SGD Help: SGD Paper page

The SGD Paper page displays bibliographic and curation information for individual references that are in SGD. "Curation" means that the reference is read by a biocurator and various types of information from it are incorporated into the SGD database (e.g., data are used to support GO annotations, mutant phenotype annotations, Gene Descriptions, etc.). Each SGD Paper page contains three sections: the reference citation and abstract, a summary table of the literature topics assigned to the paper, and an author search tool. Note that if a paper has not been curated, its Paper page lacks a summary table, but contains the bibliographic information and the author search tool.

Contents

  1. Organization of the Curated Paper page
    1. Citation and Abstract
    2. Summary Chart of Topics Addressed
    3. Author Search
  2. Accessing a Curated Paper page

Organization of the Paper page

Citation and Abstract

This section lists the paper citation, the abstract, and other relevant details including publication status and type, SGD's source for the citation, and the publication's PubMed ID. If the publication has multiple authors, only the first author is listed in the citation. All other authors can be found in the Author Search pulldown menu.

When appropriate, several icons are included in this section as links to additional information. The PubMed icon links to the PubMed entry for the publication. If full text is available online, it can be accessed through an Online Journal icon. If no Online Journal icon appears on the page, then SGD does not have ready access to online full text. If there are comments or errata relevant to this citation, either published or personal communications to SGD, they will be linked via a Comments & Errata icon. The absence of the Comments & Errata icon indicates that SGD has not cataloged any comments or errata relevant to this citation.

Summary Chart of Topics Addressed

This section contains a chart summarizing the literature topics covered by the publication. Literature topics are listed as row headings (y-axis) and are assigned in one of two ways:

  • Some topics are addressed in the paper but not with respect to any specific gene(s). These topics are assigned to the paper in general, and are listed under the heading "Topics not linked to Genes". They are designated by green balls.
  • Some topics addressed by the paper are associated with specific genes, which are listed as column headings (x-axis) and are hyperlinked to the appropriate SGD Locus Page. A blue ball in the chart indicates that the paper addresses that topic for that gene.

For example, the table below shows curation for PubMed ID:21363961:

Burrill DR, Silver PA (2011) Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes Dev 25(5):434-9

Curated Paper page

Clicking on the green ball in the table retrieves a page displaying all the references in SGD that have been annotated to that topic through association with a paper and not through association with any genes. (Note that the papers on this page may have other gene-topic associations; thus, there may be some genes listed in the "Genes Addressed" column.)

Clicking on the blue ball retrieves a page that displays other papers in SGD that address the same topic for that gene. More literature associated with a gene, as well as detailed gene information, is available through individual SGD Locus Summary pages.

Author Search

This feature allows users to find contact information or other publications by the authors of the publication. The authors are listed in the first pulldown menu while the search options are listed in the second pulldown menu. The search options include "Papers in SGD," "Colleagues in SGD," "PubMed," and "Google Scholar". Searches for "Papers in SGD" will look for other yeast publications by that author. Searching "Colleagues in SGD" will indicate if that author has voluntarily listed contact information with SGD. Finally, searches using "PubMed" or "Google Scholar" will find publications by that author on any subject. To use the Author Search, choose an author and a search parameter and then click the "Search!" button.

Accessing an SGD Paper page

There are multiple ways to access a Curated Paper page. An SGD Paper icon appears with the citation on any page the paper is referenced in SGD (for example, in the Literature Guide for a gene linked to it). Clicking on the icon leads directly to the Curated Paper page. Citations can be found by author searches or by searching the literature guide of specific genes using SGD's Search tool. Finally, typing the PubMed ID of the paper directly into the Search box will lead to the Curated Paper page.

Go to Reference Search