Digital resources in the Social Sciences and Humanities OpenEdition Our platforms OpenEdition Books OpenEdition Journals Hypotheses Calenda Libraries OpenEdition Freemium Follow us

Tag: visualization

Open Citations developments

Following the decision to merge the planned development of the Open Citations Corpus with the Related Work Project, described in the previous blog post, we proposed to develop one underlying data store, one data model and one RDF representation.

Infrastructure

We are presently creating a new OpenStack server environment on one of our Zoology Department Web servers, will host the data storage system, to be called the Open Citations Corpus Datastore (OCCD), the reference processing software, and the web server providing web sites, blog hosting and the Related Work user interfaces to the underlying data within the new enhanced Open Citations Corpus.  This will be available for use shortly.

Input data

We anticipate three primary data streams into the new expanded Open Citations Corpus, from PubMed Central, from ArXiV and from CrossRef.

PubMed Central has more than doubled the number of its Open Access full-text papers since they were last harvested into the Open Citations Corpus early in 2011.  There are now over 530,000 articles in the Open Access Subset, the majority of which are new for the Open Citations Corpus.  These contain approx. 16 million references to approx. 9 million individual cited papers.  The PubMed Central articles have rich metadata, marked up using the National Library of Medicine DTD v3.  The current Open Access Corpus from PubMed Central has now been downloaded, prior to processing.

ArXiV has approximately 750,000 papers, containing references to approx. 16 million papers, about 2 million of which are within ArXiV itself.  These are held in LaTeX format, and are accompanied by basic Dublin Core elements metadata.  The ArXiV corpus was downloaded in October, and will be updated in the near future.

CrossRef holds the reference lists for approx. 18.8 million articles provided by publishers participating in the CrossRef ‘CitedBy Linking’ service.  These are marked up in XML according to the CrossRef data schema that differs from the NLM DTD.  Access to these reference lists via CrossRef will require specific permission from the publishers concerned, that is currently being sought, as detailed in a recent blog post.  Trial downloads of CrossRef-derived reference lists will begin shortly.

New data model

The metadata requirements for the revised Open Citations Corpus, closely based on the data model originally developed by Alex Dutton during the initial JISC Open Citations Project, is now available online at http://goo.gl/eeDe8.

One task that we have already undertaken is to determine from each of the anticipated data input streams those metadata entities (e.g. title) that are already clearly marked up and can be recognisable automatically in the input data from each source – these we call ‘raw’ metadata terms – and those (e.g. author affiliation) that will have to be deduced or parsed out from the text of the input source – referred to as ‘derived’ metadata terms. A spreadsheet showing these mapping is available at http://goo.gl/XTlQ1.

Data format

The native format chosen for storing the reference data within is BibJSON, and the mapping from BibJSON to RDF will be achieved using an RDF metadata mapping that closely reflects that already in use for the original Open Citations Corpus, currently being finalized.  BibServer will be used as the underlying storage technology for the OCCD, which handles BibJSON natively.

Data processing

The existing data processing pipeline developed for the Open Citations Corpus is currently being reviewed to handle the new data, and to modularize it and fit it into a messaging system, which will allow simultaneous execution and status controlling of the various tasks that have to be performed at import.

Technical developments on the unified data store and the unified processing pipeline will be undertaken by intimate collaboration between Cottage Labs and Related Work staff, that has already commenced.  These tasks include:

  1. Zip extraction.
  2. Checking the incoming data for each article from each source for completeness and correctness according to the supplier’s data schema.
  3. Extraction of the article’s bibliographic metadata and its reference list.
  4. Conversion from the input format into the common BibJSON format.
  5. Data clean-up – correction of errors within the references.
  6. Data augmentation, by use of Web services accessing information from PubMed, CrossRef and other authorities for bibliographic records and DOI identifiers. (Well over half of references in published reference lists lack DOIs – if these exist, they will be found and added).
  7. Matching of citation targets: many papers cite the same target article in slightly different ways.  We will determine whether or not references are to a unique target, and then ensure that the correct bibliographic record for that cited article is used.
  8. Conversion of the BibJSON records to RDF using an XSLT transformation.
  9. Authoritative versions of semantically described bibliographic records for the citing and cited articles, together with the citation links, will then be held in both BibJSON and RDF formats in the Open Citations Corpus Datastore, to be used by front-end Related Work services.

Data indexing

The bibliographic reference information will then be indexed and held in an Elastic Search system, which deals natively with JSON data.  A variety of indexes will be built, to provide rapid response times for the user-facing services.

User interfaces

The interface provided to data in the original Open Citations Corpus was limited in functionality.

During the short Open Citations Extension Project, which extends into 2013, we will experiment with two sets of user interfaces, that will be developed and maintained over the new data, to permit a ‘show and tell’ comparison at the end of the project, before deciding on which of these demonstration interfaces we will retain for the on-going service.

First, the BibServer software developed to use Elastic Search by Cottage Labs during the JISC Open Bibliography Project will be employed to provide faceted search and browse over the data.

Additionally, the user interfaces currently under development for Related Work will be employed, using additional text-mining activities ‘under the hood’.  These will have an emphasis on social media interactions, with personalized auto-completion and instant filtering of reference lists.  This will permit the user to move from a selected paper to semantically related papers, to find other papers by the same author, to look at co-authorship and self-citation patterns, etc.

Finally, we hope to develop some time-line visualizations of citation networks.

We aim to provide a clean separation between the underlying data and the services built on top, using RESTful APIs, providing maximum flexibility for future development.

Web site

For the time being, until our new combined project server becomes available, the existing Open Citations Corpus and Related Work web sites will be kept active on their existing separate servers, but will eventually be phased out.

Blogs

At present, each project (Open Citations and Related Work) has its own blog.  This will change. I will open this blog to contributions from other members of the Open Citations and Related Works team, and will rename it Open Citations and Related Work. In addition, I will create a new blog, named Semantic Publishing and available at http://semanticpublishing.wordpress.com/, and will use that to host all new posts concerning semantic publishing and related topics that do not specifically relate to our joint open citations work. Previous semantic publishing posts within this blog will also be copied to the new Semantic Publishing blog.

Further plans

Further development of Related Work and the Open Citations Corpus will be dependent upon additional funding, for which we will apply early this year.

There are two developments that seem particularly beneficial to pursue in the near future:

  1. Improvements of the reference string matching for the bibliographic reference strings that appear in reference lists, for which DOIs or other identifiers are not given, so that the correct bibliographic record for the cited paper can be associated with the reference string.  At present, only two million out of the 16 million reference targets in the ArXiV data are correctly matched in this way.
  2. User generated annotations, particularly provision of CiTO-based citation typing to characterize why one paper cites another.  Tanya Gray has already created a plug-in to Chrome that permits this over native PubMed Central articles, and we are seeking to adapt this to use as a Related Work service with any browser.

Future scope

While our initial data sources have been in the physical and biomedical sciences, respectively, we hope to expand our services for people in the social sciences, humanities and arts, and provide broad coverage in these other disciplines, if we can tap into open sources of bibliographic reference lists from publications in these areas.

The Five Stars of Online Journal Articles

Many people will be familiar with Tim Berners-Lee’s five stars of linked data, categorising the publication of data on the web in levels of increasing usefulness.  To complement these, I wish to propose the Five Stars of Online Journal Articles, in particular to characterize the potential for improvement to the primary medium of scholarly communication made possible by web technologies, including the semantic publishing approaches I have recommended and exemplified in recent presentations, blog posts and papers [1-5].

While Tim’s five stars of linked data are hierarchical, all relating to the same thing and each building on the preceding one, the five stars of online journal articles shown in the diagram below are complementary, forming a constellation arranged along five independent axes within a multi-dimensional publishing universe.

Five stars of online journal articles Diagram

 

★  Peer review   Ensure your your article is peer reviewed, to provide assurance of its scholarly value, quality and integrity.

★  Open Access  Ensure others have cost-free open access to your published article, to ensure its greatest possible usefulness and readership.

★  Enriched content  Use the full potential of web technologies and web standards to provide interactivity and semantic enrichment to the content of your online article.

★  Available datasets  Ensure that all the data supporting the results you report are fully published under an open license, with sufficient metadata to enable their re-interpretation and reuse.

★  Machine-readable metadata  Publish machine-readable metadata describing both your article and your cited references, so that these can be discovered automatically.

At present, many publishers primarily use the web simply as a cheap and convenient distribution medium for PDF documents that are essentially electronic facimiles of the printed page, ignoring the Web’s greater potential.  The Five Stars of Online Journal Articles proposed here encapsulate a richer vision. Each star is highly desirable in its own right, but it is only by achieving them all in combination that we will really advance scholarly communication.  Of course, the degree of achievement along each of these publishing axes can vary, analogous to the different stars within the constellation shining with varying luminosities.

So I want you to ask yourself:

“How do my online journal articles rate against these five stars?”

As an exercise in ‘drinking my own champagne’, I have evaluated references [1] to [4] against the five stars, and present those results, together with a full explanation of the five-point evaluation scale for each star, in an article [6] for which this blog post is summary.  Here, to give you a flavour of that, I show the evaluations for Reis et al. (2008) (Reference [3]) before and after our semantic enhancements to that article that are separately described in Reference [2].

Original version of Reis et al. (2008)  (http://dx.doi.org/10.1371/journal.pntd.0000228).   Publisher: Public Library of Science.

Reis et al. original

Rating

Peer review (P)                              3    Conventional peer review with author feedback.

Open Access (O)                           4    Published in an open access journal with a Creative Commons attribution license.

Enriched content (E)                   0    Article lacks useful web links in the text and lacks direct links to referenced papers.

Available datasets (A)                 1    Figures and table within the article have their own DOIs, but are only downloadable as images, so that the data in the graphs and table are not available as actionable spreadsheets.

Machine-readable metadata (M)   1    Structural markup available in the XHTML version of the article.

Overall rating                             9

Semantically enhanced version of Reis et al. (2008)  (http://dx.doi.org/10.1371/journal.pntd.0000228.x001).  Publisher: David Shotton, Oxford University.

Reis et al. enhanced

Rating

Peer review (P)                              3    Conventional peer review of the original article, with author feedback.

Open Access (O)                           4    Enhanced version republished with a Creative Commons attribution license.

Enriched content (E)                   4    Of many types, as fully described in Reference [2].

Available datasets (A)                 2    Data for table and some figures kindly provided by the authors, and made available as downloadable actionable spreadsheets with their own DOIs.

Machine-readable metadata (M)   3    Structural and semantic markup within the text available as XHTML; embedded RDFa provides basic bibliographic information; two downloadable RDF files with their own DOIs accompany the enhanced article, one giving full bibliographic metadata about the article and the second providing bibliographic details, citation typing information and citation frequencies for all the cited references.  Article summary available as a separate document, but not in machine-readable format.

Overall rating                           16

Acknowledgements

I am most grateful to Bob DuCharme who, inspired by Berners-Lee’s five stars of linked data, challenged me to come up with five stars of online journal articles, following a talk I gave on semantic publishing.  I also thank Tanya Gray and Katherine Fletcher for wise comments after reading preliminary drafts of the full paper [6], and wish particularly to acknowledge the specific input made by Silvio Peroni , who insisted that I specify evaluation scales for all five stars, and whose wise proposals concerning peer review and open access I have incorporated into the full paper.

References

[1]      Shotton D (2009) Semantic Publishing: The coming revolution in scientific journal publishing. Learned Publishing 22: 85-94. doi:10.1087/2009202.

[2]      Shotton D, Portwin K, Klyne G, Miles A (2009) Adventures in semantic publishing: exemplar semantic enhancement of a research article. PLoS Computational Biology 5: e1000361. doi: 10.1371/journal.pcbi.1000361.

[3]      Reis RB, Ribeiro GS, Felzemburgh RDM, Santana FS, Mohr S, et al. (2008) Impact of environment and social gradient on Leptospira infection in urban slums  PLoS Neglected Tropical Diseases 2: e228.

[4]      Shotton D (2010) CiTO, the Citation Typing Ontology. J. Biomedical Semantics 1 (Suppl. 1): S6.  doi:10.1186/2041-1480-1-S1-S6.

[5]      Silvio Peroni S and Shotton D (2011).  FaBiO and CiTO: ontologies for describing bibliographic resources and citations.  (Submitted for publication).  Preprint available at http://imageweb.zoo.ox.ac.uk/pub/2011/publications/fabiocito_ontology_paper_PREPRINT.pdf.

[6]      Shotton D (2011).  The Five Stars of Online Journal Articles – an article evaluation framework.  (Submitted for publication).  Preprint available at http://precedings.nature.com/documents/6542/version/1/files/npre20116542-1.pdf and at http://imageweb.zoo.ox.ac.uk/pub/2011/publications/Shotton_TheFiveStarsOfOnlineJournalArticles.pdf.

JISC Open Citations Project web site

The JISC Open Citations Project website at http://opencitations.net exists for several purposes:

and, most importantly,

The JISC Open Citations Project Home Page

For the purposes of this demonstration, we are running an instance of Fuseki, that provides access to the Open Citation Corpus in an underlying TDB quad store, with a local patch to enable query timeouts, as was done for the SPARQL endpoint of CLAROS, a related project in which we have been intimately involved.

The web site and the underlying RDF citation data follow key linked data principles:

  • We don’t use blank nodes
  • All URIs are dereferenceable and content-negotiable.
  • Where possible we use standard identifiers based on DOIs, ISSNs and ISBNs.

For users wishing to jump into the data, we provide tabs to access data about journals and articles, each giving greater detail about the contents as one clicks in.

The Journals page

Each Journal page displays metadata about the journal, and links to useful information and the ability to download the journal metadata in a variety of formats.


Details of one journal

The articles tab displays a subset of about 10% of the entire corpus, for speed of loading the demonstration.

The Articles Page

Each ‘article’ page displays details about the selected article and its citation network, using graphviz, along with a user input form to customise the display of the network, namely for input or output citations, and for different forms of display. The article metadata and the citation diagrams can be downloaded in various formats.

Input citations for Codon, C. (2007). Maturation and degradation of RNA in bacteria. Current Opinion in Microbiology 10(3): 271-278. doi:10.1016/j.mib.2007.05.008.

We also display the RDF properties of each entity, allowing a ‘follow your nose’ style of data discovery. Each page lists the SPARQL queries that were run to generate it, enabling the user to see how the site works and to tweak the queries for their own ends.

Further work is planned to display citations along a time axis, and to develop other tools to permit users to exploit the data.

Functional clustering of CiTO properties

CiTO v2.0 contains just two main object properties, cito:cites and its inverse cito:isCitedBy, each of which as thirty-two sub-properties. Intentionally, these properties are not constrained as to domain or range, thereby maximising their applicability in a wide range of citation contexts. Additionally, CiTO contains one additional generic object property, cito:shareAuthorsWith, that may be used even outside a citation context.

Some have criticised CiTO for having too many properties, making it confusing for potential users, and Martin Fenner chose to use only the ten ‘most popular’ properties in his CiTO plug-in for WordPress, previously mentioned in this blog post. In response, I would point out that each property has a distinct and clearly defined meaning, and that together they provide an appropriate level of expressivity for effective use. Nevertheless, it is clearly difficult to conceptualize all the CiTO properties at one time, if they are being viewed using an ontology editor such as Protégé. I have thus created the following figure that groups CiTO properties by similarity, in the hope that this will facilitate choice of the most appropriate one.

Clustering of CiTO relationships by similarity

As shown in the figure, the CiTO properties and sub-properties (and, consequently, their inverses) may be classified as rhetorical (upper oval) and/or factual (lower oval, dark blue text), with the rhetorical properties being grouped in three sets depending on their connotation: positive (green), neutral or informative (blue) and negative (red). Five properties (in purple, within the overlap of the ovals) have both factual and rhetorical characteristics. The inverse properties are not shown.

Graffoo, a Graphical Framework for OWL Ontologies

Graffoo, a Graphical Framework for OWL Ontologies [1], is a wonderful new open source tool developed by Silvio Peroni that can be used to present the classes, properties and restrictions within OWL ontologies, or sub-sections of them, as clear and easy-to-understand diagrams. Several Graffoo diagrams have been developed to explain SPAR ontologies, or portions of them, and are to be found in the appropriate ontology directories at https://sempublishing.svn.sourceforge.net/svnroot/sempublishing/.

For example, in Figure 1 the diagram, BiRO.png, illustrates the structure of BiRO, the Bibliographic Reference Ontology:


Graffoo diagram of BiRO, the Bibliographic Reference Ontology

The upper part of this diagram shows how a bibliographic record, which in FRBR terminology is a Work, (a) is a set of components (author names, publication year, title, volume number, ISSN, publisher, dates of submission, acceptance and publication, etc.), (b) references a published entity (a FRBR Endeavor), and (c) can form part of a bibliographic collection such as a library catalogue, which is also a set of components, in this case of bibliographic records.

The lower part of the diagram shows how such a bibliographic record can be realized (i.e. expressed in a specific form, forming what in FRBR terminology is an Expression) as a bibliographic reference, such as you might find in an article’s reference list. The bibliographic reference, while referencing the same published entity, differs from a bibliographic record in two important ways.

  • First, a bibliographic reference typically does not include all the components of the full bibliographic record. References typically exclude the ISSN, the name of the publisher, and the submission and acceptance dates; may exclude the publication date and some of the authors’ names if there are many authors; and in certain journal (e.g. Nature) also exclude the title.
  • Second, the components of a bibliographic reference form an ordered list rather than a set, although the precise order of components can vary from journal to journal (e.g. whether or not the publication year immediately follows the authors’ names).

The diagram also shows that, just as bibliographic records may be grouped into bibliographic collections, so bibliographic references may be grouped into bibliographic lists such as reference lists (which, of course, are themselves ordered lists), nicely exposing the symmetry within the BiRO ontology in a manner that would be hard to grasp simply by looking at the class structure within an ontology editor such as Protégé.

The advantages of using such a Grafoo diagram are thus that it displays the logical relationships between elements of an ontology, or a sub-section of an ontology, in a manner that is relatively straightforward to understand, once one has grasped the meaning of the different elements of a Graffoo diagram. These elements are shown and defined in the Graffoo key (Figure 2).

Figure 2: The legend for all possible Graffoo objects

From our preliminary empirical studies, it appears that Graffoo allows us to create representations of OWL ontologies that can be comprehended in detail without the person viewing them having to understand the details of OWL 2 or of any of its linearizations (Turtle, RDF/XML, Manchester Syntax, or OWL/XML).

Graffoo has been developed using the standard library of the yEd diagram editor, a free diagram editor running on Windows, Mac and Linux. The graphml format version of those Graffoo objects is also available here. We commend the use of Graffoo to other ontologists.

[1] Graffoo, the Graphic framework for OWL ontologies. http://www.essepuntato.it/graffoo.