Biologists use scientific research on selected biological species to reveal a certain life phenomenon with universal laws. This selected biological species, the model organism, is an important material for scientific research, and an ideal research system. At present, common model organisms used in scientific research are mice, fruit flies, yeasts, nematodes, zebrafish, and Arabidopsis. They have made great contributions to the revealing of life phenomena and the treatment and exploration of human diseases, and they play an irreplaceable role in the process of promoting life science research and medical progress. The development of sequencing technology has led to the accumulation of the genetic information of model organisms, followed by the emerging databases of different model organisms. These databases serve as a platform for researchers to share existing research results and data, and also provide a data basis for subsequent research.
1. MGI
− The Mouse Genome Informatics (MGI) is the international database resource for mice used in the laboratory, and provides a common access point to two large databases at The Jackson Laboratory, the Mouse Genome Database (MGD) and the Gene Expression Database (GXD). As a major model in the Human Genome Project, the inbred mouse is a central experimental animal. MGI provides a well-documented phenotypic, expression and genotypic data resource for mouse for the scientific research community. Information on mouse genes, markers and phenotypes, molecular probes and segments, maps and mapping data, polymorphisms, are all supported with bibliographic references. Totally, MGI provides integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
2. RGD
− The Rat Genome Database (RGD) at the Wisconsin University, collects, consolidates, and integrates data generated from ongoing rat genetic and genomic research. RGD is one of the core resources of rat genomics, dedicated to providing support for disease-based research using rat models.
3. SGD
− The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.
4. TAIR
− The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive linkouts from its data pages to other Arabidopsis resources.
5. LIS
− Developed by the National Center for Genome Resources in cooperation with the USDA Agricultural Research Service (ARS), Legume Information System (LIS) is a comparative legume resource that integrates genetic and molecular data from multiple legume species enabling cross-species genomic and transcript comparisons. LIS is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.
6. Wormbase
− WormBase is an important knowledge resource for biomedical researchers worldwide. WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans, as well as the genome information of other related nematodes and parasitic flatworms.
7. Xenbase
− Xenbase, the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research.
8. ZFIN
− Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio). ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data.
9. Flybase
− FlyBase is the primary repository of genetic and molecular data of the insect family Drosophilidae. As a most extensively studied species, a wide range of data on Drosophila melanogaster are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions.
10. IGSR
− International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set.
11. PomBase
− PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
References
- Jo Wixon. The Jackson Laboratory Mouse Genome Informatics Site: Version 2.3.2[J]. Yeast, 2011, 17(2):134-45.
- Simon N T, et al. The Rat Genome Database, update 2007--easing the path from disease to data and back again [J]. Nucleic Acids Res. 2007 Jan;35(Database issue):D658-62.
- Gonzales M D, et al. The Legume Information System (LIS): an integrated information resource for comparative legume biology[J]. Nuclc Acids Research, 2005 (suppl_1): D660-D665.
- Lee Raymond Y N, et al. WormBase 2017: molting into a new stage[J]. Nuclc Acids Research, 2018(D1):D1.
- Bowes J B, et al. Xenbase: gene expression and improved integration[J]. Nuclc Acids Research, 2010, 38(suppl_1):D607-D612.
- Rachel A D, et al. FlyBase: genes and gene models[J]. Nucleic Acids Res, 2005 Jan 1;33:D390-5. doi: 10.1093/nar/gki046.
