Abstract
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 intestinalisembryonic 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. intestinalisgenome. 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | D808-D818 |
| Journal | Nucleic Acids Research |
| Volume | 44 |
| Issue number | D1 |
| DOIs | |
| State | Published - Jan 1 2016 |
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ASJC Scopus subject areas
- Genetics
Cite this
ANISEED 2015 : A digital framework for the comparative developmental biology of ascidians. / Brozovic, Matija; Martin, Cyril; Dantec, Christelle; Dauga, Delphine; Mendez, Mickaël; Simion, Paul; Percher, Madeline; Laporte, Baptiste; Scornavacca, Céline; Di Gregorio, Anna; Fujiwara, Shigeki; Gineste, Mathieu; Lowe, Elijah K.; Piette, Jacques; Racioppi, Claudia; Ristoratore, Filomena; Sasakura, Yasunori; Takatori, Naohito; Brown, Charles; Delsuc, Frédéric; Douzery, Emmanuel; Gissi, Carmela; McDougall, Alex; Nishida, Hiroki; Sawada, Hitoshi; Swalla, Billie J.; Yasuo, Hitoyoshi; Lemaire, Patrick.
In: Nucleic Acids Research, Vol. 44, No. D1, 01.01.2016, p. D808-D818.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - ANISEED 2015
T2 - A digital framework for the comparative developmental biology of ascidians
AU - Brozovic, Matija
AU - Martin, Cyril
AU - Dantec, Christelle
AU - Dauga, Delphine
AU - Mendez, Mickaël
AU - Simion, Paul
AU - Percher, Madeline
AU - Laporte, Baptiste
AU - Scornavacca, Céline
AU - Di Gregorio, Anna
AU - Fujiwara, Shigeki
AU - Gineste, Mathieu
AU - Lowe, Elijah K.
AU - Piette, Jacques
AU - Racioppi, Claudia
AU - Ristoratore, Filomena
AU - Sasakura, Yasunori
AU - Takatori, Naohito
AU - Brown, Charles
AU - Delsuc, Frédéric
AU - Douzery, Emmanuel
AU - Gissi, Carmela
AU - McDougall, Alex
AU - Nishida, Hiroki
AU - Sawada, Hitoshi
AU - Swalla, Billie J.
AU - Yasuo, Hitoyoshi
AU - Lemaire, Patrick
PY - 2016/1/1
Y1 - 2016/1/1
N2 - 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 intestinalisembryonic 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. intestinalisgenome. 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.
AB - 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 intestinalisembryonic 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. intestinalisgenome. 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=84976905632&partnerID=8YFLogxK
U2 - 10.1093/nar/gkv966
DO - 10.1093/nar/gkv966
M3 - Article
C2 - 26420834
AN - SCOPUS:84976905632
VL - 44
SP - D808-D818
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
ER -