jiscexpo – OpenCitations blog

Open Citations Extension Project

I am pleased to announce that the JISC have funded an extension to the Open Citations Project to run from 1st August 2012 until 31st January 2013, during which we will review and revise the technology used to create the Open Citations Corpus, will update the content provided by PubMed Central, and will improve its presentation. We will also prototype value-added services over the open citations data, to demonstrate their usefulness and to justify further funding that will permit a major expansion of the corpus in 2013 to include reference lists from subscription-access journals, including those from Nature Publishing Group, Science and other AAAS publications, and Oxford University Press. In preparation for this, we will collaborate with CrossRef to determine how best to ingest reference data into the Open Citations Corpus in an on-going manner.

Full details are given in the Case for Support. Watch this space!

Oxford University Press to support Open Citations

I am delighted to announce that Cathy Kennedy, OUP’s Senior Publisher for Journals, has just written to me as follows:

“Oxford University Press is delighted to support the Open Citation Corpus initiative in the interest of furthering and disseminating scholarship. We are making the reference lists of articles in a number of journals we own available for inclusion in the Open Citations Corpus, and will be consulting further with our partner societies on extending the initiative to include their journals in due course”.

OUP thus becomes the third publisher of subscription-access journals, and the first university press, to declare its willingness to make the reference lists in journal articles publicly available. Congratulations, OUP!

Are we starting to see the beginning of a sea change in attitudes? Watch this space.

Nature to open its reference list data

Bibliographic references are the links that knit together independent scholarly endeavours. I am thus delighted to announce that Nature Publishing Group, publisher of Nature, Nature Genetics and many other leading journals, has agreed to open its articles’ reference lists, initially for a selected number of NPG journals, and contribute the bibliographic citations contained in these lists as open linked data to an expanded Open Citations Corpus, where they will be freely available for everyone to use in whatever manner they choose. Preparations to expand the corpus in this manner, by integration with the reference processing pipeline of the CrossRef Cited-By Linking service, will be undertaken over the next six months of this year, and incorporation of the references from the selected NPG journals into the expanded Open Citations Corpus is planned to commence in the first half of 2013.

As the first subscription-access publisher to opening its reference lists in this way, Nature Publishing Group is further demonstrating its commitment to ‘lead from the front’ in its embrace of new semantic publishing technologies. Only two months ago, this publisher announced its decision to open up the bibliographic records of its journal articles as open linked data. On 4th April, NPG’s Linked Data Platform press release read:

“Nature Publishing Group (NPG) today is pleased to join the linked data community by opening up access to its publication data via a linked data platform. NPG’s Linked Data Platform is available at http://data.nature.com. The platform includes more than 20 million Resource Description Framework (RDF) statements, including primary metadata for more than 450,000 articles published by NPG since 1869. In this first release, the datasets include basic bibliographic information (title, author, publication date, etc) as well as NPG-specific ontology terms. These datasets are being released under an open metadata license, Creative Commons Zero (CC0), which permits maximal use/re-use of this data. NPG’s platform allows for easy querying, exploration and extraction of data and relationships about articles, contributors, publications, and subjects. Users can run web-standard SPARQL Protocol and RDF Query Language (SPARQL) queries to obtain and manipulate data stored as RDF. The platform uses standard vocabularies such as Dublin Core, FOAF, PRISM, BIBO and OWL, and the data is integrated with existing public datasets including CrossRef and PubMed. More information about NPG’s Linked Data Platform is available at http://developers.nature.com/docs. Sample queries can be found at http://data.nature.com/query. ”

We very much hope that NPG’s example will encourage other subscription-access publishers to open their own journal article reference lists, and become early adopters of Open Citations. Reasons why subscription-access publishers should willingly join NPG and open their citation data are given in my previous blog post. While at first coverage among subscription-access publishers will be incomplete, this expanded Open Citation Corpus will, I am sure, draw in increasing numbers of publishers, and in true Web 2.0 style will become more useful the more publishers participate, resulting in value-added bibliographic and bibliometic services being created over the open data. Other subscription-access publishers who would like to contribute their journal article references to the Open Citations Corpus should contact me at <david.shotton@zoo.ox.ac.uk>.

Why publishers should open their references

Why should the publishers of subscription-access journals, who presently generate income from the sale of access to peer-reviewed full text scholarly articles, be willingly open the reference lists of these articles, and contribute these to the Open Citations Corpus for publication as open linked data? I would like to suggest the following reasons:

1. There is a general move towards open data, which is widely regarded as a common good. This includes citation data, i.e. bibliographic references from one article to another (in RDF Turtle format: A cito:cites B . ).
2. The reference lists at the end of journal articles are works of scholarship by the authors, who have chosen to include certain references and exclude other potentially citable papers from the reference list. However, the references themselves are simply items of bibliographic data, formatted according to the journal style, and do not benefit from the author’s creative input.
3. The reference list, together with the front matter (including the bibliographic information about the article itself) and the abstract, has traditionally been included within the copyright protection enjoyed by the article as a whole. However, the bibliographic information about the article and the article’s abstract are commonly made freely available, for example through PubMed. This same openness should now be afforded to the reference list within each article.
4. There is a home for such reference citation data: the Open Citations Corpus has been specifically created to house and publish scholarly bibliographic citation data, and is now preparing to welcome article reference lists from subscription-access journals, to supplement those already contributed from open-access journals.
5. For those publishers who already contribute their reference information to CrossRef as part of its Cited-By Linking service, this can be accomplished without any change to the publisher’s own publishing workflows, just by giving permission for CrossRef to flag the articles of certain journals as having open references. Open Citations intends to collaborate with CrossRef by harvesting the reference lists from such flagged articles, parsing them into RDF, and adding them to the Open Citations Corpus. Provided that the references are already being submitted to CrossRef, no work will have to be done by the publisher, and no changes in publishing procedure will be involved.
6. Open Citations will publish each reference list as an independent RDF Named Graph, with a unique URI, thereby protecting the integrity of the article reference list as a unit of scholarship, the source of which will be explicitly acknowledged.
7. The open citations data will then be offered back to publishers to use as they wish, e.g. for visualization of citation networks, calculation of metrics, etc., providing easier and more usable access to their own citation data than is currently afforded by commercial providers, who do not provide such data in linked data format.
8. Publishers will also be free to host their own open citations data, should they wish to do so.
9. For the majority of publishers, who would still receive subscriptions on the full articles themselves, opening their article reference lists in this way will cost nothing in terms of lost revenue.
10. Indeed, participation in the Open Citation Corpus will bring the following benefits to subscription-access publishers:
– Access to services to be built over the aggregated open citations data, for example an automated reference correction service available to editors upon receipt of a manuscript, for the automated pre-publication correction of errors in reference lists prior to article publication.
– Increased exposure to users of the references to the publisher’s own journal articles – a form of advertising. While at first coverage among subscription-access publishers will be incomplete, this expanding Open Citation Corpus will, in true Web 2.0 style, become more useful the more publishers participate.
– Even while coverage is incomplete, the Open Citations Corpus by its very nature contains reference citations to all the key papers published in every field covered – currently to all the key papers published in every biomedical field, enabling readers more easily to identify and find the most highly cited papers of each contributing publisher.
– Opening citations data will result in white-listing and general good-will from funding agencies, government and other advocates of open data, who might otherwise mandate publication by grantees in alternative open-access journals.
– Opening citations data will lead to support from scholars and researchers themselves, who wil be more inclined to publish in that publisher’s journals, feeling that at last the publishers would be giving back to them some of their own data, rather than selling it back to them as at present.

As my next blog post shows, one leading subscription-access publisher is now willing to open its journal article references in the way I have suggested. Others who would like to so the same should contact me at <david.shotton@zoo.ox.ac.uk>.

IBRG projects to facilitate data publication and data citation

In the previous post, I outlined reasons why researchers don’t publish data, presented as evidence to the Royal Society’s Policy Study “Science as a Public Enterprise” Call for Evidence. Here, I summarize activities by members of my Image Bioinformatics Research Group (IBRG) at Oxford University to facilitate data publication and data citation, and thus to help catalyze a cultural shift to a situation in which data publication is as natural a part of research life as is undertaking experiments.

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Data management services and data repositories

We are developing tools and services to assist researchers in their local data management, for their own personal benefit, while facilitating automated data submission to appropriate institutional or subject-specific data repositories, in ways that fit with their normal working practices and impose as little as possible in terms of cognitive overhead – what we term sheer curation. These include the two-stage data management services we are currently funded to develop by the University Modernization Fund through the JISC DataFlow Project, namely (a) DataStage, a private local data management file system, with automated backup, Web access, and security access control, for use by individual research groups, and (b) DataBank, a cloud-deployable data repository for use by universities, research institutes or large research consortia. These open source services will be made available for installation by third parties on the Eduserv academic cloud and elsewhere, as required by research groups, institutions and universities both in the UK and internationally. We seek early adopters!

Curation by addition

For automated data submissions from DataStage to DataBank, that will use the SWORDv2 repository submission protocol to standardize data package ingest, we are intentionally lowering the barriers in terms of metadata requirements for initial data submission, with the the possibility of enriching the metadata at a later date – what we call curation by addition – in order to kick-start the cultural sea change required for data deposition to become routine. We are trying to avoid the best – the requirement for perfect and complete metadata – becoming the enemy of the good – data publication by any means.

Dryad

We are, through the JISC Dryad-UK Project, working to promote the Dryad Data Repository, a domain-specific repository for biological datasets linked to peer-reviewed journal articles, by bringing additional publishers and journals on board, and enabling Dryad metadata to be published as open linked data.

SWORD

We are also promoting the adoption of SWORDv2 repository communication protocol for data package wrapping, to permit automated deposit to DataBank, Dryad or other SWORD-compliant repositories, and the exchange of metadata between them.

SPAR (Semantic Publishing and Referencing) Ontologies

To enable Dryad, DataBank and similar repository metadata to be published as open linked data, we are creating appropriate data description and data citation ontologies, including FaBiO and CiTO4Data, as part of our suite of SPAR Ontologies, and are using them to provide mappings from the DataCite XML Metadata Kernel to RDF.

Data citation

We are working with DataCite to assign DOIs to Dryad and DataBank datasets, so that data publications become citable, gaining academic credit for the data depositor.

These data citations, when they exist, will fit naturally within the Open Citations Corpus, a collection of some 3.4 million bibliographic citations from within PubMed Central that we have recently established as open linked data, as part of the JISC Open Citations Project.

We have also worked to establish best practice for citing data publications from within the literature, and with one open access journal publisher to influence their Data Publishing Policies and Guidelines to Authors regarding data citation, as detailed in earlier posts on this blog.

Tools for metadata curation

The above tools and services are generic. Specifically in the biomedical area, we are developing MIIDI, a Minimal Information standard for reporting an Infectious Disease Investigation, to specify the metadata that should for completeness accompany such an investigation, and have recently developed MIIDI Forms, a web tool that facilitates the entry of such metadata, that involves interaction with appropriate web services to enable autocompleting of bibliographic information and specification of geo-coordinates for place names, and permits automated look-up of ontology terms from the NCBI BioPortal.

Open Research Reports

We are working to create Open Research Reports, open access structured digital abstracts in both human- and machine-readable form that describe datasets or journal articles that relate to infectious disease, based on MIIDI and to be published in an instant data journal format with DOIs to permit referencing and citation.

Tools for creating data management plans

We have recently started working with the Digital Curation Centre to help improve their DMPonline data management planning tool for creating the data management plans increasingly required to accompany grant applications, and useful for managing the flow of data from funded projects. If our current funding application is successful, this work will be carried forward in the OXFORD DMPonline Project, in which, in addition to adoption, adaption, customization and integration of the tool for use by University of Oxford researchers, we will develop the following generic improvements to the tool that will be fed back to the DCC as open source enhancements for general use across UK academia and internationally:

a) creation of DaMO, a simple data management ontology,

b) use of DaMO to create RDF metadata for data management plans,

c) SWORDv2-wrapping of data management plans for repository submission, and

d) creation of DMPBank, a DataBank instance specifically tailored for archiving and publishing data management plans.

Why researchers don’t publish data

Evidence submitted by David Shotton in response to the Royal Society’s Policy Study “Science as a Public Enterprise” Call for Evidence, addressing the following two topics raised by that call:

Getting Researcher buy-in. How do we get researchers to be more willing to share data? What is there to be learned from disciplines such as genomics which have norms which favour wide sharing of data?

Ensuring we generate useful metadata. For open data to be useful, it needs to be sufficiently well described. The researchers creating the dataset are in the best position to create the metadata; but as things stand, the incentives for them to do a thorough job of this are not always very strong. Do we need to change incentives?

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“I guess I have been invited to contribute evidence to the evidence session on digital curation at the Royal Society on 5th August 2011 to present the view from the shop floor – or rather from the laboratory bench. I would like to mention three pressures that presently combine to prevent researchers from publishing their data.

Pressure one: Information volume

When I started research, you could, if you were very fortunate (as I was), solve a protein structure to low resolution within six months and to medium resolution within three or four years, and you could hope to know something about all the protein structures that had so far been determined. Today, you can collect the crystallographic structure factor data for a new protein in a few minutes at the Diamond Light Source, and can compute its 3D structure on your laptop during the train ride home. PDB currently contains the structures of about 74,000 macromolecules, and you are unlikely to know the structures of more than a handful of these.

Looking at the same problem from a different perspective, PubMed currently received a million articles per year. If you imagine there might be a thousand biomedical specialisms – if you slice the salami thinly enough -, as a specialist you can expect to have on average twenty new papers in your field each week – an impossible number to carve out time for, from your other activities, if you wish to read them properly.

Thus you will never catch up – there is just too much scientific information around now. You would like to know about it all, to keep abreast of your field, but the task is impossible. Researchers are thus under overwhelming pressure, and have to run just to stand still. They have no spare time to undertake data curation activities for which they receive little or no academic reward in terms of peer esteem, tenure or promotion.

Pressure two: Institutional pressures

The principal pressures researchers are under from their departments and institutions are (a) to win grants and (b) to publish in high impact journals, because these things influence departmental income both (a) directly through full economic costs from funding agencies, and (b) through high RAE/REF scores that in England determine funding from HEFCE. From the viewpoint of a Head of Department trying to establish or maintain his department’s reputation and financial health, nothing else matters. I have known these factors as the deciding ones in academic appointments. Nobler concepts of scientific excellence and of scientific altruism in the form of data publication become submerged beneath these pressures.

Pressure three: Cognitive overheads of data management

Appropriate ontologies and technical infrastructures for data preservation increasingly exist, but the concepts surrounding metadata creation, repository deposit and data accessibility are foreign to most biomedical researchers, leading to cognitive and skill barriers that prevent them from undertaking routine best-practice data management.

Put crudely, the large amount of effort involved in preparing data for publication, coupled with the negligible incentives and rewards, prevents researchers in most biomedical specialisms from doing so.

Having said that, research scientists are perfectly able to provide structured metadata when it is necessary to do so. With the switch to on-line journal article submission, publishers have devised lengthy web forms that require completion with details of co-authors and their affiliations, funding agencies, etc. before you are permitted to upload your manuscript – forms that for certain publishers can take the best part of an afternoon to complete for a new submission involving many authors, figures and supplementary files. Since researchers have no choice but to comply with the metadata requests, they do so, since this is the only way in which to achieve their desired goal of publication in the chosen journal.

That the fields of genomics and macromolecular structures are exceptions to the rule that data are not widely published is due to two factors:

First, their datasets are relatively simple, homogeneous and well-defined – linear nucleotide or amino acid sequences, lists of structure factors, and lists of atomic coordinates – in comparison with the heterogeneity of data in fields such as ecology or animal behaviour, simplifying the tasks of data management and metadata creation.
Second, and more important, is the fact that in the early 1970s journals such as Nature started to mandate database accession numbers as a precondition of publishing sequence or structure papers – this brought about an almost instantaneous change in attitudes among our research community!

For other disciplines, while I commend journals’ and research councils’ recent policies regarding data publication, I believe we will only achieve radical change when funders and publishers mandate data publication as a pre-condition of applying for a further grant or of article submission. Toothless research council data policies, however laudable, are of little use unless backed up by some policing. ‘Sticks’ are required to achieve desired policy aims, as well as the ‘carrots’ of better personal data management and data security obtained by employing easy-to-use tools and systems.”

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The following post describes what we are doing, with funding help from the JISC, to help mitigate these pressures and provide tools and services to assist researchers in data publication.

Current Projects at the Image Bioinformatics Research Group in Oxford

Alistair Miles, of SKOS fame, who formerly worked in our research group, spent yesterday afternoon catching up with us, and has written a nice blog post on the MalariaGEN Informatics Blog describing our current activities, including our work on the Open Citations Corpus, and how they might intersect with the data management activities of the MalariaGEN, the Malaria Genome Epidemiology Network for which he now works.

He has also written a separate blog post reflecting on the work he did when in our group working on the JISC FlyWeb Project to develop openflydata.org, as an update on his earlier post, which is well worth a read if you wish to understand how semantic web techniques can be used to integrate data from heterogeneous and non-compatible databases in distributed locations.

Graham Klyne, who was part of that FlyWeb Project, has been instrumental in taking those same ‘data web’ data integration techniques and re-applying them to data integration in the classical arts, using the CIDOC-CRM data model developed for the museum community, to underpin CLAROS, The World of Art on the Semantic Web. It now looks as though Graham’s current work with Jun Zhao and others on the provenance of bioinformatics workflows, within the EU Workflows4Ever Project, might be of assistance to Al in his current work with Plasmodium SNP discovery and genotyping pipelines for MalariaGEN.

It’s nice to stand back from time to time and see all these activities interlinking as a whole. Thanks, Al.

My next two posts follow on from this, in that the first explores reasons why the majority of researchers don’t presently publish the datasets underlying their research articles , and the second summarizes the various JISC projects in which we are involved as a research group, including the Open Citations Project, that seek to mitigate this problem and provide tools and services that make data publication and subsequent data citation easier.

JISC Administrative Data for Open Citations Project

Data copied from JISC Expo DOAP (Description of a Project) spreadsheet at https://spreadsheets.google.com/ccc?key=0ArsNASxXZiL6dC1mWWFMMjRWSmVha0E1WmdlQ05KcEE&hl=en#gid=7.

Project title: The Open Citations Project

Project tag: jiscopencite

Short project description

We will publish reference lists from Open Access biomedical journal articles as Linked Open Citation Data at http://opencitations.net.

Long project description

The Open Citations Project is global in scope, designed to change the face of scientific publishing and scholarly communication. Specifically, it aims to make it possible to publish bibliographic and citation information in RDF and to make citation links as easy to traverse as Web links.

To achieve this goal, we have had four primary aims:

To create a semantic infrastructure that makes possible the description of citations, references and bibliographic entities in RDF, since we found existing ontologies inadequate for our purpose.
To extend that semantic infrastructure to handle data citations and data entities, as well as bibliographic citations and bibliographic entities, mindful of Philip Bourne’s prediction that soon there will be no meaningful difference between a journal article and a database entry.
To provide exemplars of how these ontologies can be applied to real-world data, by creating mappings from existing encodings to RDF, and by creating RDF metadata relating to bibliographic and data entities and their citations.
To convert the reference lists within all the PMC Open Access subset articles to RDF, and to publish them as open linked data that third parties can use in novel ways.

Principle deliverables and outputs

The SPAR (Semantic Publishing and Referencing) Ontologies.
Graffoo and LODE, two novel tools for ontology visualization and documentation.
Mappings of various existing metadata schemes to RDF using SPAR.
Development of data citation methods and protocols
The Open Citations Corpus of bibliographic citation data encoded in RDF and published as Open Linked Data.
The OpenCitations.net web site, to provide user access to the Open Citations Corpus.
The Open Citations Project software used for processing the Pubmed Central Open Access corpus into Open Linked Data.

The net result is open citation data from life science journal articles available on the web, for utilization by academics, for citation network analysis applications, and for tracking the impact of research grant funding.

Secondary deliverables and outputs

Blog posts describing the experience and process by which the primary products from the project was produced: http://opencitations.wordpress.com/.

JISC Website Keywords

Data & Text Mining

Data Services & Collections

Open Technologies

Resource Discovery

Standards, Tools & Techniques

Web 2.0

Name of lead institution: University of Oxford

Department where project is primarily locate: Department of Zoology

Postcode where the project team is primarily based: OX1 3PS

Name of person(s) responsible for JISC project documentation and reporting: Dr David Shotton

Email of person responsible for project documentation and reporting: david.shotton@zoo.ox.ac.uk

Phone / Skype for Person responsible for project documentation: 01865-271193 / skype: davidshotton

Names and roles of all people working on the project team

Dr David Shotton, Principal Investigator and Project Manager

Mr Benjamin O’Steen, Technical Developer – employed 50% FT from 01-07-2010 to 30-06-2011

Mr John Mansfield, Citation Data Manager – employed 100% FT from 14-07-2010 to 13-08-2010

Mr Alex Dutton, Citation Data Manager – employed 50% FT from 04-10-2010 to 30-06-2011

Names and roles of any and all project partners: None

Emails of all the team members, consultants, partners and any other person who will be working on or with the project

David Shotton <david.shotton@zoo.ox.ac.uk>

Benjamin O’Steen <bosteen@gmail.com>

John Mansfield <jbmansfield@gmail.com>

Silvio Peroni <speroni@cs.unibo.it>

Peter Murray-Rust <pm286@cam.ac.uk> (PI of Open Bibliography sister project – liaison)

Named end users who will be testing or using your software outputs

Anusha Ranganathan <anusha.ranganathan@bodleian.ox.ac.uk>

Steve Pettifer <steve.pettifer@manchester.ac.uk>

Tim Clark <twclark@nmr.mgh.harvard.edu>

Paolo Ciccarese <paolo.ciccarese@gmail.com>

Rahul Dave <rahuldave@gmail.com>

Alberto Accomazzi <aaccomazzi@cfa.harvard.edu>

Martin Fenner <fenner.martin@mh-hannover.de>

Egon Willighagen <egon.willighagen@gmail.com>

Number of named end users: 8

Project gmail account: None. Use <david.shotton@zoo.ox.ac.uk>

Project blog URI: http://opencitations.wordpress.com

RSS2 or ATOM feed for project blog: http://opencitations.wordpress.com/?feed=atom

URL of the code repository for versioned source code produced by project: https://github.com/opencitations/

See also http://github.com/benosteen/pairtree http://github.com/benosteen/rdfobject http://bitbucket.org/okfn/ofs http://code.google.com/p/opencitations/source/browse

URL for instructional documentation: http://opencitations.net/

OSS license you will you be using for the code generated from project: MIT license

Analytics Engine on your project blog, code repository and any other project web presence: Google Analytics being installed.

Creative Commons Licence used for project presentations and documentation: Creative Commons Attribution 3.0 Unported License

Creative Commons Licence used for project content: CCZero waiver

Project Start Date: 2010-06-01

Project End Date: 2011-06-30, extended to 2011-08-01

Total amount of money awarded to the project in Grant Letter: £99,998

Name of Institutional Budget Manager: Miriam Wood <miriam.wood@zoo.ox.ac.uk>

Link to final project post: https://opencitations.wordpress.com/2011/07/01/jisc-open-citations-project-%E2%80%93-final-project-blog-post/

PIMS URL for Project: https://pims.jisc.ac.uk/projects/view/1866

Link to Final Approved Published Budget: Pending.

Like a kid with a new train set! Exploring citation networks

As part of the Open Citations Project, Alex Dutton recently completed a graphing plug-in for the Open Citations web site, that permits users to generate different kinds of graphs of citation networks by querying the Open Citation Corpus for a particular article, and either display the network of papers citing that article (input citations), papers cited by that article (output citations), or both. These can be displayed on screen in the web browser in a variety of layouts, or conveniently downloaded in a number of useful formats.

THIS IS SOOOOO COOL!

Having survived the preparation and posting of the JISC Open Citations Project Final Blog Post last night, minutes before the midnight deadline, I’m now like a kid with a new train set, playing with this display tool and exploring the citation networks present in the Open Citation Corpus, something I have dreamed of doing for two years now.

Remember first that in the Open Citations Corpus we have some 200,000 citing articles – those within the Open Access Subset (OASS) of Pubmed Central – citing ~3.4 million papers out there in the big wide world, which are only recipients of citations. The consequence of this limited corpus is that the majority of citation chains are of length one – from a paper in the OASS to a paper outside the OASS. Not very interesting. Add to this the fact that PubMed Central is new – over 90% of the papers in the Open Access Subset were published in the 21st Century, and 77% of them in the last 5 years. Thus there are only a very few citation from articles within the OASS to other articles within the OASS. That means that the maximum length of our citation chains, at present, to three or four on links the input side – a selected article may be cited by a chain of three or four other OASS articles, and three or four on the output side – the selected article may cite other OASS articles in addition to non-OASS articles, and these in turn will cite others. However, in most cases, the citations chains are much shorter.

simple networkFigure 1. A simple citation network of input citation chain length of 2 links within the Open Citations Corpus, and an output chain length of 1 link – the selected article (red) receives citations from other OASS articles (green), and itself cites only articles outside the OASS (white).

Let’s start with something familiar – the article in PLoS Neglected Tropical Diseases by Reis et al. (2008) [1] that I used for our semantic publishing exemplar [2]. Its inward citation graph, limited to a citation chain length of two links, created by and copied from the Open Citations Project web site, looks like this:

input citations of Reis — Figure 2. The input citation network of Reis et al. (2008), limited to an citation chain length of 2 links.

I, of course, cited the Reis et al. (2008) paper [1] in our 2009 Adventures paper [3] that we based upon it, and also in my first paper on CiTO in 2010 [3], which also cites the Adventures paper. Reis et al. (2008) is also cited by Fink et al. (2010) [4], who also cited our Adventures paper, and by Bourhy et al. (2010) [5], another PLoS Neglected Tropical Diseases paper in the OASS, which in turn is cited by Galloway and Levett (2010) [6], while our Adventures paper is also cited by Gerner and Nenadic (2010) [7].

The following image shows this graph as it was originally created within the Open Citations web page:

Input citations of Reis in web page — Figure 3. The same input citation network of Reis et al. (2008), as shown in the Open Citations web site.

Since Reis et al. (2008) has a reference list containing 52 references, its output citation graph is much more complex, even when limited to a citation chain length of 2, since several of its cited papers are also members of the Open Access Subset. The following figure shows the whole output citation network a citation chain length of 2, which is too demagnified to be legible.

Citations by Reis — Figure 4. The outward citation network of Reis et al. (2008), limited to a citation chain length of 2 links.

The next figure shows a close-up of part of the previous diagram – the output citation network of Reis et al. (2008), again showing the Reis et al. (2008) paper in red, and one of the key papers it cites, Maciel et al. (2010) [8], a slightly earlier paper from the same research group, forming a second key node in the top right of the diagram.

Cited by Reis closeup — Figure 5. A close-up of a central portion of the outward citation network of Reis et al. (2008), limited to a citation chain length of 2 links.

Clearly, there is lots of information that can be extracted from these graphs, particularly when we display them in a tool like GraphViz that permits interactions with the data. While the Open Citations web site simply displays such citation graphs created using one of several layout algorithms selected by the user, the raw data can also be downloaded in a variety of formats including GraphViz, GraphML and SVG, while the resulting network images can be downloaded in as PNG, JPEG and PDF images, and the underlying RDF metadata can be downloaded as RDF/XML. N-triples, Notation3 and Turtle.

Having used our new Open Citations web site and its network display interface for a short while, I am already aware of many shortcomings and limitations that we will attempt to improve upon in the next few days. However, we would very much like to hear from you – as a user of the Open Citations web site – both to learn what you like about what we have done and to hear what you find to be shortcomings of the functionality and new features that you would like to see implemented, which we will record as user stories to input into our next round of development. These can either be recorded as comments on this blog post, or can be e-mailed with the subject line “Open Citations web site” either to me <david.shotton@zoo.ox.ac.uk> or to Alex Dutton <Alexander.dutton@zoo.ox.ac.uk>, who is the person who deserves all the credit for the present system. We look forward to hearing from you.

[1] Reis RB, Ribeiro GS, Felzemburgh RDM, Santana FS, Mohr S, Melendez SXTO, Queiroz A, Santos AC, Ravines RR, Tassinari WS, Carvalho MS, Reis MG, Ko AI (2008). Impact of environment and social gradient on Leptospira infection in urban slums. PLoS Negl Trop Dis 2(4): e228. doi:10.1371/journal.pntd.0000228.

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

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

[4] Fink JL, Fernicola P, Chandran R, Parastatidis S, Wade A, Naim O, Quinn GB, Bourne PE (2010). Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics 11:103. doi:10.1186/1471-2105-11-103.

[5] Bourhy P, Collet L, Clément S, Huerre M, Ave P, Giry C, Pettinelli F, Picardeau M (2010). Isolation and Characterization of New Leptospira Genotypes from Patients in Mayotte (Indian Ocean). PLoS Negl Trop Dis 4(6): e724. doi:10.1371/journal.pntd.0000724.

[6] Galloway RL, Levett PN (2010) Application and Validation of PFGE for Serovar Identification of Leptospira Clinical Isolates. PLoS Negl Trop Dis 4(9): e824. doi:10.1371/journal.pntd.0000824.

[7] Gerner M, Nenadic G (2010). LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics 11:85. doi:10.1186/1471-2105-11-85.

[8] Maciel EAP, Carvalho ALF, Nascimento SF, Matos RB, Gouveia EL, Reis MG, Ko AI (2008). Household transmission of Leptospira infection in urban slum communities. PLoS Negl Trop Dis 2: e154. doi:10.1371/journal.pntd.0000154.

JISC Open Citations Project – Final Project Blog Post

Executive summary

Introduction

To general readers of this blog, this post will appear different from normal posts. Rather than being about a particular topic, it pulls together a summary of the work undertaken over the past year within the Open Citations Project supported by the JISC, and is primarily intended to assist JISC evaluation of the project and its outputs. Details of the work undertaken and the outputs from this project have mostly been described in previous blog posts, to which this post will frequently refer.

Project scope and purpose

The Open Citations Project is global in scope, designed to change the face of scientific publishing and scholarly communication. Specifically, it aims to make it possible to publish bibliographic information in RDF and to make citation links as easy to traverse as Web links.

Project aims

To achieve this goal, we have had four primary aims:

To create a semantic infrastructure that makes possible the description of citations, references and bibliographic entities in RDF, since we found existing ontologies inadequate for our purpose.
To extend that semantic infrastructure to handle data citations and data entities, as well as bibliographic citations and bibliographic entities, mindful of Philip Bourne’s prediction that soon there will be no meaningful difference between a journal article and a database entry.
To provide exemplars of how these ontologies can be applied to real-world data, by creating mappings from existing encodings to RDF, and by creating
RDF metadata relating to bibliographic and data entities and their citations.
To convert the reference lists within all the PMC Open Access subset articles to RDF, and their publication as open linked data that third parties can use in novel ways.

Principle deliverables and outputs

The SPAR (Semantic Publishing and Referencing) Ontologies.
Graffoo and LODE, two novel tools for ontology visualization and documentation.
Mappings of various existing metadata schemes to RDF using SPAR.
Development of data citation methods and protocols
The Open Citations Blog in which activities and outputs are described.
The Open Citations Corpus of bibliographic citation data encoded in RDF and published as Open Linked Data.
The OpenCitations.net web site, to provide user access to the Open Citations Corpus.
The Open Citations Project softwareused for processing the Pubmed Central Open Access corpus into Open Linked Data.The net result is open citation data from life science journal articles available on the web, for utilization by academics, for citation network analysis applications, and for tracking the impact of research grant funding.

Primary beneficiaries

Scholars worldwide, particularly in the biomedical sciences, by providing better access to bibliographic and citation data.
Academic publishers and repository managers, by providing a semantic infrastructure and tools to enable their outputs and holdings to join the semantic web of open linked data.

Background

In 2008, Katie Portwin and I had an enjoyable summer ‘souping up’ a PLoS Neglected Tropical Diseases article by Reis et al. (2008) [1] that I had downloaded as an XML file from the journal web site in late April, one week after it had been published. The resulting enhanced publication, available here, became an exemplar of what is possible in the realm of semantic publishing, while undertaking that work was very influential in shaping the course of my more recent activities.

One of the things we undertook was to mark up the reference list with annotations that clarified the nature of the cited entity (e.g. book, journal article, medical report) and the reason the authors had cited those entities (used data from, obtained background from, extended, etc.) – annotation that we took care to verify with the authors themselves before publishing them!

While we undertook that work manually, it quickly became apparent that what we needed was an ontology from which a controlled vocabulary of such terms could be used to create both human- and machine-readable metadata describing the citations and the cited entities. We therefore developed a draft ontology that we subsequently split to form the basis of the first two ontologies of the suite of SPAR (Semantic Publishing and Referencing) Ontologies described elsewhere on this blog, namely CiTO, the Citation Typing Ontology to describe the relationships between the citing and cited entities, and FaBiO, the FRBR-aligned Bibliographic Ontology, to describe the cited entities themselves.

Using these tools, we were able to mark up the reference list from Reis et al., and publish it as RDF.

From there it was but a small step to dream of the day when the references from all biomedical research articles would be published as open linked data, and to think what we could do to make that dream a reality.

And it was obvious where to start – with the Open Access subset of journal articles available in PubMed Central (PMC), all nicely marked up in XML using the National Library of Medicine DTD.

Table of contents

The various aspects of the Open Citations Project and its outputs are described in the following blog posts, complete with diagrams, data tables, and screen shots where appropriate. These are organized into the following set of distinct topics:

Standards
The SPAR ontologies for bibliographic and data entities and their citations
Graffoo and LODE – tools for ontology visualization and documentation
Third-party applications of our ontologies
Mappings to the SPAR ontologies, and exemplar RDF encodings
Development of data citation methods and protocols
The creation of the Open Citation Corpus of linked bibliographic citation data

1 Standards

Advantages of Ontological Standards in Scholarly Publishing

Nomenclature for citations and references

2 The SPAR ontologies for categorizing bibliographic and data entities and their citations

The SPAR ontologies described in the following blog posts were developed jointly with Silvio Peroni, a brilliant graduate student from the University of Bologna, who spent the last six months of 2010 working with me as an intern in Oxford, where he became an honorary member of the Open Citations Project, contributing very significantly to our achievements. His supervisor Fabio Vitali and the Department of Information Science at the University of Bologna are to be congratulated and thanked for their enlightened requirement that all their graduate students spend an internship overseas, since without his collaboration and great skill, much of this development would not have been possible within the available time, if at all.

Introducing the Semantic Publishing and Referencing (SPAR) Ontologies

New web site for the SPAR ontologies

Functional clustering of CiTO properties

Extending FRBR within FaBiO

Categorising bibliographic resources with FaBiO and SKOS

CiTO4Data – a new data-centric citation typing ontology

Using FaBiO to describe data entities

3 Graffoo and LODE – tools for ontology visualization and documentation

These tools have been developed by Silvio Peroni, an honorary member of the Open Citations Project, as explained above.

Graffoo, a Graphical Framework for OWL Ontologies

Using LODE for ontology visualization

4 Third-party applications of our ontologies

Our work to develop a standard semantic infrastructure for bibliographic and data entities and their citation is new. Nevertheless, we have received encouraging responses when we have presented our work at international publishing venues such as the 2010 ALPSP Conference and the 2010 STM Innovation Conference.

Apart from local applications at the University of Oxford, the University of Bologna, and the University of Manchester (for the Utopia Project), and adoption of the SPAR ontologies by the University of Harvard both to complement SWAN (Semantic Web Applications in Neuromedicine) and to mark up astrophysics data (Accomazzi and Dave (2011) Semantic Interlinking of Resources in the Virtual Observatory Era. arXiv:1103.5958), we have expressions of interest from PLoS, Nature and Il Mulino, a major academic publisher in Italy, who are looking to improve their metadata encoding as RDF. We are also interacting with the British Library in mapping the DataCite Metadata Kernel to RDF (see below), and with the Dryad Data Repository in creating RDF mappings of Dryad metadata to RDF and, as part of the JISC Dryad-UK Project, in developing MIIDI and MIIDI-structured RDF metadata for infectious disease papers and datasets, using SPAR ontologies where appropriate, with the aim of permitting authors to submit rich metadata to Dryad.

The following blog posts describe uptake and use of CiTO in CiteULike and WordPress.

Use of CiTO in CiteULike

How to employ CiTO in CiteULike

Using CiTO in WordPress

5 Mappings to the SPAR ontologies, and exemplar RDF encodings

Comparison of BIBO and FaBiO

BIBO2SPAR, an RDF Mapping of BIBO to the SPAR Ontologies

DataCite2RDF – Mapping DataCite Metadata Scheme Terms to ontologies

6 Development of data citation methods and protocols

Nomenclature for data publications and citations

Questions of granularity – Dryad’s use of DataCite DOIs for data citation

How to cite data

Pensoft Journals policy and author guidelines on data publication and citation

7 The creation of the Open Citation Corpus of linked bibliographic citation data

This achievement is almost entirely as the result of the excellent work of our chief data wrangler Alex Dutton, whose skill and natural feel for linked data has done wonders for this project.

The following set of blog posts describe the starting corpus from PubMed central, our transformation of it to RDF, the problems we encountered along the way, the resulting Open Citations Corpus, and the potential uses to which the resulting open citation data can now be put.

Input data for Open Citations – the PMC Open Access Subset

Garbage in, garbage out – problems with bibliographic references

Who wrote this paper? Author list problems in PubMed Central references

Citation correction methods

The citation processing pipeline and the Open Citations Corpus

JISC Open Citations Project web site

Like a kid with a new train set! Exploring citation networks

JISC Administrative Data for Open Citations Project

This information, extracted from the JISC Expo DOAP (Description of a Project) spreadsheet, is to be found in a separate blog post, here.

The Future

While this is the formal Final Blog Post for the JISC-funded Open Citations Project, that was funded for a year from 1^st July 2010, our work is not yet finished. We cherish grand ideas for the liberation of the reference lists from all scholarly journal articles, using the Open Citations Corpus as an exemplar, in collaboration with publishers and organizations such as CrossRef who handle such citation data on behalf of publishers on a daily basis.

This work will only be finished when it is longer up to an individual academic research group to take on the task of citation liberation, but when each publisher publishes the citation data from each of their journal articles as open linked data on their own web sites, marked up using agreed ontological standards that we have proposed, freely available for scholar around the world, from Bangladesh to Zimbabwe, and from Holland to New Zealand, to use and explore, independent of their ability to afford subscription access to the journal articles from which the citations are made.