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Pheno-Pub: a total support system for the publication of mouse phenotypic data on the web

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Abstract

We have developed an open-source database system named “Pheno-Pub” to support a series of data-handling and publication tasks, including statistical analyses, data review, and web site construction, for mouse phenotyping experiments. This system is composed of three applications. “Mou-Stat” provides semiautomatic statistical analyses for a batch of phenotypic data, including a variety of conditions for group comparisons (e.g., different scales of measurement parameters). “Genotype Viewer” and “Strain Viewer” provide representation of genotype-driven and measurement parameter-driven views of phenotypic data; they highlight significant differences in genotypes and between strains, respectively. Direct links from the Strain Viewer web site to the Genotype Viewer web site provide flexible navigation in the exploration of phenotypic data. With these publication tools, phenotypic data can be made available on the Internet by simple operations. This system is expandable for a wide range of uses in phenotypic comparative analyses, including comparisons among different genotypes and strains and comparisons among groups exposed to different environmental conditions. Finally, Pheno-Pub provides advanced usability for both producers of experimental data and consumers of phenotypic information. Therefore, Pheno-Pub contributes significantly to the publication of data in various fields of phenotyping research and to broad data sharing, thereby promoting the understanding of the functions of the entire mouse genome.

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Acknowledgments

We thank Mr. Hideki Tanomura at Hitachi Solutions Co., Ltd., and Mr. Takeshi Matsubara at Visible Information Center Co., Ltd., for the development of Pheno-Pub. We also thank Mr. Kiyota Toguchi and Mr. Tetsuo Miyagi for their help with the implementation of Pheno-Pub. This study was supported by a Grant-in-Aid for Scientific Research from the Japanese Ministry of Education, Culture, Sports, Science and Technology.

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Authors and Affiliations

  1. Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan

    Tomohiro Suzuki, Tamio Furuse, Ikuko Yamada, Yasuyo Kozawa & Shigeharu Wakana

  2. Team for Advanced Development and Evaluation of Human Disease Models, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan

    Hiromi Motegi

  3. Technology and Development Unit for Knowledge Base of Mouse Phenotype, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan

    Hiroshi Masuya

Authors
  1. Tomohiro Suzuki
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  2. Tamio Furuse
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  3. Ikuko Yamada
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  4. Hiromi Motegi
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  5. Yasuyo Kozawa
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  6. Hiroshi Masuya
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  7. Shigeharu Wakana
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Correspondence to Hiroshi Masuya or Shigeharu Wakana.

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Suzuki, T., Furuse, T., Yamada, I. et al. Pheno-Pub: a total support system for the publication of mouse phenotypic data on the web. Mamm Genome 24, 473–483 (2013). https://doi.org/10.1007/s00335-013-9482-y

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  • DOI: https://doi.org/10.1007/s00335-013-9482-y

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