This form of semantic integration allows the components to cooperate flexibly in the analysis of document content and structure, and allows plugins to be developed independently of one another, with sensible relationships and behavior being inferred at run-time rather than being pre-determined: e. Via its plugins, Utopia Documents has access to a wealth of bioinformatics data.
Each plugin can use whatever client libraries are appropriate to access web-service endpoints both SOAP- and REST-style , as well as other remotely accessible resources, such as relational databases and RDF stores. This both offers a single mechanism via which Utopia Documents can search multiple primary databases, and enforces a consistent naming scheme between sources, allowing results to be interrelated. Although containing much information that is irrelevant to the life sciences, Wikipedia and thus DBPedia has evolved to represent a significant and mostly authoritative corpus of scientific knowledge—a study performed by the journal Nature concluded that its entries were as accurate or indeed, as error prone as those published in Encylopaedia Britannica Giles, , The combined application of ontologies and RDF in DBPedia allows queries performed by Utopia Documents to traverse only the portions of the DBPedia network that are semantically related to the life sciences.
We welcome any feedback on the software. Utopia Documents was developed in response to the need to achieve tighter coupling between published articles and their underlying data, ultimately to facilitate knowledge discovery. The tool was designed with two classes of user in mind; the reader, as consumer of published material; and the journal editor, as curator. To this end, the software was piloted with Portland Press Limited PPL with the goal of rendering the content of BJ electronic publications and supplemental data richer and more accessible.
With the customized software in-house, article annotation was fairly swift, individual papers taking 10—30 min, depending on their suitability for mark-up. Entities relating to protein sequences and structures have been, of necessity, the main targets for mark-up, because this was the functionality built into the original Utopia toolkit. The kinds of additional mark-up provided by the software include links from the text to external web sites, term definitions from ontologies and controlled vocabularies, embedded data and materials images, videos, etc.
The tool installs easily on the desktop as an alternative PDF viewer. Once opened, it displays a window consisting of three regions Fig. Below this, thumbnail images give an overview of the document and allow rapid navigation through it. The sidebar on the right displays the contents of annotations, providing term definitions and access to auxiliary data as the article is explored.
When no specific terms are selected, the sidebar defaults to displaying document-wide metadata [including the title, authors, keywords, abbreviations, etc. Where the PDF version is not available to the reader, clicking on the reference currently launches a Google Scholar search instead. Similar marks are added to the corner of the corresponding thumbnail in the pager, to indicate that additional information exists somewhere on that page. Mousing-over a glyph highlights the nearby terms, or document regions, that contain annotations; selecting these areas causes the associated data to be displayed—this may involve populating the sidebar with definitions, or may activate an embedded interactive visualization.
Highlighting any word or phrase in the paper 3a initiates a context-sensitive search of the online resources to which Utopia Documents is connected, all results again appearing in the sidebar. Selecting a term invokes the display of all possible definitions, allowing the reader or editor to select for themselves the most appropriate version. The provenance of these definitions is indicated in their headers, as illustrated in Figure 3 : the icon on the left 3c represents the item's origin [e.
The current version of Utopia Documents supports three forms of embedded interactive content; as with term definitions, these are indicated by red glyphs in the margins. Each type of interactive content has its own functionality: 3D molecules Fig.
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Figure 4 illustrates the simple transformation from static images of tables and figures into semantically annotated, interactive objects. Image sequences showing the transformation of a 2D image left-hand panel and of a static table of figures right-hand panel into interactive objects: i. Utopia Documents provides new ways of reading, of interacting with and ultimately of assimilating the knowledge embodied within research articles. The approach taken here departs from many initiatives in scholarly publishing in that the focus for enrichment is the hitherto-largely-neglected static PDF file, rather than HTML- or XML-based files.
Utopia Documents is hence an attempt to provide a semantic bridge that connects the benefits of both the static and the dynamic online incarnations of published texts. Inevitably, those who prefer to read articles online in a web browser will view the need to download a new, desktop-based PDF reader as a weakness. The philosophy embodied in Utopia Documents is to hide as much of the underlying complexity as possible, to avoid requiring users whether editors, authors or readers to change their existing document-reading behaviors, and to present no significant extra hurdles to publication.
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Like the initiatives in semantic publishing outlined earlier, the Semantic BJ , powered by Utopia Documents, is a pilot, the success of which will depend on various factors, including whether the barriers to adoption are sufficiently low, and whether the approach is considered to add sufficient value. Although it is too early to assess the impact of the pilot on readers of the Semantic BJ , the take-up of the software by the BJ 's full editorial team, and it use to mark up every issue since the launch, is a testament to the software's ease-of-use.
Of course, as the project with PPL develops, we will gather relevant usage and usability data in order to provide a more meaningful evaluation. Many of the projects discussed in this article have exploited fairly traditional text-mining methods, in conjunction with controlled vocabularies and ontologies, to facilitate the launch of relevant external web pages from marked-up entities in documents.
As such, they come with all the limitations in precision of current text-mining tools; this brings a significant overhead to readers in terms of having to identify errors. Of course, the difficulty for non-experts in any given field is to be able to recognize when particular annotations really are errors, and failure to identify them as such leads to the danger of error propagation. In light of these issues, we took a slightly different approach to entity mark-up in this first incarnation of Utopia Documents, taking advantage of linked-data initiatives to facilitate mark-up and add value to published texts.
However, because the functionality of the system is easily customizable via its flexible plugin architecture, any text-mining tool or database that is accessible via web services can be trivially added to the suite. As a demonstration of the potential of this architecture, in collaboration with their developers, three prototype plugins that link Utopia to other systems have been implemented:. Its entity-recognition engine, however, may also be accessed programmatically via a web service, which, given a section of text, identifies objects of biological interest and returns links to the summary pop-ups.
Integration of Reflect's functionality with Utopia Documents is therefore a comparatively straightforward task: as a user reads a PDF document, its textual content is extracted and sent to the Reflect web service; the resulting entities are then highlighted in the PDF article, and linked to the appropriate pop-up, which is displayed when a highlighted term is selected.
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A particular advantage of this integration is that it provides the reader with a light-weight mechanism for verifying or cross-checking results returned from multiple sources e. Its recently developed web-service interface provides programmatic access to much of its content, enabling Utopia Documents to identify and highlight receptors and their associated mutants when encountered in PDFs.
Thus, the presence of a GPCR in an article triggers the creation of a link to a description of that receptor in the database, which is displayed in the sidebar. As with the Reflect plugin, integration with these systems via their web services provides a straightforward way of migrating functionality previously only available for HTML content to scientific PDF articles.
Utopia Documents is at an early stage of development and there is more work to be done. In the future, as well as opening its APIs to other developers, we plan to extend its scope to systems and chemical biology, and to the medical and health sciences, as many of the requisite chemical, systems biology, biomedical, disease and anatomy ontologies are already in place and accessible via the OBO Foundry Smith et al.
Ultimately, allowing users to append their own annotations in addition to those endorsed by publishers should help to involve authors in the manuscript mark-up process.
Click on an option below to access. Log out of ReadCube. When participants were primed with either of these utopias, the Green utopia was perceived to entail a range of other positive characteristics e. Furthermore, the Green utopia was shown to elicit greater perceptions of participative efficacy, which in turn predicted the increase in social change motivation.
Utopia X: Wilson: aserlozronsvi.gq: Books
The full text of this article hosted at iucr. If you do not receive an email within 10 minutes, your email address may not be registered, and you may need to create a new Wiley Online Library account. If the address matches an existing account you will receive an email with instructions to retrieve your username. Fernando Corresponding Author E-mail address: julianwf unimelb. Nicholas J.
Tools Request permission Export citation Add to favorites Track citation. Share Give access Share full text access. Share full text access. Please review our Terms and Conditions of Use and check box below to share full-text version of article. Get access to the full version of this article. So I thought it was a very appropriate ending, with some relationship drama, some action and a nice HEA for all concerned. Great series though, really, for those who like fantasy or UF it's so worth it. Aug 10, Ami rated it really liked it Shelves: mm-fantasy-pnr-futuristic-scifi. Win, who is in loving relationship with Pablo, feels that since he and his compadres Tole and Zee are all now in relationship with other people, they no longer can stimulate sex with each other to work on the Celestine.
26b. Experiments with Utopia
So the three of them visit the Academy to look for answer. Pablo, left alone, decides to have fun with his old friends. When the Coven of Three returns, Win finds Pablo with traces of sex and their place ransacked. Win, in anger, tells Pablo to get out from the apartment. Pablo Win, who is in loving relationship with Pablo, feels that since he and his compadres Tole and Zee are all now in relationship with other people, they no longer can stimulate sex with each other to work on the Celestine.
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Pablo decides to find out the truth about what happens. The last book of the Utopia X series switch focus to Win and Pablo. While I miss Ridley he's my favorite character but Win and Pablo also have my heart. Seeing how deep the two of them love each other.