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.

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 PubMed search that looks for papers whose titles or abstracts contain the words "yeast" or "cerevisiae". These papers are reviewed manually by SGD curators, and relevant papers are added to SGD and linked to the appropriate genes. During this process, the references are also classified regarding 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. Please let us know if you think a paper should be added to the database, by using our suggestion form or emailing sgd-helpdesk@lists.stanford.edu. You can also submit specific information about your own publications using our Submit Data form.

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, or protein structure.

Additional Literature: References that use the gene in experiments or describe its homologs 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 (as curated by BioGRID). All references used to make GO and/or Phenotype annotations for a gene are automatically categorized as Primary Literature for that 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 annotations.