Table

[fred-atherden]

Tables within an article.

User Stories

Author

1. A an author, I want to be able to see the title and legend for a table so that I can check the content is correct.
2. As an author, I want to be able to edit the title and legend for a table so that I can correct any errors.
3. As an author, I want to be able to add a reference or asset citation to a table title or legend so that I can cite other articles or items in this context.
4. As an author, I want to be able to add, edit or remove equations in a table title or legend so that I can include mathematical content.
5. As an author, I want to be able to add new rows and columns to a table so that I can add new content.
6. As an author, I want to be able to remove rows and columns from a table so that I can remove content.
7. As an author I want to be able to add text to new cells so that I can add new content.
8. As an author, I want to be able to edit or remove the existing content in a cell so that I can correct any errors.
9. As an author, I want to be able to paste multiple cells copied from a spreadsheet into a table so that I can add new content in bulk.
10. As an author, I want to be able to add, edit or delete a reference or asset citation in the content of a cell so that I can cite other articles or items in this context.
11. As an author, I want to be able to add, edit or delete an equation in the content of a cell so that I can include mathematical content in a table.
12. As an author, I want to be able to apply style formatting (bold, italic etc) to the content in a cell so that I can add emphasis.
13. As an author, I want to be able to remove style formatting from the content in a cell so that I can remove emphasis.
14. As an author, I want to be able to add and remove style formatting across multiple cells at once so that I can make mass formatting changes in a table.
15. As an author, I want to be able to set the vertical and horizontal alignment of content in one or more cells so that I can improve the readability of the table.
16. As an author, I want to be able to designate one or more rows as header rows so that I can indicate the headings for my table.
17. As an author, I want to be able to remove header row status from one or more rows so that I can correct errors.
18. As an author, I want to be able to merge two or more cells into cells that cross rows and/or columns so that I can improve the readability of the table.
19. As an author, I want to be able to unmerge cells that cross rows and/or columns so that I can improve the readability of the table.

Production staff

20. As production staff, I want to be able to add a new table so that I can capture missing content.
21. As production staff, I want to be able to chose whether a new table should be a main table (label, title and legend) or an inline table (just the cells and footnotes) so that I can pick the most appropriate option for the content.
22. As production staff, I want to be able to add a title to a new table so that I can describe the content.
23. As production staff, I want to be able to add a legend to a new table so that I can describe the content.
24. As production staff, I want to be able to remove a table so that I can correct errors.

Érudit

25. As production staff, I want to be able to add an image to represent a table so that I can capture table content supplied in this manner.
26. As production staff, I want to be able to replace the image representing a table so that I can correct any errors.
27. As production staff, I want to be able to add an attribution to a table so that I can acknowledge the source of the content.
28. As production staff, I want to be able to edit the attribution for a table so that I can correct any errors.
29. As production staff, I want to be able to remove the attribution for a table so that I can correct any errors.

But what if . . . ?

Considerations

• Labelling. eLife currently allows unlabelled tables, labelled tables (Table 1, Table 2 etc) and a special case labelled table (Key resources table). Unlabelled tables won't have titles or legends and are generally used by authors to give shorter sets of data.
• We need to support header rows at any point in the table, not just the first row(s).
• eLife currently uses the @position attribute for tables, with two different values - either 'float' (for main tables) or 'anchor' (for inline/unlabelled tables). The idea was to fix inline tables at certain points in the text and to allow main tables to move about. This, however, is mostly a PDF issue the attributes may not be needed for this.
• PKP use both @postion and @orientation attributes, with @orientation being required in PDF generation.

XML requirements

Tables are captured using table-wrap. table-wrap may or may not have a child label element. Similarly they may or may not have a caption or title.

A table-wrap may have the attributes @position and @orientation, which are generally used for the purposes of PDF generation. Typical values are position="float", position="anchor", orientation="portrait", orientation="landscape".

Every table-wrap should contain one and only one table element. This table element may have a thead or a tfoot, and must have a tbody. Rows are determined by the element tr which can contain th and td elements. th must be allowed as a descendant of both thead and tbody, whereas td should be allowed as a descendant of tbody and tfoot.

The @colspan attribute can be used in order to specify if a th/td spans more than one column. The @rowspan attribute can be used in order to specify if a th/td spans more than one row. The @align attribute can be used in order to specify th/td data horizontal alignment. The @valign attribute can be used in order to specify th/td data vertical alignment.

The break element should be used in order to add line breaks within th/td elements.

<table-wrap id="table1" position="float" orientation="portrait">
    <label>Table 1.</label>
    <caption>
        <title>Data collection and refinement statistics</title>
        <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus consequat justo lacinia tortor placerat pretium. ...</p>
    </caption>
    <table frame="hsides" rules="groups">
        <thead>
            <tr>
                <th colspan="2" valign="top">Protein:RNA</th>
                <th valign="top">PUF-8: <break/>PBE</th>
                <th valign="top">FBF-2 SS/Y: <break/>PBE</th>
                <th valign="top">FBF-2 AS/Y: <break/>PBE</th>
                <th valign="top">FBF-2 AQ/Y: PBE</th>
            </tr>
            <tr>
                <th colspan="2" valign="top">Data collection</th>
                <th valign="top"/>
                <th valign="top"/>
                <th valign="top"/>
                <th valign="top"/>
            </tr>
        </thead>
        <tbody>
            <tr>
                <td colspan="2" valign="top"> Space group</td>
                <td valign="top">C2</td>
                <td valign="top">P61</td>
                <td valign="top">P61</td>
                <td valign="top">P61</td>
            </tr>
            <tr>
                <td rowspan="2" valign="top"> Unit Cell</td>
                <td valign="top"><italic>a</italic>, <break/><italic>b</italic>,
                        <break/><italic>c</italic> (Å)</td>
                <td valign="top">109.2, <break/>189.0, <break/>63.2</td>
                <td valign="top">96.4, <break/>96.4, <break/>99.9</td>
                <td valign="top">96.5, <break/>96.5, <break/>101.1</td>
                <td valign="top">95.9, <break/>95.9, <break/>100.4</td>
            </tr>
            <tr>
                <td valign="top">α, <break/><italic>β,</italic>
                    <break/><italic>γ</italic> (°)</td>
                <td valign="top">90, <break/>103.6, <break/>90</td>
                <td valign="top">90, <break/>90, <break/>120</td>
                <td valign="top">90, <break/>90, <break/>120</td>
                <td valign="top">90, <break/>90, <break/>120</td>
            </tr>
            <tr>
                <td colspan="2" valign="top">Resolution (Å)</td>
                <td valign="top">50–2.55 <break/>(2.59–2.55)<sup>*</sup></td>
                <td valign="top">50–2.25 <break/>(2.29–2.25)<sup>*</sup></td>
                <td valign="top">50–2.25 <break/>(2.33–2.25)<sup>*</sup></td>
                <td valign="top">50–2.85 <break/>(2.9–2.85)<sup>*</sup></td>
            </tr>
            <tr>
                <td colspan="2" valign="top"><italic>R</italic><sub>sym</sub> or
                        <italic>R</italic><sub>merge</sub></td>
                <td valign="top">0.191 (0.692)</td>
                <td valign="top">0.101 (0.704)</td>
                <td valign="top">0.104 (0.772)</td>
                <td valign="top">0.191 (0.957)</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"><italic>I</italic> /σ<italic>I</italic></td>
                <td valign="top">9.4 (1.9)</td>
                <td valign="top">19.2 (3.42)</td>
                <td valign="top">17.1 (2.98)</td>
                <td valign="top">12.8 (2.34)</td>
            </tr>
            <tr>
                <td colspan="2" valign="top">Completeness (%)</td>
                <td valign="top">98.9 (98.0)</td>
                <td valign="top">99.9 (100)</td>
                <td valign="top">99.9 (100)</td>
                <td valign="top">99.6 (99.2)</td>
            </tr>
            <tr>
                <td colspan="2" valign="top">Redundancy</td>
                <td valign="top">6.9 (3.6)</td>
                <td valign="top">5.7 (5.7)</td>
                <td valign="top">5.7 (5.7)</td>
                <td valign="top">10.7 (8.8)</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
            </tr>
            <tr>
                <th colspan="2" valign="top">Refinement</th>
                <th valign="top"/>
                <th valign="top"/>
                <th valign="top"/>
                <th valign="top"/>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Resolution (Å)</td>
                <td valign="top">33.8–2.6</td>
                <td valign="top">32.0–2.3</td>
                <td valign="top">31.6–2.3</td>
                <td valign="top">27.5–2.9</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> No. reflections</td>
                <td valign="top">37,625</td>
                <td valign="top">25,089</td>
                <td valign="top">25,386</td>
                <td valign="top">12,185</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> <italic>R</italic><sub>work</sub>/<italic>R</italic><sub>free</sub></td>
                <td valign="top">0.229/ <break/>0.285</td>
                <td valign="top">0.158/ <break/>0.204</td>
                <td valign="top">0.167/ <break/>0.223</td>
                <td valign="top">0.219/ <break/>0.272</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> No. atoms</td>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Protein</td>
                <td valign="top">8415</td>
                <td valign="top">3197</td>
                <td valign="top">3194</td>
                <td valign="top">3189</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> RNA</td>
                <td valign="top">507</td>
                <td valign="top">150</td>
                <td valign="top">168</td>
                <td valign="top">168</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Solvent</td>
                <td valign="top">229</td>
                <td valign="top">169</td>
                <td valign="top">109</td>
                <td valign="top">21</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> <italic>B</italic>-factors (Å<sup>2</sup>)</td>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Wilson B</td>
                <td valign="top">29.7</td>
                <td valign="top">36.6</td>
                <td valign="top">35.5</td>
                <td valign="top">48.4</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Protein</td>
                <td valign="top">32.8</td>
                <td valign="top">45.3</td>
                <td valign="top">45.1</td>
                <td valign="top">50.2</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> RNA</td>
                <td valign="top">43.6</td>
                <td valign="top">51.4</td>
                <td valign="top">58.8</td>
                <td valign="top">64.8</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Solvent</td>
                <td valign="top">32.7</td>
                <td valign="top">49.6</td>
                <td valign="top">44.3</td>
                <td valign="top">23.1</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> R.m.s deviations</td>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
                <td valign="top"/>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Bond lengths (Å)</td>
                <td valign="top">0.002</td>
                <td valign="top">0.007</td>
                <td valign="top">0.007</td>
                <td valign="top">0.002</td>
            </tr>
            <tr>
                <td colspan="2" valign="top"> Bond angles (°)</td>
                <td valign="top">0.45</td>
                <td valign="top">0.77</td>
                <td valign="top">0.78</td>
                <td>
                    <p>bar charts</p>
                    <p>flow charts</p>
                </td>
            </tr>
        </tbody>
    </table>
    <table-wrap-foot>
        <fn>
            <p><sup>*</sup>Values in parentheses are for the highest-resolution shell.</p>
        </fn>
    </table-wrap-foot>
</table-wrap>

Example of PKP content:

    <table-wrap specific-use="rules" id="IDb259e5ef-e160-4d78-9588-cc16787d10bb"
                        position="float" orientation="portrait">
                        <table>
                            <tr>
                                <td colspan="3"><p content-type="centered"/></td>
                            </tr>
                            <tr>
                                <td><p><bold>Complexity type</bold></p></td>
                                <td style="vertical-align:top;"><p><bold>Natural Language Processing
                                            methods used</bold></p></td>
                                <td><p><bold>Visualization methods used</bold></p></td>
                            </tr>
                            <tr>
                                <td><p>Language complexity</p></td>
                                <td><p>Readability measures, proportion of rare words, proportion of
                                        foreign words, density of entities, &#160;proportion of part
                                        of speech types, occurrence of topics discussed (topic
                                        lists, LIWC lexicon), emotions (NRC Emotion Lexicon),
                                        sentiment (Stanford Sentiment Analyzer), high-level verb and
                                        noun types (WordNet lexicographer files)</p></td>
                                <td>
                                    <p>paragraph squares</p>
                                    <p>bar charts</p>
                                    <p>aligned bar charts</p>
                                    <p>flow charts</p></td>
                            </tr>
                            <tr>
                                <td><p>Interaction complexity</p></td>
                                <td><p>Named entity recognition and classification (person,
                                        location, organization), entity graph (strength of
                                        relationship metrics)</p></td>
                                <td><p>co-occurrence matrices</p></td>
                            </tr>
                            <tr>
                                <td><p>Character complexity</p></td>
                                <td><p>Speaker identification, emotion development analysis,
                                        sentiment development analysis, WordNet lexicographer files
                                        for individual character&#8217;s activities</p></td>
                                <td><p>bar charts</p>
                                    <p>flow charts</p></td>
                            </tr>
                        </table>
                    </table-wrap>

The following elements should be allowed as children of th/td:

• bold
• italic
• sup
• sub
• sc
• underline
• ext-link
• xref
• break
• named-content
• preformat
• code
• inline-graphic
• inline-formula
• list
• p

Érudit example

Érudit capture tables as images:

<table-wrap id="ta2" position="float">
    <label>TABLEAU 2</label>
    <caption>
        <title>Résultats des régressions Tobit</title>
    </caption>
    <graphic xlink:href="table2_figure_1.png">...</graphic>
    <table-wrap-foot>
        <fn-group>
            <fn>
               <label><sup>a</sup></label>
               <p>Pharmacie, CLSC et organismes communautaires collectant les seringues à moins de 100 mètres (variable muette).</p>
            </fn>
            <fn>
               <label><sup>b</sup></label>
               <p>Poste de quartier à moins de 100 mètres (variable muette).</p>
            </fn>
            <fn>
               <label><sup>c</sup></label>
               <p>Autoroute, nationale, collectrice ou artère.</p>
            </fn>
        </fn-group>
    </table-wrap-foot>
</table-wrap>

Published HTML

Taken from: https://github.com/elifesciences/TextureRequirements/issues/46

[fred-atherden]

Tagged as partial support because:

• No way of tagging a th instead of td in the tbody (i.e. adding a header in the body)
• Line breaks are not supported (br for example)

Note that we should consider also the use of horizontal rule hr, as demonstrated in Table 3 of this Hindawi article :

[NickDuf]

• We can include inline math to a table legend but not block level equations. Is this sufficient?
• It is not possible to add equations to table cells at present
• Text style formatting can only be done on a per cell basis
• Setting cell alignment is not possible at present
• It is not possible to remove cell heading status after it has been applied
• It is not possible to unmerge cells
• There is no inline table option (just the cells and footnotes)
• Erudit only
  • No ability to represent tables as images
  • No attribution for tables option
• Removal of rows can be buggy at times