Take our Survey

SGD Help: Literature page

The Literature page for a gene can be accessed via the gene's Literature tab and lists all manually curated references for the specified gene. The references can be browsed by literature type (Primary, Additional, Review) or by their annotations to the gene in SGD. Each citation includes links to the paper in SGD and PubMed, as well as PubMed Central and/or a Full-Text article, whenever available. SGD gathers references via an automated search of PubMed for papers whose titles or abstracts contain “yeast” or “cerevisiae;” these papers are reviewed manually by curators and linked to relevant genes and literature topics by SGD curators.

Contents

  1. Literature Collection & Curation
  2. Literature page Organization
    1. by Reference Type
      1. Primary Literature
      2. Additional Literature
      3. Review
    2. by Annotation Associations

Literature Collection & Curation

SGD gathers references via an automated search that looks in PubMed records for papers whose titles or abstracts contain the word "yeast" or "cerevisiae". These papers are reviewed manually by SGD curators, and relevant papers are added to the database and linked to the appropriate genes. During this process, the references are also classified as to the type of information they contain for a gene. A reference may be further reviewed and used to make annotations to phenotype, Gene Ontology (GO), or Regulation annotations and/or to update the Locus Summary page for a gene.

Literature curation is an ongoing project at SGD. For some loci, we have not yet reviewed all of the literature. The Literature Curation Summary shows the number of curated references and the date a paper was last curated for this feature.

In addition, SGD users often let us know when we have missed a paper relevant to S. cerevisiae. Please contact us if you think a paper should be added to the database, by using our suggestion form or emailing sgd-helpdesk@lists.stanford.edu

Literature page Organization

by Reference Type

Primary Literature: Literature that either focuses on the gene or contains information about the gene’s function, biological role, cellular location, phenotype, regulation, structure, or disease homologs in other species.

Additional Literature: References that show experimental evidence for the gene or describe homologs of the gene in other species, but for which the gene is not the paper’s principal focus.

Review: A review article that contains information about the gene of interest. These papers general do not contain original research.

Note: The initial assignment of "Primary Literature" and "Additional Literature" topics for papers added to SGD before 2013 was made in a semi-automatic fashion based on their past assignments to a different set of topics. If you see a paper listed in "Primary Literature" that would be better categorized as "Additional Literature" (or vice versa), please contact us by using our suggestion form or emailing sgd-helpdesk@lists.stanford.edu.

by Annotation Associations

SGD curators read the full text of papers to make experimentally based annotations to Gene Ontology (GO) terms, phenotypes, and regulation information. In addition, SGD displays interaction data for a gene based on BioGrid, associating each piece of interaction evidence with the reference BioGRID uses to make the annotation. All references used to make annotations for a gene are automatically Primary Literature for the gene, although not all Primary Literature references for a gene are used to make annotations. The references on a Literature page for a gene can therefore be browsed for those specifically associated with 1) GO terms, 2) phenotypes, 3) interactions, or 4) Regulation evidence.