Archive for the ‘Semantic Enrichment’ Category

Utopia Documents highlights RSC Publishing’s semantic chemistry

RSC Publishing and its free database ChemSpider have integrated chemical semantic publishing across its chemical publications, and in collaboration with University of Manchester has made it accessible from the article PDF via the highly regarded Utopia Documents reader.

RSC Semantic Publishing

RSC has extracted chemical names from all its journal publications from 2008-2010 (over 30,000 articles), and has integrated the primary compounds of interest into ChemSpider. Readers of the article HTML on the RSC’s Publishing Platform can highlight compounds, and click on them to link directly through to ChemSpider’s compound record to discover additional data and compound information sources. The compounds will also shortly be visible from the article’s abstract page. Users of ChemSpider can discover these compounds via a text or structure search and, from a result, find the relevant references from RSC journal content and other integrated information sources. The project will run routinely on all new journal articles published by RSC and be extended further back into the RSC’s 170-year archive.

Integration with Utopia Documents

The free Utopia Documents reader can use this semantic information in the RSC’s enhanced articles to deliver this highlighting and linking functionality to RSC PDFs. Now readers of RSC PDF articles can use Utopia Documents to highlight and link from compounds directly through to ChemSpider and other information sources, thanks to the extension of Utopia by the software’s creators at The University of Manchester.

Richard Kidd, Informatics Manager at the RSC comments “expanding the integration of ChemSpider with our Publishing content, and applying routine semantic markup across ongoing and backfile content is a real milestone for how chemical science information can link together across the web. Being able to view all this through the PDF just makes it more accessible, and Utopia has continued to impress since it was first released.”

Steve Pettifer says, “Utopia Documents grew out of a need in the life sciences to regain some control of the mushrooming body of literature; it’s been really exciting for us to work with the RSC to expand into the field of chemistry and to bring our technology to a new audience.”

Example document to view the HTML and download a PDF:
Hydrogen bonding patterns in a series of 1-arylcycloalkanecarboxamides
Andreas Lemmerer and Joseph P. Michael, CrystEngComm, 2008, 10, 95-102
DOI: 10.1039/B708333E

Download Utopia Documents from getutopia.com

With this extension of semantic linking across our publications, RSC will now retire the use of the terms RSC Prospect & Project Prospect, used to describe the evolving project to enhance our articles which began back in 2007.

Both RSC and the Utopia Documents team are part of the Open PHACTS drug discovery consortium, which will be using the same technology to link disparate pharmacological data sources together under one view.

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Announcing launch of Release 6.1.2 of RSC Publishing Platform

This update includes further performance improvements and improved functionality for the RSC Publishing Platform:  

Article Landing Page 

  1. A new Compounds tab now displays the key chemical compounds from a journal article when it has been semantically enriched via RSC’s Project Prospect. Each compound links back to ChemSpider to access its 400 chemical data sources for compounds and users can also find related RSC journal articles containing the same compound. Try it now by clicking on the ‘Compounds’ tab in the article – Total synthesis of (±)-Vertine with Z-selective RCM as a key step, Laetitia Chausset-Boissarie, Roman Àrvai, Graham R. Cumming, Céline Besnard and E. Peter Kündig, Chem. Commun., 2010, 46, 6264.
  2. Our Rich HTML (Project Prospect view) has been greatly simplified and visually improved. Try now for Chem. Commun., 2010, 46, 6264 by following the Rich HTML link. Compounds highlighted in the Rich HTML also link through to ChemSpider.
  3. We fixed a bug where it was not possible to access RSC free content using an institutional username or federated access (Athens/Shibboleth) from the  article landing page.
  4. For older articles, where we do not have author abstracts (for a variety of reasons), we now display an image of the first page of the article, so that you can now use this as an abstract.  Try now for this historic article, On some analyses of modern “dry” champagne, Otto Rosenheim and Philip Schidrowitz, Analyst, 1900, 25, 6.
  5. To accommodate the new first-page abstracts, the login box for any users not recognised through IP authentication now appears above the PDF download link. This is a more logical placement.

Journal Landing Page / Home Page 

  1. We have created an issue tab for archive journals to provide consistency in the interface with the current titles.
  2. We’ve made the article finder more prominent on the journal page as users were not finding it below the page fold. We may consider moving the Article Finder higher up the page, depending on your feedback.
  3. Following your feedback, we’re in the process of removing the expanding ‘tree’ navigation in ‘Browse Journal’ on the journal homepages in favour of a drop-down menu system.  The tree navigation was complex for some titles (such as Organic & Biomolecular Chemistry) as it displayed the previous names for each journal, providing a ‘journal family’ history. This journal family history has been removed following your feedback and for the moment we are displaying navigation only for the single journal being viewed. This is the same level of functionality that will be available when we launch the drop-down menu navigation in the next release.

 Mobile Site 

  1. Mobile versions of the journal home pages are now available and give quick access for our mobile users. We do not display graphical abstracts for speed considerations. This is particularly important when accessing content over 2G and 3G networks. Graphical abstracts are available on the mobile pages for individual articles.

 

Site Homepage
  1. Added a link to watch the demo video of the RSC Publishing Platform.

Librarians Portal 

  1. The IP addresses registered for your institution can now be viewed. [21 Dec 2010, Updated – this functionality will now be released in Jan or Feb 2011.]
  2. If an institutional branding logo is smaller than the 150×30 pixels template, white space is now added to the image rather than stretching it to fit.
  3. Improvements were made to the profile management for librarians to allow name changes.
  4. The registration process for a librarian account has been simplified.
  5. A new form has been created to enable new customers to register their IPs.

Bug Fixes 

  1. We have fixed the broken navigation when navigating between issues where there was a change of journal name / ISSN.
  2. PDFs were downloading with file names such as “1996-01-01.pdf”, and are now correctly named by article ID, which is unique.
  3. We fixed a navigation error when the expanding tree navigation redirected users to the wrong  issue.
  4. Front and back matter for older content (pages starting X) was breaking the page range description on the issue home page. 

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PDF compound galleries

Another way of putting our award-winning markup into PDFs (see earlier), we’re using the structure drawing capabilities of ChemSpider to produce compound galleries here and here.  We’ve sorted the compounds by relevance into three broad categories, primary, secondary and routine.

What we’d really like is some feedback on how we can make this most useful for you, the reader. Here are some questions:

  • Is it more useful to have the compound gallery at the front, as a sort of index page, or at the back?
  • Currently we’re showing the routine compounds (solvents, drying agents and the like). Do we need to do this at all?
  • Is the article PDF even the best place for this? Would it be better to have a PDF for each issue, or for the current advance articles, or something else entirely?

Do let us know in the comments below!

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PDFs enhanced with XMP

Our readers still read most of our articles on the web as PDFs rather than HTML, so we thought we’d experiment with making some of our award-winning Prospect markup available through PDFs as well as through HTML.

Our first experiment is with XMP, a format which has hitherto mainly been used for metadata in photographs. We’re including compound data as InChIs, specifically pointers to the RSC InChI resolver, and incorporating other entities of interest with reference to OBO and RSC ontologies.

Examples, and instructions for how to see what we’ve included with an ordinary PDF viewer, available here: http://www.rsc.org/Publishing/Journals/ProjectProspect/Examples.asp

They’re not really intended to be directly read by human beings; we’d anticipate that these will be picked up and indexed by search engines or desktop search, and that people will use Adobe’s SDK to extract the data into a triplestore where it can be reasoned over.

We should also acknowledge that Omer Casher and Henry Rzepa at Imperial College London were experimenting with XMP back in 2006, and that NPG’s Tony Hammond has been blogging extensively on this subject on the CrossTech blog.

More experiments soon, but do let us know what you think in the comments below!

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