This guidelines describes the tagging requirements for processing XML and guidelines on how to optimize data for Nova system.
Nova has chosen the Journal Publishing Tag Library NISO JATS version 1.0 (JATS tag set)—successor to the NLM Journal Publishing Tag Set Tag Library version 3.0 as the standard for loading XML content into Nova. The elements defined by the JATS DTD are descriptive. For instance, the < journal-title> holds the Journal title. To know details about description of the tag set, tagging details and an extensive library of the descriptive tags, refer the below link.
Because of the size of the JATS tag set, Nova does not accommodate all features available in the tag set. This document depicts the Nova implementation of the JATS tag set. Content that is substantial against this specification will also be legitimate against the JATS tag set, yet the opposite isn’t really evident.
Please ensure that your XML files must valid against the NISO JATS version 1.0 tag set before uploading to Nova.
XML must be well-structured XML according to the Nova XML Recommendation, fully tagged and valid to the JATS 1.0 schema. XML must also meet the requirements in this Nova specification.
Nova accepts Journals in two forms:
- Fully tagged (preferable).
- Metadata-only (for Journals available in PDF only).
Article metadata for both forms must be complete as described here.
Note: Guidelines regarding body tagging do not apply to metadata-only documents.
Declarations required at the top of each XML file are:
- XML version
- Character encoding
- Document Type Definition
<?xml version=”1.0″ encoding=”UTF-8″ standalone=”no”?>
<!DOCTYPE article PUBLIC “-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.0 20120330//EN” “http://jats.nlm.nih.gov/publishing/1.0/JATS-journalpublishing1.dtd”>
UTF–8 character encoding is needed to ensure that characters are translated properly upon import into the Nova database. Content XML may also contain numeric character references (e.g. ř or ř) or the character entity references that JATS supports for special characters. Predefined entities for the ampersand, less-than, and greater-than should be used where the motive is to display the actual characters ampersand (&), less-than (<), or greater-than (>) respectively; the predefined entities ought not be utilized where those characters are part of markup or encodings.
Each article is tagged in XML as an <article>.
Article type attribute
Article types are utilized for indexing and recovery. Imprint the <article> element with the proper @article-type attribute. Article types must be set up in Nova before loading. NLM givesproposed article types at http://jats.nlm.nih.gov/publishing/tag-library/1.0/n-eqr0.html, but any values may be used. Spaces and variations in punctuation and spelling will be read and handled as different article types. The article type is not case-sensitive, however. Article types must be set up in Nova before importing articles.
If the article is part of conference proceedings the article-type must be “proceedings” so that the article will be formatted as conference proceedings.
Correction articles should have <article article-type=”correction”>. In that article, the <related-article> element should have the attribute @related-article-type=”corrected-article”.
<article article-type="correction"> <front> <journal-meta>…</journal-meta> <article-meta> … <related-article xmlns:xlink="http://www.w3.org/1999/xlink" related-article-type="corrected-article" elocation-id="10.1117/1.JBO.17.1.9765173" /> </article-meta> </front> … </article>
Nova will display a warning if the ISSN provided does not match the ISSN configured in Nova for a publication. To enable ISSN matching, use the @pub-type=”ppub” or @pub-type=”epub” attribute on the <issn> element.
|Recommended element||Recommended Attributes|
|< issn>||@pub-type="ppub" for print ISSN @pub-type="epub" for EISSN||Journal ISSN. Use the pub-type attribute to specify what type of ISSN is provided.|
|< journal-id>||@journal-id-type||Use the @journal-id-type attribute to name the type of identifier.|
|< journal-title>||Full title of the journal|
|< abbrev-journal-title>||Abbreviation version used for PubMed and other third party deliveries|
<journal-meta> <journal-id journal-id-type="coden">JBOPFO</journal-id> <journal-id journal-id-type="publisher-id">JBO</journal-id> <journal-title-group> <journal-title>Journal of Cancer Research</journal-title> <abbrev-journal-title>J. Cancer. Research.</abbrev-journal-title> </journal-title-group> <issn pub-type="ppub">1083-3668</issn> <issn pub-type="epub">1560-2281</issn> <publisher> <publisher-name>Society of Photo-Optical Instrumentation Engineers</publisher-name> </publisher> </journal-meta>
Ensure to give at least the following article metadata at whatever point appropriate. Metadata is needed for both articles with full text and articles that are provided in PDF only. The values provided here will be shown in the article and utilized for indexing and retrieval of articles.
Required Article Metadata
|Required element||Required Attributes||Notes|
|< article-title>||Contained in a < title-group> element. Articles without titles will be assigned a default title to make them navigable on the website.|
|< pub-date>||One of the following for each element: @pub-type="ppub" @pub-type="epub" @pub-type="epreprint"||See section Article and issue publication dates|
|< volume>||Note that values are not normalized in processing; vol 01 and vol 1 are treated as two separate volumes. Volume numbers are not required for Publish Ahead of Print articles.|
|< issue>||Note that (as with volume) issue 01 and issue 1 are treated as two separate issues. Issue numbers are not required for Publish Ahead of Print articles or proceedings.|
|< fpage>||First page number. Non-numeric values such as “1a” are acceptable if this reflects the article’s pagination. If page numbers are not used, a value that is the equivalent of page number (e.g. CID) should be put in < fpage>.|
|< lpage>||Last page number. Required if different in value from < lpage>.|
|< self-uri>||@xlink:href="article_pdf.pdf"||Required if a PDF of the article is present.|
|< related-article>||Required for errata and any other related proceeding link. See section Related article links|
Recommended Article Metadata
|Recommended element||Required Attributes||Notes|
|< article-id>||One of the following for each element: @pub-id-type="doi" @pub-id-type="publisher-id"||DOIs are required to enable some Nova functionality, including automated article replacement, duplication checking, and PubMed and CrossRef deposits. Articles may have multiple < article-id>.|
Nova will utilize an article’s DOI or publisher ID to automatically recognize duplicate articles and make substitutions. DOI will trump publisher ID for matching articles. If the journal or conference is live, then an imported article will replace an article already in the system that has a matching DOI or publisher ID. If the journal or conference is not live—for example, while importing backfile content—at that point articles will be imported as new regardless of whether they have a duplicate DOI or publisher ID.
Article and issue publication dates
Article and issue dates ought to be included in a < pub-date> node. At least one < pub-date> is needed to be valid against the JATS tag set. However, Nova supports dynamically fills the article date depends on the date the article goes live on the site. If this behavior is desired and you do not want to supply any date information, include the < pub-date> element with empty < year> values, and no @iso-8601-date attribute.
< pub-date>< year /></pub-date>
To supply a date, the following options are available:
- Supply at least a < month> and < year> in numerical form (< day> is optional).
- Supply a date in an @iso-8601-date attribute in the format YYYY-MM-DD.
Dates can be provided in non-numerical form (e.g. < month>January</month>).
The < season> tag can also be used instead of day and month (e.g. < season>Fall</season> or < season>1st Quarter</season>). If the date is provided in a state other than numerical month and year, then the @iso-8601-date attribute must be included to supply a numerical article date. In this case, the day and month or season provided can be used for display, while the @iso-8601-date value is used as the underlying article date by the system.
The @pub-type attribute is required if a < pub-date> element is included with values. The following @pub-type attribute values may be used:
- < pub-date pub-type=”ppub”> assigns the date an article appears in a print publication. The ppub date is also used as the issue date when a new issue is created. For traditional (non-continuous) publishers, the ppub date is the article date.
- < pub-date pub-type=”epub”> assigns the date an article appears online. For continuous publishers, the epub date is the article date. For traditional publishers, the epub date is ignored.
- < pub-date pub-type=”epreprint”> assigns the date an article appears as a Publish Ahead of Print article or Just Accepted Manuscript. When the article is (re)published as part of an issue, the article must be resupplied with a pub-type of epub or ppub, depending on the publishing model.
The article metadata is not mandatory, so you can provided it when possible.
The < permissions> element holds copyright information and license material.
Copyright may include:
- <copyright-statement>: The information that will display on the site should be the complete statement of copyright for the article. It is likely that this will duplicate information in the <copyright-year> and <copyright-holder> elements.
- <copyright-year>: The year of copyright.
- <copyright-holder>: The name of the copyright holder.
The < license> element contains the set of conditions under which people are allowed to use an article, or other license-related information or restrictions.
- @license-type attribute: The access type to be stored in the database. The following licenses will make the content available on the site without authentication. Other license types will default to private.
- @xlink:href attribute: A URL to a resource describing the license. To submit the license URL to CrossRef, include a value in this attribute.
|@license-type="open-access"||Open Access article|
- < license-p>: A paragraph of text within the description of a < license>.
… < license license-type=“open-access” xlink:href=“http://creativecommons.org/licenses/by/2.0/”> This is an open-access article distributed under the terms of the Creative Commons Attribution License, which allows unrestricted use, distribution, and reproduction in any medium,provided the original work is properly cited.
If a funder for an article has an embargo period, then the article will automatically become available outside the paywall after the embargo period.
History is used as a holder for dates such as received date and accepted date recognized with the processing history of the document. Values for date-type are customer-specific and must be set up in Nova before loading. Use a combination of day, month, year, and iso–8601-date as depicted in Articles and issue publication dates to give a legitimate date.
<article-meta> … <history> <date date-type="received"> <day>05</day> <month>01</month> <year>1998</year> </date> <date date-type="rev-recd"> <day>24</day> <month>05</month> <year>1998</year> </date> <date date-type="accepted"> <day>06</day> <month>06</month> <year>1998</year> </date> </history> … </article-meta>
Authors and affiliations
<contrib-group> <contrib contrib-type="author"> <name> <surname>Maria</surname> <given-names>Steffy</given-names> </name> <degrees>PhD</degrees> <xref ref-type="aff" rid="aff1" /> </contrib> … </contrib-group> <aff id="aff1"> <label>1</label> Information Systems, Charlottesville, VA 22902. </aff>
Affiliations that are not linked from a < contrib> element will be overlooked.
The <aff> nodean likewise be incorporated as as a child of the < contrib> element to which the affiliation applies. Utilizing this strategy, affiliations must be repeated for every contributor if multiple contributors have the same affiliation, and the @id attribute is not required.
Each affiliated organization should be included in a separate <aff> node.
Use < collab> instead of < name> if the author is a grouped under a single name or the author is an organization (collaborative groups or collectives). Members of each group can be provided inside a < contrib-group> node that is a child of the < collab> element. These contributing members are not treated as authors and will not appear in the by-line, but will be submitted to PubMed as investigators/collaborators.
Notes that are not affiliations but are specific to a contributor can be included in an < author-comment> node within the < contrib> node to which the note applies. The @content-type attribute must be included to indicate the type of note. Permitted attribute values are:
- < author-comment content-type=”disclosure”>
- < author-comment content-type=”deceased”>
- < author-comment content-type=”other”>
Link to PDF of article
Link an article PDF to the article using <self-uri>, for example <self-uri xlink:title=”pdf” xlink:href=”2011.11010094.pdf”/> where the xlink:href value is the exact file name as it occurs in the pdf subdirectory. Do not prepend the file name with a directory path.
The <self-uri> element is intended to link to the same portion of content in different forms. For links to data supplements use the <supplementary-material> element . For links within the same document, use the <xref> element. For links to external resources, use the <ext-link> element.
Data supplements such as PDFs, images, etc. and information in external files have to be linked in the article using the <supplementary-material> element. Give the relevant data supplement file name, with the extension, in the @xlink:href attribute value, as in <supplementary-material xlink:href=”supplement.pdf”>. Do not include a file path.
For data supplements, use the attribute @content-type=”data-supplement”. For disclosures, use the attribute @content-type=”disclosure”. If no @content-type attribute is provided, then the material will be treated as a data supplement. A title for supplementary data have to be placed in <label> and any explanatory text in the <caption>, inside the element. The supplementary material must be placed inside the <article-meta> section within the <front> of the article.
<supplementary-material id="sup1" content-type="data-supplement" xlink:href="data_supplement.pdf"> <label>Data Supplement Title.</label> <caption> <p>Detailed diagram of the topic under discussion.</p> </caption> </supplementary-material>
Page range and count
You can also include page range and page count of an article in the metadata. The page range should be included in <page-range>. Use <page-range> if pages are discontinuous. Include <fpage> and <lpage> even if <page-range> is provided. The page count of the article can be provided as the value of the @count attribute of the <page-count> element within a <counts> element. We accept only the page count.
<page-count count=”6″ />
Author notes show up as an extended section or pop-up from a link under the article title and authors. Utilize this section for additional notes about article contributors. The authors notes can be incorporated by utilizing the <author-notes> element within the <article-meta> section.
Abstracts are included in the <abstract> node within the <article-meta> element. The authored abstract should have no @abstract-type attribute, or it should have the attribute @abstract-type=”abstract”. The attributes @abstract-type=”teaser” and @abstract-type=”precis” will also be imported. Within an abstract, you may include titled sections using <sec> nodes and the <title> element in each <sec>. Abstracts tagged with titled sections will be sent to PubMed as structured abstracts.
Article metadata that are ignored
The following elements will be ignored during import when included as children of the <article-meta> element.
Sections and paragraphs
See the JATS tag set description of the tag for a general description of sections (https://jats.nlm.nih.gov/publishing/tag-library/1.3d1/index.html). Sections can be nested to form sub-sections. Sub-sections intended to be at the same sub-section level should appear in the XML in elements at the same nested level. Nova will ignore the @sec-type attribute if it is included.
The paragraph element
describes block-level text. Paragraph elements cannot be nested. Each
element does not necessarily need to represent a single key point, thought, or topic as in the common definition of a paragraph. For example, if a list appears in the middle of a paragraph (in the common sense), then the paragraph should be split into two separate
elements with a element in between.
Automatic numbering of figures (and analogous elements such as tables and boxed text) is not provided. If numbering is wanted the numbers should be provided in the
<fig id="f1"> <label>Fig. 1</label> <caption><p>A schematic of … </p></caption> <graphic xlink:href="JBO_17_2_026001_f001.png"/> </fig>
Nesting special content elements
Nova enables special display behaviors to some contents elements like figures, tables, boxed-text, graphics, media, supplementary material, lists, and verse groups (poems). For instance, clicking on a figure may enlarge the image, or tables may be listed in an index of tables. Avoid nesting of the elements, because nesting these elements inside other special element may cause failure to its display behavior.
Figures (<fig>) should be placed only after the paragraph in which they are cited, not in the mid-paragraph. If more than one figure or table is cited in any particular paragraph, they have to be placed in the order they are cited. If they are cited in a list item, they must be placed after the (outermost) closing list tag.
<p>… in <xref ref-type=”fig” rid=”f1″>Fig. 1</xref>. The …</p>
<fig id=”f1″><label>Fig. 1</label><caption><p…</p></caption><graphic xlink:href=”XXX_22_2_026001_f001.png”/></fig>
Use <fig> elements for formal figures, especially when numbered and/or captioned. If your site includes features such as an index of figures, figure carousel, or tab of figures, the <fig> element designates the items that appear in those features. Use the <fig-group> element if a figure has more than one image part, and the image parts require labels. For example, the group of figures may have a caption, with the internal figures each having their own label and caption.
The @id attribute must be used on the <fig> or the <fig-group> if they will be referenced from the body of the text using an <xref>.
The <graphic> element within the <fig> is used to point to the external file containing a still image. A <graphic> must have an attribute @xlink:href, whose value should be the exact file name of the image. Give only the exact file name relative to the directory specified for the file in the proper packaging guidelines. For example, a figure image stored directly in the FigureImages directory should use xlink:href=”image.png” without a file path preceding the file name.
The <graphic> element can also be used without a <fig>. A <graphic> can be placed either outside or inside a paragraph, and will show up on its own line in either case. This tagging should be used for images without number and label, such as author headshots. These images will appear within the text of the document, without a pop up, and will not appear in the table of figures.
Inline graphics appear within a line of text, and are tagged using the < inline-graphic> element. An < inline-graphic> must have an attribute @xlink:href, whose value should be the exact file name of the image.
<p>The temperatures rose 20 degrees <inline-graphic xmlns:xlink=”http://www.w3.org/1999/xlink” xlink:href=”sparkline.png” /> in 20 minutes. …</p>
As like figures, tables should also be placed after the paragraph in which they are cited, and not mid-paragraph. Tables are tagged with the < table-wrap> element and may contain a < label> and < caption>, and must contain a < table> or < graphic> element. Include XML content for the table in < table>. Use the < graphic> element to point to the image file instead of using the < table> element, provide the table content in the form of an image,
A < graphic> must have an attribute @xlink:href, whose value should be the exact file name of the image. Provide only the literal file name relative to the directory specified for the file in the appropriate packaging guidelines. For example, a table image stored directly in the TableImages directory should use xlink:href=”image.png” without a file path preceding the file name. The @id attribute must be used on the < table-wrap> if the table will be referenced by an <xref> from elsewhere in the article.
Use the table-wrap element with the @specific-use=”inline” attribute, to apply tabular formatting to content without the complete table treatment (e.g. listing in table of tables, expandable thumbnails, downloads)
By default, this Tag Set uses the NISO JATS (XHTML-inspired) table model, as defined in NISO JATS version of the XHTML Table Module. However, this Tag Set can be set up to use the OASIS XML Exchange (CALS) table model either instead of or in addition to the XHTML-inspired model.
The modules that enable the OASIS XML Exchange (CALS) table model are distributed as part of this Tag Set, and a separate OASIS XML Exchange (CALS) Table Tag Library (https://jats.nlm.nih.gov/options/OASIS/tag-library/19990315/index.html) describes the OASIS XML Exchange (CALS) table model elements, attributes, and parameter entities.
To enable two different tagging schemes for the same material (row and column tables), all OASIS XML Exchange (CALS) table model elements have been given a namespace and use the namespace prefix “oasis”. Since DTDs do not really work with namespaces, the namespace prefix has been hard-coded into the names of the OASIS table elements. This differentiates the two sets of table elements, allowing both NISO JATS XHTML-inspired and OASIS XML Exchange (CALS) table models to be used together.
To illustrate how this works and for use by the user community, a separate OASIS XML Exchange (CALS) Table Archiving DTD is available as part of this Tag Set. It uses the OASIS XML Exchange (CALS) table elements instead of the NISO JATS XHTML-inspired table elements (filename JATS-archive-oasis-article1.dtd).
NISO JATS XHTML-inspired Table
The modules that implement the NISO JATS table coding are:
- NISO JATS XHTML-inspired Table Setup Module (JATS-XHTMLtablesetup1.ent) Sets all parameter entities needed by the NISO JATS version of the XHTML Table Module, and then references (invokes) the NISO JATS XHTML-inspired Table Module.
- To include the NISO JATS XHTML-inspired Table model in a tag set, a DTD must reference this module.
- NISO JATS XHTML-inspired Table Module (xhtml-table-1.mod) The public XML DTD version of the XHTML Tables Module. This contains the NISO JATS version of the W3C-developed XHTML table model. This module is invoked from the module %XHTMLtablesetup.ent;.
- NISO JATS XHTML-inspired Table Style Module (xhtml-inlstyle-1.mod) Declares the @style attribute, which supports inline style markup for elements such as <td> and <tr> and within NISO JATS table model.
OASIS CALS Tables
The XHTML-inspired table model is the NISO JATS default, but versions of the models (DTD, XSD, and RNG) have been provided for archives and publishers that use OASIS XML Exchange (CALS) table model. As set up, these are separate models that define both the XHTML-inspired and the OASIS Exchange (CALS) table models, with the OASIS table model namespaced (prefix “oasis”) to prevent name clashes. An XML expert can readily turn off the XHTML-based table model, and (once there is only the single OASIS Exchange (CALS) table model, remove the OASIS namespace using NISO JATS-provided overrides (the OASIS Table Module need not be touched). The following files are necessary to use the OASIS Exchange (CALS) table model:
- Journal Archiving and Interchange DTD with OASIS Tables (JATS-archive-oasis-article1.dtd) Complete Archiving (Green) DTD for the creation of new journal articles. This extension of the Journal Archiving and Interchange DTD replaces the Archiving DTD module and invokes both the XHTML table and the CALS OASIS XML Exchange Table models.
- Journal Archiving and Interchange DTD with OASIS Tables DTD-Specific Modules (JATS-archive-oasis-custom-modules1.ent) The DTD-specific modules for the new Journal Archiving and Interchange DTD that includes OASIS Tables.
- Journal Archiving and Interchange DTD with OASIS Tables Customize Classes Module (JATS-archivecustom-classes1.ent) The class overrides for this new DTD. These repeat all the class overrides of the regular Archiving DTD, with the table and alternative classes modified to use the OASIS XML Exchange (CALS) table elements. There is no equivalent mix override module, because this DTD uses the ordinary Archiving mix overrides.
- JATS OASIS Table Namespace Module (JATS-oasis-namespace1.ent) This modules establishes the prefix for the OASIS Exchange (CALS) table model, by default “oasis” (“<oasis:table”)
- JATS Namespaced OASIS XML Table Setup Module (JATS-oasis-tablesetup1.ent) Sets all parameter entities needed by the OASIS XML Exchange (CALS) table model, and then references (invokes) the OASIS XML Exchange (CALS) Table Model Module. for declarations of all the table elements.
- OASIS XML Exchange (CALS) Table Model Module (oasis-exchange.ent) This is the OASIS XML Exchange (CALS) table model DTD fragment, modified to use the OASIS namespace and the “oasis” prefix. This module is invoked from the JATS OASIS XML Exchange (CALS) setup module.
Sidebars and boxed-text
Sidebars can be numbered or unnumbered, and placed in the content based on publisher preference, but avoid placing in mid-paragraph. The placement of sidebars and bored text in XML reflects in the online placement, i.e, in the web site. Nova supports sidebars marked as <boxed-text> elements with special flags on a @content-type attribute. There are three types of sidebars allowed, in three sizes, as indicated by the value of the @content-type attribute:
- <boxed-text content-type=”sidebar-small”>
- <boxed-text content-type=”sidebar-medium”>
- <boxed-text content-type=”sidebar-large”>
The <boxed-text> element without a @content-type attribute should be used for boxed-text that is not a sidebar. We can customize the actual display based on each client, please contact us if you need any adjustments.
Like figures and tables, sidebars and boxed-text may be numbered by using <label>, and can include a <caption>. The @id attribute must be used on the <boxed-text> if the table will be referenced by an <xref> from elsewhere in the article.
<video width="320" height="240" controls> <source src="movie.mp4" type="video/mp4"> <source src="movie.ogg" type="video/ogg"> Your browser does not support the video tag. </video>
Media hosted by Nova
To include audio content, first include the video files in the DataSupplements folder of the package and mention the media in the Journals XML as follows:
<media id="audio1" content-type="audio" xlink:href="sounds-good.wmv"> <label>1</label> <caption><title>Biography</title><p>Recording of a person's life experience.</p></caption> </media>
The must have an attribute @xlink:href, whose value should be the exact file name of the multimedia. Provide only the exact file name relative to the directory specified for the file in the proper packaging guidelines. For example, an audio file stored directly in the DataSupplements directory should use xlink:href=”audio.mp3″ without a file path preceding the file name.
Math and equations
Equations have to placed in a <disp-formula> element or an <inline-formula> element. Both formula elements may contain text, MathML, or images. The <inline-formula> may not contain a <graphic>, but may contain an <inline-graphic>.
Equations appearing on their own line should be contained in a <disp-formula> element. The <disp-formula> element may be placed inside or outside a <p>. To label the formula—for example, with a number that appears to the right of the formula—include the label text in a <label> within the <disp-formula>. The <disp-formula> may be referenced by an <xref>; if the formula will be referenced, an @id attribute must be included.
Equations appearing within a line of text should be placed in an <inline-formula> element. The element should appear within a paragraph (<p>) or other element containing text. Inline formulas cannot be referenced by an <xref>.
Mathematical equations can be depicted using MathML contained in the <mml:math> element. If both an image and MathML are provided in a particular equation, we will display the image. The image file name is declared in the @altimg attribute value on the <mml:math> element and it must match the file supplied. If no image is provided, we will display the formatted MathML.
MathML elements must use “mml” as the namespace prefix to validate to the JATS DTD.
Provide lists inside the <list> element. The <list> element should not be placed within a <p> element. The @list-type attribute can be used to assign the type of list as follows. If no @list-type is provided, the list will default to a simple list. Do not include the list item character (i.e. numbering or bullets) in the content; this will be generated automatically.
|List-type attribute||Default list item character||Notes|
|simple||n/a||Gets list indentation, but no character in front of each item. Sometimes called “unordered”.|
|number||1, 2, 3|
|alpha-lower||a, b, c|
|alpha-upper||A, B, C|
|roman-lower||i, ii, iii, iv|
|roman-upper||I, II, III, IV|
Use <verse-group>` element to include poems. The <verse-group> element should not be placed within a <p> element.
Use the < ext-link> element for links external to the content, except when mentioning to an alternate form of the same article or data supplements. The @xlink:href attribute should be used to indicate the location of the external content.
The <ack>, <app-group>, <bio>, <fn-group>, <ref-list>, <notes>, and <sec> elements can be used in the back matter.
References or bibliographic citations should be tagged inside <ref-list> in the back matter. Each bibliographic entry should be in a <ref> element. References should be tagged in highly detailed way to support display and indexing. The JATS tag set recommends to tag the below elements:
We can match citation dynamically and provide functionalities such as display, linking, and analysis functionalities exactly, if tagging of the above information are done correctly. If the tagging is not detailed, it may leads to failure of the link references to CrossRef, PubMed, and other external resources. Nova can create links to PubMed and CrossRef for journal articles referenced in the references section. For Nova to determine and create these links, the @publication-type=”journal” attribute must be included in the <element-citation> or <mixed-citation> element.
CrossRef and PubMed information may optionally be supplied with the references by including a <pub-id> element. Use the attribute @pub-id-type=”doi” for a DOI and @pub-id-type=”pmid” for PubMed ID.
We support both <element-citation> and <mixed-citation> for references. The system provides formatting and punctuation for <element-citation>, while <mixed-citation> is formatted and punctuated from the source data. (See http://jats.nlm.nih.gov/publishing/tag-library/1.0/index.html?elem=element-citation and http://jats.nlm.nih.gov/publishing/tag-library/1.0/index.html?elem=mixed-citation for explanations and examples of each.)
If you are using <element-citation>, we suggest you preview the rendition of your data in our system to ensure good results.
<element-citation publication-type="journal" publication-format="print"> <name><surname>John</surname><given-names>RC</given-names></name> <name><surname>Adam</surname><given-names>JM</given-names></name> <name><surname>Jeff</surname><given-names>LE</given-names></name> <name><surname>Fedrick</surname><given-names>L</given-names></name> <article-title>Life after Cancer</article-title> <source>J Dem Diseases</source> <year>2006</year> <month>Feb</month> <volume>32</volume> <issue>1</issue> <fpage>112</fpage> <lpage>116</lpage> </element-citation>
If you are using <mixed-citation> the XML must include all punctuation and spacing (such as the space between the <surname> and <given-names> below) as it should be displayed.
<?xml version="1.0" encoding="UTF-8"?> <mixed-citation publication-type="journal" publication-format="print"> <string-name> <surname>John</surname> <given-names>RC</given-names> </string-name> , <string-name> <surname>Adam</surname> <given-names>JM</given-names> </string-name> , <string-name> <surname>Jeff</surname> <given-names>LE</given-names> </string-name> , <string-name> <surname>Fedrick</surname> <given-names>L</given-names> </string-name> . <article-title>Life after Cancer</article-title> . <source>J Dem Diseases</source> . <year>2006</year> <month>Feb</month> ; <volume>32</volume> ( <issue>1</issue> ): <fpage>112</fpage> – <lpage>116</lpage> . </mixed-citation>
Note: some users prefer to use for citations types such as articles, where automatic formatting is likely to be satisfactory and use for unusual citation types (e.g., court cases, unpublished letters) where the citation format is more unique. The < xref> element must have an @id attribute if it is linked from elsewhere in the content using an < xref>.
Footnote must have to includes in <fn-group> element, with each footnote in an <fn>. In case, if the footnote is linked with any other section in the content using an <xref>, then the <fn> element must have an @id attribute, hence footnotes will display in the section where they appear instead of as a separate footnotes section.
Related article links
<related-article> is used for linking content to an article. For example, you can link an erratum to the original article or a response to a Letter to the Editor. Related articles must be limited to articles within the publisher’s content. Place the <related-article> node in the article metadata; <related-article> elements in the body of the article will not generate links between articles. The XML containing the <related-article> and the target content can be imported in any order in relation to each other.
There are two methods for indicating which article to link to:
1. DOI of the related article
2. Volume and first page number of the related article
DOI is strongly preferred. Volume and page number can be used for articles that do not have an assigned DOI, however links may not always be created if the system cannot find a match or finds more than one match and cannot determine which is correct. This can happen if there are numerous articles on a single page, e.g. various letters to the editor.
To link via DOI, two methods are available:
- Use @elocation-id. The following attributes are required:
- @elocation-id=”[DOI of the related article]”
- Use @xlink:href. The following attributes are required:
- @xlink:href=”[DOI of the related article]”
To link via volume and page number, the following attributes are required:
- @journal-id—set to the ISSN of the journal
- @page—set to first page of the related article
Related articles that use the @xlink:href attribute to identify the target will be ignored by the Nova system, unless the target value is a DOI and the element includes the @ext-link-type=”doi” attribute. Currently supported values for @related-article-types are listed below. Contact your Project Manager if other types are needed.
|Link type||JATS definition|
|commentary||Used in an article to name its associated commentary or editorial.|
|companion||Used in an article to name a companion (related or sibling) article.|
|corrected-article||Used in a correction or erratum to name the article being corrected.|
|letter||Names a letter to the publication or a reply to such a letter.|
|retracted-article||Used in a retraction to name the article being retracted.|
You may link articles to other content or objects within an article.
Use the < related-object> element in the < article-meta> to assign a relation to another piece content.
Use the @document-type, @document-id-type, and @document-id attributes to designate the type of content and document to target.
Use the @object-type, @object-id-type, and @object-id attributes with the appropriate values, to link to an object (e.g. figure, table) within a portion of content. You must designate both the document and the object when linking to an object.
Links to the following content types can be created from articles. For links to non-standard content, the target content must be imported first, or be in the same package when creating a link. For links to books or books content, the article XML and the target XML can be imported in any order.
|Target document/content type||Tagging format|
|Non-standard||< related-object document-type="non-standard" document-id-type="publisher-id" document-id="gbos123-12345"/>|
|Book (using ISBN 13)||< related-object document-type="book" document-id-type="isbn13" document-id="5-321-44667-1"/>|
|Book (using ISBN 10)||< related-object document-type="book" document-id-type="isbn10" document-id="3478932145"/>|
|Book (using eISBN)||< related-object document-type="book" document-id-type="eisbn" document-id="4-009-23145-2"/>|
To target objects within document, additionally include the following attributes:
|Target object||Tagging format|
|Main Division (in non-standard only)||< … object-type="main-division" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
|Part (in book only)||< … object-type="part" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
|Chapter (in book only)||< … object-type="chapter" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
|Section||< … object-type="sec" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
|Figure||< … object-type="fig" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
|Table||< … object-type="table" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
|Video||< … object-type="video" object-id-type="publisher-id" object-id="legacySectionID-value"/>|
For example <related-object document-type=”non-standard” document-id-type=”publisher-id” document-id=”gbos123-12345″ object-type=”fig” object-id-type=”publisher-id” object-id=”legacySectionID-value”/>
Links to objects within non-standard content will not be maintained if the target content is replaced. Use the @link-type attribute to designate the link type. The link-type must match a value in our system. If the link-type is directional in nature (e.g. A is a correction for B vs. B is corrected by A), the link-type should follow the logic: “The content in this XML is a/the [linkType] of/for the target content.”
Hierarchical article categories
Articles can be assigned to categories such as subjects or groupings of any sort that span each site. Use the and elements to designate categories for the article. Each category should be placed in a element within the element. Nova does not create categories on the fly. They must be set up in Nova before importing.
Nova supports hierarchical article categories, which allows for parent-child relationships between categories. When assigning a child-level category to an article, the parent categories must also be supplied in case more than one subcategory shares the same name. Nova can currently import up to a 2-level hierarchy. The example below shows an article with a category structure of:
- Sensor Networks
- Rainwater Harvesting Systems
<article-categories> <subj-group subj-group-type="category"> <subject>Sensor Networks</subject> <subj-group subj-group-type="category"> <subject>Rainwater Harvesting Systems</subject> </subj-group> </subj-group> </article-categories>
Since the JATS only allows nested <subj-group> elements after the <subject> elements, use multiple top-level <subj-group subj-group-type=”category”> nodes to designate multiple parent-child categories.
If multiple facets of organization are required and the same category name exists for multiple facets, add a hyphen and the the category type to the end of the @subj-group-type value. For example, if the categories such as Research (with category type of Journal Categories) and Research (with category type of Article Categories) are set up in Nova for the same site, then specify the latter in the XML by including:
<subj-group subj-group-type="category-Article Categories"> <subject>Research</subject> </subj-group>
Table of contents headings
Use <subj-group subj-group-type=”toc-heading”> element, to assign articles to a table of contents (TOC). TOC headings will be created on the fly during import. The TOC and TOC headings will be created for each issue and cannot be used to sort or group articles across different issues.
The top level <subj-group> element (the one with the @subj-group-type=”toc-heading” attribute) ought to contain the top-level (issue or conference volume) TOC arranging strategies. Place each TOC heading relevant to the article in subsequent nested <subj-group> elements. The most minimal level <subj-group> element must represent the article itself. Include an ordinal for the article in this last level. If the article needs no ordinal, incorporate the final <subj-group> element with an empty child element (<subject/> or <compound-subject/>).
Nova permits utilization of various sort algorithms at each level of the TOC, and diverse sort algorithms for sub-headings and articles. Sort algorithms for the top-level and each TOC heading assign how its children will be arranged. For instance if “Heading 1” has a sub-heading sort set to in alphabetical and article sort set to page number, at that point its sub-headings will be arranged alphabetically and its child articles will be arranged by page number.
Other rules regarding the TOC are as follows:
- Both a sub-heading sort algorithm and an article sort algorithm must be given at the top level (issue or conference volume).
- An article may show up just a single time in the TOC. Incorporate just a solitary way of TOC headings to the article.
- A heading that has not had a sort technique specified indicated will acquire that sort strategy from its parent head or the top-level entry.
- A heading that exists in an issue, that is imported in an article subsequent to the heading being created, and that does exclude sort strategies will hold the current sort strategy for the heading.
- A heading that exists in an issue, that is imported in an article subsequent to the heading being created, and that incorporates a sort strategy will update the sort method for the heading.
Include the heading name and sort methods using <compound-subject-part> elements in a <compound-subject> under each <subject-group>. Use the following attributes on the <compound-subject-part> elements to specify the heading information:
|@content-type="subhead-sort"||Sort algorithm for subheadings under the current heading|
|@content-type="article-sort"||Sort algorithm for articles under the current heading|
|@content-type="text"||The text displayed for the heading|
|@content-type="ordinal"||The ordinal assigned to the heading itself (or article if applied at the lowest < subj-group> node). Required if the parent heading has a sort method of ordinal.|
The following values are permitted inside <compound-subject-part content-type=”subhead-sort”> elements:
|inherit||inherit from parent heading|
|ordinal||by manually assigned ordinal|
The following values are permitted inside <compound-subject-part content-type=”article-sort”> elements:
|inherit||inherit from parent heading|
|alpha||alphabetical on article title|
|ordinal||by manually assigned ordinal|
|page||by first page|
|date||by pub date|
The start and end of arbitrary portions of text can be mentioned using the <milestone-start> and <milestone-end> elements. These tags can demonstrate the portions of text to highlight in an article that is linked from a CME or quiz to portray the correct answer.
Since these are empty elements, they can be utilized to show non-hierarchical portions of the text that cannot otherwise be indicated using standard opening and closing element tags without violating XML standards. Where a <milestone-start> element is used, a matching <milestone-end> element must be used.
The <milestone-start> element must have an @id attribute. The <milestone-end> element must have an @rid attribute whose value equals the @id of the matching <milestone-start> element.
Funding information for deposit to FundRef
Include information about funding of the research in the <funding-group> tag. Nova can import the funder’s name, funder’s identifier, and associated award identifiers, and deposit this information to FundRef. Inside the <funding-source> element, use the <named-content content-type=”funder-name”> and <named-content content-type=”funder-identifier”> tags to designate the funder name and identifiers, respectively.
<?xml version="1.0" encoding="UTF-8"?> <funding-group> <award-group award-type="grant"> <funding-source> <named-content content-type="funder-name">National Science Foundation</named-content> <named-content content-type="funder-identifier">14.12674.10000441</named-content> </funding-source> <award-id>psychoceramics-1152342</award-id> </award-group> <award-group award-type="grant"> <funding-source> <named-content content-type="funder-name">Example Org</named-content> <named-content content-type="funder-identifier">00.00000.441</named-content> </funding-source> <award-id>abc-001</award-id> <award-id>abc-002</award-id> </award-group> </funding-group>
If an embargo period is stored in Nova for a funder, articles associated with an award from that funder will automatically become available outside the paywall after that embargo period. Embargo periods for funding agencies are maintained in Nova and are not included in the XML. The initial access type for an article is set during import. A license URL for an article can also be sent to CrossRef. See section Permission for information about setting access type and including licensing information.
Proceedings XML requirements
Proceedings usually follow the same requirements as for journal articles. Details are given in this section for information specific to proceedings.
Conference proceedings journal metadata
The following metadata in the <journal> element are suggested for conference proceedings. Nova will display a warning if the ISSN provided does not match the ISSN configured in Nova for a publication. To enable ISSN matching, use the @pub-type=”ppub” or @pub-type=”epub” attribute on the <issn> element.
|< issn>||This is required by NLM to be valid against the DTD.|
|< isbn>||If the conference has an ISBN, include it. Use no attribute or give the attributes @content-type="ISBN10" or @content-type="ISBN13" for print ISBN. Use the attribute @content-type="eISBN" for electronic ISBN.|
|< publisher>/< publisher-name>|
Conference article metadata
The article element requires an @article-type attribute.
Article Element for Proceedings
The following is the required article metadata for conference proceedings.
|Required element||Required attributes||Notes|
|< article-title>||Contain in < title-group> element. Proceedings without titles will be assigned a default title to make them navigable on the website.|
|< contrib-group>||@content-type="article" @content-type="volume"||Use @content-type="article" for proceedings authors. Put volume editors within a < contrib-group> with @content-type="volume". Volume editors will be updated every time an article is loaded to that volume.|
|< contrib>||@contrib-type="author" (use for proceedings authors) @contrib-type="editor" (use for volume editors)||Contain in < contrib-group> element.|
|< collab>||Use for groups of authors credited under a single name.|
|< volume>||Note that vol 01 and vol 1 are treated as two separate volumes. This information must match that provided in the conference metadata.|
|< fpage>||First page number. Non-numeric values such as “1a” are acceptable if this reflects the article’s pagination. If page numbers are not used, a value that is the equivalent of page number (e.g. CID) should be put in < fpage>.|
|< lpage>||Required if different in value from < lpage>.|
|< self-uri>||@xlink:href="article_pdf.pdf"||Required if a PDF of the proceeding is present.|
|< permissions>||Copyright statements go here. Multiple copyright statements, years, and holders are permitted.|
Required Article Metadata for Proceedings
|Recommended element||Required attributes||Notes|
|< article-id>||One of the following for each element: @pub-id-type="doi" @pub-id-type="publisher-id"||DOIs are required to enable some Nova functionality, including automated article replacement, duplication checking, and CrossRef deposits. Articles may have multiple < article-id>.|
Nova will use an article’s DOI or publisher ID to automatically distinguish duplicate articles and make replacements. DOI will trump publisher ID for coordinating articles. On the off chance that the journal or conference is live, at that point an imported article will replace an article already in the system that has a matching DOI or publisher ID. In the event that the journal or conference is not live, for instance, while importing backfile content—then articles will be imported as new regardless of whether they have a copy DOI or distributer ID.
Conference hierarchy metadata
The conference metadata includes the full conference hierarchy for the proceeding, plus information about the volume and the session within the volume. The metadata must match for each proceeding in the volume; otherwise the system will create a new volume with the conference hierarchy specified in the metadata.
Conference hierarchy metadata
|Required element||Required attributes||Notes|
|< conference>||@content-type="conf-level-1" or @content-type="conf-level-2"||Up to two conference levels are supported. conf-level-1 indicates the conference series information. conf-level-2 indicates the conference itself. The < conference> element is the parent of the following elements.|
|< conf-date>||To indicate only the start date of the conference, the format is < conf-date>YYYY-MM-DD< /conf-date>. If you want to specify start and end dates for a conference, please use the format < conf-date>YYYY-MM-DD|YYYY-MM-DD< /conf-date> (note the pipe delimiter between the dates). If you’d like for the conference to have only a month as the date, please include 00 in place of the day. Example: < conf-date>2012-05-00< /conf-date> would display as May 2012. If there is no date—for example, for the conference series—include as empty element to satisfy JATS requirements.|
|< conf-name>||Spelling, case, and punctuation must be consistent for all proceedings in a conference.|
|< conf-acronym>||This is a short identifier for the conference.|
|< conf-loc>||Spelling, case and punctuation must be consistent for all proceedings in a conference.|
Conferences with multiple parents
A conference can have more than one parent. To indicate this, use a separate < conference> tag for each parent.
In the example below, the “Annual Yearly Conference for 2012” belongs to both the “Yearly Conference” and the “Annual Conference” and would be assigned to both parents. On the site, the “Annual Yearly Conference” would show up in Conference Browse pages under both parents.
<conference content-type="conf-level-1"> <conf-date /> <conf-name>Yearly Conference</conf-name> <conf-acronym>YC</conf-acronym> <conf-num>36</conf-num> </conference> <conference content-type="conf-level-1"> <conf-date /> <conf-name>Annual Conference</conf-name> <conf-acronym>AC</conf-acronym> <conf-num>30</conf-num> </conference> <conference content-type="conf-level-2"> <conf-date>2010-09-02|2010-09-03</conf-date> <conf-name>Annual Yearly Conference for 2010</conf-name> <conf-acronym>YC12</conf-acronym> <conf-num>1234567</conf-num> <conf-loc>Charlottesville, VA USA</conf-loc> <conf-sponsor>Society of Conference Sponsors</conf-sponsor> <conf-theme> Managing Change</conf-theme> </conference> <conference content-type="volume"> <conf-date/> <conf-name>Managing Change 2010</conf-name> <conf-num>123</conf-num> </conference> <conference content-type="session"> <conf-date/> <conf-name>Change in Organizations</conf-name> </conference>
|Required element||Required attributes||Notes|
|< conference>||@content-type="volume"||Information about the conference volume will go here. The < conference> element is the parent of the following elements.|
|< conf-date>||If no date is supplied for the volume, the volume date will be set to the date the volume is published to the site. If no date is provided, include an empty element to satisfy JATS requirements.|
|< conf-name>||Put volume name here. The volume name must be consistent across all proceedings in the volume.|
|< conf-num>||Volume number goes here. It must match the volume number given in the article metadata.|
A conference session is also known as a conference section. These are different headers within the volume.
|Required element||Required attributes||Notes|
|< conference>||@content-type="session"||The < conference> element is the parent of the following elements.|
|< conf-date>||A session date cannot be assigned. Include as an empty element to satisfy JATS requirements.|
|< conf-name>||Put session name here.|
To specify one or more volume editors, use a <contrib-group> with the attribute @content-type=”volume” as follows:
<contrib-group content-type="volume"> <contrib contrib-type="editor"> <name><surname>Philips</surname><given-names>Adam E.</given-names></name> </contrib> </contrib-group>
The <contrib-group> should be included in the <article-meta> section. Conference volume editors will be updated every time an article is loaded to that volume. Conference volume editors must therefore be included with all content.
Authors go into a contrib-group as follows:
<contrib-group content-type="article"> <contrib contrib-type="author"> <name><surname>Philips</surname><given-names>Adam E.</given-names></name> </contrib> </contrib-group>
1. Conference location, start date, and end date will be updated every time an article is loaded to the conference. The information must therefore be included with all content.
2. The volume date and volume name will be updated every time an article is loaded to that volume. The volume date and name must therefore be included with all content.