Utopia Documents

Getting Started

Utopia Documents is a PDF reader optimised for scientific literature (right now, many of its functions work particularly well with life science articles). When you read an article with Utopia, it will connect you with a wealth of online resources to help you explore an article's content, and to discover other related material in a focused way (needless to say, if you're not connected to the internet when using Utopia Documents, several of its features won't be available).

Working with documents

Start-up screen

When you first run Utopia Documents, it will start up with an empty document window. The interface will appear similar whether you're running the software on a PC or a Mac; the only real difference will be the window's 'close' and 'minimise' functions, which behave as normal for your operating system.

Viewing PDFs

You can use Utopia Documents in the same way as any other PDF reader, such as Adobe Acrobat Reader or the Preview application on a Mac. You can open a file in one of two ways:

  1. Select 'Open' from the File menu
  2. Drag and drop a file from somewhere in your file system on to the Utopia Documents window.

You can use Utopia Documents to read most PDF files; however, the software really comes into its own as a reader for scholarly articles.

There are three main sections to the Utopia Documents workspace: on the far left is a tab bar allowing multiple documents to be open at once; in the centre is the main PDF reading pane; and to the right is a sidebar in which information appears as you read and interact with an article.

Pager

The pager shows thumbnails of the article's pages. Selecting a thumbnail with the mouse moves the article to that page. The pager is hidden and revealed from the main View menu.

Figure browser

The figure browser gives you an overview of the images that appear in an article, and can be opened and closed from the main View menu. Clicking on an image brings it to the centre of the browser, and double clicking the central image changes the article page to show that figure.

Sidebar

The sidebar shows information relating either to the whole article, or to specific terms that have been selected. Its contents are separated out into different sections, which can be expanded or collapsed by clicking on their section title. The sidebar can be opened and closed from the main View menu. Certain activities, such as opening a paper or exploring a term cause the sidebar to open automatically if there's new information to show, but it can be hidden again at any time.

Lookup Search Box

The search function allows you to query a number of online life science services. The results appear in the sidebar. The lookup search box can be toggled from the main View menu.

Article overview: putting articles into context

When you first open a paper, Utopia Documents will analyse its content, and attempt to link it to online resources that provide up-to-date information about what you're reading. In the sidebar, you'll see various different things appearing. The exact content, and the order in which the content appears depends on the information that's available at the time, so it will vary from paper to paper. Typical examples include:

  1. A formatted citation for the article, provided by CrossRef. You can change the citation style (including bibtex), and copy-and-paste this into other documents.
  2. The Altmetric score for the current article, which gives you an indication of the impact an article is having in blogs, on social networking sites, and in the media.
  3. Links to other articles provided by Mendeley's social network and algorithms.

Clicking on the title of a content section expands or collapses the section. By default, the Altmetric and CrossRef sections appear in their 'open' state, and everything else appears closed. The icon in the content section header shows you information about that content provider, and a link to the appropriate website.

Other sections will appear if relevant. For example, if the article is Open Access, and has been deposited in Pubmed Central, then you'll get a section with clickable links to the papers cited by the current article. If the cited articles are themselves in Pubmed Central, clicking on the [PDF] link in the citation will fetch the article directly, and open it up for you in Utopia Documents. Or, if data sets have been deposited in the Dryad repository that relate to what you're reading, then that information will be displayed too.

Some publishers (such as Portland Press or the Royal Society of Chemistry) have also made additional information available about their articles. If available, this will automatically be displayed.

Exploring an article's content

You can find out more about any term or phrase in an article using the 'Explore' function. Select the text you want to explore with the mouse and click the right mouse button. Simply select the 'Explore' option in the context menu, and the sidebar's contents will be replaced by information relating to whatever you've selected. As with the overview information, exactly what appears will depend on the nature of the term selected, and the ordering may vary. A spinning progress icon at the top right of the sidebar will show whether the search is still in progress, and clicking on the section titles that appear will expand and collapse the sections.

If you'd like to look something up that's not explicitly mentioned in the article's text, selecting to 'Toggle Lookup Search Box' from the View menu brings up a search box into which you can type any term or phrase.

Structure View

If the region annotated represents a molecule, click and drag with the mouse to rotate the view, or hold the control key (or command key on a Mac) to zoom in and out.

Sequence View

If the region annotated represents a protein sequence or set of sequences, use the mouse to scroll through the sequence, or click and drag to insert and remove gaps within the sequences.

Plot View

If the region annotated represents a set of numerical data, it wil be shown as a table of the information. Use the mouse to select which data you would like to plot, and click the 'plot' button to see the data as a 2D scatter-plot. Individual data items can also be edited - click the 'plot' button again to toggle between the two views of the data.

For articles published by the Royal Society of Chemistry, chemical terms will appear as blue text, linked to definitions in ChemSpider and elsewhere.

Dynamic content enhancement

You can use Utopia to enhance life science articles from any publisher/journal; from the PDF panel's context menu (opened with 'right click' – or 'ctrl click' on a Mac – in any white space in the PDF itself), select one of the 'annotate' options. These will cause the article to be processed by the selected algorithm, with any annotations created as a result appearing as red highlights.

Data sources

The following data sources are accessed whatever kind of article you're reading, and activate automatically when there's something useful to show.

Altmetric

http://altmetric.com/

Altmetric watches social media sites, newspapers and online magazines for mentions of scholarly articles and generates a measure of the quality and quantity of attention that a scholarly article has received. Utopia Documents brings this information directly to the article you're reading, giving you an indication of its impact in its field.

Mendeley

http://mendeley.com/

Mendeley provides an academic social network to help you discover the latest research in your area. Reading a paper in Utopia Documents seamlessly shows you other related articles from the Mendeley community.

CrossRef

http://crossref.org/

CrossRef is the official Digital Object Identifier registration agency for scholarly and professional publications, with a citation-linking network covering tens of millions of articles. As well as for getting hold of high-quality metadata, Utopia Documents uses CrossRef services to provide you with formatted citations for the articles you read.

Sherpa/RoMEO

http://www.sherpa.ac.uk/romeo/

Sherpa/Romeo provides information about publisher copyright and archiving policies, so you can easily tell whether an article can be re-distributed to your colleagues.

figshare

http://figshare.com/

figshare allows researchers to publish data auxiliary to an article in an easily citable, sharable and discoverable manner. Through figshare, Utopia Documents can provide direct links to this material while reading an article.

Life-science-specific sources

These features are specific to the life sciences; their content will appear in the sidebar automatically.

Open PHACTS

http://www.openphacts.org/

The Open PHACTS Discovery Platform is a freely available, integrated pharmacological database, sourcing its data from a variety of information resources and providing tools and services to question this integrated data to support pharmacological research.

The Semantic Biochemical Journal

http://biochemj.org/

Where the Utopia Documents story started! With over a 1000 articles manually curated by the editorial team, Portland Press’ Biochemical Journal provides links to online definitions, and interactive visualisation of tabular data, protein sequences and structures.

Dryad

http://datadryad.org/

Dryad is an international repository of the data behind published articles in basic and applied biosciences. If there's data in Dryad associated with whatever you're reading, Utopia Documents will let you know.

SciBite

http://scibite.com/

SciBite is a biomedical search engine and information alerting service focussed on drug discovery. It indexes thousands of papers, patents, blogs, grants, clinical trials and news feeds. Utopia Documents puts this information right at your fingertips, showing news relating to the article you're reading, and giving you the latest information on concepts within the paper.

Royal Society of Chemistry

http://rsc.org/

RSC has extracted chemical names from all its journal publications between 2008-2010 (over 30,000 articles). Utopia Documents displays these chemicals as annotations, linking them to the RSC's ChemSpider database. Annotations for articles published between 2010 and March 2012 will be available soon, with future articles being enhanced at the time of publication.

AQnowledge

http://aqnowledge.com/

AQnowledge provides detailed information about many hundreds of thousands of very specific laboratory materials and products, from a wide range of suppliers. This makes learning about, and sourcing, the materials mentioned in relation to a given experiment or protocol, or relevant to a given term or phrase in the text (e.g. a protein), easy and convenient, just by clicking the term or phrase in question.

Annotators

The following annotator features can be invoked manually from the Annotation context menu.

GPCRDB and NuclearDB

http://www.gpcr.org/7tm/ http://www.receptors.org/nucleardb/

GPCRDB and NuclearDB are molecular-class information systems that collect, combine and validate large amount of information about particular classes of protein. Relevant information relating to genes, residues and mutations is automatically retrieved and integrated with the article you're reading.

Reflect

http://reflect.ws/

EMBL's Reflect tool highlights proteins and small molecules found in your articles, linking them to online definitions and data. Previously only available for HTML content, Utopia Documents brings this functionality to any PDF.