SGD

SGD Help: SGD Curated Paper Pages

Contents


Description & Usage

An "SGD curated paper" is any reference (published or unpublished) that is relevant to SGD and may or may not be manually curated. The SGD Curated Paper page displays bibliographic and curation information for individual references that are in SGD. Each Curated Paper page contains three sections: the reference citation and abstract, a summary table of the topics assigned to the paper by an SGD curator, and an author search tool. Note that if a paper has not been curated, its SGD Curated Paper page lacks a summary table, but contains the bibliographic information, the author search tool, and (when applicable) a sentence indicating that the paper is not yet curated for the genes to which the paper has been linked. Descriptions of the three sections follow:

(1) Citation & 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 communication 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.

(2) 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:
  1. 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.

  2. 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:16452116:

    Schluter A, Ripp R, Fourcade S, Mandel JL, Poch O, Pujol A (2006) The Evolutionary Origin of Peroxisomes: An ER-Peroxisome Connection. Mol Biol Evol 23(4):838-845

    This paper compares nineteen representative eukaryotic genomes to identify peroxisomal proteins that are in common and thus serve as peroxisomal markers. Because the paper specifically discusses several yeast proteins, these proteins are annotated to the relevant topics (in this case, the topics "Fungal Related Genes/Proteins" and "Non-Fungal Related Genes/Proteins"). In addition, because the paper discusses some evolutionary aspects of peroxisomes in general (for example, it provides evidence against a prokaryotic ancestor of peroxisomes), the topic "Evolution" is assigned. Topics that are assigned to the paper but not to genes indicate that the paper provides information about yeast that is more general and cannot be captured by curation to individual genes.

    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.

(3) 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 a Curated Paper page

There are multiple ways to access an SGD Curated Paper page. An SGD Curated Paper icon SGD Papers Entry 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 SGD 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 SGD Curated Paper page.

Other Relevant Links

  1. SGD Pages
    1. SGD Help: Literature Guide
    2. SGD Help: Colleagues
    3. SGD Help: Locus Page
    4. Search SGD

  2. External Sites
    1. PubMed
    2. PubMed Journal Browser: can be used to find the full length journal name from the abbreviation; SGD uses the MEDLINE abbreviations used at PubMed.

Associated Glossary Terms

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