SGD: Saccaromyces Genome Database
- SGD comes from the Department of Genetics at the School of Medicine, Stanford University, and is described by its creators thusly:
- SGDTM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
- [online; accessed 1/28/03; http://genome-www.stanford.edu/Saccharomyces/
Schema in CLSD
SGD tables are found under the 'sgd' schema.The following README files available from th SGD's ftp site provide information about the data that has been loaded into CLSD:
| Table | Field | Type | Description |
|---|---|---|---|
| chrom_feature | Feature | varchar(20) | |
| Gene | varchar(20) | ||
| Alias | varchar(80) | ||
| Feature_Type | varchar(20) | ||
| Chromosome | int | ||
| Start_Coord | int | ||
| Stop_Coord | int | ||
| Strand | varchar(1) | ||
| SGDID | varchar(8) | ||
| SGDID2 | varchar(100) | ||
| Description | varchar(900) | ||
| Date | timestamp | ||
| Version | timestamp | ||
| Genetic_position | numeric(5,2) | ||
| Enzyme | varchar(900) | ||
| reservation_date | timestamp | ||
| standard_name | varchar(1) | ||
| annotation_change | Feature_Action | varchar(20) | |
| Feature_Type | varchar(20) | ||
| Chr | int | ||
| Start_Coord | int | ||
| Stop_Coord | int | ||
| Strand | varchar(1) | ||
| SGDID | varchar(8) | ||
| SGDID2 | varchar(100) | ||
| Feature_cur | varchar(20) | ||
| SGDID_cur | varchar(8) | ||
| Description | varchar(900) | ||
| Note | varchar(900) | ||
| Date | timestamp | ||
| clone | ATCC_name | int | |
| WashU_name | int | ||
| Chr | int | ||
| Start_coord | int | ||
| Stop_coord | int | ||
| external_id | External_ID | varchar(100) | |
| External_Src | varchar(100) | ||
| Gene_ORF | varchar(20) | ||
| SGDID | varchar(8) | ||
| genetic_map | exp_name | varchar(100) | |
| parental_ditype | int | ||
| nonparental_ditype | int | ||
| tetratype | int | ||
| first_division | int | ||
| second_division | int | ||
| distance | numeric(5,2) | ||
| stderr | numeric(5,2) | ||
| interference | numeric(5,2) | ||
| interference_stderr | numeric(5,2) | ||
| note | varchar(100) | ||
| gene1 | varchar(20) | ||
| gene1_ORF | varchar(20) | ||
| gene1_chr | int | ||
| gene1_genetic_pos | numeric(5,2) | ||
| gene1_sgdid | varchar(8) | ||
| gene2 | varchar(20) | ||
| gene2_ORF | varchar(20) | ||
| gene2_chre | int | ||
| gene2_genetic_pos | numeric(5,2) | ||
| gene2_sgdid | varchar(8) | ||
| SGD_CDS_xref | Acc_Numr | varchar(20) | |
| PROTEIN_ID | varchar(20) | ||
| SGDID | varchar(20) | ||
| ORF | varchar(20) | ||
| intron_exon | Feature_name | varchar(20) | |
| Gene | varchar(20) | ||
| Primary_SGDID | varchar(8) | ||
| Feature_type | varchar(20) | ||
| Chr | int | ||
| Start_coord | int | ||
| Stop_coord | int | ||
| Feature_type_sub | varchar(20) | ||
| Start_coord_sub | int | ||
| Stop_coord_sub | int | ||
| registry_genenames | Locus_name | varchar(20) | |
| Other_name | varchar(100) | ||
| Description | varchar(900) | ||
| Gene_product | varchar(900) | ||
| Phenotype | varchar(900) | ||
| ORF | varchar(20) | ||
| SGDID | varchar(8) | ||
| orf_go | ORF | varchar(20) | |
| Gene | varchar(20) | ||
| Length | int | ||
| Process | varchar(100) | ||
| Function | varchar(900) | ||
| Component | varchar(100) | ||
| SGDID | varchar(8) | ||
| orf_go_all | ORF | varchar(20) | |
| Gene | varchar(20) | ||
| SGDID | varchar(8) | ||
| Ontology_aspect | varchar(100) | ||
| GO_Term | varchar(900) | ||
| GOID | int | ||
| Is_not | varchar(1) | ||
| Evidence_Code | varchar(3) | ||
| Reference_no | int | ||
| PubMedID | int | ||
| SP_GI | varchar(20) | ||
| go_annotation | ORF | varchar(20) | |
| Gene | varchar(20) | ||
| SGDID | varchar(8) | ||
| GO_Aspect | varchar(1) | ||
| GO_Term | varchar(900) | ||
| GOID | int | ||
| Evidence_Code | varchar(3) | ||
| go_terms | GOID | int | |
| GO_Term | varchar(900) | ||
| GO_Aspect | varchar(1) | ||
| GO_Term_Definition | varchar(1800) | ||
| phenotypes | ORF | varchar(20) | |
| Gene | varchar(20) | ||
| SGDID | varchar(8) | ||
| Phenotype_type | varchar(100) | ||
| Phenotype | varchar(1000) | ||
| Description | varchar(100) | ||
| gene_literature | pubmed_ID | int | |
| citation | varchar(900) | ||
| gene | varchar(20) | ||
| feature | varchar(20) | ||
| literature_topic | varchar(900) | ||
| SGDID | varchar(8) | ||
| protein_properties | ORF | varchar(20) | |
| SGDID | varchar(20) | ||
| MOLECULAR_WEIGHT | int | ||
| PI | numeric(5,2) | ||
| CAI | numeric(5,3) | ||
| PROTEIN_LENGTH | int | ||
| N_TERM_SEQ | varchar(20) | ||
| C_TERM_SEQ | varchar(20) | ||
| CODON_BIAS | numeric(5,3) | ||
| ALA | int | ||
| ARG | int | ||
| ASN | int | ||
| ASP | int | ||
| CYS | int | ||
| GLN | int | ||
| GLU | int | ||
| GLY | int | ||
| HIS | int | ||
| ILE | int | ||
| LEU | int | ||
| LYS | int | ||
| MET | int | ||
| PHE | int | ||
| PRO | int | ||
| SER | int | ||
| THR | int | ||
| TRP | int | ||
| TYR | int | ||
| VAL | int | ||
| FOP_SCORE | numeric(5,3) | ||
| GRAVY_SCORE | numeric(7,6) | ||
| AROMATICITY_SCORE | numeric(7,6) |
