Data citation

[Daniel-Mietchen]

Now that data citation is en route to become available in JATS and thus for machines, I think it would be good to take a JATS4R perspective on it and come up with some tagging recommendations, so that we can give the harvesting of data citations a cleaner start than other forms of reuse of JATS.

[Melissa37]

I am just preparing a sample for testing on our host's display. Before going through that process, I wanted to include what I have for analysis by the group. Currently we call out Data citations in a separate section of the article. I plan to carry on doing so, but will also add them to the reference list.

This will be the reference entry:

<ref id="bib46">
  <element-citation publication-type="data">
    <person-group person-group-type="author">
      <name><surname>Ly</surname>
        <given-names>T</given-names></name>, <name><surname>Endo</surname>
        <given-names>A</given-names></name>, <name>
        <surname>Lamond</surname><given-names>Angus I</given-names></name>
    </person-group>
    <year>2014</year>
    <source>Proteomics database</source>
    <ext-link ext-link-type="uri" xlink:href="http://proteomecentral.proteomexchange.org"
      >http://proteomecentral.proteomexchange.org</ext-link>
  </element-citation>
</ref>

And this is how we will mark it in the Data citation section (the bib call out is subject to change):

<sec sec-type="datasets">
  <title>Major dataset</title>
  <p>The following dataset was generated:<xref ref-type="bibr" rid="bib46"/></p>
  <p>
    <related-object content-type="generated-dataset" id="dataro1">
      <name><surname>Ly</surname><given-names>T</given-names></name>,
      <name><surname>Endo</surname><given-names>A</given-names></name>,
      <name><surname>Lamond</surname><given-names>Angus I</given-names></name>,
      <year>2014</year><x>, </x><source>Proteomics database</source><x>, </x>
      <object-id pub-id-type="art-access-id">PXD001610</object-id><x>; </x>
      <ext-link ext-link-type="uri"
        xlink:href="http://proteomecentral.proteomexchange.org"
        >http://proteomecentral.proteomexchange.org</ext-link><x>, </x>
      <comment>ProteomeXchange Consortium.</comment>
    </related-object>
  </p>
</sec>

Any input welcome!

[Melissa37]

I have found another variation on this:

<ref id="bib46">
  <element-citation publication-type="web">
    <person-group person-group-type="author">
      <name>
        <surname>Schuman</surname>
        <given-names>M</given-names>
      </name>
      <name>
        <surname>Barthel</surname>
        <given-names>K</given-names>
      </name>
      <name>
        <surname>Baldwin</surname>
        <given-names>IT</given-names>
      </name>
    </person-group>
    <year>2012</year>
    <comment>Data from: Herbivory-induced volatiles function as defenses increasing
      fitness of the native plant <italic>Nicotiana attenuata</italic> in nature.
      Dryad Digital Repository.</comment>
    <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5061/dryad.gs45f"
      >http://dx.doi.org/10.5061/dryad.gs45f</ext-link>
  </element-citation>
</ref>

It has proven a bit difficult for us because it does not have a title or a source, just a comment.

Looking at the bibtex file from Dryad:

@misc{dryad_gs45f,
  title = {Data from: Herbivory-induced volatiles function as defenses increasing fitness of the native plant Nicotiana attenuata in nature},
  author = {Schuman, MC and Barthel, K and Baldwin, IT},
  year = {2012},
  journal = {eLife},
  URL = {http://dx.doi.org/10.5061/dryad.gs45f},
  doi = {doi:10.5061/dryad.gs45f},
  publisher = {Dryad Digital Repository}

So maybe it should be given title in JATS XML and not comment?

[Melissa37]

Examples on JATS:

http://jats.nlm.nih.gov/archiving/tag-library/1.1d2/chapter/tag-cite-archving-e5.html#arc-tag-cite-archving-e5

[Klortho]

See minutes from 7/23/2015 meeting for some notes/decisions.

We need to start drafting recommendations on the wiki, here.

[Klortho]

I still have some concerns that perhaps we should add some more examples to the data citations draft.

Here are some sources for examples:

• JATS Tag library
• Our own references-citations.md file.