The ability to add semantic tagging to text in order to designate them as, for example, gene sequences, RRIDs and so on. Currently, gene sequences at eLife is the only live use case.
User stories
Author
As an author, I want to be able to tag a piece of text as a gene sequence so that this information can be picked out for special display, data mining etc.
As an author, I want to be able to see when text has been tagged as a gene sequence so that I can check this has been done correctly.
As an author, I want to be able to remove gene sequence tagging from a piece of text so that I can correct errors.
As an author, I want to be able to add styling (bold, italic etc) to text within a tagged gene sequence so that I can emphasise particular letters.
As an author, I want to be able to edit text tagged as a gene sequence so that I can correct any errors.
But what if . . . ?
Consideration
The only use case for eLife here is the use of named-content[@content-type="sequence"], which is employed for display purposes (so that HTML renderers/CSS can hook onto that element and break a long sequence across multiple lines).
This idea can definitely be expanded to other kinds of content using different @content-type values.
XML requirements
named-content[@content-type="sequence"] is used for gene sequences/primers:
<p>We used the following primer <named-content content-type="sequence">5´-AGCATCGGACCGGCTTTTTCGAACTGCGGGTGGCTCCAGCTAGCCATGGATCCGCGCCCGATGGTGGGACGGTATG-3´</named-content> ... </p>
On occasion these also include other formatting, used for emphasis, such a bold or italic, and this formatting needs to be retained:
If this needed to be extended to other concepts, presumably this could be done with different @content-type values on a named-content element, or similarly with other elements, such as @content-type on p.
Description
The ability to add semantic tagging to text in order to designate them as, for example, gene sequences, RRIDs and so on. Currently, gene sequences at eLife is the only live use case.
User stories
Author
But what if . . . ?
Consideration
named-content[@content-type="sequence"], which is employed for display purposes (so that HTML renderers/CSS can hook onto that element and break a long sequence across multiple lines).@content-typevalues.XML requirements
named-content[@content-type="sequence"]is used for gene sequences/primers:On occasion these also include other formatting, used for emphasis, such a bold or italic, and this formatting needs to be retained:
If this needed to be extended to other concepts, presumably this could be done with different
@content-typevalues on anamed-contentelement, or similarly with other elements, such as@content-typeonp.Mock ups
Proposal