ANISEED 2015: A digital framework for the comparative developmental biology of ascidians

Matija Brozovic; Cyril Martin; Christelle Dantec; Delphine Dauga; Mickaël Mendez; Paul Simion; Madeline Percher; Baptiste Laporte; Céline Scornavacca; Anna Di Gregorio; Shigeki Fujiwara; Mathieu Gineste; Elijah K. Lowe; Jacques Piette; Claudia Racioppi; Filomena Ristoratore; Yasunori Sasakura; Naohito Takatori; Titus C. Brown; Frédéric Delsuc; Emmanuel Douzery; Carmela Gissi; Alex McDougall; Hiroki Nishida; Hitoshi Sawada; Billie J. Swalla; Hitoyoshi Yasuo; Patrick Lemaire

doi:10.1093/nar/gkv966

ANISEED 2015: A digital framework for the comparative developmental biology of ascidians

Matija Brozovic, Cyril Martin, Christelle Dantec, Delphine Dauga, Mickaël Mendez, Paul Simion, Madeline Percher, Baptiste Laporte, Céline Scornavacca, Anna Di Gregorio, Shigeki Fujiwara, Mathieu Gineste, Elijah K. Lowe, Jacques Piette, Claudia Racioppi, Filomena Ristoratore, Yasunori Sasakura, Naohito Takatori, Titus C. Brown, Frédéric DelsucEmmanuel Douzery, Carmela Gissi, Alex McDougall, Hiroki Nishida, Hitoshi Sawada, Billie J. Swalla, Hitoyoshi Yasuo, Patrick Lemaire

Molecular Pathobiology

Research output: Contribution to journal › Article › peer-review

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	https://doi.org/10.1093/nar/gkv966
State	Published - 2016

ASJC Scopus subject areas

Genetics

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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, E. K., Piette, J., Racioppi, C., Ristoratore, F., Sasakura, Y., Takatori, N., Brown, T. C., ... Lemaire, P. (2016). ANISEED 2015: A digital framework for the comparative developmental biology of ascidians. Nucleic acids research, 44(D1), D808-D818. https://doi.org/10.1093/nar/gkv966

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 2016, 'ANISEED 2015: A digital framework for the comparative developmental biology of ascidians', Nucleic acids research, vol. 44, no. D1, pp. D808-D818. https://doi.org/10.1093/nar/gkv966

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title = "ANISEED 2015: A digital framework for the comparative developmental biology of ascidians",

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.",

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doi = "10.1093/nar/gkv966",

language = "English (US)",

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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, Titus C.

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

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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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ER -

ANISEED 2015: A digital framework for the comparative developmental biology of ascidians

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