Additions to the IOP DTD in Version 1 4 6

Additions to the IOP DTD in version 1_4_6

The changes to the DTD in changing from version 1_4_5 to 1_4_6 are additions to cater for additional functionality in some of out new journals. There should be no change in the existing journals other than to advance the DTD identifier to the new version.

Glossaries

The journal Physical Biology contains glossaries to papers which appear immediately before the reference list. A new element <glossary> has been included in the DTD for these; it is an optional element in <body>, with content similar to an unnumbered section. Glossaries would normally have a heading of Glossary and contain a <definition-list> with terms and their definitions. In print the term is rendered in italic, with the definition run-on. Items are not indented and there's a line space (which can be variable) between entries.

A simplified version of the XML code is:

<definition-list id="pb169159dl1" spacing="compact">

<def-list-item id="pb169159dl1.1">

<term<italic>Adaptation.</italic</term>

<list-text<p type="run-on">The loss … stimulus.</p</list-text>

</def-list-item>

<def-list-item id="pb169159dl1.2">

<term<italic>All-points amplitude histogram.</italic</term>

<list-text<p type="run-on">A histogram of the current … histogram.</p</list-text>

</def-list-item>

</glossary>

Biographies

Another feature of Physical Biology is that it can have biographies of the authors at the end of the article. To accommodate this a new optional element <biographies> has been added to <back>. <biographies> is a container for one or more individual <biography> elements, the content of which is an optional graphic (a mug shot of the author) and paragraph text containing a brief biography of the author.

In print each biography is preceded by a column width rule with a 5pt space below. The mugshot is 5 pica (60 points) wide and separated from the text (which should align with the top of the figure) by a 6pt space. The text is set unjustified to the rest of the column width in 9 on 10 points Times. The name of the person is in bold.

Colour can be used for mugshots in the Electronic Journals version but for print should be greyscaled unless instructed otherwise.

An extra attribute biog has been added to the <author> element to provide a link from an authors name to his/her biography. This is an implied attribute and only required when a biography for that author is present.

<graphic-file version="print" format="EPS" file="physbio123456bio1.eps" width="5pc"/>

<graphic-file version="ej" format="JPEG" file="physbio123456bio1.jpg" width="5pc"/>

</graphic>

<p<bold>Aaron Fenster</bold> is a Professor of Medical Physics

at The John P Robarts Research Institute, London, Canada and the Department of

Diagnostic Radiology and Nuclear Medicine, The University of Western Ontario, London, Canada</p>

</biography>

<graphic-file version="print" format="EPS" file="physbio123456bio1.eps" width="5pc"/>

<graphic-file version="ej" format="JPEG" file="physbio123456bio1.jpg" width="5pc"/>

</graphic>

<p<bold>Fred Smith</bold> is …</p>

</biography>

</biographies>

Subject areas and keywords

Additions have been made to the subject areas and keywords sections of the DTD to accommodate the specific classification schemes used by the journals we jointly publish with SISSA (Journal of Statistical Mechanics and Journal of Cosmology and Astroparticle Physics).

Subject areas

For subject areas, new attributes have been added to both the <subject-area> and the <category> elements. <subject-area> now has a type attribute to indicate which scheme of subject classification is being used, and <category> has a code attribute so that the category can be specified by a `code’ rather than the textual description of it where appropriate. Journal of Statistical Mechanics is the first journal to use the subject area elements and the coding would be

<subject-area type="jstat">

</subject-area>

<subject-area type="jstat">

<category code="1">Low dimensional quantum mechanics and quantum field theory</category>

</subject-area>

(While the second example contains more information it is more open to typos and other errors so we strongly recommend that the code should be the data inputted and if the text is included it should be automatically added from a master list to avoid errors.)

The subject area information isn’t included in the PDF or HTML files but is used to allow subject views of the journal content within the Electronic Journals service.

Keywords

In a similar way to subject areas a type attribute has been added to <keywords> and a code to <keyword>. This allows keywords (actually short phrases) to be selected from a controlled list for a particular journal. Both Journal of Statistical Mechanics (JSTAT) and Journal of Cosmology and Astroparticle Physics (JCAP) have their own keyword lists and code allocated to each individual keyword. For JSTAT the keywords are divided by subject area so a code might be 1/010 or 12/020 where the portion before the / indicates the subject area the code belongs to. (Note that an article may be given keywords from several subject areas but allocated to fewer subject areas.)

An example of coding might be

<keyword code="cwd" /

<keyword code="exd" /

<keyword code="stc" /

</keywords>

<keyword code="cwd">cosmology with extra dimensions</keyword>

<keyword code="exd">extra dimensions</keyword>

<keyword code="stc">string theory and cosmology</keyword>

</keywords>

(Again while the second example contains more information it is more open to typos and other errors so we strongly recommend that only the code should be the data inputted and if the text is included it should be automatically added from a master list to avoid errors rather than being keyed each time.)

Types of article number

Two new attributes (jcap, jstat) have been added to <art-number> for specific types of article number for which external links can be generated knowing only the number and type of link. A jcap article number (journal J. Cosmol Astropart. Phys.) is of the form JCAP01(2004)001, while a JSTAT (journal J. Stat. Mech.) one is JSTAT01(2004)P001 for a paper or JSTAT01(2004)L001 for a Letter. In each case the first two digits indicate the month of publication so can range from 01 to 12 and the final three digits are the sequence number for the article in that month and can range from 001 to 999 (001 to 099 in practice).

External links

Both JCAP and JSTAT have external reference linking from their PDF files. The linking can be to the original article on the publisher’s web site, to the SPIRES database at SLAC (Stanford Linear Accelerator Laboratory) or to a preprint at ArXiv. Four new types of external link have now been defined and are available for use as part of the %f.extrefs; entity. The <links> element which was previously unused should now be used for JCAP and JSTAT and it’s content has been enhanced to include %f.extrefs;.

Two different types of link can now occur within the <links> group:

· elements with content which should provide a link from their content and will appear in the PDF after the main reference, e.g. <spires> links. In these cases the link is not to the primary source of the article but a secondary source.

· elements with no content but which refer to the primary source of the article (i.e. the article at its publisher’s web site) and indicate the previous elements in that reference from where the link is to be placed (e.g. <aps>, <edp> and <stacks>)

The new external linking elements are:

<spires> provides a link to the SPIRES database at the Stanford Linear Accelerator Center, a SPIRES link requires pieces of information journal, volume and page. Note that where a journal has parts, all parts have the same journal identifier but the part letter is included with the volume. For instance for all parts of Physical Review the jnl attribute is “PHRVA” but the vol attribute is A.. for part A, B.. for part B etc. The normal usage of the <spires> element would be within the <links> element, for example:

<links>[<spires jnl=”PHLTA” vol=”B516” page=”388”>SPIRES</spires>]</links>

which would provide a link from the word SPIRES to http://www-spires.slac.stanford.edu/spires/find/hep/www?j=PHLTA%2CB516%2C388

In the PDF the Spires links are coloured pale blue.

<extdoi> provides a link to an article for which a DOI is given (it is different from the <doi> which provides the DOI of the current article). The <extdoi> needs data in the doi attribute and provides a link to http://dx.doi.org/ with the doi appended. For example

would provide a link to http://dx.doi.org/10.1088/0305-4470/37/6/L02

<aps> and <edp> provide links to publisher’s web sites for references to articles in journals published by the APS and EDP respectively. In these cases the link should be made from the journal reference itself (normally from the volume and page combination) rather than from some additional text following after it as in the case of Spires links. Thus the content of the <aps> and <edp> links is normally empty and the attributes `start’ and `end’ indicate which piece of the text is to be linked. There are again attributes jnl, vol and page to provide the information needed for linking in addition to the base URL.

For example the reference

Senami M and Yamamoto K, 2002 Phys. Rev. D 66 035006

could have a link to the article at the APS web and the XML would be coded

the link would be to http://links.aps.org/abstract/PRD/v66/p035006 from the 66 035006 in the reference. In the PDF these links are coloured blue.

<edp> links are similar in structure to APS ones and a URL is http://publish.edpsciences.org/abstract/AA/v37/p1234 for

(the start and end attribute would also normally be present and the element empty).

The <stacks> element has also gained the attributes start and end so that it can be used to provide a link to an IOP element in the same way as <aps> and <edp> do.