1. David Shotton Image BioInformatics Research Group Department of Zoology University of Oxford, UK http:/ibrg.zoo.ox.ac.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 e-mail: david.shotton @ zoo.ox.ac.uk

2. 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

3. 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

4. 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

5. Semantic themes in the SPIDER Project The Web as a platform for science The ‘semi-mantic’ Web “A little semantics goes a long way” Developing a new scientific publishing framework that can respond quickly and flexibly to emerging trends Text mining and machine learning to assist the discovery of knowledge Multiple channels for the dissemination of scientific results Recognition of the role of social networks in generating new science and of human insight in making links across scientific disciplines Encouragement of such communication and cross-discipline linking as a driver of innovation

6. The publishing challenges of the SPIDER Project For subscription-access and open-access publishers to make common cause in pre-competitive R&D that will develop best practices and common standards for semantic publishing To fulfil the commitment of the Brussels Declaration on STM Publishing to change and innovation that will make science more effective, and for the free availability of raw research data and datasets submitted with a paper To adapt established production practices in order to add value  Richard Kidd, Manager for Editorial Production Systems, RSC: “The main overall challenge has been to implement change in an existing production workflow that already has world-class publication times “But these enhancements offer real benefits for authors and readers “To a great extent success is due to our technical editors, who have developed new skills to judge the meaning and context of terms - as they’re experienced highly qualified chemical scientists we feel that this is a great application of their skills and knowledge”

7. The research challenges of the SPIDER Project Research at a frontier of information management  between semantic technologies to provide machine-processable markup  and text mining technologies to give concepts for semantic annotation New applications of description logics reasoning for query rewriting, partitioning and distribution over a variety of data sources Social computing, by enabling user annotation of research findings Web 2.0 aspects, involving the ‘wisdom of crowds’ in terms of Web surveillance for disease information, and data mashups Grid aspects of ‘cloud computing’ for Web-based data storage services Aspects of complexity science, for analysis of citation networks Web Science, because of the insistence of the Web as the platform The ultimate objective is to server biomedical researchers and enhance epidemiological research, with the purpose of saving lives

8. The EPSRC Digital Economy Programme What is the digital economy?  The transformational impact that ICTs are having on business  “We should measure our performance by how fast we move into knowledge intensive goods and services.” The EPSRC Digital Economy Programme (http://www.epsrc.ac.uk/ResearchFunding/Programmes/DE/default.htm) will support ICTs in three multidisciplinary research areas:  Transport, Healthcare and the Creative Industries (incl. Publishing) The EPSRC Digital Economy Programme will fund ‘risky’ projects that bring about paradigm shifts in the creative industries These “must strengthen UK plc” Details of the programme are currently awaited, “to be announced shortly”  Autumn application submission, project start Spring 2009

9. Anticipated shape and funding of SPIDER Academic partners from biology, veterinary and computer science, with research assistants funded by EPSRC A number of STM publishers, each of whom commits to semantic enhancements on a journal of relevance to infectious diseases, e.g.  Epidemics (Elsevier)  The Cochrane Library (Wiley-Blackwell)  International Journal of Epidemiology (Oxford Journals) CrossRef to integrate effort and spread standards among publishers ICT technical partners who can provide state-of-the-art software and infrastructure for data management Anticipated duration: 3 years Anticipated funding from EPSRC: £1.5 million - £2.0 million Non-academic partners expected to contribute ‘in kind’

10. Anticipated outcomes of the SPIDER Project Development of best practices and promotion of standards for semantic publishing Developments guided bottom-up by the real user requirements of epidemiological researchers, not top-down by the idealistic notions of knowledge engineers or publishers Publication of exemplar journals relevant to infectious disease epidemiology that put these best practices and standards into effect Development of added-value services – citation networks, data integration – that enhance the value of the exemplar journals and provide additional business opportunities for the publishers involved A positive effect on epidemiological research by more rapid, more convenient and more complete access to reliable disease information

11. Future SPIDER Project activities Formation of a stable consortium of enthusiastic partners Development of an outline funding application for EPSRC Exploration of supplementary funding opportunities, particularly for a project manager to integrate the activities of the non-university partners Develop a consortium agreement to protect partners’ IPR Plan a future pre-application meeting to agree the funding application

12. Many thanks for your interest and presence here today