Monica Duke

Enhancing access to research data: the challenge of crystallography

This paper describes an ongoing collaborative effort across digital library and scientific communities in the UK to improve access to research data. A prototype demonstrator service supporting the discovery and retrieval of detailed results of crystallography experiments has been deployed within an Open Archives digital library service model. Early challenges include the understanding of requirements in this specialized area of chemistry and reaching consensus on the design of a metadata model and schema. Future plans encompass the exploration of commonality and overlap with other schemas and across disciplines, working with publishers to develop mutually beneficial service models, and investigation of the pedagogical benefits. The potential improved access to experimental data to enrich scholarly communication from the perspective of both research and learning provides the driving force to continue exploring these issues

Knowledge Discovery in an Agents Environment

We describe work undertaken to investigate automated querying of simple forms of ontology by software agents to acquire the semantics of metadata terms. Individual terms as well as whole vocabularies can be investigated by agents through a software interface and by humans through an interactive web-based interface. The server supports discovery, sharing and re-use of vocabularies and specific terms, facilitating machine interpretation of semantics and convergence of ontologies in specific domains. Exposure, and hence alignment through ontological engineering should lead to an improvement in interoperability of systems in particular sectors such as education, cultural heritage and publishing.

eCrystals: A Route for Open Access to Small Molecule Crystal Structure Data.

Recently the funding councils in the UK stated that ‘the data underpinning the published results of publically-funded research should be made available as widely and rapidly as possible’. Thirty years ago a research student would present about five crystal structures as their PhD thesis, however with modern technologies and good crystals this can now be achieved in the timespan of a single morning. This increase in pace of generation further exacerbates a problem in the communication of the results. Additionally, the general route for the publication of a crystal structure report is coupled with and often governed by the underlying chemistry and is therefore subject to the lengthy peer review process and tied to the timing of the publication as a whole. This bottleneck in the dissemination of crystal structure data hinders the potential growth of databases and the data mining studies that are reliant on these collections. Just 500,000 small unit cell crystal structures are available in the CSD, ICSD & CRYSMET databases, while it is estimated that at least twice this number have been determined in research laboratories and are likely to remain unpublished. In addition, publication in the mainstream literature still offers only indirect (and often subscription controlled) access to this data. The work of the eBank-UK project (http://www.ukoln.ac.uk/projects/ebank-uk/) has addressed this problem by establishing an institutional data repository that supports, manages and disseminates metadata relating to the crystal structure data it contains (i.e. all the files generated during a crystal structure determination). This process alters the traditional method of peer review by openly providing crystal structure data where the reader or user may directly check correctness and validity. The repository (http://ecrystals.chem.soton.ac.uk) makes available all the raw, derived and results data from a crystallographic experiment with little further researcher effort after the creation of a normal completed structure in a laboratory archive. Not only does this approach allow rapid release of crystal structure data into the public domain, but it can also provide mechanisms for value added services that allow rapid discovery of the data for further studies and reuse, whilst ownership of the data is retained by the creator. The details of the preparation of data, upload process, files supported and automatic report generation will be presented. Additionally, the process whereby metadata relating to each archive entry is disseminated, using current Digital Libraries technologies, for discovery and reuse by will be summarised. Strategies for the installation of archives at new sites, the construction of harvesting and aggregator services and the interaction with crystallographic data holding bodies, such as IUCr and CCDC, will also be outlined. Additionally links to educational tools, specifically the Schools eMalaria project (http://emalaria.soton.ac.uk), will also be presented.