1 Enriching UK PubMed Central SPIDER launch meeting, Wolfson College, Oxford Paul Davey, UK PubMed Central Engagement Manager

2 Partners University of Manchester -Hosts UK PubMed Central -Builds ‘small scale developments’ -Engagement with HE community (working with British Library) British Library -Prime contractor -Manages grantee database -Mark up author submissions European Molecular Biology Laboratory - European Bioinformatics Institute -Creates links to data -Integrates data with other repositories -Develops the discovery interface

3 Funding organisations Investing around £1.5 million over three years

4 July 2008 onwards Four areas, that will be brought together to: - Enhance the user experience - Deliver metrics and the ability to analyse impact in new ways - Provide access to a fuller range of biomedical and health journal literature - Enable access to a wider range of information resources

5 1. Text mining – Improved retrieval and knowledge discovery European Bioinformatics Institute – leader, term extraction, linking to databases University of Manchester National Centre for Text Mining – fact extraction University of Manchester MIMAS – integration with UK PubMed Central portal

6 Outcomes and Benefits Researchers/Scientists will - Experience enhanced search capability - Be able to explore, more efficiently, the content of publications and the background knowledge in biomedical databases

7 Types of terms and facts - Gene symbols, protein names, Gene Ontology (GO) terms, species, database accession numbers (EMBL/GenBank, UniProtKB, PDB etc) - Chemical entities, drugs, phenotype such as disease, nomenclatures such as karyotypes and mutations - Facts and relations, such as protein-protein interactions, gene- phenotype relationships, drug-proteins, protein functional annotation

8 2. Delivering additional content and creating a user interface (BL) Cater for wider information needs of biomedical & health researchers Deliver tools and services via well designed web-site Increasing use and usability of UKPMC Datasets, supplementary data, clinical guidelines, reports and policy literature, protocols, funder publications, patents, images, theses Integration of CiteXplore bibliographic data; text mining and dataset linking; grant reporting

9 3. Providing comprehensive bibliographic metadata to UK PubMed Central Partners: European Bioinformatics Institute – leader, service API provider University of Manchester – integration with UKPMC portal

10 Outcomes and Benefits UK PubMed Central search service which is comprehensive in coverage of biomedical domain Search will include ~20m bibliographic records in addition to 1m UKPMC articles. Provision of ‘cited/cited-by’ feature

11 Content to be provided to UK PubMed Central (via EBI’sCiteXplore webservice API) PubMed (daily-updated)17,883,539 Agricola 453,127 Patents1,547,082 Own content 600+

12 4. Grant Reporting Tool –To be delivered by University of Manchester –Anticipated October 2008 start

13 UKPMC Grant Reporting System - Objectives Provide metrics and views to: - enable the Funders to monitor the effectiveness of their open access policy; - assess the impact/output of individual grants/grant holders; - assess value of whole research portfolios (targeted schemes etc). In addition development of: - user-orientated functions to enable grant holders to report research outputs to their respective funders and other agencies - a range of value-added services such as “My Bibliography”, “My Grants” and “My UKPMC Impact” - meaningful and targeted data on how their research is being used

14 Some similarities with SPIDER harnessing web technology to promote knowledge discovery in the field of biomedicine providing access to fuller range of biomedical and health journal literature, and wider range of information resources, with semantic enrichment of the information through innovation benefit of the research community, and health of the nation contribute knowledge and expertise activities - text mining and providing additional content such as “grey literature”

15 And the future? Share work as things develop, particularly challenges and how to overcome these practically SPIDER can use UK PubMed Central data, we have an OAI-PMH 2 interface to allow harvesting of our content Could be a minor partner: publisher and/or data provider More information: UK PubMed Central Engagement Manager, British Library – Paul Davey UK PubMed Central Programme Manager, British Library – Phil Vaughan