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!

Open Citations and Semantic Publishing

Given the renewed interest among publishers in the Open Citations Corpus, following the decisions by Nature Publishing Group, publisher of Nature, and by the American Association for the Advancement of Science, publisher of Science, to open their citation data for inclusion in the corpus, I thought it would be helpful to provide links to videos of two conference presentations I gave that describe the Open Citations Corpus in the context of our other work in the area of semantic publishing.

The first of these was an invited contribution with the title Enriching Scientific Citations to Facilitate Knowledge Discovery, given to publishers at the Scientific, Technical and Medical Publishers Innovations Seminar 2010 entitled “Flows in Flux: how publishing technologies change the researcher’s life”, held in London, UK, on 3rd December 2010:

lecture: http://river-valley.tv/media/conferences/stm-innovation-2010/0202-David-Shotton/

slides: http://imageweb.zoo.ox.ac.uk/pub/2010/Presentations/SHOTTON_Citations_STM-Innovations-Seminar-03Dec2010.pdf

abstract: http://imageweb.zoo.ox.ac.uk/pub/2010/Presentations/STM_Innovations_Seminar_2010_ABSTRACTS.pdf

The second presentation, given almost a year later, was an invited contribution with the title The SPAR (Semantic Publishing and Referencing) Ontologies and the Open Citation Corpus, given to librarians at SWIB11 (Semantic Web in Bibliotheken; Semantic Web in Libraries Conference 2011) “Scholarly Communication in the Web of Data”, held in Hambrug, Germany on 30th November 2011:

lecture: http://www.scivee.tv/node/39208

slides: http://imageweb.zoo.ox.ac.uk/pub/2011/presentations/Shotton_SWIB11_SPARandOpenCitationCorpus_30Nov2011.pptx.pdf

abstract: http://imageweb.zoo.ox.ac.uk/pub/2011/presentations/Shotton_Abstract_for_Presentation_at_SWIB11.pdf

Further details of the Open Citations Corpus and the SPAR ontologies, and their applications are, of course, given in this Open Citations and Semantic Publishing blog, for which the following two posts provide the best introduction for those coming here for the first time:

JISC Open Citations Project – Final Project Blog Post

Introducing the Semantic Publishing and Referencing (SPAR) Ontologies

Access to Citation Data

The JISC, in response to its invitation to tender, has recently funded Curtis+Cartwright Consulting Ltd, a research and strategy consultancy, to undertake an independent study entitled Access to Citation Data: A Cost-Benefit and Risk Review and Forward Look.  Evidence gathering for the study has just started, and the consultants are due to produce a report on this subject by next February.  This report will be one of a series of high profile reports that the JISC is commissioning to inform the UK FE/HE sector on key issues relating to digital infrastructure.

The JISC has invited me to serve on the steering group for this study, which will in particular be reviewing the Open Citations Corpus, both to provide intelligence and to act as a case study and as a potential recommended corpus of citation data.

I look forward to working with the review team, starting later this month, and anticipate that we will benefit from this investigation as well as contribute to it, since we anticipate that Curtis+Cartwright will be able to advise on sustainable business models for such open access citation data corpora.

The plate tectonics of research data publication

In biology, the fields of macromolecular structural biology and sequence bioinformatics have, since the 1970s, had established international databases for the deposition of data, and journal policies mandating such deposition prior to acceptance for publication of manuscripts describing the data.  Similar good practices have developed more recently in other disciplines, notably astronomy.  But these are the exceptions, and over the majority of scientific fields data publication remains a minority activity.  For the most part, this is because the technical barriers to publication of research datasets remain so high, and the academic rewards so low, that such publication is undertaken only by the few who regard it as a moral imperative.  However, new policies are combining with new technological capabilities to bring significant change to this publication landscape.

An analogy can perhaps be made with geological plate tectonics.  The new policies of funders and journal publishers towards the open publication of research datasets arising from publicly funded research can be likened to a tectonic plate slowly moving forward with inexorable force, that is colliding with the massive stationary continental plate of established scientific practice, in which data are traditionally regarded as belonging to the research group that generated them, in which data sharing occurs only between trusted colleagues on the basis of personal request, and in which the only publications that are truly valued are those of journal articles.

This traditional position is reinforced by the metrics employed in the assessment of research quality, which, while giving lip service to the value of data publication, regard articles in high impact factor journals as of paramount importance.  And there is good reason why the scholarly research article is so highly regarded, since it is a rhetorical construct in which the authors attempt by the selective presentation of evidence to convince the readers that particular hypotheses are proven.  As such, it can both demonstrate the competence and achievements of the authors, and be evaluated against other such publications by peer review.  In contrast, the publication of a research dataset is primarily a presentation of facts, with no rhetorical content, that can only be validated on the basis of internal self-consistency, information about instrument calibrations, resolution and error estimates, and the possession of adequate descriptive metadata in appropriate formats – much more pedestrian stuff.

However, to return to our analogy, these tectonic plates are colliding, with the traditional plate of data retention facing ultimate subduction beneath the advancing plate of open data publication.  At present there is friction between them, and along much of the sheer zone there seems to be little movement, leading to a build-up of pressure.  Small projects that result in some local movement towards better data management can be likened to minor earthquakes having only local impact.  But these are the precursors to an inevitable major re-positioning of the plates to relieve the mounting pressure for change.  This will result in a major general realignment of attitudes along the whole plate boundary, resulting in a tsunami of open data publication.  We are thus on the cusp between the traditional status quo and a new dramatically reshaped scientific publication landscape, in which open data publication will take its proper place as underpinning the publication of ideas and evidences supporting hypotheses.

Technological projects such as the JISC ADMIRAL Project and its successor the JISC UMF DataFlow Project serve to facilitate this transition by ‘lubricating’ the plate boundary and enabling movement.  In particular, the two-tiered federated data management infrastructure they provide, with local services to meet the private data management needs of individual research groups (DataStage filestore instances) being linked to institutional repositories (DataBank repository instances) by automated procedures for the easy archiving and publication of selected datasets, makes the whole process easier, as illustrated by the following figures taken from the original ADMIRAL Project grant application.

Figure 1: The conventional research data lifecycle  

Four phases mark the activities undertaken in traversing the conventional data lifecycle: formulation, experimentation, interpretation and publication.       The publication outputs from one cycle provide the input to the next.  However, only selected research data are conventionally published.  The original research datasets are frequently abandoned on local hard drives or CD-ROMs, and neither datasets nor papers are submitted to institutional repositories.

Figure 2: The ADMIRAL enhanced research data lifecycle

Raw research data are first organized and annotated in a local research data filestore.  From there they can be shared and used to support publications, and can be automatically archived to institutional repositories, from which they can optionally be published as Linked Open Data on the Semantic Web for public dissemination and reuse.  This figure differs from the DCC Data Cycle model by emphasizing the importance of the local research data filestore.

Figure 3: The effort involved in submitting data to an institutional repository  

As investment is made in the local organization and annotation of research datasets, the effort involved in data submission to an institutional repository reduces to the point where it becomes feasible on a routine basis.

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>

See also Final Blog Post http://opencitations.wordpress.com/2011/07/01/jisc-open-citations-project-%E2%80%93-final-project-blog-post/.

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.

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