Keywords and categories

[michael]

Description

Author supplied keywords and categories into which content is sorted.

User stories

Keywords

Author

• (1) As an author, I want to be able to check the keywords so that I can make sure they are correct.
• (2) As an author, I want to be able to edit the keywords so that I can correct mistakes.
• (3) As an author, I want to be able to add new keywords so that I can include missing information.
• (4) As an author, I want to be able to delete keywords associated with my manuscript so that I can make sure that my work is correctly.
• (5) As an author, I want to be able to organize keywords associated with my manuscript by category so that I can make my work more discoverable.

Production staff

• (6) As production staff, I want to be able to add a new keyword category to help organize the content of my journal.

EMBO SourceData

• (7) As an author, I want to add keywords to figure panels so that I can capture the corresponding metadata.
• (8) As an author, I want to be able to edit keywords associated with figure panels so that I can correct errors.
• (9) As an author, I want to remove keywords from figure panels so that I can correct errors.
• (10) As an author, I want to be able to organize keywords associated with my figures by category so that they can be sorted into a database.
• (11) As an author, I want to be able to add a new keyword category to help organize the metadata for a figure.

Categories

Author

• (12) As an author, I want to be able to see which subject areas my manuscript has been associated with so that I check that this information is correct.

Production staff and Erudit

• (13) As production staff, I want to be able to associate subject areas with a manuscript so that I can correct any missing information.
• (14) As production staff, I want to be able to remove subject areas associated with a manuscript so that I can adjust this information when it is incorrect.

But what if . . . ?

Consideration

• eLife has two categories of keywords, 'Author keywords' and 'Research organisms'. Research organisms are populated from a pre-set list, though we should also be able to add custom values to this category.
• At eLife, one or two major subject areas are allowed per research-type article. Non-research content does not need to have a major subject area.
• At Erudit we need to support multiple levels of categories with a maximum of 3 levels.

XML requirements

Article keywords:

There are two categories of keyword for eLife - Author Keywords and Research Organisms. The <kwd-group> element is used for each category. <kwd> for each keyword - all of them are distinct, e.g.

<article-meta>
        ...
        <kwd-group kwd-group-type="author">
                <kwd>long non-coding RNA</kwd>
                <kwd>intellectual disabilities</kwd>
                <kwd>autism</kwd>
                <kwd>genomics</kwd>
                <kwd>gene regulation</kwd>
                <kwd>neuronal development</kwd>
                <kwd><italic>Homo sapien</italic></kwd>
        </kwd-group>
        <kwd-group kwd-group-type="research-organism">
                <kwd>Human</kwd>
                <kwd>Mouse</kwd>
        </kwd-group>
</article-meta>

They are captured as children of article-meta.

<kwd-group> may also contain an @xml:lang attribute and a title:

<kwd-group xml:lang="pt">
  <title>Palavra-chave</title>
   <kwd>Broncoscopia</kwd>
</kwd-group>

Which suggests that there might be more than one kwd-group, one for each language.

eLife only needs <kwd-group> to have the following children:

• title
• kwd

eLife only needs <kwd> to have the following children:

• italic
• sub
• sup

Categories

Captured as <subject> elements in a <subj-group subj-group-type="heading"> element. They are captured as children of article-categories. 0-2 subjects allowed in eLife articles

<article-categories>
     <subj-group subj-group-type="heading">
          <subject>Epidemiology and Global Health</subject>
          <subject>Human Biology and Medicine</subject>
     </subj-group>
</article-categories>

<article-categories>
        <subj-group subj-group-type="heading">
          <subject>Articles</subject>
          <subj-group subj-group-type="heading">
            <subject>Review Articles</subject>
            <subj-group subj-group-type="heading">
              <subject>Report</subject>
            </subj-group>
          </subj-group>
        </subj-group>
        <subj-group subj-group-type="heading" xml:lang="en">
          <subject>Articles english</subject>
          <subj-group subj-group-type="heading" xml:lang="en">
            <subject>Review Articles english</subject>
            <subj-group subj-group-type="heading" xml:lang="en">
              <subject>Report english</subject>
            </subj-group>
          </subj-group>
        </subj-group>
      </article-categories>

eLife are not wedded to the @subj-group-type value given.

@xml:lang can be used on the subj-group element if needed.

Keywords are currently under JATS4R public review .

Examples of keywords in figures as required by EMBO SourceData:

<fig>
<kwd-group kwd-group-type="exp-system">
  <label>Exp. System</label>
  <kwd>immunostaining</kwd>
  <kwd>confocal microscopy</kwd>
</kwd-group>
<kwd-group kwd-group-type="measured-variables">
  <label>Measured-Variables</label>
  <kwd>immunostaining</kwd>
  <kwd>confocal microscopy</kwd>
</kwd-group>
</fig>

Mock ups

Proposal

This will be added by the Texture team after the feature request is discussed and agreed.

[michael]

@Melissa37 please add your user stories here.

[Melissa37]

@michael I have pulled this out of the ticket but it is kept here for now. They cannot be in the ticket without user stories attached to them.

Figure Metadata keywords:

<fig>
<kwd-group kwd-group-type="exp-system">
  <label>Exp. System</label>
  <kwd>immunostaining</kwd>
  <kwd>confocal microscopy</kwd>
</kwd-group>
<kwd-group kwd-group-type="measured-variables">
  <label>Measured-Variables</label>
  <kwd>immunostaining</kwd>
  <kwd>confocal microscopy</kwd>
</kwd-group>
</fig>

[obuchtala]

@Melissa37 I sense some source of confusion re <fig> level keywords. IMO the user-stories are essentially the same as for <article-meta> level keywords. Also there we might consider more scopes for keywords, such as table-wrap or supplementary-material. Wouldn't it make sense to cover all of such cases with one set of user-stories, and add refinements where necessary?

[Melissa37]

Yes I agree. Shall we pull in the figure metadata ones here and close the ticket https://github.com/substance/texture/issues/1249

The tickets we're generating have good user stories that have been verified by Nick, so we'd like to keep that process going. Also, we want to provide the Consortium tickets as we produce them and I am happy to pull the ScourceData use cases and examples into them, with good user stories added, but we can't have our user stories generated by anyone else and before we get to them :-)

[JGilbert-eLife]

@Melissa37, @michael, @source-data - I have added user stories related to figure-specific keywords here. I am assuming these will be at the panel level, but will update if that's not right.