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SGD Help: Reference page

The SGD Reference page displays bibliographic and curation information for each individual reference in SGD. SGD Biocurators read each paper, associating any relevant genes and deriving any possible annotations from the paper. The Reference page displays all of these curated associations. In some cases, it is not possible to derive either specific gene names or more detailed information from the reference, so none will appear on its Reference page.

Contents

  1. Reference information
    1. How are references collected?
    2. How are references curated?
  2. The Reference page
    1. Title (citation)
    2. Abstract Section
      1. Abstract & links to reference
      2. Reference type
      3. Authors
      4. Associated genes
    3. Related references
    4. Annotations made from Reference
      1. Gene Ontology
      2. Phenotype
      3. Interaction
      4. Regulation
  3. Accessing a SGD Reference page


Reference information

How are references collected?

Nearly all references in SGD are identified in PubMed through an automated script, reviewed for relevance to the biology of Saccharomyces cerevisiae, and imported into the database accordingly. On occasion, papers not picked up by the automated search are added to the database by curators.

How are references curated?

All references added to SGD are read and curated by SGD Biocurators. "Curation" means the reference is classified as to the type of information it contains for any mentioned genes (Primary, Additional, Review) and, whenever possible, it is also used as a source for additional annotations to Gene Ontology terms, phenotypes, gene Descriptions, etc. (please see Literature Help for more information).

The Reference page

Title (citation)

The title of the reference page is the citation for the reference, as found in PubMed, including authors, title, journal, volume and issue, and page numbers.

Abstract Section

Abstract & links to reference

The full abstract of the paper, whenever available. Below the abstract is its PubMed ID (PMID), a link to its entry in PubMed, and, when available, a link to the full text article.

Reference type

The publication type (PT), as classified by Medline. This is most often "Journal Article," but can include other information such as categories of Research Support.

Authors

A list of authors for the reference, each author linked to his/her respective author page that lists his/her publications.

Associated genes

Curated lists of genes, categorized according to their degree of study within the paper. Genes listed under "Primary Literature" for the reference are those for which the paper contains functional, process, structural, phenotypic, or other descriptive information about the gene. Genes categorized under "Additional Literature" represent genes that are studied in the paper, but are not the paper's primary focus. For Review articles, genes that are specifically mentioned within the paper are listed. For more information, please the the Literature Guide Help page.

Related References

Related references include any that are either a comment or erratum for the current paper or are the subject of a comment or erratum. This section appears only if there are related references for the given paper. The Related References section provides the citation information, PMID, and relevant links for the related reference. When there is an abstract for the related reference, it also appears in this section.

Annotations made from reference

Gene Ontology

This section appears only when the given reference has been used to make one or more annotations to a Gene Ontology term. In this case, a table will appear, each row listing the gene annotated, its corresponding Gene Ontology (GO) term, any qualifiers, the evidence code used, the annotation source, the date on which the annotation was assigned, and any extension information. This table is sortable and can be filtered, downloaded, and/or fed into the Analyze page. Please see the Gene Ontology Help page for more information.

Phenotype

This section appears only when the given reference has been used to make one or more phenotype annotations. In this case, a table will appear listing the phenotype annotations made from the given reference, including the gene annotated, its phenotype, the type of experiment, any mutant information, strain background, any involved chemicals, and phenotypic details. This table is sortable and can be filtered, downloaded, and/or fed into the Analyze page. For more information on phenotypes, please visit the Phenotype Help page.

Interaction

This section appears only when the given reference has been used to make one or more Interaction annotations. In this case, a table will appear listing the interaction annotations made from the given reference and includes the two interacting loci, the type of interaction (physical or genetic), the assay used to identify the interactions, the action (Bait, Hit), and any modifications or phenotypes. This table is sortable and can be filtered, downloaded, and/or fed into the Analyze page. Note that all of SGD's interaction annotations are from those curated by BioGRID. For more information on interaction annotations, please visit the Interaction Help page.

Regulation

This section appears only when the given reference has been used to make one or more regulation annotations. In this case, a table will appear listing the regulation annotations made from the given reference, including the regulator, its target, the experiment type, the assay used, any construct information, experimental conditions, and strain background. This table is sortable and can be filtered, downloaded, and/or fed into the Analyze page. For more information on regulation data, please visit the Regulation Help page.

Accessing a SGD Reference page

There are multiple ways to access a curated Reference page. A link to the reference contains the first author name, the date, and the PMID and appears on various pages throughout the database. Citations can be found by author searches or on the Literature page for a specific gene. Finally, typing the PubMed ID of the paper directly into the Search box will lead to the corresponding Reference page.