PNAS Reference style?

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2009-04-14
2013-05-28
  • Knut Krüger
    Knut Krüger
    2009-04-14

    Hi together,
    is there a soulution for the PNAS Style?
    f.e http://www.pnas.org/content/106/14/5693.full.pdf

    text:

    MPAs must be simultaneously self-sustaining (7, 8) and ...

    References:
    1.
    2. ....

    7. Hastings A, Botsford LW (2006) Persistence of spatial populations depends on returning
    home. Proc Natl Acad Sci U S A 103:6067–6072.
    8. Jones GP, Planes S, Thorrold SR (2005) Coral reef fish larvae settle close to home. Curr
    Biol 15:1314–1318.

    With kind regards Knut

     
    • Hi Knut,

      the PNAS style itself could probably adopted easily from the refbase Polar Biol or APA styles. However, since it's a numbered style, references get listed in the bibliography section according to their first occurrence in the article text. The refbase 'extract.php' script currently has no support for numbered styles.

      Some background: The refbase function (in 'search.php') that analyses the output from 'extract.php' currently just extracts reference IDs (serial numbers or cite keys) from the given source text and generates an appropriate SQL query (including the ORDER BY statement). The query is then executed by 'search.php' as usual and any found results are displayed. Unless I'm overlooking something, to display found records according to their occurrence in the article text, refbase would need to save the list of extracted serial numbers and re-order found records in memory according to that list.

      This is certainly doable but I fear it's not a quick hack (though I might be wrong). And I'm not sure how important this feature would be for the majority of our users...

      Matthias

       
      • Knut Krüger
        Knut Krüger
        2009-04-20

        Hi Matthias,
        i found a code part below in extract.php and I am wondering why I do not see the options.
        Wouldn't It be easy to adapt "order as in document"  or "no sort order"
        to get the same order as in the pasted text?
        Regards Knut

        echo "\n\t\t</select>&nbsp;&nbsp;&nbsp;"
                    . "\n\t\tsort by:&nbsp;&nbsp;"
                    . "\n\t\t<select name=\&quot;citeOrder\&quot; title=\&quot;choose the primary sort order for your reference list\&quot;>"
                    . "\n\t\t\t<option value=\&quot;author\&quot;>author</option>"
                    . "\n\t\t\t<option value=\&quot;year\&quot;>year</option>"
                    . "\n\t\t\t<option value=\&quot;type\&quot;>type</option>"
                    . "\n\t\t\t<option value=\&quot;type-year\&quot;>type, year</option>"
                    . "\n\t\t\t<option value=\&quot;creation-date\&quot;>date created</option>"
                    . "\n\t\t</select>&nbsp;&nbsp;&nbsp;"
                    . "\n\t\treturn as:&nbsp;&nbsp;"
                    . "\n\t\t<select name=\&quot;citeType\&quot; title=\&quot;choose how your reference list shall be returned\&quot;$citeFormatDisabled>";

         
      • Knut Krüger
        Knut Krüger
        2009-04-23

        Hi Matthias,

        >This is certainly doable but I fear it's not a quick hack (though I might be >wrong). And I'm not sure how important this feature would be for the majority >of our users...

        Very important, because Nature and Science have the same reference Style ;-)

        Regards Knut

         
    • Hi Knut,

      > Wouldn't It be easy to adapt "order as in document" or
      > "no sort order" to get the same order as in the pasted text?

      No, unfortunately not. The currently available sort options refer to appropriate "ORDER BY ..." SQL statements. But the document's citation order cannot be readily converted into an SQL "ORDER BY ..." clause. Instead one would need to loop over all citations from the document and resort the returned MySQL result set accordingly.

      Matthias