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Maria Costanzo, Ph.D. Saccharomyces Genome Database

Organization and Presentation of Biological Information in the Saccharomyces Genome Database (SGD). Maria Costanzo, Ph.D. Saccharomyces Genome Database Department of Genetics • Stanford University School of Medicine. The Locus page is SGD’s basic unit.

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Maria Costanzo, Ph.D. Saccharomyces Genome Database

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  1. Organization and Presentation of Biological Information in the Saccharomyces Genome Database (SGD) Maria Costanzo, Ph.D. Saccharomyces Genome Database Department of Genetics • Stanford University School of Medicine

  2. The Locus page is SGD’s basic unit • Information from the literature is sorted to the appropriate Locus pages. • Principles of Locus page design: • user-friendly, clear and logical navigation paths • consistent format that becomes familiar to users • centralized data: all information relevant to each locus is displayed on or linked to its Locus page

  3. Short tour of a typical Locus Page http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=his7

  4. How do users access Locus pages? • SGD Quick Search takes text as input, searches 6 fields • Chromosomal Features Search allows users to combine multiple criteria http://db.yeastgenome.org/cgi-bin/SGD/search/featureSearch • GO Term pages list all genes annotated to a term http://db.yeastgenome.org/cgi-bin/SGD/GO/go.pl?goid=5739 • Many other avenues

  5. GO term page

  6. Brief outline of the curation process • Literature loaded automatically • Curators review literature associations to genes • Curators read abstracts, select Literature Guide topics • Based on content of abstracts, curators may decide to update GO annotations, Description, other information on Locus page. In this case, they often read the full text. • Literature curation often leads to addition of new terms to the Gene Ontology, or to revisions of existing terms

  7. Summary • We aim to: • collect all information relevant to a locus • organize and display it in a logical, easily understandable fashion • change the content of the Locus page as frequently as necessary to accommodate new types of data, while preserving the familiar look and layout of the page

  8. SGD staff E-mail: yeast-curator@genome.stanford.edu

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