORE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-09 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10408360
• 关键词: Address; Administrative Supplement; Advanced Development; Atlases; Authorization documentation; BRAIN initiative; Basic Science; Bioinformatics; Biological; Biological Sciences; Cells; Cochlea; Communication impairment; Complex Analysis; Country; Data; Data Scientist; Data Security; Data Set; Development; Ear; Education and Outreach; Educational workshop; Engineering; Epigenetic Process; Equilibrium; FAIR principles; Feedback; Fostering; Funding; Future; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Generations; Goals; Hearing; Hearing problem; Institute of Medicine (U.S.); Institutes; Laboratories; Labyrinth; Maryland; Metadata; Multiomic Data; Mus; Names; Ontology; Organ; Parents; Performance; Persons; Privatization; Public Domains; Publications; Publishing; Research; Research Personnel; Resources; Role; Scientist; Secure; Standardization; Structure; Surgeon; Surveys; Technology; Therapeutic; Training; Translations; Universities; Validation; Visit; Visualization; Work; analytical tool; base; cell type; cloud based; data dissemination; data exchange; data sharing; deafness; equilibration disorder; experience; genome sciences; improved; indexing; insight; interoperability; medical schools; member; multidisciplinary; multimodality; multiple omics; operation; scaffold; skills; therapeutic development; tool; transcriptomics; trustworthiness

ABSTRACT Discovery in biological sciences has shifted to increasingly rely on high throughput multi-omic data. The advent of single cell (sc) transcriptomics further revolutionized research in our field, given the intricate structure of the inner ear organs consisting of numerous distinct cell types that function in concert to properly sense hearing and balance. Harnessing the wealth of existing and future multi-omic, multi-modality and multi-species data is challenged by their ever-increasing data size and relative inaccessibility to biologists that are not trained in bioinformatics. The gEAR, gene Expression Analysis Resources (umgear.org), is a cloud-based `one-stop- shop' where inner ear-related multi-omic data can be explored and analyzed by biologists without requiring programming skills. Over the past five years, the gEAR has become a critically valuable resource to our field. The impact of the gEAR on the field is reflected by its 846 registered users, 440 datasets (over 70 organized in thematic profiles in the public domain), and thousands of monthly visits. The goal of this proposal is to implement necessary improvements in the gEAR that will significantly enhance the ability of researchers to infer biological insights from the omics data generated by their own laboratories and from omics datasets in the public domain. We will: (1) continuously upload and curate ear- related multi-omic data from contributing laboratories and the public domain; (2) construct an integrated epigenetic and transcriptomic atlas of the developing and mature mouse cochlea (a) as a necessary scaffold for cross dataset integration, and (b) as necessary data for bridging the gap between gene expression and gene regulation; (3) implement advanced bioinformatic analytical tools in the gEAR; (4) enhance the user- interface; (5) make scalability, performance and stability improvements; (6) integrate the gEAR with analytical notebooks to allow more complex analyses with minimal training; and (7) continue our education and outreach efforts. In addition to user-surveys, we will establish both user and technology expertise advisory boards to provide feedback and guide development. Diverse expertise is required for the efficient operation and development of the gEAR bioinformatics platform. Our multi-disciplinary team members are a surgeon-scientist (PI), bioinformaticians (Co-Is), biologists and engineers. Our experience in turning the gEAR from an abstract idea to a successful platform, widely adapted in the ear field, and with multiple successful clones including NeMO Analytics (nemoanalytics.org) for the BRAIN initiative should attest to our experience, expertise, and ability to deliver. Completion of the proposed gEAR advancements will boost fulfillment of the great promises expected from omics data generation and analyses and foster reuse of existing data, thereby catalyzing both basic science discovery and advance development and translation of therapeutics for hearing and balance disorders.

摘要 生物科学中的发现已经转向越来越依赖于高通量多组学数据。的 单细胞（sc）转录组学的出现进一步革新了我们领域的研究， 由许多不同类型的细胞组成的内耳器官，这些细胞共同发挥作用， 听觉和平衡利用现有和未来的多组、多方式和多物种生物多样性 数据面临着不断增加的数据大小以及未经培训的生物学家相对难以访问的挑战 在生物信息学中。基因表达分析资源（umgear.org）是一个基于云的“一站式”服务， 在这里，生物学家可以探索和分析内耳相关的多组学数据，而不需要 编程技能。在过去的五年里，gobble已经成为我们这个领域的一个非常宝贵的资源。 该平台对该领域的影响体现在其846个注册用户、440个数据集（70多个数据集以 公共领域的专题简介），以及每月数千次的访问。 本提案的目标是对gesture进行必要的改进， 增强研究人员从自己产生的组学数据中推断生物学见解的能力 实验室和公共领域的组学数据集。我们将：（1）不断上传和策划耳- （2）从贡献实验室和公共领域的相关多组学数据;（3）构建一个综合的 发育和成熟小鼠耳蜗的表观遗传和转录组图谱（a）作为必要的支架 用于交叉数据集整合，以及（B）作为用于弥合基因表达和基因表达之间的差距的必要数据， 基因调控;（3）在基因组中实施先进的生物信息学分析工具;（4）提高用户- 接口;（5）提高可伸缩性、性能和稳定性;（6）将gcss与分析 笔记本电脑，使更复杂的分析与最低限度的培训;和（7）继续我们的教育和推广 努力除了用户调查外，我们还将设立用户和技术专家咨询委员会， 提供反馈并指导开发。 生物信息学的有效运作和发展需要各种专门知识 平台我们的多学科团队成员是外科医生科学家（PI），生物信息学家（Co-Is），生物学家 和工程师。我们的经验，把gesture从一个抽象的想法，以一个成功的平台，广泛 适应在穗领域，并与多个成功的克隆，包括NeMO分析（nemoanalytics.org）， BRAIN计划应该证明我们的经验、专业知识和交付能力。完成 拟议中的基因组学进展将促进实现从组学数据中预期的伟大承诺 生成和分析并促进现有数据的再利用，从而促进基础科学发现和 促进听力和平衡障碍治疗方法的开发和翻译。

项目成果

The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain.

• DOI: 10.1093/nar/gkac962
• 发表时间: 2023-01-06
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Ament, Seth A.;Adkins, Ricky S.;Carter, Robert;Chrysostomou, Elena;Colantuoni, Carlo;Crabtree, Jonathan;Creasy, Heather H.;Degatano, Kylee;Felix, Victor;Gandt, Peter;Garden, Gwenn A.;Giglio, Michelle;Herb, Brian R.;Khajouei, Farzaneh;Kiernan, Elizabeth;McCracken, Carrie;McDaniel, Kennedy;Nadendla, Suvarna;Nickel, Lance;Olley, Dustin;Orvis, Joshua;Receveur, Joseph P.;Schor, Mike;Sonthalia, Shreyash;Tickle, Timothy L.;Way, Jessica;Hertzano, Ronna;Mahurkar, Anup A.;White, Owen R.
• 通讯作者: White, Owen R.

Avian auditory hair cell regeneration is accompanied by JAK/STAT-dependent expression of immune-related genes in supporting cells.

• DOI: 10.1242/dev.200113
• 发表时间: 2022-04-15
• 期刊: Development (Cambridge, England)