references

It’s All About Access

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Amanda Ehrhardt, MA, JAMA Network

Let’s take a little jaunt through time to before the pandemic days (remember those?) and look at one of the most downloaded and cited articles in the history of the JAMA Network. Perhaps you’ll recognize the title (or, more likely, the author).

As you move toward the reference section of this article by our former president, you may notice that something looks a bit different about the first citation.

It’s subtle, but according to the newest edition of the AMA Manual of Style, 3.15.3, the location of the published and access dates now comes before the URL in electronic references, and there is no longer a period after the URL.

If President Obama’s article were published today, that reference would look like this:

  1. Centers for Medicare & Medicaid Services. National Health Expenditure Data: NHE tables. Published December 3, 2015. Accessed June 14, 2016. https://www.cms.gov/Research-Statistics-Data-and-Systems/Statistics-Trends-and-Reports/NationalHealthExpendData/NationalHealthAccountsHistorical.html

Just as access to health care is important, so is the access date in articles!

Citing Online Journal Articles and Data from Repositories

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The new edition of the AMA Manual of Style is here, and it has nearly 200 more pages on everything from reference citations to the ethical and legal issues associated with medical publishing.

If the amount of new content seems overwhelming, may I suggest starting with the basics?

I dove in by reviewing the References chapter.

Online Journal References

According to section 3.11.4, “Online Journal Articles, Preprints, and Manuscripts,” the basic components of an online journal reference haven’t changed: authors’ surnames and initials, the title of the article, abbreviated name of the journal, publication year, pagination, the date the article was accessed, and the DOI or URL.

What has changed it that the date accessed should now be listed before the DOI or URL, and the URL is not followed by a period.

Data Repositories

I’ve also edited a few articles that included an analysis of data sets from a repository. Data repositories serve as archives for isolated data sets that allow data to be mined for secondary use in research. In a situation like this, the data set used and the original source for the data should be cited.

In the example shown below, the information for the original source for the data is listed first, followed by the name of depository, the date of data deposit, and the DOI for the data set.

DeLeon TT, Almquist D, Kipp BR, et al. Data from: Assessment of clinical outcomes with immune checkpoint inhibitor therapy in melanoma patients with CDKN2A and TP53 pathogenic mutations. Dryad Digital Repository. Deposited March 12, 2020. doi:10.5061/dryad.m0cfxpp0g

Accurate references are a critical element of any published article. The updated guidelines on references ensure that readers are directed to additional resources for more information.—Juliet Orellana

Preprints in the Time of COVID

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Fans of the 1985 Gabriel García Márquez novel Love in the Time of Cholera are all too familiar with the concept of pining over something long desired, but luckily for medical editors, the 11th edition of the AMA Manual of Style has been quick to provide necessary and accessible updates for editors to use during the time of coronavirus disease 2019 (COVID-19).

The worldwide effort to provide research on COVID-19 has led to a substantial emerging literature, and many study results and manuscripts have been posted on preprint servers prior to peer-reviewed publication. Thus, medical editors who are working with COVID-19 articles may find that more authors are citing sources from preprint servers, leading to references that are, just like Florentino Ariza’s love life, a bit…complicated.

However, medical editors will not need to inhabit a world of magical realism to solve this dilemma. They only have to refer to the recent update to chapter 3.11.4.1, Preprint and Publication of Unedited Manuscripts. In it, they’ll find that many of the things that made citing these sources cumbersome, such as duplicative ID numbers, have been removed and that the order of elements is similar to other, perhaps more familiar, references.

This update hopefully makes life easier for medical editors during a high-volume time. It may even leave more time for reading for pleasure! I can make a great book suggestion 😉–Amanda Ehrhardt

Where in the World Is the Publisher’s Location?

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If you’re into vintage video games or, like me, came of age watching copious amounts of PBS programming, you may be familiar with a certain raven-haired, scarlet-bedecked, UNESCO World Heritage Site–stealing woman of mystery.

bustle.com

Where was the elusive Carmen headed, and what thrills were in store on the journey to find her and thwart her devious plans?

In the 10th edition of the AMA Manual of Style, reference citations for books and edited books included the publisher’s location, which at times could be as hard to pinpoint as Ms Sandiego herself. However, the journey to find this information lacked the glamor of international espionage and instead featured fruitless online searches and squinting at the minuscule copyright page of a volume from the 70s that Google allowed for preview.

Particularly perplexing were the occasions when a publisher with multiple offices was listed but no indication was given as to which one produced the book in question. So where in the world was the publisher’s location? Boston? London? Berlin? Hoboken?

Luckily, the 11th edition of the AMA Manual of Style recognizes that this struggle was indeed real, and the publisher’s location is no longer required for reference citations for books and edited books (3.12.8). Now the publisher appears directly after the italicized book title and is followed by the publication year. For example: Tinker R. Who in the World is Carmen Sandiego? HMH IP Company Unlimited Company; 2019.

Hopefully eliminating the publisher’s location from references will save you time during your editing process, time that can be better spent spanning the globe in pursuit of a jet-setting villainess…if you can find her.–Amanda Ehrhardt

Resources for References

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Sometimes editing requires a little detective work, especially when the manuscript you’re working on has several incomplete references. You could query the author for the missing information, but with minimal time and effort, you may be able to the find the information you need using 2 free resources: PubMed and Worldcat. Both of these resources have extensive features, and editors can use the basic search interface to find missing reference information.

PubMed is an essential resource for medical editing—I use it nearly every day. If you need to fact-check data from a published journal article or online book, find an abstract for background information on a study cohort, or search for a missing volume or issue number for a journal reference, PubMed is the tool for the job. Let’s use it to find the missing volume and last page of the article in this reference:

Hui D, Hannon BL, Zimmermann C, Bruera E. Improving patient and caregiver outcomes in oncology: team-based, timely, and targeted palliative care. CA: a Cancer Journal for Clinicians. 2018;_(5):356.

We’ll start by typing in the author names in the PubMed search field and hitting enter.

Let’s see what we get!

Voila! Now we have the complete reference, and we can even update the journal title. As an added bonus, the full-text article is available with a click of a button on this page. If I need to do any fact-checking, I can access the article directly from PubMed.

That was quick and easy, but PubMed doesn’t index print books. No problem! Worldcat, the world’s largest library catalog, is another free resource that editors can use to find missing publication information. Worldcat allows you to search the collections of libraries around the world; it’s a great resource for materials published in languages other than English. I primarily use it to find chapter titles and publication information for print books. Let’s give it a try with this incomplete reference:

Erinnerungen, Träume, Gedanken von C.G. Jung 1961; Carl Gustav Jung and Aniela Jaffé.

Although I’m almost certain that this is a reference for a book, I’m going to select the “Everything” tab in the Worldcat search field to capture all of the potential results.

This yields 130 results, but in this case, the first result is a close match for the title and authors. The year doesn’t match the information in the incomplete reference, but if we click the “View all editions” link underneath the reference, we can narrow the results even further.

This is what we get:

This looks like a good match! The title and authors match those listed in the incomplete reference. The year doesn’t quite match, but it’s close. I can now ask the author to confirm the complete reference.

Searching for complete publication information for journal articles and books is quick and simple with PubMed and Worldcat. Although these free databases offer many more features, I use the basic search feature most often. Give them a try, and, of course, always check with the author to confirm that the information that you have is correct.–Juliet Orellana

Looking Forward to the 11th Edition

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At the most recent annual conference of the American Medical Writers Association, we received a sneak peek at some of the changes to come with the AMA Manual of Style 11th edition. AMA Manual of Style Committee Members Cheryl Iverson, Stacy Christiansen, and Annette Flanagin gave an overview of some highlights, including changes to the way references are styled, updates taking into account the growing presence of social media, and changes to nomenclature. Other topics included updates to corrections processes, clarification of authorship guidelines, and data sharing rules.

In this post, I thought I’d share some of the changes that I’m most excited about as an editor, many of which promise to make the editing process easier and more intuitive. Several new guidelines for styling references caught my attention. For example, electronic references in the current edition mirror traditional references with the addition of a URL in the middle of the reference and a date accessed at the end. The new edition will put URLs at the end of a reference, similar to how DOIs currently appear. Another welcome change is the omission of publisher locations from references to books and reports, which seems sensible given the multinational nature of publishing and the increasing move toward digital formats.

An update to the style of tables and figures was also covered in the presentation. Starting with the 11th edition, column heads in tables and axis labels in graphs will appear in sentence case capitalization rather than title case. Table and figure headings and labels in scientific publishing often contain a great deal of text, making it all the more important to display that text in a way that’s as easy as possible for readers to parse. In addition to saving space, the use of sentence case capitalization throughout figures and tables will make these elements appear more standardized and easier to read.

The new edition also makes some helpful distinctions between AMA style preference and alternatives considered acceptable. For example, it is now acceptable to use of “they” as a singular pronoun. In addition to circumstances in which “they” is a person’s preferred pronoun, this construction can also be helpful in preserving patient confidentiality (eg, avoiding the disclosure of patients’ sex in a small sample size to preserve anonymity).

Many other exciting changes are anticipated with the upcoming 11th edition. Stay tuned for more!—Heather Green

 

 

Pharmaceutical Company Names

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The pharmaceutical industry is ever-changing, and it’s hard to keep up with new ownership and branding. When editing sections of manuscripts with a lot of pharmaceutical company names, such as the conflict of interest disclosures, I typically find all sorts of spellings of the names, even for the same company within the same paragraph. According to the Business Firms subsection (14.7) of the AMA Manual of Style, the name of the company should appear exactly as the company uses it but with omission of the period after abbreviations. Furthermore, terms such as Company and Corporation should be spelled out if the term is spelled out in the company name. The best way to determine how to spell a company’s name is to check the official company website. Following are a few examples of company names that I frequently see misspelled or misrepresented:

Boehringer Ingelheim

Bristol-Myers Squibb

Daiichi Sankyo (hyphenated in the logo but not elsewhere on the company website)

Eli Lilly and Company

GlaxoSmithKline

Merck & Co

Also keep in mind that some pharmaceutical companies have multiple business units (ie, biologics, medical devices) or different names depending on the country. In these cases, it may be necessary to query the author to ensure that the correct name is used.—Sara M. Billings

 

Questions From Users of the Manual

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Q: Section 3.12.5 describes how to cite books with editors and translators but there is no example showing how to cite a book with both an editor and an editor in chief. Should only the editor in chief be cited if one is given for a book?

A: No, I would not exclude other editors’ names if an editor in chief is given. You could extrapolate from the example in section 3.12.5 that shows how to cite an editor and a consulting editor. In that example, repeated below, just replace “consulting ed” by “ed in chief.”

Klaassen CD. Principles of toxicology and treatment of poisoning. In: Hardman JG, Limbird LE, eds. Gilman AG, consulting ed. Goodman and Gilman’s The Pharmacological Basis of Therapeutics. 10th ed. New York, NY: McGraw-Hill Book Co; 2001:67-80.

Q: When you cite an online reference that will require a password to access the reference, should you include in the reference citation some indication that access is restricted?

A: We wrestled with this question when preparing the current edition and decided against it because different users would have different access rights.

Q: When citing the same work 2 or more times in a manuscript, do you continue to use the same superscript reference number, or do you use a different superscript reference number and relist the work multiple times in the reference list?

A: It is our style to give a reference one number and to refer to it by that number every time it’s cited. This policy is not stated specifically in the manual and perhaps in the next edition it should be. In the current edition, page 44 discusses the situation in which an author might want to cite different (and specific) page numbers from the same reference. The style used is based on the assumption that a reference number “sticks” throughout a manuscript.

Q: Your manual (pp 22 and 183 in print) advises that clinical trials should be registered and that the URL of the registry and the identifying number should be published as a part of the manuscript. Is this still true if the clinical trial has been terminated?

A: Yes, the identifier should be given even if the clinical trial has been terminated. Anyone who chooses to go to the URL provided will be able to read about the trial and will also see there that it has been terminated.—Cheryl Iverson, MA

Questions From Users of the Manual

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Q: I am writing a manuscript in which I want to include the dates that a list of products were first marketed. The database from which I got the information is a subscriber-only database. This seems to be the only place that has the information I want to use. Are such subscriber-only databases allowable to include in a reference list?

A: This question was one we had to address when working on the chapter on reference citation style and the answer we decided on was YES, these may be included in a reference list. (We did not address it specifically for a subscriber-only database, but this question also arises with reference to journal articles that are password-protected/available only to subscribers.) The rationale was 2-fold. First, if there is another place that the information can be obtained that is not behind a “wall,” then of course you might want to consider using that reference instead of the one that is not easily available to all. But, as you indicated in your case, sometimes there is no “free” site for the information you want to reference, and it’s important to acknowledge your source—even if access to it is limited. Second, thinking back to the days before people were citing much online material (and those days were not that long ago, were they?), reference lists frequently cited books that might be out of print or other sources that might not allow easy access. This doesn’t seem a reason not to include the material, even though it might be an annoyance to online readers to find that the source is not freely available, so YES.

Q: How would you cite a webinar?

A: I would extrapolate from the style recommended for citing an audio presentation:

Christiansen S. Medical copyediting with AMA style [webinar]. December 15, 2011.  http://www.copyediting.com.  Accessed April 6, 2012.

Q: In section 14.12, you state “Use the abbreviation [of units of time] only in a virgule construction and in tables and line art.” Does this mandate the use or merely allow the use of these abbreviations in these instances?

A: The answer is short. It does not mandate so much as allow, although units of measure are almost always abbreviated in column heads and stubs in tables and on axes in line art in our journals because of space considerations.—Cheryl Iverson, MA

 

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