Abstracts

fred-atherden commented 4 years ago

The abstract(s) for an article.

User Stories

Author

[x] As an author, I want to be able to clearly see the abstract for my article so that I can check it is correct.
[x] As an author, I want to be able to edit an abstract so that I can correct any errors.
[ ] As an author I want to be able to add sub headings to an abstract so that I can structure the content.
[x] As an author, I want to be able to add and remove styling to the text in an abstract so that I can correct any errors.
[ ] As an author, I want to be able to add and remove equations to an abstract so that I can correct any errors.
[ ] As an author, I want to be able to indicate the language for an abstract so that I can add translated summaries to an article.

Production staff

[ ] As production staff, I want to be able to add one or more abstracts so that I can capture a summary of the article.
[ ] As production staff, I want to be able to remove an abstract so that I can correct errors.
[ ] As production staff, I want to be able to set the type of abstract so that I can indicate what kind of summary it is.
[ ] As production staff, I want to be able to change the type of the abstract so that I can correct any errors.

SciELO

[ ] As production staff, I want to be able to add a figure to an abstract so that I can create a graphical abstract.

But what if . . . ?

Considerations

At eLife, when an article is reporting the results of a clinical trial, its abstract will need to be structured with sections and sub-headings as will be detailed in ticket #45. Therefore, we need to allow multiple sections in abstracts.
Some publishers may wish to add more than one type of abstract so that they can include translations, different kinds of summary etc.
Examples of this include eLife's Digest and Impact statement, and SciELO's visual abstracts.
For eLife's digest (@abstract-type="executive-summary"), we want this to be editable by staff but not by authors, since they approve the content before it is loaded to the article.
There are validation requirements on eLife's impact statement (it must be a complete sentence, no longer than 30 words). Are there similar validation requirements for other abstract types and should they be considered as part of the design for abstract?

XML requirements

Structured abstracts must be allowed:

<abstract>
     <sec>
          <title>...</title>
          <p>...</p>
     <sec>
     ...
     <p>...</p>
</abstract>

As well as more simple ones:

<abstract>
     <p>...</p>
</abstract>

The main abstract never has any attributes on it in eLife use-case.

Visual abstracts

SciELO use abstract-type="graphical" for graphical abstracts, containing figures:

...
<abstract abstract-type="graphical">
  <title>Visual Abstract</title>
    <p>
      <fig id="vf01">
         <caption>
            <title>Título</title>
         </caption>
         <graphic xlink:href="1234-5678-zwy-12-04-0123-vs01.tif"/>
      </fig>
    </p>
</abstract>
...

And allow title as a child of abstract (see above).

Translated abstracts

The element trans-abstract should be used. It should have an @xml:lang. Simple translated abstract:

...
<article-meta>
  ...
  <trans-abstract xml:lang="en">
    <title>Abstract</title>
    <p>This article analyses the language ideological debate surrounding the relationship between the future of the Canadian Francophonie, the quality of the language, and the duty of young people to preserve it. The idea that young people in particular are responsible for the deterioration of a language is part of an old and recurring discourse. We examine its resurgence between the fall of 2012 and the spring of 2013 in Acadie, as seen in media texts that share strong argumentative similarities. Through a critical approach, we show that the positions staked out in this debate draw their legitimacy and authority from the ideological foundations of modern political nationalism, which construe language as the central feature of identity and language proficiency as a skill that is accessible to all.</p>
  </trans-abstract>
  ...
</article-meta>
...

Translated abstract with sections:

...
<article-meta>
    ...
    <trans-abstract xml:lang="en">
        <title>Abstract</title>
        <sec>
            <title>Objective</title>
            <p>To analyze the association between socioeconomic situation, clinical characteristics referred and the family history of cardiovascular disease, with the Self-perceived health of young adults education and their implications for clinical characteristics observed.</p>
        </sec>
        <sec>
            <title>Method</title>
            <p>Analytical study conducted with 501 young adults who are students in countryside city in the Brazilian Northeast. We used binary logistic regression.</p>
        </sec>
    </trans-abstract>
    ...
</article-meta>
...

Impact statement

Impact statement's should be captured as abstract[@abstract-type="toc"]

...
<abstract abstract-type="toc">
     <p>Crystal structures of the mouse CMP-sialic acid transporter in complex with both CMP and CMP-sialic acid reveal the mechanisms of substrate selectivity and transport.</p>
</abstract>
...

eLife digest

eLife has content called digests (jargon-free descriptions of the findings in research content). These should be captured as abstract[@abstract-type="executive-summary"]

...
<abstract abstract-type="executive-summary">
   <title>eLife digest</title>
   <p>The cells in our body are tiny machines which, amongst other things, produce proteins. One of the production steps involves a compartment in the cell called the Golgi, where proteins are tagged and packaged before being sent to their final destination. In particular, sugars can be added onto an immature protein to help to fold it, stabilize it, and to affect how it works.</p>
   <p>Before sugars can be attached to a protein, they need to be ‘activated’ outside of the Golgi by attaching to a small molecule known as a nucleotide. Then, these ‘nucleotide-sugars’ are ferried across the Golgi membrane and inside the compartment by nucleotide-sugar transporters, or NSTs. Humans have seven different kinds of NSTs, each responsible for helping specific types of nucleotide-sugars cross the Golgi membrane. Changes in NSTs are linked to several human diseases, including certain types of epilepsy; these proteins are also important for dangerous microbes to be able to infect cells. Yet, scientists know very little about how the transporters recognize their cargo, and how they transport it.</p>
   <p>To shed light on these questions, Ahuja and Whorton set to uncover for the first time the 3D structure of a mammalian NST using a method known as X-ray crystallography. This revealed how nearly every component of this transporter is arranged when the protein is bound to two different molecules: a specific nucleotide, or a type of nucleotide-sugar. The results help to understand how changes in certain components of the NST can lead to a problem in the way the protein works. Ultimately, this knowledge may be useful to prevent diseases linked to faulty NSTs, or to stop microbes from using the transporters to their own advantage.</p>
</abstract>
...

Digests will never contain fig, table-wrap, or xref in eLife's use case - it will only contain quite simple paragraphs and formatting elements - p, italic, bold, ext-link, sub, sup, sc, underline.

JATS abstract types - https://jats.nlm.nih.gov/archiving/tag-library/1.2/attribute/abstract-type.html

Taken from: https://github.com/elifesciences/TextureRequirements/issues/26

fred-atherden commented 4 years ago

I had added the affects-downstream label as I'd assumed abstract[@abstract-type="teaser"] would display on PMC, but having tested this in their article previewer, this is not the case (only the other abstracts appear):

So I am removing it.

NickDuf commented 4 years ago

We feel that the input is duplicated on both the details tab and article tab
See inVision file for design proposal

fred-atherden commented 4 years ago

Note, changed <abstract abstract-type="teaser"> to <abstract abstract-type="toc">.

Melissa37 commented 4 years ago

Note, changed <abstract abstract-type="teaser"> to <abstract abstract-type="toc">.

This is because we're thinking about how Libero Publisher will work. It seems sensible to use an attribute that most other publishers will probably use (or is written into the JATS spec as a suggestion) for content that is for use on the TOC and not the article itself.

libero / editor

Abstracts #38

User Stories

Author

Production staff

SciELO

But what if . . . ?

Considerations

XML requirements

Abstracts

Visual abstracts

Translated abstracts

Impact statement

eLife digest