CBSE citation format

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We have standardized on the PubMed citation format throughout the Genome Browser website.

Here is a link to the PubMed Journal Article Citation Format. If you can't find an existing example on this page of how to create a citation, just look up the article in PubMed, then cut/paste the entire citation.

PubMed, in turn, uses the ANSI/NISO Z39.29-2005 Bibliographic References standard pdf as the basis for their format standards.

Direct links to journal articles rather than PubMed are preferred if the journal article is open access.

Note (2/12/2013): All of our NIH-related reports and grants now require PMIDs as part of the citation, so we should probably start including them in our refs moving forward. The hitch is that the PMID isn't always available right away when an article is published, so sometimes must be added later. Some articles also have a PMCID -- those are articles for which PubMed Central has the rights to directly provide free open access. We should include the PMCID when available. In summary: At the end of a standard citation add "PMID: xxxxxx; PMCID: xxxxx"

NOTE (2022): Most references can be automatically built from a URL with the getTrackReferences script (http://genomewiki.ucsc.edu/genecats/index.php/Details_pages_--_conventions).


Citing Works in the References Section

Basic format

Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4;441(7089):87-90. PMID: 16625209

Chapter in a book

Meltzer PS, Kallioniemi A, Trent JM. Chromosome alterations in human solid tumors. In: Vogelstein B, Kinzler KW, editors. The genetic basis of human cancer. New York: McGraw-Hill; 2002. p. 93-113.

The Publications page in the Genome Browser has been updated to reflect this style. Please follow this style for all future citations used in the browser.

To cite electronic sources

If you are citing an electronic source like a web page or web-based software, first see if the web site itself lists guidelines on how you should cite it.

Here is an example of a site whose FAQ section addresses this: RepeatMasker

Format details

  • If there are more than ten authors, list only the first 10 then use et al.
  • If the journal name is abbreviated, do not include periods within the abbreviated name (but do include a period after the journal name, as always). You can find the correct abbreviation for the journal name by viewing the citation in PubMed.
  • If the PubMed or journal website clearly indicates that the paper is open access, link to the full-text version of the article. If a subscription is required, or if you are unsure about whether the article is freely available without a subscription, point to the abstract version instead. (Not all users have access to full-text versions without paying a fee.)
  • List citations in alphabetical order.

Citing Works in Text

Citations format:

(LASTNAME, YEAR)

(LASTNAME et al., YEAR)

Examples:

(Kent, 2010)

(Haussler et al., 2011)

Editing pubs.html

Note that the publications page usually lists the full author list for publications listed in alphabetical order by year. You can output the references with full author list and PMID/PMCID using getTrackReferences with the -v flag (run it with -h to see the help message) e.g.:

getTrackReferences -v 23537068

When you add a publication that includes an author from our group, please also send the link out to the browser-staff email address (or even genecats if it seems broadly interesting). This will help keep the team more informed about what everyone is working on.

Additional Help

The following pages are also helpful:

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