ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.
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DOI：
10.1093/nar/gkv966
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Lemaire P
中科院分区：
文献类型：
--
作者：
Brozovic M;Martin C;Dantec C;Dauga D;Mendez M;Simion P;Percher M;Laporte B;Scornavacca C;Di Gregorio A;Fujiwara S;Gineste M;Lowe EK;Piette J;Racioppi C;Ristoratore F;Sasakura Y;Takatori N;Brown TC;Delsuc F;Douzery E;Gissi C;McDougall A;Nishida H;Sawada H;Swalla BJ;Yasuo H;Lemaire P
海鞘属于被囊动物，脊椎动物的姐妹群，并且是胚胎发育、再生和干细胞领域中公认的模式生物。ANISEED是海鞘发育生物学研究的主要信息系统。本文报告了该系统自2010年首次发布以来的发展情况。在过去的五年中，我们将系统从初始的自定义模式重构为Chado模式的扩展版本，并重新设计了所有用户和后端界面。基于改进的基因组组装和基因模型集、精细的功能基因注释和解剖本体以及完整ORF cDNA的新集合，这种新架构被用于改进和丰富玻璃海鞘胚胎发育的描述。自C.染色体组。在ANISEED 2015中，所有九个新的海鞘物种都可以通过专用的基因组浏览器进行探索，并通过Blast进行搜索。此外，ANISEED还提供了六个具有最高质量基因组的物种的完整功能基因注释，解剖本体和一些基因表达数据。ANISEED可在http://www.aniseed.cnrs.fr上公开获取。
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.