What is all the fuss about?
Portland Press Limited and the University of Manchester are proud to present The Semantic Biochemical Journal, powered by Utopia Documents.
Utopia Documents offers a completely new way of reading PDF files. See the revolution for yourself - video demo now available
Once you have downloaded and installed Utopia Documents, open any PDF in the current issue, and watch it come to life.
A user guide is available here, and there are further FAQs below.
This is just the beginning. Come back soon and see what else you can do with all those flat, boring PDFs...
Why did we embark on the Semantic Biochemical Journal experiment?
With researchers drowning in a sea of data and knowledge highly fragmented across huge databases and millions of journal articles, publishers have been keen to find ways to unlock this information.
'Calling International Rescue: knowledge lost in literature and data landslide!' explains why the University of Manchester and Portland Press Limited embarked on this experiment and invites you to take part.
Why is using the term lookup feature in Utopia Documents any different to using, say, Google or a specific database?
First, Utopia Documents searches numerous appropriate databases for definitions and records, so it's rather more convenient than having to search them individually. Second, even though the software searches some quite generic sources (such as Wikipedia: DBpedia) for information, these searches are guided by semantics that mean that only results relevant to biochemistry and molecular and cell biology are returned.
Where does the additional information come from?
Everything that appears in the sidebar has an icon identifying the source of the data; for example, molecular structures are likely to come from the Protein Data Bank, definitions of terms are likely to have been sourced from the Glossary of Biochemistry and Molecular Biology by David M. Glick, or from Wikipedia. Other data sources will be being added all the time, and will appear with suitable icons. If you have a specific source that you'd like to see included, please email firstname.lastname@example.org.
Why are some items in the sidebar marked with a 'BJ' icon?
As you browse through a paper, you'll see that some words have been annotated by the editorial staff of the Biochemical Journal. Clicking on these causes that information to be displayed in the sidebar. Items that have been annotated by the editorial staff are marked with a BJ icon on the right hand side -- so you can be confident they are sensible definitions. Utopia Documents will also search various other databases for definitions or records associated with the term you've selected; if these appear without the BJ icon, then these haven't been curated by the editorial staff. They may well be appropriate and accurate definitions, but as with all web-based information, you'll have to use your own judgement as to their validity.
Online databases and encyclopedia change all the time -- how do I know what I'm seeing is what the editorial staff meant me to see?
The terms that appear in the sidebar are frozen at the point at which the editorial staff added them, so for curated items you can be sure they are what the editorial staff meant. However, many databases and encyclopedias change all the time, and the web page you'll be redirected to when you click the 'more' link on an item will be whatever is most current.
Do I have to download new PDFs to see additional content?
No - none of the additional features of Utopia Documents rely on information that's 'in' a PDF file, it's all calculated on-the-fly by inspecting the paper itself and fetching any new content via the internet. Even old copies of papers can be retrospectively annotated by the journal's editorial staff.
There seem to be more annotations in this paper than there were last time I looked! Is that possible?
Yes, that's perfectly normal. The Editorial staff can 'push' errata, updates, and new information on to already published papers, and you don't need to do anything special to receive these.
Utopia Documents appears to be able to manipulate the content of a PDF document -- how can I be confident I'm seeing what the author(s) intended?
It's true that the software can in theory change any aspect of what is displayed when a paper is read, but the software never modifies the PDF itself. We've gone to a lot of effort to make anything that's added to a document by software really obvious to the reader while at the same, minimizing its disruption to the experience of reading an article. You can always confirm that what you're seeing is 'the genuine article' by looking at the PDF in some other reader.
Are there any privacy issues associated with using Utopia Documents?
When you read a paper with this software, a number of searches are performed in order to find additional data. No personally identifiable information is sent from your client during this process, but it does mean that our servers (and other databases such as PubMed and PubMed Central) will get a query from your IP address for the particular document. In reality there are no privacy issues here that are any different from manually querying these databases, but you should be aware that this is happening automatically.
Can Semantic Biochemical Journal articles be read with normal PDF readers?
Yes - the PDFs themselves are no different to any other PDF, and you can read them with any normal PDF viewing software. You just won't get the extra features!
Does Utopia Documents only work for Semantic Biochemical Journal papers?
The software will display any article in PDF format, and you'll be able to use the dynamic lookup facilities to find your own definitions of biochemical terms. At present, only Biochemical Journal articles contain additional realtime material and curated annotations.