Edifix uses the JATS specific-use attribute in five different contexts within the JATS XML returned from the service:
- font face format changes in elements where JATS does not support font face markup (e.g. person-group)
This FAQ describes how Edifix uses specific-use in all five contexts.
Edifix uses the JATS specific-use attribute in the mixed-citation element for three purposes:
- to indicate reference status for billing
- the status of a reference for an end processor
- font face changes for specific JATS elements
mixed-citation specific-use attribute values
For each reference processed, Edifix uses one of the four following values in the specific-use attribute of the mixed-citation element:
- restruct: the reference has been fully parsed (i.e., semantically meaningful tags have been applied to all significant text in the reference), and the reference has been restructured with a reference template. This value will only appear in journal, book, and book chapter references, because those are the only reference types for which Edifix applies a reference template to restructure the reference.
- parsed: Edifix has fully parsed the reference, but has not restructured it. This value will typically appear in references to preprints and data sets. It will appear in references to conference proceedings when they are fully parsed by Edifix. This value may also appear in references to online sources if the content is fairly simple (e.g., author, title, URL, and access date) and fully parsed.
- unparsed: Edifix has partially parsed the reference (e.g., authors and year, but nothing else), or Edifix has not parsed the reference at all. Common examples of unparsed references are complex references to books or conference proceedings that include elements not expected or recognized by Edifix, references to dissertations, and references to legal documents.
- linked: Edifix has not restructured the reference, which may be either parsed or unparsed, but Edifix has successfully linked the reference to Crossref. In many cases Edifix is unable to fully parse a reference, but it is able to tag the author(s), title, and year. Using these three elements, Edifix may be able to link the reference to Crossref. In this situation, specific-use will have the “linked” value rather than the “unparsed” value.
mixed-citation specific-use values for billing
To account for billable references, Edifix considers the specific-use attribute of the mixed-citation element and the editorial style template with which it restructures the reference
- For all editorial styles except "No Format," Edifix counts as billable all references where specific-use is "restruct" or "linked".
- For the “No Format” editorial style template: Edifix bills all references that are "parsed" or "linked". When using this editorial style template, references are never restructured, therefore processing completes when references are fully parsed, with specific-use="parsed".
→ Any reference with a valid DOI is considered “linked”, even if the DOI was provided by the author. Edifix verifies that DOI is valid using multiple link services including Crossref.
mixed-citation specific-use values for processing
These specific-use attribute values provide the ability to control the display or subsequent processing of references. The attribute is left to your system to leverage or ignore.
For example, in the user interface Edifix displays references with specific-use=“restruct” in black type. Edifix displays all other references in gray when using any template except “No Format.” The display formatting indicates that any reference in gray may need additional copyediting. However, when the “No Format” template is used, any reference that is “parsed” is displayed in black, and all other references appear in gray to indicate those which may need additional tagging.
When an original reference submitted to Edifix contains a DOI provided by the author/user, the pub-id element applied to the DOI will have the additional attribute specific-use=“author” to distinguish it as an author-provided DOI.
In June 2020, Edifix added validation of all author-provided DOIs, whether registered with Crossref or any other registration agency. The status of all DOIs will be one of the following:
- Verified as a Crossref DOI: no comment added
- Verified as registered with a registration agency other than Crossref: Edifix adds a mixed-citation annotation comment that indicates the registration agency where the DOI has been deposited (e.g., DataCite)
- Unverifiable with any registration agency: Edifix includes a mixed-citation annotation comment that indicates the DOI is invalid
Note: If the original reference has no DOI, and a DOI is added to the reference via Crossref lookup, no specific-use attribute is added to the pub-id element.
annotation / p@content-type="warning"
Since June 2021, when Edifix adds a comment to a reference, the p element (with @content-type=“warning”) containing the comment also has a specific-use attribute with a numeric code specific to the comment added. The numeric code corresponds one-to-one to comments found in the Edifix configuration files.
By interpreting this number, a processor can reliably further post-process the comments (e.g., dropping comments that may not be of concern to a specific audience, or replacing the text of comments with text that may be more appropriate to a specific audience).
For a list of these comments and the associated numbers that Edifix may insert into the resulting JATS XML, please contact Inera.
Since May 2021, when Edifix flags a reference for having a journal title that is in the Cabells Predatory Reports database, the source element will have the hash ID for the specific Cabells record in the specific-use attribute.
Note that the initial implementation of Cabells reference processing in Edifix is available to all Edifix customers. When the beta period ends, a Cabells account will be required to obtain detailed information about references that appear in the Cabells Predatory Reports database. At that time, the Cabells hash ID will only be available in the specific-use attribute if the Edifix account processing the reference is associated with a valid Cabells account.
Also note that in some infrequent cases, Edifix will match a journal name to more than one Cabells record. In these cases, two or more hash IDs will appear in the specific-use attribute, delimited with a “|”.
<pub-id pub-id-type=“doi” specific-use=“author”>
<p content-type=“warning” specific-use=“9999999”>
specific-use to indicate font face format changes
In some cases, Edifix includes a specific-use attribute to indicate font face changes (bold, italic, underline). This happens when the JATS DTD does not allow these font face changes inside the element and does not allow the font face changes to include a semantic element. For example, in some editorial styles, the year is presented in bold. But even in the JATS archiving and interchange DTD, the following markup examples are not valid:
To accommodate this situation, when a year needs to be presented in bold, Edifix uses this markup:
The elements where Edifix may use specific-use to represent font face changes are:
- person-group (when an entire author group is presented in bold, as in the reference style for ASM Press)
The values that may appear in the specific-use attribute in this context are "bold", "italic", and "underline".
Note: Edifix includes these specific-use format values in both exported JATS XML and exported Display JATS XML. When using the Display JATS XML and converting it to HTML, you will need to include handlers for these cases of specific-use in your transformation so that font face changes will be correctly shown to the end user.