PMID:19906697
| Citation |
Engel, SR, Balakrishnan, R, Binkley, G, Christie, KR, Costanzo, MC, Dwight, SS, Fisk, DG, Hirschman, JE, Hitz, BC, Hong, EL, Krieger, CJ, Livstone, MS, Miyasato, SR, Nash, R, Oughtred, R, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Dolinski, K, Botstein, D and Cherry, JM (2010) Saccharomyces Genome Database provides mutant phenotype data.Nucleic Acids Res. 38:D433-6 |
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| Abstract |
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD. |
| Links | |
| Keywords |
Computational Biology; DNA, Fungal; Databases, Genetic; Databases, Nucleic Acid; Databases, Protein; Genes, Fungal; Genome, Fungal; Information Storage and Retrieval; Internet; Mutation; Phenotype; Protein Structure, Tertiary; Saccharomyces cerevisiae; Software |
| edit table |
What phenotypes are displayed in SGD?
- Single mutant phenotypes for every gene in the yeast genome
- "representative" phenotypes
- classical yeast phenotypes from pivotal papers
- phenotypes from newly published papers
- Genetic interactions
- Suppression
- Complementation
- Synthetic lethality
- Data from large scale screens for genetic interactions
- Synthetic Genetic Analysis
- Diploid-based Synthetic Lethality Analysis on Microarrays
What is not recorded?
- Mutant phenotypes inferred from assays performed in vitro or in organello
- SGD does not curate every possible phenotype from every paper
How are the phenotype data recorded?
- controlled vocabularies
- an "observable"- main feature of the phenotype
- a "qualifier"- describes the direction or type of change relative to the wild type
- Additional aspects of the phenotype are also described using controlled vocabularies
- mutant type (causal mutation)
- conditions of its occurance (strain background)
- assay preformed (experiment type, chemicals)
Phenotype Annotations
See Help:AnnotationTable for details on how to edit this table.
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| Species | Taxon ID | Strain | Gene (if known) | OMP | Phenotype | Details | Evidence | Notes |
|---|---|---|---|---|---|---|---|---|
| edit table |
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Notes
References
See Help:References for how to manage references in omp dev.
