references

URLs Gone Bad: Fixing Broken Links

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Link rot is a term that describes the tendency of URLs to fail over time because the page has been deleted or moved. Because of the lag between writing and publication, link rot can be a problem even before content is posted, so all URLs should be checked for dead links.

URL-Checking Software

A number of tools exist that check and verify URLs. Well-written URL-checking software can report dead links and some redirected (forwarded) links. Even if a URL appears to work and is not obviously broken, however, the content of the page may have changed, and it may no longer be what the author intended to cite. Because of this issue and others explained below, it’s not possible to detect all bad links automatically. Therefore, a copy editor should check all URLs manually at least once during the publication process, verifying that the content of the page matches the citation context.

The Link Works, but Is the Content Right?

The content of a web page can change at any time. For example, many government agencies report statistics regularly, archiving or deleting the old report once the new one becomes available. Here’s a reference from the Administration on Aging:

Department of Health and Human Services. A profile of older Americans: 2007. http://www.aoa.gov/AoARoot/Aging_Statistics/Profile/index.aspx. Accessed April 7, 2012.

This URL is valid, but the title on the page is now “A Profile of Older Americans: 2011.” As you scroll down the page there are links to previous profiles, including the 2007 version cited by the author, which now has a new URL:

http://www.aoa.gov/AoAroot/Aging_Statistics/Profile/2007/index.aspx

In this case no change is really needed; the URL is still valid, and the report the author referenced is available from this same page. If there’s any doubt about whether the content of the URL is what the author meant to cite, he or she should review and verify changed URLs (assuming time permits).

Broken Link? Google It

Here’s a sentence from an author-submitted manuscript that includes a broken URL:

To search for gene network pathways, we searched BioCarta, KEGG, and Reactome pathways and available software programs (https://www.affymetrix.com/products/software/compatible/pathway.affx).

A good tool to investigate and repair a broken link is Google. Search the title or a detailed description, in this case “Affymetrix compatible gene network pathways software.” The first result of this search,

http://www.affymetrix.com/partners_programs/genechip_compatible/genechip_compatible.affx

looks promising, and, if you click on the Pathway tab on this page, the heading is “Pathway/Network Analysis,” indicating that this new URL fits the citation context well.

It’s Really Broken: Keep the URL but Kill the Hyperlink

If a title or detailed description search fails to find a match for a source with a broken URL, ask the author to provide another source or another way to access the same source. If there’s not time to consult the author or if the author replies that there is no other way to access the reference, leave the URL in place to indicate how the author accessed the source, but remove the hyperlink.

Here’s an example from another author-submitted reference list, with the URL in place but the hyperlink removed:

Kittler H. Dermatoscopy: introduction of a new algorithmic method based on pattern analysis for diagnosis of pigmented skin lesions. Dermatopathol Practical Conceptual. 2007;13(1). http://www.derm101.com/dynaweb/resources/milestones/49057/@Generic__BookView/49067;cs=chapview.wv;ts=chaptoc.tv;chap=dpc1301a03. Accessed February 15, 2010.

A detailed title search doesn’t help in this case. There are no obvious errors in the URL. Also, entering the author’s name in the site search box provided at the home page, http://www.derm101.com/, produces this result: “The term ‘kittler’ was not found.”

Typos in URLs

Copy editors must also be alert for typos, especially errors in punctuation. These are common, and some of them, like the first example below, can be spotted and repaired before checking the reference:

Bad URL: http://www.hospitalcompare.hhs.gov/Hospital/Search/Welcomeasp

Good URL: http://www.hospitalcompare.hhs.gov/Hospital/Search/Welcome.asp

Bad URL: http://www.plosmedicine.org/article/info:doi/10.1371/journal-pmed.0050120

Good URL: http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0050120

Bad URL: https://www.cdc.gov/nchs/nhanes.htm

Good URL: http://www.cdc.gov/nchs/nhanes.htm

Redirected URLs

If, when you attempt to verify a URL, the landing page has a URL different than the one you tested, the URL has been redirected, or forwarded. Redirection is used most often to allow URLs to be updated without breaking the old URLs. The cited URL jumps automatically to the updated URL. To identify redirected URLs, check the browser address window. Here are 2 examples:

Cited URL: http://wwwn.cdc.gov/travel/yellowbookch4-hepb.aspx Redirected to: http://wwwnc.cdc.gov/travel/yellowbook/2012/chapter-3-infectious-diseases-related-to-travel/hepatitis-b.htm

The Rule: When URLs are redirected, it’s preferable to cite the destination URL, both because redirection is sometimes temporary and because redirection sometimes fails.

The Exception to the Rule: Another tye of redirection is the use of vanity URLs to promote a product or a brand. For example, the vanity URL http://jama.com redirects to http://jama.jamanetwork.com/journal.aspx. Unlike updated URL redirects, vanity URLs should be left intact.

More Information

See §3.15, Electronic References in the AMA Manual of Style (pp 64-67 in print) for more information about the correct format for URLs in electronic references.—Paul Frank

Questions From Users of the Manual

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Q: How can a user of your online manual tell if use of a particular word (such as namely) is discouraged?

A:  The first place to look might be chapter 11, Correct and Preferred Usage. But the word you used as an example is not included therein. Or you could try a search in the online manual for the word in question. But that too produces nothing helpful, most likely because we have no “official” policy on this word. Next you might consult a good usage book or the usage notes in the American Heritage Dictionary. Finding nothing anywhere, you could decide on a policy for your publication or the document you are working on, if this seems appropriate or desirable.

Q:  Several questions about the citation of abstracts in a reference list.

  • Section 3.11.9 (Abstracts and Other Material Taken From Another Source) states on page 50 that for abstracts published in the society proceedings of a journal, “the name of the society before which the paper was read need not be included” and that “if a[n abstract] number is included, it is placed in brackets along with the ‘abstract’ designation.” What is not made clear is whether including an “abstract” designation is mandatory or voluntary.   

Should an “abstract” designation be included in the citation to an abstract published in the society proceedings of a journal if neither the society’s name nor an abstract number is being provided? In other words, using example 3 of the book as a base, which of the following would be correct?  

  •  . . . Lemli-Opitz syndrome. Invest Ophthalmol Vis Sci. 2001;42(suppl):S627.  (the reference is not identified as being an abstract)

        or

  • . . . Lemli-Opitz syndrome [abstract]. Invest Ophthalmol Vis Sci. 2001;42(suppl):S627.  (the reference is identified as being an abstract)

If the “[abstract]” designation is not mandatory, is it AMA style to delete it when an author includes it (without an accompanying society name or abstract number) in such a reference?

Also, if an abstract is given an abstract number in the place where it is published, is it considered mandatory or voluntary for its number to be included in the reference citation? The text in the manual says “if a number is included” but the meaning of this is possibly ambiguous (included by the journal in which it was published; or voluntarily included by the author who submits the manuscript as a matter of the submitting author’s preference? It seems most likely that it is the latter, but I’m not certain). 

A:  In order:

  • The if  is meant to signify that the designation as an abstract should be included if it is provided.
  • The second version you provided would be preferred. It’s a nice service to readers to let them know that what is referenced is an abstract.
  • Absolutely not. We would never delete it. It too provides a service to readers, helping them to find the abstract referred to, should they be so inclined.
  • You interpreted the manual correctly—the latter is what is intended.—Cheryl Iverson, MA

Questions From Users of the Manual

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Q: Does your style require parenthetical page numbers after the superscript citation of the reference number on all references or just direct quotations?

A: The manual does not “require” page numbers with any in-text citations. If an author wishes to cite different page numbers from a single reference source at different places in the text, the page number or page numbers may be included in the superscript citation and the source appears only once in the reference list. The superscript may include more than a single page number and/or citation of more than a single reference, and all spaces are closed up.

  • These patients showed no sign of protective sphincteric adduction.3(p21),9
  • Westman5(pp3,5) reported 8 cases in which vomiting occurred.

An author may also wish to use such a reference to an exact page after citing a quotation, directing the reader to the page on which the quotation appears. See section 3.6  for more details on this point.

Q: When a reference is cited in the text and the author is named as part of the citation, how should a 2-author citation be mentioned? Or a citation involving 3 or more authors?

A: We recommend the following:

  • Doe and Roe8 reported on the survey.
  • Doe et al10 reported on the survey.

Of course it is also acceptable to cite a reference and not give an author’s name (or authors’ names) in the text, or to use “and colleagues” or “and associates” or similar phrases rather than “et al.”  See the examples below and section 3.7 for more on this.

  • Several investigators13-16 corroborated these findings.
  • Friedman and colleagues11 reported on this at the 2011 American Heart Association meeting.—Cheryl Iverson, MA

 

Citing Electronic Editions: or, Getting on the Same Page

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Copyediting.com recently posted a tip on how to cite a book read on a Kindle or other similar e-reader,1 noting that with the lack of page numbers in such electronic editions this was a “peculiarity” that editors could use guidance on. They provided the guidance offered by the Chicago Manual of Style and the Publication Manual of the American Psychological Association. They noted that the AMA Manual of Style was “quiet on the subject.”

Not liking to remain quiet for long, Stacy Christiansen, our manual’s “Tweeter,” sent a tweet2 using the same example used in the Copyediting.com tip. To wit:

Barr C; senior editors at Yahoo. Shape your text for online reading. In: The Yahoo Style Guide. Kindle ed. New York, NY: St Martins Griffin; 2010.

Tweets don’t allow much space to delve into the finer points, such as how multiple specific citations in this book could be referenced in a single manuscript, which would also help readers who are not seeking the citation on a Kindle find the specific citation. Here is a little more information for a more specific citation, indicating not only the chapter name but also the paragraph number within the chapter:

Barr C; senior editors at Yahoo. Shape your text for online reading. In: The Yahoo Style Guide. Kindle ed. New York, NY: St Martins Griffin; 2010:¶1.

An article in the New York Times3 indicated that this question is of interest to more than manuscript editors—for example, to members of a book group, some of whom read the book under discussion in print and others of whom read it on an electronic reader, but all of whom want to be able to be “on the same page” when they are discussing the book. Furthermore, this desire has been taken seriously by Amazon, which markets the Kindle. The article noted that the Kindle “will now supplement its ‘location numbers’ with page numbers that correspond to physical books.”

Bravo, we might say. The author of the article, however, offers a different perspective by saying that the attempt to “incorporate cues to keep people grounded in what has come before [eg, the page number] or scrap convention completely” is a dilemma for designers of these new technologies. So, as we leap to the future, some of us still find it useful to keep one foot in the not-so-distant past. And there’s a word for that (also noted in the article): skeuomorphs. Long may we live and long may we leap (with glee but caution).—Cheryl Iverson, MA

1. Nichols W. Copyediting Tip of the Week: Citing electronic editions. Copyediting blog. Posted January 18, 2011. http://www.copyediting.com/copyediting-tip-week-citing-electronic-editions. Accessed May 7, 2012.

2. To cite an e-reader. http://twitter.com/AMAManual/status/32154562768928768. Posted January 31, 2011. Accessed May 7, 2012.

3. Brustein J. Why innovation doffs an old hat: Breakthroughs like the Kindle and the iPad retain cues to keep users grounded in what came before. New York Times. February 13, 2011;Week in Review:2.

Digital Object Identifiers (DOIs) for Electronic References

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Electronic references are widely used in scientific publications. Most people are familiar with the URL (uniform resource locator), the address for a page on the Internet. A serious problem with URLs is described by the slang term link rot, the tendency of URLs to fail over time because the content has been deleted or moved. Markwell and Brooks1 found that science education URLs went bad at a rate of more than 10% per year (63% were bad after 5 years 11 months).

The DOI was created in part to address this problem. At the time of publication, DOI names are assigned to content objects themselves; in contrast, URLs are assigned to locations of objects. DOIs are permanent; once assigned, they cannot be changed. Because of the DOI system’s technology, DOI links are persistent—an object’s DOI link continues to work even if its URL changes.

All DOI names have a prefix and a suffix, separated by a forward slash; for example, 10.1001/jama.2009.2. All DOI prefixes begin with the directory code 10, followed by a period and a number identifying the entity that registered the DOI (usually the publisher), in this case the American Medical Association. The DOI suffix is a unique identifier for the content object and is assigned by the entity that registers the DOI; the suffix does not have to have any meaning, although some publishers use the object’s bibliographic information or its ISBN. In this case the suffix comprises the journal abbreviation (jama), the year of editorial processing (2009), and a sequential number (2). By convention, when a DOI is cited, “doi:” precedes the DOI and is set closed up to it.

The process by which a DOI is used to link to a content object is called resolution. There are 2 easy ways to resolve DOIs:

• Any DOI can be converted to a URL by adding the prefix “http://dx.doi.org/”; for example, http://dx.doi.org/10.1001/jama.2009.2. Enter the URL in any Web browser’s address window.

• The International DOI Foundation provides a Web page that resolves DOIs, http://dx.doi.org/. Paste the DOI into the box on this Web page.

To find the correct DOI for an electronic reference:

• The DOI registration agency CrossRef’s simple text query page (http://www.crossref.org/SimpleTextQuery/) locates DOIs for references input as text. Paste the reference into the box on this Web page.

• CrossRef’s fielded search page (http://www.crossref.org/guestquery/) supports a more targeted search.

• Use the click-through link from the PubMed service of the National Library of Medicine (http://www.ncbi.nlm.nih.gov/pubmed/). There’s often a link at the top right of an article’s citation page on PubMed to the article on the publisher’s Web site, and the DOI usually appears there.

See §3.15, Electronic References in the AMA Manual of Style (pp 64-67 in print) for more information about the correct format for DOIs in electronic references.—Paul Frank

1. Markwell J, Brooks DW. Broken links: just how rapidly do science education hyperlinks go extinct? http://www-class.unl.edu/biochem/url/broken_links.html . Updated July 24, 2006. Accessed January 17, 2012.

Citations a-Twitter

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The dizzying speed at which technology has been evolving often leaves those of us entrenched in the world of crediting sources and editing reference lists running to keep up. We have standard citation formats for Web sites (§3.15), publish ahead of print articles (§3.15.1), and e-reader content (Tweet on January 31, 2011). Those of us who edit scientific content do not regularly (if ever) come across a citation to Twitter. That does not mean, however, that Twitter does not offer anything useful to science writers and editors. Government agencies, scientific journals, researchers, and others involved in publishing Tweet constantly.

How, then, should one cite a Tweet? In deciding AMA style position on this, we first had to resolve whether Twitter constituted a standard citable source or was more in the realm of “personal communications” (such as e-mail). We agreed that Twitter does belong in the citations list because it’s in the public domain, anyone can follow the Tweets of a journal or agency, and the individual posts are maintained by date with a lasting link. In addition, the US Library of Congress is to begin archiving all public Tweets, ensuring their searchability and permanence (http://www.loc.gov/today/pr/2010/10-081.html).

The second decision we had to make was what should be included in the citation. Our final Twitter citation style is based on that of a regular Web site reference:

1. @AMAManual. Many now accept “data” as singular. However, JAMA & Archives Journals retain the use of the plural verb with “data.” http://t.co/auYSgGb. http://twitter.com/#!/AMAManual/status/94117252009431040. Posted July 21, 2011.

2. @AMAManual. Style update! “CI” no longer requires expansion at first mention in AMA Style. So, 95% CI instead of 95% confidence interval (CI). http://twitter.com/#!/AMAManual/status/96287318616440833. Posted July 27, 2011.

In the first position is the author, in this case the “handle” or username on Twitter (@AMAManual). Then follows the full Tweet, the URL of that post (found by clicking on the date stamp), and finally the date of posting.

For those writing and editing in the social and behavioral sciences, the APA style blog also has addressed the citation of Twitter (http://blog.apastyle.org/apastyle/2009/10/how-to-cite-twitter-and-facebook-part-ii.html).

We hope this can help avoid citations sounding like a cacophony of Angry Birds.—Stacy L. Christiansen, MA