D702 Nucleic Acids Research, 2012, Vol. 40, Database issue controlled vocabulary called the ChEBI ontology (11). Phenotypes representing over 17 000 classical and high-throughput phenotype assays have been described and are available from SGD (12). Biochemical pathways Biochemical pathways are manually curated by SGD and provided using the Pathway Tools browser version 15.0 (13). The SGD biochemical pathways data set for S. cerevisiae, one of the most highly curated data sets among all Pathway Tools data sets available, is the gold standard for budding yeast; SGD supports an ongoing effort to update and enhance these data. The Pathway Tools interface provides a complete description of each pathway, with molecular structures, E.C. numbers and full reference listing. The updated pathways browser provides several enhanced features, including download of a list of genes found in a pathway for further analysis with other tools available at SGD. The pathway browser is hyperlinked via the ‘Pathways’ section of the Locus Summary page. The Pathway display is available from http://pathway.yeastgenome.org. Nomenclature SGD continues to maintain the S. cerevisiae genomic no- menclature. Our job is to promote the community-deﬁned nomenclature standards and to ensure that the agreed-upon guidelines are followed in naming new genes or assigning new names to previously identiﬁed genes. Community guidelines state that the ﬁrst published name for a gene becomes the standard name. However, prior to publication, a gene name may be registered and displayed in SGD in order to notify the community of its intended use. If there are disagreements or naming con- ﬂicts, we communicate with the relevant researchers within the community and negotiate an agreement whenever possible. The majority of those working on the gene in question must agree to any nomenclature change before it is implemented in SGD. In addition to maintaining genetic names, SGD ensures that the names of ORFs, ARS elements, tRNAs and other chromosomal features also conform to agreed-upon formats. Over the past 2 years 154 new gene names have been assigned and 21 community-initiated name changes have been processed. Maintenance of the S288C reference genome SGD maintains, updates and distributes the S. cerevisiae reference genome sequence of the commonly used lab strain S288C. The original reference sequence, released in April 1996 (14), was the ﬁrst available eukaryotic genome sequence and has been maintained by SGD ever since (S. cerevisiae S288C reference genome sequence NCBI accession numbers: NC_001133, NC_001134, NC_001135, NC_001136, NC_001137, NC_001138, NC_001139, NC_001140, NC_001141, NC_001142, NC_001143, NC_001144, NC_001145, NC_001146, NC_001147 and NC_001148). Between its original release and 2010, there have been a total of 239 changes to the sixteen nuclear chromosomes. In 2010, a newly determined reference sequence was released, from strain AB972, a direct descendant of S288C and one of the strains used in the original 1996 published sequence (14). The new reference sequence (version 64) was determined by mapping next-generation sequence reads to the previous reference (version 63) then manually inspecting any disagreements between the new sequence and the old reference. The AB972 sequence was released in February 2011 as the new reference genome for S. cerevisiae strain S288C, providing even higher quality sequence from a single consistent strain background for all 16 nuclear chromosomes. Concurrent with the update of the refer- ence sequence we have adopted a reference versioning system; the current version of the reference sequence with chromosomal feature annotation was released as version 64.1. The ﬁrst part of the version number incre- ments when the sequence changes and second part incre- ments when there are changes to the gene models. The current and all previous versions can be downloaded from SGD (http://downloads.yeastgenome.org/sequence/ S288C_reference/genome_releases). With this comprehen- sive update in place, we plan that future differences between the reference and sequenced genes will primarily be represented as variations from the reference. However, a reference genome must take into consideration the best case for that strain and not simply the sequence of one individual; therefore, we will accommodate corrections to non-functional alleles unique to S288C. We have conﬁ- dence that in the near future, the genomes of additional isolates of AB972 and other direct derivatives of S288C will be determined. Differences between these genomes will also be provided as alleles or observed variation of the current reference sequence. Continued annotation and analysis of the S. cerevisiae genome Our understanding of the S. cerevisiae genome is no longer limited to a few commonly studied strains such as S288C (genomics) (15), W303 (cell cycle and budding) (16) and SK1 (sporulation and meiosis) (17). Nextgen sequencing methods have already provided the genomic sequences of tens of S. cerevisiae laboratory and industrial strains (http://downloads.yeastgenome.org/sequence/strains), and will soon provide the genomic sequences for thou- sands of wild isolates. As with other model organisms, comparative genomics of many isolates will provide a new understanding of the full genetic constituent parts of a species. We are compiling S. cerevisiae genomes avail- able from NCBI, selecting genomes based on scientiﬁc or industrial relevance and sequence quality. We currently provide 26 strain genomes available for download and include them in our BLAST and pattern matching (PatMatch) search tools. In addition, homologs to protein-coding genes present in the reference strain have been automatically predicted for 18 genomes. The pre- dicted ORF sequence as well as a ClustalW alignment of all predicted ORFs in all strains is available from the Locus Summary page for each protein-coding ORF. We are developing a pan-genomic representation of S. cerevisiae that includes all protein encoding genes, and their variation, found within any strain of