social media – OpenCitations blog

The OpenCitations team is growing – announcing three new appointments!

This is a summer of great news for OpenCitations. Thanks to the generous support received from the scholarly community during the first year of SCOSS adoption, we’re happy to announce the appointment of three new colleagues to work for OpenCitations at the Research Centre for Open Scholarly Metadata (University of Bologna).

Here’s some information about their backgrounds, positions and roles at OpenCitations.

Claudio Fabbri (Administrator and Research Manager):

Claudio has taken responsibility for all the day-to-day administrative activities of OpenCitations, including financial arrangements with those organisations supporting OpenCitations and bureaucratic interactions involving our host institution, the University of Bologna.

“After graduating in philosophy, I worked for several years as a librarian in university libraries. Considering my professional background, it came naturally to me to get in touch first with the Open Access movement and then, in a broader view, with Open Science principles. Now, as the Research Manager for OpenCitations, I’m proud to lead the administrative work for this great infrastructure. I’m interested in the history of science, especially how scientific communication has changed over the years”.

Chiara Di Giambattista (Communications Director and Community Development Manager):

Chiara takes care of all communications and social interactions made on behalf of OpenCitations, in terms of outreach to the scholarly community, contacts with present and potential supporting organisations, and OpenCitations’ communications via social media. She is developing a comprehensive mission statement and communications strategy for OpenCitations, designed to enhance the community’s understanding of OpenCitations’ global mission and awareness of its financial needs, to increase usage of OpenCitations services, and to foster collaborative interactions with like-minded infrastructures and institutions.

“I graduated in Visual Arts at the University of Bologna with the thesis “Presenting the future in the Digital Age. The semiotic convergence between art and IxD design in the practice of Future Casting”. Being deeply passionate about the adaptive potential of language in all its forms, from classical linguistics to visual semiotics, I have various experiences in web journalism and publishing. My role in OpenCitations is to improve the engagement of OpenCitations with the scholarly community, to develop OpenCitations’ social media platforms (LinkedIn and Twitter) and the OpenCitations blog, and to communicate and promote the values, services and impact of OpenCitations throughout the world”.

Giuseppe Grieco (Software and Systems Developer):

As a skilled computer scientist, Giuseppe will take charge of all the technical development related to the OpenCitations services, data acquisition, and bibliographic metadata and citations provision.

“I have a degree in computer science. I have been passionate about this field since I was thirteen years old, when I started to learn the basics of algorithms and programming. Most recently, I have been dedicating myself to artificial intelligence by pursuing Masters studies at the University of Pisa. I have always tried to take every opportunity to put into practice what I’ve been studying . Now, with my appointment at OpenCitations, I will do so by developing upgrades and enhancements to the existing software infrastructure”.

More new people will be getting involved in OpenCitations in the autumn. Watch this space!

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:

Zip extraction.
Checking the incoming data for each article from each source for completeness and correctness according to the supplier’s data schema.
Extraction of the article’s bibliographic metadata and its reference list.
Conversion from the input format into the common BibJSON format.
Data clean-up – correction of errors within the references.
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).
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.
Conversion of the BibJSON records to RDF using an XSLT transformation.
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:

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.
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.

Why openness benefits research

David writes: Dr Heinrich Hartman is a new colleague of mine, who, having been working in the Mathematical Institute of Oxford University, has just returned to Germany to start a new job in a leading semantic web research group, that of Steffan Staab at the Institute for Web Science and Technologies, University of Koblenz-Landau. What follows are our thoughts about research openness, that relates to our decision, described in the next blog post, to merge our bibliographic citation projects.

The following text is jointly authored by David Shotton (david.shotton@zoo.ox.ac.uk) and Heinrich Hartmann (hartmann@uni-koblenz.de)

Transparency is essential for trust and credibility in the research community, and true openness brings great opportunities for academia. The internet facilitates the free flow of information and knowledge, and permits new forms of communication both for researchers and for the general public. Already, today’s children can listen freely on the internet to university courses taught by world-leading scientists, and everybody has the best encyclopaedia ever written (Wikipedia) at their fingertips. These are real game changers. Opening up the research literature is the next logical step.

Open publishing

We believe that the current academic publishing model – whereby researchers give their content to commercial publishers and then buy it back from them at enormous cost by means of journal subscription fees – has become absurd, since it is no longer helping the researcher to distribute his or her findings, but rather prevents the work from being widely read, by hiding it behind subscription pay walls. Would it not be much better to let this information flow freely, accessible to everybody who wants to read it!

Of course, such a vision of openness for academic publishing raises issues of finance and quality control – who will pay for open access publishing, and how can we ensure that scientific rigor accompanies open publication. While the internet enables dissemination of information at a fraction of the cost of traditional print publication, publishing clearly involves more than electronic dissemination. It is for this reason that we, with others, are presently planning a high level conference on modern scientific communication, entitled Rigor and Openness in 21st Century Science, to be held in Oxford next spring.

However, new publication funding models are being developed, particularly in the United Kingdom, where Research Councils UK and the Wellcome Trust are insisting that papers reporting research results obtained as a result of their research funding should be published under an open Creative Commons CC-By attribution licence when an article processing charge (APC) is levied, so that the works are freely available for text mining and re-use [1]. What is significant is that they are backing their words with funding to enable it. Cameron Neylon has recently written a commentary in Nature about the importance of this [2].

Furthermore, peer review is being carefully examined by several forward-looking publishers to determine how well open alternatives to the present system of confidential review actually work.

The role of social media in science

Much academic research is done in relative isolation, because topics have become so specialized that there may be only a few experts in the whole world who really understand each particular research problem. These experts may be located on different continents, and may not know about one another – a situation that is particularly true for Ph.D. students and other young researchers, who may not yet be familiar with the literature in their field, and who may have formed few personal relationships with colleagues in other institutions through attendance at research conferences. New forms of academic social media can play a role here, to catalyse interactions between geographically separated academics, and many experiments in this area are being conducted.

Academic social media can also play an important role in filtering the wealth of new articles published every day, and in alerting people to the small fraction of these that are most relevant to them. Typically, junior researchers rely on recommendations from friends and colleagues about which articles are worth reading, but if academic social media can be used to broaden this recommendation network, they will provide a significant service.

Fears and benefits of openness

Of course researchers, particularly early in their careers, are cautious about sharing their discoveries too early or too widely, for fear they may get ‘scooped’, since they naturally and quite properly wish to obtain credit for their own work by being the first to publish it. However, what is often missed by people of this mind-set is that working openly with other people can have benefits too. It can be a lot more fun, can lead to more sustainable motivation, can result in incredibly rapid collaborative progress, and hence can often lead to better results. An essential pre-requisite for this is the willingness to share one’s ideas and making contact with like-mined people. An example of a researcher who practices openness in his day-to-day research is Georgio Gilestro, Lecturer in Systems Neurobiology with the Department of Life Sciences at Imperial College London, who publishes his research group’s Open Lab Book online.

Our personal experience, not at least in the joint Open Citations and Related Work developments described in the next blog post, is that you gain more than you loose by being open!

Reference

[1] Wellcome Trust announcement: Open access: CC-BY licence required for all articles which incur an open access publication fee – FAQ. Available from http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/WTVM055715.pdf.

[2] Cameron Neylon (2012). Science publishing: Open access must enable open use. Nature 492: 348–349. doi:10.1038/492348a.

‘Likes’ joins the semantic web: cito:likes

A ‘like’ button is a well-known feature in communication software such as social networking services, Internet forums, news websites and blogs that permits a user to indicate that he/she likes, enjoys or supports certain content. Internet services that feature ‘like’ buttons usually also display the number of users who have expressed that they ‘like’ a particular item of content, providing a quantitative estimate of the strength of support for it.

In particular, the ‘Like’ button is one of Facebook’s social plug-ins, which can be use on websites outside Facebook as part of Facebook’s Open Graph. It is valued by advertisers who wish to attract ‘likes’ for their products (and who pay Facebook for the privilege), but its use has aroused privacy concerns because it permits Facebook to track visitors to participating sites, even if they not Facebook users, giving Facebook a vast amount of information about who visits which sites.

Like it or not, however, this form of social communication has now become an integral feature of online social interactions. For this reason, we thought it would be worthwhile to enable encoding of such ‘likes’ as open linked data, in the form of a new object property in CiTO, the Citation Typing Ontology.

This new property, cito:likes, has the following definition:

“A property that permits you to express appreciation of or interest in something, or to express that it is worth thinking about even if you do not agree with its content, enabling social media ‘likes’ statements to be encoded in RDF. Use of this property does NOT imply the existence of a formal citation of the entity that is ‘liked’.”

An exemplar usage of cito:likes (in Turtle format) is:

sioc: <http://rdfs.org/sioc/ns#> .
foaf: <http://xmlns.com/foaf/0.1/> .
today: <http://opencitation.wordpress.com/2012/07/13/> .

today:cito-likes a sioc:Post ;
	sioc:has_creator [ 
		a sioc:UserAccount ; 
		sioc:account_of [ 
			a foaf:Person ;
			foaf:givenName "David" ;
			foaf:familyName "Shotton" ] ] .

<https://www.facebook.com/silvioperoni> a sioc:UserAccount ;
	sioc:account_of <http://www.essepuntato.it/me>;
	cito:likes today:cito-likes .

To our surprise, we found that existing ontologies did not include such a property – a search in the excellent new LOV (Linked Open Vocabularies) service revealed that no other open ontology contains the same concept as is now represented by cito:likes.

The Trait Ontology has trait:likes, but this object property has a gender-related domain, and its definition indicates that its usage is designed for expressing sexual fetish preferences.

Schema.org at first sight appears to have something resembling cito:likes, but inspection of schema:UserLike reveals this use to be specific for events.

Even the SIOC ontology, a product of the SIOC initiative (Semantically-Interlinked Online Communities) aimed at enabling the integration of online community information, which is described in an award-winning paper from DERI [1], lacks the concept ‘likes’.

So here we offer cito:likes, a property (like all other cito properties) without domain or range constraints, permitting it to be used in a wide variety of situations.

Like it? Click the Like button below!

David Shotton
Silvio Peroni

Reference

[1] John G. Breslin, Andreas Harth, Uldis Bojars, and Stefan Decker (2005). Towards Semantically-Interlinked Online Communities. In Proc. ESWC 2005 (A. Gómez-Pérez and J. Euzenat, Eds.); Lecture Notes in Computer Science 3532, pp. 500–514. doi:10.1007/11431053_34. Available from http://bit.ly/KQ2iK4.