David Shotton Image BioInformatics Research Group Department of Zoology University of Oxford, UK SPIDER Project Launch Meeting Wolfson College, Oxford Friday 27 June 2008 SPIDER – Semantic Publishing for Infectious Disease Epidemiology Research © David Shotton, 2008 Published under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Licence zoo.ox.ac.uk

The SPIDER Project Objective:  To change the world in terms of research publications relating to infectious disease epidemiology – both papers and datasets – and thereby improve epidemiologists’ access to disease data, by assisting authors, data producers, publishers and information consumers to use the Web to its full potential The SPIDER Project partnership will undertake pre-competitive multi- disciplinary R&D that individual research groups and companies have neither the capacity nor the skills to undertake individually It will seek to demonstrate enhanced “end-to-end” data management for epidemiological research Early adopters of semantic publishing will benefit by increasing the desirability of their journals, and by developing added value services Biomedical researchers will benefit by better, faster, cheaper access to data for epidemic prediction and countermeasures

The anticipated SPIDER Project partnership Biological and veterinary researchers, and others who create or consume infectious disease incidence data (DEFRA and HPA) Computer scientists with technologies that can assist in data management My Image Bioinformatics Research Group (IBRG), which employs semantic and Web technologies to enhance the usefulness of biological data, particularly image data Leading scientific publishers publishing journals relevant to disease The partnership should as far as possible be geographically local, to enhance collaborative potential

Infectious diseases are a continuing threat UK Government’s 2006 Foresight Report  Future threats from infectious diseases are at least as great as in the past century, with an undiminished rate of emergence of new diseases and increasing resistance being shown by many disease agents to antimicrobial drugs Malaria and TB are major global health problems HIV-AIDS, SARS, West Nile fever, bluetongue and avian influenza present new hazards Bioterrorism (e.g. anthrax, smallpox) presents potential threats Lives depend upon the timely availability of reliable disease incidence data that permit predictions of the severity and spread of epidemics

Biological and veterinary researchers Angela McLean, Oxford University – epidemiologist David Rogers, Oxford University – uses remote sensing satellite data to predict disease spread Joe Brownlie, Royal Veterinary College, London – one of the prime movers behind the Foresight Report: Infectious Diseases: Preparing for the Future – is in Turin today and sends his apologies Jane Gibbens, DEFRA: “Apologies for not responding earlier - we are currently dealing with an outbreak of avian flu, and unlikely to be able to field a participant” Health Protection Agency

The potential of the Web Tim Berners-Lee, 2001: “The semantic web will profoundly change the very nature of how scientific knowledge is produced and shared, in ways that we can now barely imagine” Semantic publishing will enable new knowledge to be more effectively linked into the existing knowledge network It will make explicit the rhetorical claims of each paper, and assist users in accessing data, both within the paper and in the underpinning datasets It will enable this by imparting publications with machine-readable metadata, allowing computers to assist in the task of information discovery and integration

Computer science and ICT input Andy Seaborne Hewlett Packard Research Labs, Bristol “I’m sorry I can not make June 27, but the area of semantic publishing that SPIDER is addressing is of interest to us and we support this work. “We are interested in developing a platform around scalable RDF storage, query and inference, and to create and deploy a live service for a specific use case could form the basis for joint work” Nigel CollierBioCaster, presently in Tokyo “I am very keen to be part of the SPIDER Project” Ian HorrocksInformation Systems Group, Oxford Inigo Surguy Chief technologist, 67 Bricks, Oxford Siegfried HandschuhDigital Enterprise Research Institute (DERI), GalwayDERI

Nigel Collier’s BioCaster Global Health Monitor Biocaster automatically scours the Internet and aggregates news of infectious diseases, employing text mining tools to analyse it Nigel has developed an extensive ontology of infectious diseases which we will use for the SPIDER Project

Integrating heterogeneous data from distributed sources IBRG is using Semantic Web tools and standards to develop data webs  All identifiers are mapped to URIs  RDF is used as the standard format for sharable metadata  The RDF query language SPARQL is used for data web queries

Scholarly publishing in the UK UK researchers contribute 9% of the world’s research publications and 12% of the world’s citations Many academic publishers are based in the UK, particularly in Cambridge, Oxford and London The English-language scientific, technical and medical (STM) journals market was estimated to be worth around $5 billion globally in 2004 Scholarly journals are the primary dissemination channel and public record of new research and development effort The original research article is the key commodity which drives this marketplace The new UK Research Assessment Framework will use metrics based on research articles published

The information overload

... but publishing has changed very little We still have a linear narrative, with references The norm is that the online version of a journal article is a PDF file  PDF is an electronic embodiment of a static printed page  This is antithetical to the spirit of the Web, and ignores its great potential Rather, we need lively journal content  Semantic mark-up of text  Interactive figures  Actionable numerical data  Links between papers and datasets

The Brussels Declaration on STM Publishing Published by the international scientific, technical and medical (STM) publishing community ( “STM publishers are committed to change and innovation that will make science more effective, and believe that raw research data and datasets submitted with a paper to a journal should, wherever possible, be made freely accessible to other scholars”

Publishers invited to participate in the SPIDER Project Anita de Waard, Elsevier: “SPIDER is a most interesting endeavor - we will provide support, input and access to content” Timo Hannay, Nature: “Unfortunately I cannot attend and haven’t been able to find a good substitute to attend from Nature. Keep us informed with any resulting documentation and further meeting announcements” Mark Patterson, PLoS: “I’m very interested in the SPIDER Project, and if there are some specific things that you need from PLoS, I’ll do my best to see what we can provide” Nick Royle, The Cochrane Collaboration: “We are trying to find someone - snag is that the most appropriate people are in Australia and Canada” Matthew Cockerill, BioMed Central: “Very interested – cannot come but will send a colleague” (Matt Hodgkinson) Philippa Scoones, Wiley-Blackwell: “We have a lot of relevant content and are very keen to be participants” (Will Wilcox) Richard O’Beirne, Oxford Journals

Other stakeholders in academic publishing Stephane GoldsteinResearch Information Network:  “This certainly looks like an interesting project, clearly relevant to the work that we've been doing of late on data stewardship and publication. We would certainly wish to be kept abreast of developments” Ed Pentz Executive Director, CrossRef, Oxford On seeing the Royal Society of Chemistry’s efforts in semantic publishing: “This is fantastic. I’ve just seen the future of the journal” Robert Kiley Head of e-Strategy, Wellcome Trust Library Paul Davey UK PubMed Central (STM), British Library

Aspects of semantic publishing Primary enhancements  Enhancements of the authoring process  Enhancement of the online paper  Enhancement of data publication Subsequent enhancements  Better integration between papers, and between papers and datasets  Creation of added-value services on top of these publications

Enhancements of the authoring process Anita de Waard of the Elsevier Advanced Technology Group is currently developing a system, in conjunction with the editors and authors of Cell, whereby the authors are enabled to mark-up while writing the paper Microsoft have a plug-in for MS-Word 2007 ( for the creation of structural mark-up that supports the National Library of Medicine’s document format Organizing committee included  Siegfried Handschuh and Nigel Collier (co-chairs) and Anita de Waard

Enhancement of the online paper Some journals, particularly those of the Royal Society of Chemistry, have taken the lead in this area Enhancement of data publication Few examples yet in the scholarly journals, but some excellent examples from other data sources  e.g. SourceOECD, the Online Library of Statistical Databases, Books and Periodicals of the Organisation for Economic Co-operation and Development (OECD)

The Elsevier Grand Challenge The Elsevier Grand Challenge: Knowledge Enhancement in the Life Sciences  “To improve the interpretation and identification of meaning in online journals and text databases relating to the life sciences” First prize of US$35,000, second prize of US$15,000

The paper we have chosen to semantically ‘enliven’

The morning agenda 09:30 Coffee 10:00David Shotton Welcome, introductions, SPIDER Project vision 10:30Angela McLeanEpidemiology researchers and data access 10:45David RogersRemote sensing geospatial data and disease 11:00 Coffee 11:30Ian Horrocks Can computer science help research publishing? 11:45 Siegfried Handschuh DERI and semantic publishing 12:00Katie Portwin, Alistair Miles, Jun Zhao, Graham Klyne The IBRG semantic publishing vision 12:45 Discussion of biological and computer science issues

The afternoon agenda 14:00Richard O’BeirneThe challenge of the Web 14:10Matt Hodgkinson BioMed Central's interest and activities in semantic publishing and data sharing 14:20Will WilcoxWiley-Blackwell and semantic publishing 14:30Ed Pentz CrossRef, citations and information linking 14:40Paul Davey Enriching UK Pubmed Central holdings 14:50Robert Kiley The Wellcome Trust’s view 15:00Discussion of publishing issues 15:15David ShottonThe SPIDER project and the EPSRC Digital Economy funding opportunity 15:40General discussion, conclusions and future actions