vocab
Vocabulary/Taxonomy Name
The name of a taxonomy, ontology, database, term list, thesaurus, index, controlled vocabulary (defined formally), or generic vocabulary (subject area defined informally), etc. that is the source of terms such as keywords and subjects.
Remarks
Usage: There is no fixed list of term sources, and each JATS organization may point to its chosen taxonomies, ontologies, keyword lists, etc. For keywords, named vocabularies include “inspec”,
“medical-devices”, etc. For subjects, named vocabularies include “ipc”, “mesh”, and “unspsc” etc. In cases where there is no named vocabulary, the @vocab attribute may be set to “uncontrolled”.
Vocabulary Attributes: Four attributes are used in this Tag Set to identify terms from a controlled or an uncontrolled vocabulary:
vocab | Name of the controlled or uncontrolled vocabulary, taxonomy, ontology, index, database, or similar that is the source of the term. For example, for a subject term, a value might be the IPC Codes (“ipc”) or MESH headings
(“mesh”). For an uncontrolled term, the value might be
an area of study such as “medical-devices” or merely the word “uncontrolled”. |
|---|---|
vocab-identifier | Unique identifier of the vocabulary, such as (but not limited to) a URI or DOI. For example, for Dublin Core (DCC), the identifier may be http://dublincore.org/documents/2012/06/14/dces/. For CRediT, the identifier may be https://dictionary.casrai.org/Contributor_Roles. |
vocab-term | The content of the element is the display version of the vocabulary or taxonomic term. The @vocab-term attribute holds the canonical version of the same term, as it appears in the vocabulary. For example, if the attribute value is “digitized-vor”, the element might contain the display text “Digitized Version of Record”. |
vocab-term-identifier | Unique identifier of the term within a specific vocabulary, such as (but not limited to) an item number, a URI, DOI, etc. |
Used on these Elements:
<article-version>, <inline-media>, <institution-id>, <compound-kwd>, <compound-subject>, <kwd>, <kwd-group>, <named-content>, <nested-kwd>, <resource-id>, <role>, <subject>, <subj-group>, <term>
| Value | Meaning |
|---|---|
| Text, numbers, or special characters | The name of the vocabulary, taxonomy, ontology, database, term list, index, etc. that is the source of the term named in the element’s content. |
| Restriction | @vocab is an optional attribute; there is no default. |
Example 1
Vocabulary is a CRediT taxonomy term:
... <contrib-group> <contrib> <string-name><given-names>Barbara</given-names> <surname>Johnston</surname></string-name> <role vocab="CRediT" vocab-identifier="http://dictionary.casrai.org/Contributor_Roles" vocab-term="Conceptualization" vocab-term-identifier="http://dictionary.casrai.org/Contributor_Roles/Conceptualization" degree-contribution="lead">study designer</role> </contrib> <contrib> <string-name><given-names>Brooke</given-names> <surname>Jackson</surname></string-name> <role vocab="CRediT" vocab-identifier="http://dictionary.casrai.org/Contributor_Roles" vocab-term="Writing — Original Draft" vocab-term-identifier="http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_original_draft" degree-contribution="lead">writer</role> </contrib> </contrib-group> ...
Example 2
Special characters in CRediT attribute values need to be given as Unicode character references. In narrative text, Unicode character references, general entities, or characters may be used.
...
<contrib-group>
<contrib>
<string-name><given-names>Anne</given-names> <surname>Berns</surname></string-name>
<role vocab="CRediT"
vocab-identifier="http://dictionary.casrai.org/Contributor_Roles"
vocab-term="Writing — Original Draft"
vocab-term-identifier="http://dictionary.casrai.org/Contributor_Roles/Writing_%E2%80%93_original_draft"
degree-contribution="lead">Writing – Original Draft</role>
</contrib>
</contrib-group>
...
Example 3
Vocabulary is a NISO JAV article version descriptor:
...
<article-meta>
<article-id pub-id-type="other">jBMJ.v324.i7342.pg880</article-id>
<article-id pub-id-type="pmid">11950738</article-id>
<article-version vocab="JAV"
vocab-identifier="http://www.niso.org/publications/rp/RP-8-2008.pdf"
article-version-type="VoR"
vocab-term="Version of Record">version-of-record</article-version>
...
<title-group>...</title-group>
<pub-date-not-available/>
...
</article-meta>...
Example 4
Two vocabularies in one keyword group:
... <kwd-group kwd-group-type="library-classifications"> <compound-kwd vocab="LOC" vocab-term="Diseases of the respiratory system" vocab-term-identifier="RC705-779"> <compound-kwd-part>RC705-779</compound-kwd-part> <compound-kwd-part>Diseases of the respiratory system</compound-kwd-part> </compound-kwd> <compound-kwd vocab="Dewey Decimal" vocab-term="Diseases of the respiratory system" vocab-term-identifier="616.3"> <compound-kwd-part>616.3</compound-kwd-part> <compound-kwd-part>Diseases of the respiratory system</compound-kwd-part> </compound-kwd> </kwd-group> ...
Example 5
An ICD10 vocabulary:
...
<kwd-group kwd-group-type="conditions">
<compound-kwd vocab="ICD10" vocab-term="J00-J99">
<compound-kwd-part>J00-J99</compound-kwd-part>
<compound-kwd-part>Diseases of the respiratory system</compound-kwd-part>
</compound-kwd>
</kwd-group>
...Example 6
Generic subject within Dublin Core subjects:
... <kwd-group vocab="dublincore" kwd-group-type="subject"> <nested-kwd vocab="scientific name"> <kwd vocab="scientific name" vocab-term="kingdom">Plantae</kwd> <kwd vocab="scientific name" vocab-term="phylum">Anthophyta</kwd> <kwd vocab="scientific name" vocab-term="class">Monocoty</kwd> <kwd vocab="scientific name" vocab-term="order">Commelinales</kwd> <kwd vocab="scientific name" vocab-term="family">Poaceae</kwd> <kwd vocab="scientific name" vocab-term="genus">Zea</kwd> <kwd vocab="scientific name" vocab-term="species">Z. mays</kwd> </nested-kwd> </kwd-group> ...