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Topaz Release Candidate 0.8.2.1

Looks like I’ve been a bit remiss about posting release candidates on this blog as we’re on the third release candidate since RC 0.8. We’ve obviously been busy as the release candidate now has an extra numerical identifier. New features include:

  • minor and formal corrections on articles
  • advanced search
  • dynamic table of contents
  • dynamic journal archives

As with all release candidates, you may need to refresh your browser once or twice to get the new CSS changes.

And while all this development was going on, the I.T. and web teams were busy cleaning and ingesting +1400 articles to make way for PLoS Computational Biology, PLoS Genetics and PLoS Pathogens migration to the Topaz framework. Busy time at PLoS? A bit….

The most exciting features for this release are minor and formal corrections. Users can add a note and select “Correction” from the drop-down list. The PLoS staff will review the note and it will either stay as a note or be changed to a minor or formal correction. A minor correction is represented by a small red triangle “cloud” within the article text. A formal correction is signified the same way but a block appears above the title of the article displaying all formal corrections for the article. Clicking into a formal correction will also show the citation information.

These online corrections are another forward-looking feature for online STM publishing. In the past, PLoS would publish a new “formal correction article” with a link to the original article days/months after the original article published. But this “formal correction article” usually appeared in a different table of contents and could easily be overlooked by the user. Now the formal correction appears directly on the article text and all corrections for a specific article can be retrieved from a single URL. Next steps are to automatically add these corrections to the article PDF as a cover sheet when a user downloads the PDF and create a REST interface to easily retrieve the corrections for an article.

We’ve also re-indexed every published article for advanced search. Now you can search for text within the entire article, the abstract, article title or article references and search by subject category. The search fields also support a variety of search mechanisms include range searches, grouping and Boolean operators. We’ve a bit more work to do on search – look for a “quick article locator” block in the near future.

What else has been going on?!? A small crew at PLoS have been cleaning over 1400 articles from the PLoS Computational Biology, PLoS Genetics and PLoS Pathogens journals for ingest into the Topaz framework. This cleanup, spearheaded by Lynn Murdock, was necessary as we’ve been through a few rounds of XML changes in the last 2.5 years. The ingest of such a large volume of articles has been slowing PLoS ONE, PLoS Neglected Tropical Diseases and PLoS Hub – Clinical Trials down the last few weeks, but we’ve finally finished and the sites should run a bit more smoothly.

We’re still not down yet though – we’re migrating the PLoS community journals to the Topaz platform in short order. And then we’ll get to enjoy the final days of Strong Beer Month!

Here’s a rundown of all the features since RC 0.8 (saving the best for last).

Features implemented in Topaz RC 0.8.1

  • Display links to related articles on Article and Browse pages.
  • Administrative interface for collecting Articles into Issue and Issues into Volumes.
  • Administrative interface for attaching Issue Image article to Issues, and setting the current Issue.
  • Browse by Issue (Table of Contents) page.

Features implemented in Topaz RC 0.8.2:

  • Fixes to Browse by Issue (Table of Contents) to add more article types and next/previous links.
  • A dynamic Browse by Journal (Journal Archive) page.
  • A single rating field for all front matter articles (e.g. Editorial, Opinion).
  • Affiliation footnote links are displayed for group authors.
  • Minor FreeMarker and CSS fixes.
  • Updates to the volume and issue object models.
  • Migration from OSCache to ehcache for faster performance.
  • Administrative interface for viewing and releasing caches.

Features implemented in Topaz RC 0.8.2.1:

  • Minor corrections on articles.
  • Formal corrections on articles.
  • ”View All” corrections page.
  • Admin interface for converting notes to corrections.
  • Citations for formal corrections.
  • Advanced search:
    • Search by author name
    • Search article text
    • Search by date published
    • Search by subject category
  • Support for note DOIs in the DOI resolver.
  • Dynamic “Most Viewed” tab for journal home pages.

Features fixed in RC 0.8.2.1

  • Nomenclature of annotations/discussions changed to notes/comments.
  • Dynamic Table of Contents with article caching.
  • Dynamic Journal Archive with article caching.
  • Re-index of past published articles for advanced search.
  • Slideshow accommodates small thumbnail issue images.
  • Overall rating correctly calculates front matter articles.
  • Order articles in the Table of Contents and RSS feeds ordered by date published and then by article DOI.
  • Correct ordering of issues in Table of Contents.
  • Ingest correctly identifies article XML file when multiple XML files are found in the article zip file.
  • Correctly display front matter ratings when a rating is deleted.
  • Table of Contents displays “Author Summary” links for research articles.
Discussion
  1. (Feel free to redirect me)
    Is the software system behind PLoS journals
    (not the blog)
    available for others to use – or is it closed?
    If open how can I get it?

  2. The Topaz application framework has been released as Open Source. The publishing application that sits on top of Topaz will also be released as Open Source in a few months.

    More information is available on the Topaz website.

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