Literature DB >> 33455583

Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center.

Hiroshi Masuya1, Daiki Usuda2, Hatsumi Nakata3, Naomi Yuhara2, Keiko Kurihara2, Yuri Namiki2, Shigeru Iwase2, Toyoyuki Takada2, Nobuhiko Tanaka2, Kenta Suzuki2, Yuki Yamagata4, Norio Kobayashi2,5, Atsushi Yoshiki3, Tatsuya Kushida2.   

Abstract

Online databases are crucial infrastructures to facilitate the wide effective and efficient use of mouse mutant resources in life sciences. The number and types of mouse resources have been rapidly growing due to the development of genetic modification technology with associated information of genomic sequence and phenotypes. Therefore, data integration technologies to improve the findability, accessibility, interoperability, and reusability of mouse strain data becomes essential for mouse strain repositories. In 2020, the RIKEN BioResource Research Center released an integrated database of bioresources including, experimental mouse strains, Arabidopsis thaliana as a laboratory plant, cell lines, microorganisms, and genetic materials using Resource Description Framework-related technologies. The integrated database shows multiple advanced features for the dissemination of bioresource information. The current version of our online catalog of mouse strains which functions as a part of the integrated database of bioresources is available from search bars on the page of the Center ( https://brc.riken.jp ) and the Experimental Animal Division ( https://mus.brc.riken.jp/ ) websites. The BioResource Research Center also released a genomic variation database of mouse strains established in Japan and Western Europe, MoG+ ( https://molossinus.brc.riken.jp/mogplus/ ), and a database for phenotype-phenotype associations across the mouse phenome using data from the International Mouse Phenotyping Platform. In this review, we describe features of current version of databases related to mouse strain resources in RIKEN BioResource Research Center and discuss future views.

Entities:  

Keywords:  Bioresource; Database; Mouse mutation information resource; Ontology; Semantic web; data integration

Year:  2021        PMID: 33455583      PMCID: PMC7811887          DOI: 10.1186/s42826-020-00068-8

Source DB:  PubMed          Journal:  Lab Anim Res        ISSN: 1738-6055


  35 in total

1.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

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Review 2.  The mouse resources at the RIKEN BioResource center.

Authors:  Atsushi Yoshiki; Fumio Ike; Kazuyuki Mekada; Yasuyuki Kitaura; Hatsumi Nakata; Noriko Hiraiwa; Keiji Mochida; Maiko Ijuin; Masayo Kadota; Ayumi Murakami; Atsuo Ogura; Kuniya Abe; Kazuo Moriwaki; Yuichi Obata
Journal:  Exp Anim       Date:  2009-04

Review 3.  Mouse Genome Informatics (MGI) Is the International Resource for Information on the Laboratory Mouse.

Authors:  MeiYee Law; David R Shaw
Journal:  Methods Mol Biol       Date:  2018

4.  Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.

Authors:  Terry F Hayamizu; Richard A Baldock; Martin Ringwald
Journal:  Mamm Genome       Date:  2015-07-25       Impact factor: 2.957

5.  The EBI RDF platform: linked open data for the life sciences.

Authors:  Simon Jupp; James Malone; Jerven Bolleman; Marco Brandizi; Mark Davies; Leyla Garcia; Anna Gaulton; Sebastien Gehant; Camille Laibe; Nicole Redaschi; Sarala M Wimalaratne; Maria Martin; Nicolas Le Novère; Helen Parkinson; Ewan Birney; Andrew M Jenkinson
Journal:  Bioinformatics       Date:  2014-01-11       Impact factor: 6.937

6.  The DisGeNET knowledge platform for disease genomics: 2019 update.

Authors:  Janet Piñero; Juan Manuel Ramírez-Anguita; Josep Saüch-Pitarch; Francesco Ronzano; Emilio Centeno; Ferran Sanz; Laura I Furlong
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

7.  PhenoDigm: analyzing curated annotations to associate animal models with human diseases.

Authors:  Damian Smedley; Anika Oellrich; Sebastian Köhler; Barbara Ruef; Monte Westerfield; Peter Robinson; Suzanna Lewis; Christopher Mungall
Journal:  Database (Oxford)       Date:  2013-05-09       Impact factor: 3.451

8.  Ensembl 2009.

Authors:  T J P Hubbard; B L Aken; S Ayling; B Ballester; K Beal; E Bragin; S Brent; Y Chen; P Clapham; L Clarke; G Coates; S Fairley; S Fitzgerald; J Fernandez-Banet; L Gordon; S Graf; S Haider; M Hammond; R Holland; K Howe; A Jenkinson; N Johnson; A Kahari; D Keefe; S Keenan; R Kinsella; F Kokocinski; E Kulesha; D Lawson; I Longden; K Megy; P Meidl; B Overduin; A Parker; B Pritchard; D Rios; M Schuster; G Slater; D Smedley; W Spooner; G Spudich; S Trevanion; A Vilella; J Vogel; S White; S Wilder; A Zadissa; E Birney; F Cunningham; V Curwen; R Durbin; X M Fernandez-Suarez; J Herrero; A Kasprzyk; G Proctor; J Smith; S Searle; P Flicek
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971

9.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

10.  The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Authors:  Adrian M Altenhoff; Natasha M Glover; Clément-Marie Train; Klara Kaleb; Alex Warwick Vesztrocy; David Dylus; Tarcisio M de Farias; Karina Zile; Charles Stevenson; Jiao Long; Henning Redestig; Gaston H Gonnet; Christophe Dessimoz
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

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  4 in total

Review 1.  Asian Mouse Mutagenesis Resource Association (AMMRA): mouse genetics and laboratory animal resources in the Asia Pacific.

Authors:  Hsian-Jean Chin; Michael S Dobbie; Xiang Gao; James E Hennessy; Ki-Hoan Nam; Je Kyung Seong; Toshihiko Shiroishi; Toru Takeo; Atsushi Yoshiki; Jing Zao; Chi-Kuang Leo Wang
Journal:  Mamm Genome       Date:  2021-09-05       Impact factor: 3.224

Review 2.  Principles for establishment of the stem cell bank and its applications on management of sports injuries.

Authors:  Bao-Shi Fan; Yang Liu; Ji-Ying Zhang; You-Rong Chen; Meng Yang; Jia-Kuo Yu
Journal:  Stem Cell Res Ther       Date:  2021-05-29       Impact factor: 6.832

Review 3.  Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan.

Authors:  Saori Mizuno-Iijima; Toshiaki Nakashiba; Shinya Ayabe; Hatsumi Nakata; Fumio Ike; Noriko Hiraiwa; Keiji Mochida; Atsuo Ogura; Hiroshi Masuya; Shoko Kawamoto; Masaru Tamura; Yuichi Obata; Toshihiko Shiroishi; Atsushi Yoshiki
Journal:  Mamm Genome       Date:  2021-09-16       Impact factor: 2.957

4.  MoG+: a database of genomic variations across three mouse subspecies for biomedical research.

Authors:  Toyoyuki Takada; Kentaro Fukuta; Daiki Usuda; Tatsuya Kushida; Shinji Kondo; Shoko Kawamoto; Atsushi Yoshiki; Yuichi Obata; Asao Fujiyama; Atsushi Toyoda; Hideki Noguchi; Toshihiko Shiroishi; Hiroshi Masuya
Journal:  Mamm Genome       Date:  2021-11-15       Impact factor: 3.224

  4 in total

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