The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.

Prefix

sgd

Keywords

ars bibliography/documents bioresource chromatin remodeling chromosomal element nomenclature chromosome, centromeric region epigenetics eukaryotic expression expression data gene gene array gene model annotation gene name genome genome/gene go-term enrichment data image/movie interaction/pathway life science literature annotations defined by experimental results molecular interaction nucleotide ontology ontology/terminology/nomenclature organism organism-specific databases orthologous phenotype plasmid protein protein domain proteomics pseudogene reference genome rna sequence sequence feature strain synthetic genetic array transcriptomics transposable element

License

CC-BY-4.0

Links

Homepage OBO OWL OBO JSON Part of sgd

Publications

1998 Expanding yeast knowledge online

1998 Comparison of the complete protein sets of worm and yeast: orthology and divergence

1999 Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

1998 SGD: Saccharomyces Genome Database

1997 Yeast as a model organism

1997 Genetic and physical maps of Saccharomyces cerevisiae

1997 Molecular linguistics: extracting information from gene and protein sequences

1995 Genetic nomenclature guide. Saccharomyces cerevisiae

https://bioregistry.io/pubmed:39530598

2024 Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements

2016 From one to many: expanding the Saccharomyces cerevisiae reference genome panel

2015 The Saccharomyces Genome Database: A Tool for Discovery

2015 The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations

2015 The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component

2015 The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining

2015 The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes

2015 The Saccharomyces Genome Database Variant Viewer

2015 Biocuration at the Saccharomyces genome database

2015 AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae

2014 The complex portal--an encyclopaedia of macromolecular complexes

2014 Standardized description of scientific evidence using the Evidence Ontology (ECO)

2014 The reference genome sequence of Saccharomyces cerevisiae: then and now

2013 Saccharomyces genome database provides new regulation data

2013 A guide to best practices for Gene Ontology (GO) manual annotation

2013 The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

2013 The YeastGenome app: the Saccharomyces Genome Database at your fingertips

2012 CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations

2012 YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

2012 Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report

2011 Saccharomyces Genome Database: the genomics resource of budding yeast

2011 Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

2009 New mutant phenotype data curation system in the Saccharomyces Genome Database

2009 Saccharomyces Genome Database provides mutant phenotype data

2009 Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns

2007 Gene Ontology annotations at SGD: new data sources and annotation methods

2006 Expanded protein information at SGD: new pages and proteome browser

2006 Saccharomyces cerevisiae S288C genome annotation: a working hypothesis

2006 Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome

2005 Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)

2004 Saccharomyces genome database: underlying principles and organisation

2004 Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

2003 Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins

2002 Saccharomyces Genome Database

2002 Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

2001 Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

2000 Integrating functional genomic information into the Saccharomyces genome database

2009 Using Model Organism Databases (MODs)

Pattern for Local Unique Identifiers

Local unique identifiers in Saccharomyces Genome Database should match this regular expression:
^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$

Example Local Unique Identifier

S000002493   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Saccharomyces Genome Database should match this regular expression:
^sgd:((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$

Example CURIE

sgd:S000002493

Contact

J. Michael Cherry   0000-0001-9163-5180

Identifier Space Owner

Stanford University

A summary of the relations in the Semantic Farm schema can be found here.

In Collection (2)

Global Biodata Coalition - Global Core Biodata Resources Synapse.org external links

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 13 mappings to external registries with 7 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier S000002493 is used to demonstrate the providers available for Saccharomyces Genome Database. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.