Journal Publishing Tag Library NISO JATS Draft Version 1.1d2

<alternatives>

Alternatives For Processing

Container element used to hold a group of processing alternatives, for example, a single <graphic> that ships in several formats (tif, gif, and jpeg) or in different resolutions. This element is a physical grouping to contain multiple logically equivalent (substitutable) versions of the same information object. Typically these are processing alternatives, and the reader is expected to see only one version of the object.

Remarks

<alternatives> is neither inherently block nor inline in nature, because the block or inline quality is determined by context and usage. Typical examples for this element are a <graphic> that ships with a document in multiple versions (for example, as a .tif, a .jpeg, and an SVG file); or an <inline-formula> that is available as a .tif (<inline-graphic>), encoded in MathML, as well as encoded in TeX, and as a plain ASCII.
Accessibility: This element, by providing a container for alternative versions of a graphic or media object, enables providing a textual alternative to any graphic or media object as well as providing an enlarged graphic version for accessibility.

Attributes

id Document Internal Identifier
xml:base Base

Content Model

<!ELEMENT  alternatives %alternatives-model;                         >

Expanded Content Model

(array | chem-struct | code | graphic | inline-graphic | inline-supplementary-material | media | preformat | private-char | supplementary-material | table | textual-form | tex-math | mml:math)+

Description

One or more of any of:

This element may be contained in:

<addr-line>, <alt-title>, <app>, <app-group>, <array>, <article-title>, <attrib>, <award-id>, <bio>, <body>, <bold>, <boxed-text>, <chem-struct>, <chem-struct-wrap>, <collab>, <comment>, <compound-kwd-part>, <compound-subject-part>, <conf-theme>, <def-head>, <disp-formula>, <disp-quote>, <element-citation>, <fig>, <fig-group>, <fixed-case>, <floats-group>, <funding-source>, <glossary>, <inline-formula>, <italic>, <label>, <license-p>, <meta-value>, <mixed-citation>, <monospace>, <named-content>, <notes>, <overline>, <p>, <product>, <ref-list>, <roman>, <sans-serif>, <sc>, <sec>, <sig-block>, <strike>, <styled-content>, <sub>, <subject>, <subtitle>, <sup>, <supplement>, <supplementary-material>, <table-wrap>, <td>, <term>, <term-head>, <th>, <title>, <trans-subtitle>, <trans-title>, <underline>, <verse-line>

Example 1

Alternatives of a graphic:

... 
<fig id="f3" position="float">
<label>FIG. 3.</label>
<caption>...</caption>
<alternatives>
<graphic specific-use="print" xlink:href="1.4821168.figures.highres.f3.zip"></graphic>
<graphic specific-use="online" xlink:href="1.4821168.figures.online.f3.jpg"></graphic>
</alternatives>
</fig>
...

Example 2

Alternatives to a table inside <table-wrap>: 
...
<table-wrap id="pbio-0020328-t003" position="float">
<label>Table 3</label>
<caption>
<title>Systematic Inactivation of SpoIIID-Activated Genes</title>
</caption>
<alternatives>

<graphic xlink:href="pbio.0020328.t003.tif"/>

<graphic xlink:href="pbio.0020328.t003.gif"/>

<table frame="box" rules="all" cellpadding="5">
<thead>
<tr>
<td>Strain</td>
<td>Description</td>
<td>Sporulation Efficiency (Percent)<sup>a</sup></td>
</tr>
</thead>
<tbody>
<tr>
<td>PY79</td>
<td>wild type</td>
<td>100</td>
</tr>
<tr>
<td>RL2391</td>
<td><italic>asnO&Delta;::spc</italic></td>
<td>0.000001</td>
</tr>
<tr>
<td>PE563</td>
<td><italic>cotF&Delta;::cat</italic></td>
<td>83</td>
</tr>
...
</tbody>
</table>

</alternatives>
<table-wrap-foot>
<fn id="nt301">
<p><sup>a</sup>&thinsp;Sporulation efficiency is defined as the
number of heat-resistant spores ...</p>
</fn>
</table-wrap-foot>
</table-wrap>
...

Example 3

Alternatives to an equation, including MathML and a graphic:
...       
<disp-formula id="pbio-0020328-e001">
<alternatives>
<mml:math display="block" xmlns:mml="http://www.w3.org/1998/Math/MathML">
<mml:mrow><mml:msub>
<mml:mrow><mml:mtext>Strength</mml:mtext></mml:mrow>
<mml:mi>i</mml:mi></mml:msub>
<mml:mo>=</mml:mo>
<mml:mi>log</mml:mi>
<mml:mo>&ApplyFunction;</mml:mo>
<mml:mfrac>...</mml:mfrac>
<mml:mo>=</mml:mo>
...
</mml:math>
<graphic xlink:href="pbio.0020328.e001.gif"/>
</alternatives>
</disp-formula>
...

Example 4

Media alternatives:
 
...
<fig id="f1" orientation="portrait" position="float">
<label>FIG. 1.</label>
<caption>
<p>(a) Schematic of the working principles of HFM, (b) a typical application
scheme for an electric bias in HFM, (c) regulation the conformations and
dynamics (trapping, concentration, and sudden stretching) of λ-DNA molecules
in HFM, and (d) schematic of the trapping location regulation (enhanced online).
[URL: <ext-link ext-link-type="uri" xlink:href="https://dx.doi.org/10.1063/1.4762852.1">
http://dx.doi.org/10.1063/1.4762852.1</ext-link>]
<alternatives>
<media id="v1" mime-subtype="avi" mimetype="video" orientation="portrait"
position="anchor" specific-use="original-format" xlink:href="v1">
<object-id pub-id-type="doi" specific-use="metadata">10.1063/1.4762852.1</object-id>
</media>
<media mime-subtype="mpeg" mimetype="video" orientation="portrait"
position="anchor" specific-use="archival-format" xlink:href="v1"></media>
<media mime-subtype="x-flv" mimetype="video" orientation="portrait"
position="anchor" specific-use="online-format" xlink:href="v1"></media>
</alternatives>
</p>
</caption>
<graphic orientation="portrait" position="float" xlink:href="f1"/>
<graphic id="f1a" orientation="portrait" position="float" xlink:href="dummy1.png"/>
<graphic id="f1b" orientation="portrait" position="float" xlink:href="dummy2.png"/>
<graphic id="f1c" orientation="portrait" position="float" xlink:href="dummy3.png"/>
<graphic id="f1d" orientation="portrait" position="float" xlink:href="dummy4.png"/>
</fig>
...

Example 5

Alternatives to a table including supplementary material:
...
<table-wrap id="pbio-0020328-t002" position="float">
<label>Table 2</label>
<caption>
<title>Genes Activated in the Mother-Cell Line of Gene Expression</title>
</caption>
<alternatives>

<graphic xlink:href="pbio.0020328.t002.tif"/>

<table frame="box" rules="all" cellpadding="5">...</table>

<supplementary-material id="S1" xmlns:xlink="http://www.w3.org/1999/xlink"
xlink:title="local_file" xlink:href="pbio-0020328-t002.xls"
mimetype="application/vnd.ms-excel">
<label>Supporting Material</label>
<caption>
<p>Supplementary Microsoft Excel file (raw study data) supplied by authors.</p>
</caption>
</supplementary-material>

</alternatives>
<table-wrap-foot>...</table-wrap-foot>
</table-wrap>
...

Example 6

An example of a triple bond glyph. To a chemist, a triple bond is not the same as Unicode x2261, but using alternatives, as shown below, is sometimes the easiest way to display the character visually and still stay within Unicode: 
...
<alternatives>

<textual-form specific-use="unicode-look-alike">&#x2261;</textual-form>

<private-char name="Triple Bond" description="Chemistry Triple Bond">
<glyph-data id="tbond" format="PBM" resolution="300"
x-size="16" y-size="32">
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
0001111111111111111111111100000
0000000000000000000000000000000
0000000000000000000000000000000
0001111111111111111111111100000
0000000000000000000000000000000
0000000000000000000000000000000
0001111111111111111111111100000
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
0000000000000000000000000000000
</glyph-data>
</private-char>

</alternatives>
...

Journal Publishing Tag Library NISO JATS Draft Version 1.1d2

Version of December 2014

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