Contents
chromosome_number[tab]start_coordinate[tab]stop_coordinateIf no coordinates are entered, all the features in the selected chromosome will be retrieved. This latter option will not retrieve data for features that are partially within and partially outside of the input coordinates. If you are uploading a file, note that there should be one Feature/Standard gene name/SGDID per line and the file should be saved as a text file.
| Column |
|---|
| 1) Primary SGDID (mandatory) |
| 2) Feature type (mandatory) |
| 3) Feature qualifier (optional) |
| 4) Feature name (optional) |
| 5) Standard gene name (optional) |
| 6) Alias (optional, multiples separated by |) |
| 7) Parent feature name (optional) |
| 8) Secondary SGDID (optional, multiples separated by |) |
| 9) Chromosome (optional) |
| 10) Start_coordinate (optional) |
| 11) Stop_coordinate (optional) |
| 12) Strand (optional) |
| 13) Genetic position (optional) |
| 14) Coordinate version (optional) |
| 15) Sequence version (optional) |
| 16) Description (optional) |
| Column | Description |
|---|---|
| 1) DB | database contributing the file (always "SGD" for this file) |
| 2) DB_Object_ID | SGDID |
| 3) DB_Object_Symbol | see below |
| 4) Qualifier (optional) | 'NOT', contributes_to, colocalizes_with qualifier for a GO annotation, when needed |
| 5) GO ID | unique numeric identifier for the GO term |
| 6) DB:Reference(|DB:Reference) | the reference associated with the GO annotation |
| 7) Evidence | the evidence code for the GO annotation |
| 8) With (or) From (optional) | any With or From qualifier for the GO annotation |
| 9) Aspect | which ontology the GO term belongs in |
| 10) DB_Object_Name(|Name) (optional) | a name for the gene product in words, e.g. 'acid phosphatase' |
| 11) DB_Object_Synonym(|Synonym) (optional) | see below |
| 12) DB_Object_Type | type of object annotated, e.g. gene, protein, etc. |
| 13) taxon(|taxon) | taxonomic identifier of species encoding gene product |
| 14) Date | date GO annotation was made |
| 15) Assigned_by | source of the annotation (such as "UniProKB", "SGD") |
| Column | Contents |
|---|---|
| 1) Feature name (mandatory) | Systematic name of the genomic feature |
| 2) Feature type (mandatory) | Type of genomic feature, e.g., ORF |
| 3) Gene (optional) | Gene name, if one exists |
| 4) SGDID (mandatory) | The SGDID, unique database identifier, for the genomic feature |
| 5) Reference (mandatory) | PubMed identifier (PMID), if one exists, and unique SGD identifier (SGD_REF) of the reference; each row contains information derived from one reference |
| 6) Experiment type (mandatory) | Type of experiment used to detect the phenotype, e.g., "classical genetics"; additional comments may be in parentheses |
| 7) Mutant type (mandatory) | Classification of the effect that the mutation has on the gene product, e.g., "null", "conditional" |
| 8) Allele (optional) | Name of the mutant allele; additional information such as the amino acid affected may be in parentheses |
| 9) Strain background (mandatory) | Genetic background in which the phenotype was analyzed |
| 10) Phenotype (mandatory) | Observed feature of the mutant strain, and the direction of change relative to wild type |
| 11) Chemical (optional) | Name of any chemicals used in the phenotype assay; additional details such as concentration may be in parentheses |
| 12) Condition (optional) | Conditions under which the phenotype was assayed, e.g., type of growth medium |
| 13) Details (optional) | Additional information relevant to the phenotype |
| 14) Reporter (optional) | Identity of any reporter used to detect the phenotype |
geneA type1 geneB geneA type1 geneC geneA type1 geneD geneB type1 geneX or geneA type1 geneB geneC geneD'type1' in this case is the type of interaction and can take values like 'Two-Hybrid', 'Synthetic Lethality' and so on. This file includes genes that directly interact with the genes from the input list. All interaction data are provided in Cytoscape format.
Note: Interaction data is currently provided in Cytoscape format; however, data will be available in other formats (for example, Osprey, PSI-ML) soon. While we are working on providing these other formats, we are providing a sample perl script that will convert Cytoscape formatted files into Osprey formatted files. You can download this perl script and run it on your local computer.
The file name, which has the process ID appended to it, is descriptive of the type of data it contains and the size of the file is displayed in the last column of the table. Clicking on the file name should download the file to the desktop of your local machine (depending on the browser). The file that contains your data will be available for 6 hours from the time it was requested.
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