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plazi / TaxPub

TaxPub Extension of the Journal Publishing Tag Set NISO JATS Version 1.1 (ANSI/NISO Z39.96-2015)

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what is the attribute for an id for Zoobank. Phycobank etc,

myrmoteras opened this issue · comments

commented

how is the MycobankId annotated: 844399 and why?

<object-id xlink:type="simple" object-id-type="MycoBank">844399</object-id>

or

<object-id xlink:type="simple" object-id-type="MycoBank">http://phycobank.org/844399</object-id>

or

<ext-link ext-link-type="uri" xlink:href="http://phycobank.org/844399">http://phycobank.org/844399</ext-link>

or

<named-content content-type="phycobank" xlink:href="http://phycobank.org/103328">Phycobank 103328</named-content>

commented

<object-id> is defined as "Unique identifier (such as a DOI or URI) for a component within an article (for example, for a figure or a table)." That is, it is an identiifer for an object in a publication, like a table, figure, section, treatment, etc... (https://jats.nlm.nih.gov/publishing/tag-library/1.3/element/object-id.html)

<ext-link> is defined as "Link to an external file or resource.", i.e, a uri which will create a hyperlink to an extrnal resource. Note that the usage guidelines distingguish it from the <uri> element: "Loosely put, an external link ) element is intended to act as a link; a URI element identifies a URI (such as a URL) in the text, but may or may not be a traversable link" See:

https://jats.nlm.nih.gov/publishing/tag-library/1.3/element/ext-link.html

and

https://jats.nlm.nih.gov/publishing/tag-library/1.3/element/uri.html

<named-content> is defined as "Word or phrase whose content/subject matter has distinct semantics or content-related significance.". I.e.,it is a generic element which could be used for fairly anything.

In the case of a mycobank identifier <exit-link> is probably the least best option, because it is not really declaring that the the tagged content is an identifier, just a link. Strictly speaking, <uri> is probably the best option. if the identifier is indeed a URI. By my read <object-id> may be inappropriate as its arguable that the identifier string lijke the mycobank id is citing something external, not providing an identifier so that a component/object of the article can itself be cited. I confess, I was not aware of the subtlety of the definiton of <object-id>. That leaves<named-content> as the best way to mark something as an identifier when it is not a URI

commented

@tcatapano now I am confused.

here you write That leaves<named-content> as the best way to mark something as an identifier when it is not a URI and in the email you metion p28 for a correct example. But this one is using <object-id>

<tp:material-citation> <object-id content-type="arpha">B5596AA1-CDF9-DDA3-D5CD-D922E1723751</object-id>

commented

May be should differentiate:

identifiers created in the article

the case where an new material citation is published and with it an identifier created (UUID),

<object-id content-type="arpha">B5596AA1-CDF9-DDA3-D5CD-D922E1723751</object-id>

the case where an identifier is created for internal use

In the case of a figure citation (e.g. Fig 4), and internal identifier is used to link wit the respective figure.

In this case an <object-id> is used

the case where an external identifier is cited, like in the case of accession number

<named-content> as the best way to mark something as an identifier when it is not a URI

that means, this

<object-id content-type="ipni" xlink:type="simple">urn:lsid:ipni.org:names:77302868-1</object-id>

shold be rewritten like the following example as

<named-content content-type="phycobank" xlink:href="http://phycobank.org/103328">Phycobank 103328</named-content>