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Updates to the Alliance of Genome Resources Central Infrastructure.
GENETICS ( IF 3.3 ) Pub Date : 2024-03-29 , DOI: 10.1093/genetics/iyae049 , Suzanne A Aleksander 1 , Anna V Anagnostopoulos 2 , Giulia Antonazzo 3 , Valerio Arnaboldi 4 , Helen Attrill 3 , Andrés Becerra 5 , Susan M Bello 2 , Olin Blodgett 2 , Yvonne M Bradford 6 , Carol J Bult 2 , Scott Cain 7 , Brian R Calvi 8 , Seth Carbon 9 , Juancarlos Chan 4 , Wen J Chen 4 , J Michael Cherry 1 , Jaehyoung Cho 4 , Madeline A Crosby 10 , Jeffrey L De Pons 11 , Peter D’Eustachio 12 , Stavros Diamantakis 5 , Mary E Dolan 2 , Gilberto dos Santos 10 , Sarah Dyer 5 , Dustin Ebert 13 , Stacia R Engel 1 , David Fashena 6 , Malcolm Fisher 14 , Saoirse Foley 15 , Adam C Gibson 11 , Varun R Gollapally 11 , L Sian Gramates 10 , Christian A Grove 4 , Paul Hale 2 , Todd Harris 7 , G Thomas Hayman 11 , Yanhui Hu 16 , Christina James-Zorn 14 , Kamran Karimi 17 , Kalpana Karra 1 , Ranjana Kishore 4 , Anne E Kwitek 11 , Stanley J F Laulederkind 11 , Raymond Lee 4 , Ian Longden 10 , Manuel Luypaert 5 , Nicholas Markarian 4 , Steven J Marygold 3 , Beverley Matthews 10 , Monica S McAndrews 2 , Gillian Millburn 3 , Stuart Miyasato 1 , Howie Motenko 2 , Sierra Moxon 9 , Hans-Michael Muller 4 , Christopher J Mungall 9 , Anushya Muruganujan 13 , Tremayne Mushayahama 13 , Robert S Nash 1 , Paulo Nuin 7 , Holly Paddock 6 , Troy Pells 17 , Norbert Perrimon 16 , Christian Pich 6 , Mark Quinton-Tulloch 5 , Daniela Raciti 4 , Sridhar Ramachandran 6 , Joel E Richardson 6 , Susan Russo Gelbart 10 , Leyla Ruzicka 6 , Gary Schindelman 4 , David R Shaw 2 , Gavin Sherlock 1 , Ajay Shrivatsav 1 , Amy Singer 6 , Constance M Smith 2 , Cynthia L Smith 2 , Jennifer R Smith 11 , Lincoln Stein 7 , Paul W Sternberg 4 , Christopher J Tabone 10 , Paul D Thomas 13 , Ketaki Thorat 11 , Jyothi Thota 11 , Monika Tomczuk 2 , Vitor Trovisco 3 , Marek A Tutaj 11 , Jose-Maria Urbano 3 , Kimberly Van Auken 4 , Ceri E Van Slyke 6 , Peter D Vize 17 , Qinghua Wang 4 , Shuai Weng 1 , Monte Westerfield 6 , Laurens G Wilming 2 , Edith D Wong 1 , Adam Wright 7 , Karen Yook 4 , Pinglei Zhou 10 , Aaron Zorn 14 , Mark Zytkovicz 10
GENETICS ( IF 3.3 ) Pub Date : 2024-03-29 , DOI: 10.1093/genetics/iyae049 , Suzanne A Aleksander 1 , Anna V Anagnostopoulos 2 , Giulia Antonazzo 3 , Valerio Arnaboldi 4 , Helen Attrill 3 , Andrés Becerra 5 , Susan M Bello 2 , Olin Blodgett 2 , Yvonne M Bradford 6 , Carol J Bult 2 , Scott Cain 7 , Brian R Calvi 8 , Seth Carbon 9 , Juancarlos Chan 4 , Wen J Chen 4 , J Michael Cherry 1 , Jaehyoung Cho 4 , Madeline A Crosby 10 , Jeffrey L De Pons 11 , Peter D’Eustachio 12 , Stavros Diamantakis 5 , Mary E Dolan 2 , Gilberto dos Santos 10 , Sarah Dyer 5 , Dustin Ebert 13 , Stacia R Engel 1 , David Fashena 6 , Malcolm Fisher 14 , Saoirse Foley 15 , Adam C Gibson 11 , Varun R Gollapally 11 , L Sian Gramates 10 , Christian A Grove 4 , Paul Hale 2 , Todd Harris 7 , G Thomas Hayman 11 , Yanhui Hu 16 , Christina James-Zorn 14 , Kamran Karimi 17 , Kalpana Karra 1 , Ranjana Kishore 4 , Anne E Kwitek 11 , Stanley J F Laulederkind 11 , Raymond Lee 4 , Ian Longden 10 , Manuel Luypaert 5 , Nicholas Markarian 4 , Steven J Marygold 3 , Beverley Matthews 10 , Monica S McAndrews 2 , Gillian Millburn 3 , Stuart Miyasato 1 , Howie Motenko 2 , Sierra Moxon 9 , Hans-Michael Muller 4 , Christopher J Mungall 9 , Anushya Muruganujan 13 , Tremayne Mushayahama 13 , Robert S Nash 1 , Paulo Nuin 7 , Holly Paddock 6 , Troy Pells 17 , Norbert Perrimon 16 , Christian Pich 6 , Mark Quinton-Tulloch 5 , Daniela Raciti 4 , Sridhar Ramachandran 6 , Joel E Richardson 6 , Susan Russo Gelbart 10 , Leyla Ruzicka 6 , Gary Schindelman 4 , David R Shaw 2 , Gavin Sherlock 1 , Ajay Shrivatsav 1 , Amy Singer 6 , Constance M Smith 2 , Cynthia L Smith 2 , Jennifer R Smith 11 , Lincoln Stein 7 , Paul W Sternberg 4 , Christopher J Tabone 10 , Paul D Thomas 13 , Ketaki Thorat 11 , Jyothi Thota 11 , Monika Tomczuk 2 , Vitor Trovisco 3 , Marek A Tutaj 11 , Jose-Maria Urbano 3 , Kimberly Van Auken 4 , Ceri E Van Slyke 6 , Peter D Vize 17 , Qinghua Wang 4 , Shuai Weng 1 , Monte Westerfield 6 , Laurens G Wilming 2 , Edith D Wong 1 , Adam Wright 7 , Karen Yook 4 , Pinglei Zhou 10 , Aaron Zorn 14 , Mark Zytkovicz 10
Affiliation
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and Application Programming Interfaces (APIs). Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).
中文翻译：
基因组资源联盟中央基础设施的更新。
基因组资源联盟（联盟）是一个可扩展的知识库联盟，专注于深入研究的模式生物的遗传学和基因组学。该联盟是作为单独的知识中心组织的，与其研究社区和集中式软件基础设施有着紧密的联系，如下所述。目前联盟中的模型生物有芽殖酵母、线虫、果蝇、斑马鱼、青蛙、实验室小鼠、实验室大鼠和基因本体联盟。该项目正处于快速开发阶段，旨在协调知识、存储知识、分析知识，并通过门户网站、直接下载和应用程序编程接口 (API) 将其呈现给社区。在这里，我们重点关注过去两年的发展。具体来说，我们添加和增强了用于浏览基因组（JBrowse）、下载序列、挖掘复杂数据（AllianceMine）、可视化路径、文献全文搜索（Textpresso）和序列相似性搜索（SequenceServer）的工具。我们增强了现有的交互式数据表，并添加了一个交互式旁系同源表，以补充我们的直系同源表示。为了支持个体模式生物群落，我们实施了特定于物种的“登陆页面”，并将很快添加特定于疾病的门户；此外，我们还支持在 Discourse 软件中实现的公共社区论坛。我们描述了我们在支持策展的中央持久数据库、支持协调的数据建模以及集成人工智能和机器学习 (AI/ML) 的最先进的文献策展系统方面取得的进展。
更新日期：2024-03-29
中文翻译：
基因组资源联盟中央基础设施的更新。
基因组资源联盟（联盟）是一个可扩展的知识库联盟，专注于深入研究的模式生物的遗传学和基因组学。该联盟是作为单独的知识中心组织的，与其研究社区和集中式软件基础设施有着紧密的联系，如下所述。目前联盟中的模型生物有芽殖酵母、线虫、果蝇、斑马鱼、青蛙、实验室小鼠、实验室大鼠和基因本体联盟。该项目正处于快速开发阶段，旨在协调知识、存储知识、分析知识，并通过门户网站、直接下载和应用程序编程接口 (API) 将其呈现给社区。在这里，我们重点关注过去两年的发展。具体来说，我们添加和增强了用于浏览基因组（JBrowse）、下载序列、挖掘复杂数据（AllianceMine）、可视化路径、文献全文搜索（Textpresso）和序列相似性搜索（SequenceServer）的工具。我们增强了现有的交互式数据表，并添加了一个交互式旁系同源表，以补充我们的直系同源表示。为了支持个体模式生物群落，我们实施了特定于物种的“登陆页面”，并将很快添加特定于疾病的门户；此外，我们还支持在 Discourse 软件中实现的公共社区论坛。我们描述了我们在支持策展的中央持久数据库、支持协调的数据建模以及集成人工智能和机器学习 (AI/ML) 的最先进的文献策展系统方面取得的进展。
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