Using Model Organism Databases (MODs)
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Model Organism Databases (MODs) represent the union of database technology and biology, and are essential to modern biological and medical research. Research communities are producing floods of new data, of increasingly different types and complexity. MODs assimilate this information from a wide variety of sources, organize it in a comprehensible manner, and make it freely available to the public via the Internet. MODs permit researchers to sort through massive amounts of data, providing access to key information that they might otherwise have overlooked. The protocols in this unit offer a general introduction to different types of data available in the growing number of MODs, and approaches for accessing, browsing, and querying these data. Curr. Protoc. Essential Lab. Tech. 1:11.4.1?11.4.17. © 2009 by John Wiley & Sons, Inc.
Keywords: Genome project; genetics; DNA sequence; gene model; protein function
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PDF or HTML at Wiley Online LibraryTable of Contents
- Overview and Principles
- Basic Protocol 1: General Guidelines for Using a Model Organism Database Using the Saccharomyces Genome Database as an Example
- Basic Protocol 2: Obtaining a Sequence from Gbrowse
- Basic Protocol 3: Using Textpresso to Search Full Text Papers
- Commentary
- Literature Cited
- Figures
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Figure 11.4.1 The SGD home page (http://www.yeastgenome.org), like most MOD home pages, is the main point of entry to the Web site. The home page lists news items and announcements, and provides links to different areas and tools provided by SGD. Ovals indicate the database Search box, a link to the Advanced Search tool, and the Google‐based html Web site search. View Image -
Figure 11.4.2 A locus summary page in SGD showing the different types of information included on a typical gene page. A portion of the page at the top that contains the SGD toolbar and Search box is not shown. A portion of the page at the bottom that contains a gene summary paragraph and references is not shown. View Image -
Figure 11.4.3 Search Results for gene/protein information and functional annotations in SGD from a simple search using the phrase “histone deacetylase.” View Image -
Figure 11.4.4 Search Results for Gene Ontology molecular function terms that contain the words “histone deacetylase.” View Image -
Figure 11.4.5 The top portion of the Gene Ontology detail page in SGD for the molecular function term “histone deacetylase activity.” View Image -
Figure 11.4.6 A view of a portion of S. cerevisiae chromosome II in SGD's version of the GBrowse genome browser. GBrowse allows queries using the Landmark or Region search box, download of DNA sequences using the Reports & Analysis pull‐down, adjustment of the viewing window using the Scroll/Zoom menu, and customization of the tracks shown in the Details field. View Image -
Figure 11.4.7 An example of a text search (“histone deacetylase”) in SGD's version of GBrowse that generates multiple results. View Image -
Figure 11.4.8 Entry page in SGD for the Textpresso text‐mining system. View Image -
Figure 11.4.9 The top portion of a results page in SGD's version of Textpresso for the query “DNA helicase cancer.” View Image
Videos
Literature Cited
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| Arnaud, M.B., Costanzo, M.C., Skrzypek, M.S., Shah, P., Binkley, G., Miyasato, S.R., and Sherlock, G. 2009. Aspergillus Genome Database http://www.aspergillusgenome.org/ (April 8, 2009). | |
| Blake, J.A., and Harris, M.A. 2008. The Gene Ontology (GO) Project: Structured vocabularies for molecular biology and their application to genome and expression analysis. Curr. Protoc. Bioinform. 23:7.2.1‐7.2.9. | |
| Blake, J.A., Bult, C.J., Eppig, J.T., Kadin, J.A., Richardson, J.E., and the Mouse Genome Database Group. 2009. The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res. 37:D712‐D719. | |
| Cherry, J.M., Adler, C., Ball, C., Chervitz, S.A., Dwight, S.S., Hester, E.T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., and Botstein, D. 1998. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26:73‐79. | |
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| Harris, M., and the Gene Ontology Consortium. 2008. The Gene Ontology project in 2008. Nucleic Acids Res. 36:440‐444. | |
| Karolchik, D., Hinrichs, A.S., and Kent, W.J. 2007. The UCSC Genome Browser. Curr. Protoc. Bioinform. 17:1.4.1‐1.4.24. | |
| Kreppel, L., Fey, P., Gaudet, P., Just, E., Kibbe, W.A., Chisholm, R.L., and Kimmel, A.R. 2004. dictyBase: A new Dictyostelium discoideum genome database. Nucleic Acids Res. 2004. 32:D332‐D333. | |
| Müller, H.M., Kenny, E.E., and Sternberg, P.W. 2004. Textpresso: An ontology‐based information retrieval and extraction system for biological literature. PLoS Biol. 2:e309. | |
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| Reiser, L. and Rhee, S.Y. 2005. Using the Arabidopsis Information Resource (TAIR) to find information about Arabidopsis genes. Curr. Protoc. Bioinform. 9:1.11.1‐1.11.45. | |
| Rhee, S.Y. 2000. Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post‐genomic era. Plant Physiol. 124:1460‐1464. | |
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| Shaw, D. 2009. Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. Curr. Protoc. Bioinform. 25:1.7.1‐1.7.14. | |
| Stein, L.D., Sternberg, P., Durbin, R., Thierry‐Mieg, J., and Spieth, J. 2001. WormBase: Network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29:82‐86. | |
| Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610. | |
| Twigger, S.N., Smith, J.S., Zuniga‐Meyer, A., and Bromberg, S.K. 2006. Exploring phenotypic data at the Rat Genome Database. Curr. Protoc. Bioinform. 14:1.14.1‐1.14.27. | |
| Twigger, S.N., Shimoyama, M., Bromberg, S., Kwitek, A.E., Jacob, H.J., and the RGD Team. 2007. The Rat Genome Database, update 2007 – Easing the path from disease to data and back again. Nucleic Acids Res. 35:D658‐D662. | |
| Internet Resources | |
| http://www.agbase.msstate.edu | |
| Resource for functional analysis of agricultural plant and animal gene products. | |
| http://www.arabidopsis.org | |
| The Arabidopsis Information Resource (TAIR): Database of genetic and molecular biology data for the plant Arabidopsis thaliana. | |
| http://crfb.univ‐mrs.fr/aniseed | |
| Ascidian Network for InSitu Expression and Embryological Data (ANISEED): Database for Ciona intestinalis, C. savignyi, Halocynthia roretzi, and Phallusia mammillata. | |
| http://agd.vital‐it.ch | |
| Ashbya Genome Database (AGD): Database of gene annotation and microarray data for Ashbya gossypii and Saccharomyces cerevisiae. | |
| http://www.aspergillusgenome.org | |
| Aspergillus Genome Database (AspGD): Resource for genomic sequence data and gene and protein information for Aspergilli. | |
| http://bovinegenome.org | |
| Database that integrates bovine genomics data with structural and functional annotations of genes and the genome. | |
| http://www.candidagenome.org | |
| Database that serves as a resource for genomic sequence data and gene and protein information for Candida albicans. | |
| http://dictybase.org | |
| Resource for the biology and genomics of the social amoeba Dictyostelium discoideum. | |
| http://ecolihub.org | |
| Centralized resource linking various E. coli online information services, databases, and Web sites. | |
| http://flybase.org | |
| Database of Drosophila genes and genomes. | |
| http://gmod.org | |
| Generic Model Organism Database (GMOD) project: Collection of open source software tools for creating genome‐scale biological databases. | |
| http://www.gramene.org | |
| Data resource for comparative genome analysis in the grasses. | |
| http://www.beebase.org | |
| Hymenoptera Genome Database (BeeBase): Database of genes and genomes of Apis mellifera and Nasonia vitripennis. | |
| http://www.informatics.jax.org | |
| Mouse Genome Informatics: Resource for the laboratory mouse, providing genetic, genomic, and biological data for the study of human health and disease. | |
| http://paramecium.cgm.cnrs‐gif.fr | |
| Database of genomic sequence and genetic data for Paramecium tetraurelia. | |
| http://rgd.mcw.edu | |
| Rat Genome Database (RGD): Database of laboratory rat genetic and genomic data, including information for quantitative trait loci, mutations, and phenotypes. | |
| http://www.yeastgenome.org | |
| Saccharomyces Genome Database (SGD): Scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. | |
| http://www.genedb.org/genedb/pombe | |
| Schizosaccharomyces pombe GeneDB: Database of genetic features, functional annotations, and other information for fission yeast. | |
| http://smedgd.neuro.utah.edu | |
| Schmidtea mediterranea Genome Database (SmedGD): Database for information associated with the planarian genome. | |
| http://www.textpresso.org | |
| Text‐mining system for scientific literature. | |
| http://wfleabase.org | |
| Web service that provides gene and genomic information for species of the genus Daphnia, commonly known as the water flea. | |
| http://www.wormbase.org | |
| Biology and genomic information for Caenorhabditis species. | |
| http://zfin.org | |
| Zebrafish Information Network: Database for the molecular biology and genetics of zebrafish. |
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