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Database Commons - SilkDB

SilkDB

Citations: 293

z-index 7.44

Short name SilkDB
Full name
Description The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data.
URL http://www.silkdb.org
Year founded 2004
Last update & version 2010-01-01    2.0
Availability Free to all users
University/Institution hosted Southwest University
Address 216 Tiansheng Rd., Beibei District, Chongqing, China 400716
City Chongqing
Province/State Chongqing
Country/Region China
Contact name Qingyou Xia
Contact email xiaqy@swu.edu.cn
Data type(s)
Major organism(s)
Keyword(s)
  • chromosomal mapping
  • ESTs
  • functional annotation
  • gene product
  • microarray expression data
Publication(s)
  • SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. [PMID: 19793867]

    Jun Duan, Ruiqiang Li, Daojun Cheng, Wei Fan, Xingfu Zha, Tingcai Cheng, Yuqian Wu, Jun Wang, Kazuei Mita, Zhonghuai Xiang, Qingyou Xia
    Nucleic acids research 2010:38(Database issue)
    156 Citations (Google Scholar as of 2016-01-27)

    Abstract: The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). Since the draft sequence was completed and the SilkDB was first released 5 years ago, we have collaborated with other groups to make much remarkable progress on silkworm genome research, such as the completion of a new high-quality assembly of the silkworm genome sequence as well as the construction of a genome-wide microarray to survey gene expression profiles. To accommodate these new genomic data and house more comprehensive genomic information, we have reconstructed SilkDB database with new web interfaces. In the new version (v2.0) of SilkDB, we updated the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org.

  • SilkDB: a knowledgebase for silkworm biology and genomics. [PMID: 15608225]

    Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, Jun Yu
    Nucleic acids research 2005:33(Database issue)
    137 Citations (Google Scholar as of 2016-01-27)

    Abstract: The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a approximately 6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn.

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Tags

DNA Expression Phenotype Standard, Ontology and Nomenclature
Bombyx mori
chromosomal mapping ESTs functional annotation gene product microarray expression data

Record metadata

  • Created on: 2015-07-13
  • Curated by:
    • Zhang Zhang [2016-10-19]
    • Zhang Zhang [2016-05-08]
    • Lin Xia [2016-03-28]
    • Mengwei Li [2016-02-20]
Stats