Enhancing access to research data: the challenge of crystallography

ABSTRACT

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.

REFERENCES

• 1: Advanced Distributed Learning. The Sharable Content Object Reference Model (SCORM). Retrieved January 27, 2005, from: http://www.adlnet.org/
• 2: Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Cryst., B58, (2002), 380-388.
• 3: Allen, F. H. High-throughput crystallography: the challenge of publishing, storing and using the results. Crystallography Reviews, 10 (2004), 3-15.
• 4: Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. and Watson, D. G. The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Cryst., B35, (1979), 2331-2339.
• 5: Arts and Humanities Data Service. Retrieved January 27, 2005, from: http://www.ahds.ac.uk/
• 6: Bekaert, J., Hochstenbach, P. and Van de Sompel, H. Using MPEG-21 DIDL to represent complex digital objects in the Los Alamos National Laboratory Digital Library. D-Lib Magazine, 9, 11 (November 2003). doi:10.1045/november2003-bekaert
• 7: Bekaert, J., Balakireva, L., Hochstenbach, P. and Van de Sompel, H. Using MPEG-21 DIP and NISO OpenURL for the dynamic dissemination of complex digital objects in the Los Alamos National Laboratory Digital Library. D-Lib Magazine, 10, 2. doi:10.1045/february2004-bekaert
• 8: Besli, S., Coles, S. J., Davies, D. B., Hursthouse, M. B., Kiliç, A., Mayer, T. A. and Shaw, R. A. Structural investigations of phosphorus-nitrogen compounds. 5. Relationships between molecular parameters of 2,2-diphenyl-4,6-cis-oxytetra(ethyleneoxy)-4,6-R2-cyclotriphosphazatrienes (R = Cl, OCH2CF3, OPh, OMe, NHPh, NHBut) and substituent basicity constants. Acta Cryst., B58, (2002), 1067-1073.
• 9: Brase, J. Using digital library techniques: registration of scientific primary data. In Research and advanced technology fir digital libraries: 8th European Conference, ECDL 2004. Springer, Berlin, 488-494.
• 10: Brogan, M. A. A survey of digital library aggregation services. Digital Library Federation, Council on Library and Information Resources, Washington D.C., 2003. Retrieved January 27, from: http://www.diglib.org/pubs/brogan/
• 11: Brown, I. D. and McMahon, B. CIF: the computer language of crystallography. Acta Cryst., B58, (2002), 317-324.
• 12: Cambridge Crystallographic Data Centre. Retrieved January 27, 2005, from: http://www.ccdc.cam.ac.uk/
• 13: CCLRC Atlas Datastore. Retrieved January 27, 2005, from: http://www.e-science.clrc.ac.uk/web/services/datastore
• 14: Collaboratory for Multi-Scale Chemical Science (CMCS). Retrieved January 27, 2005, from: http://cmcs.ca.sandia.gov/
• 15: Combechem project. Retrieved January 27, 2005, from: http://www.combechem.org/
• 16: Crow, R. The case for institutional repositories: a SPARC position paper. Scholarly Publishing & Academic Resources Coalition, Washington, D.C., 2002. Retrieved January 27, 2005 from: http://www.arl.org/sparc/IR/ir.html
• 17: Crystallography Open Database. Retrieved January 27, 2005, from: http://www.crystallography.net/
• 18: Dempsey, L., Childress, E. R., Godby, C. J., Hickey, T. B., Vizine-Goetz, D. and Young, J. Metadata switch: thinking about some metadata management and knowledge organization issues in the changing research and learning landscape. In Shapiro, D., ed., LITA guide to e-scholarship {working title}. American Library Association, Chicago, IL (forthcoming). Preprint retrieved January 27, 2005, from: http://www.oclc.org/research/publications/archive/2004/dempsey-mslitaguide.pdf
• 19: Dublin Core Metadata Initiative. Retrieved January 27, 2005, from: http://dublincore.org/
• 20: eBank UK project. Retrieved January 27, 2005, from: http://www.ukoln.ac.uk/projects/ebank-uk/
• 21: eBank UK aggregator demonstrator. Retrieved January 27, 2005, from: http://eprints-uk.rdn.ac.uk/ebank-demo/
• 22: EMBL Nucleotide Sequence Database. Retrieved January 27, 2005, from: http://www.ebi.ac.uk/embl/
• 23: enCIFer software. Retrieved January 27, 2005, from: http://www.ccdc.cam.ac.uk/free_services/encifer/
• 24: EPrints.org. Retrieved January 27, 2005, from: http://www.eprints.org/software.php
• 25: EPSRC National Crystallography Service. Retrieved January 27, 2005, from: http://www.soton.ac.uk/~xservice/
• 26: Frey, J. G., Bradley, M., Essex, J. W., Hursthouse, M. B., Lewis, S. M., Luck, M. M., Moreau, L. A. V. M., De Roure, D. C., Surridge, M. and Welsh, A. H. Combinatorial chemistry and the Grid. In Berman, F., Fox, G. and Hey, A. J. G., eds., Grid computing: making the global infrastructure a reality. Wiley, Chichester, 2003, 945-962.
• 27: Gadd, E., Oppenheim, C. and Probets, S. RoMEO studies 6: rights metadata for open archiving. Program, 38, (2004), 5-14.
• 28: GenBank. Retrieved January 27, 2005, from: http://www.ncbi.nlm.nih.gov/Genbank/
• 29: Gray, J. and Szalay, A. Where the rubber meets the sky: bridging the gap between databases and science. Technical Report MST-TR-2004-110, Microsoft Research, Redmond, WA, December 2004. Retrieved January 27, 2005, http://research.microsoft.com/research/pubs/view.aspx?tr_id=815
• 30: Hall, S. R., Allen, F. H. and Brown, I. D. The Crystallographic Information File: a new standard archive file for crystallography. Acta Cryst., A47, (1991), 655- 685.
• 31: Harnad, S., Brody, T., Vallières, Carr, L., Hitchcock, S., Gingras, Y., Oppenheim, C., Stamerjohanns, H. and Hilf, E. R. The access/impact problem and the green and gold roads to open access. Serials Review, 30, (2004), 310-314. Retrieved January 27, 2005: eprints.ecs.soton.ac.uk/9939/
• 32: Heery, R., Duke, M., Day, M., Lyon, L., Hursthouse, M. B., Frey, J. G., Coles, S. J., Gutteridge, C. and Carr, L. A. Integrating research data into the publication workflow: the eBank UK experience. PV-2004: Ensuring the Long-Term Preservation and Adding Value to the Scientific and Technical Data (Frascati, Italy, October 5-7 2004). Retrieved January 27, 2005, from: http://www.ukoln.ac.uk/projects/ebank-uk/dissemination/
• 33: Hey, T. and Trefethen, A. The data deluge: an e-science perspective. In Berman, F., Fox, G. and Hey, A. J. G., eds., Grid computing: making the global infrastructure a reality. Wiley, Chichester, 2003, 809-824.
• 34: Hursthouse, M. B. High-throughput chemical crystallography (HTCC): meeting and greeting the combichem challenge. Crystallography Reviews, 10, (2004), 85-96.
• 35: IMS Content Packaging Specification. Retrieved January 27, 2005, from: http://www.imsglobal.org/content/packaging/
• 36: Interoperable Informatics Infrastructure Consortium (I3C). Retrieved January 27, 2005, from: http://www.i3c.org/
• 37: IUCr checkCIF. Retrieved January 27, 2005, from: http://checkcif.iucr.org/
• 38: IUCr Crystallographic Data File. Retrieved January 27, 2005, from: http://www.iucr.org/cif/
• 39: IUPAC Chemical Identifier (InChI). Retrieved January 27, 2005, from: http://www.iupac.org/projects/2000/2000-025-1-800.html
• 40: ISO/IEC 21000-2:2003. Information Technology -- Multimedia framework (MPEG-21) -- Part 2: Digital Item Declaration. International Organization for Standardization, Geneva, 2003.
• 41: Lagoze, C., Van de Sompel, H., Nelson, M. and Warner, S., eds., The Open Archives Protocol for Metadata Harvesting, v. 2.0, 14 June 2002. Retrieved January 27, 2005, from: http://www.openarchives.org/
• 42: Lynch, C. A. Institutional repositories: essential infrastructure for scholarship in the digital age. ARL Bimonthly Report, 226 (2003). Retrieved January 27, 2005, from: http://www.arl.org/newsltr/226/ir.html
• 43: Lyon, L. eBank UK: building the links between research data, scholarly communication and learning. Ariadne, 36 (July 2003). Retrieved January 27, 2005, from: http://www.ariadne.ac.uk/issue36/lyon/
• 44: Lyon, L., Heery, R., Duke, M., Coles, S., Frey, J., Hursthouse, M., Carr, L. and Gutteridge, C. eBank UK: linking research data, scholarly communication and learning. Third UK e-Science Programme All Hands Meeting (AHM 2004) (Nottingham, UK, August 31 - September 3 2004). Retrieved January 27, 2005, from: http://www.allhands.org.uk/proceedings/papers/237.pdf
• 45: Metadata Encoding and Transmission Standard (METS). Retrieved January 26, 2005, from: http://www.loc.gov/standards/mets/
• 46: Murray-Rust, P., Rzepa, H.S. and Wright, M. Development of Chemical Markup Language (CML) as a system for handling complex chemical content. New J. Chem., 25, (2001), 618-634.
• 47: Open Archives Initiative (OAI). Retrieved January 27, 2005, from: http://www.openarchives.org/
• 48: Open Archives Initiative. Frequently asked questions. Retrieved January 27, 2005, from: http://www.openarchives.org/documents/FAQ.html
• 49: Open Language Archives Community (OLAC). Retrieved January 26, 2005, from: http://www.language-archives.org/
• 50: Pancerella, C., Hewson, J., Koegler, W., Leahy, D., Lee, M., Rahn, L., et al. Metadata in the Collaboratory for Multi-scale Chemical Science. DC-2003: the 2003 Dublin Core Conference (Seattle, WA, USA, 27 September - 2 October 2003). Retrieved January 27, 2005, from: http://purl.oclc.org/dc2003/03pancerella.pdf
• 51: Paskin, N. Digital Object Identifiers for scientific data. 19th International CODATA Conference (Berlin, Germany, 7-10 November 2004). Retrieved January 27, 2005, from: http://www.doi.org/topics/041110CODATAarticleDOI.pdf
• 52: PDB Protein Data Bank. Retrieved January 27, 2005, from: http://www.rcsb.org/pdb/
• 53: Powell, A. DC Architecture WG meeting report, DC2004. Mail to DCMI Architecture Group mailing list <[e-mail]>, 28 October 2004. Retrieved January 27, 2005, from: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0410&L=dc-architecture&T=0&F=&S=&P=4565
• 54: Powell, A., Nilsson, M., Naeve, A. and Johnston, P. DCMI abstract model. DCMI Working Draft, 8 December 2004. Retrieved January 27, 2005, from: http://www.dublincore.org/documents/abstract-model/
• 55: Proffitt, M., Pulling it all together: use of METS in RLG cultural materials service. Library Hi Tech, 22, (2004), 65-68. doi:10.1108/07378830410524503
• 56: PSIgate. Retrieved January 27, 2005: www.psigate.ac.uk
• 57: Reciprocal Net. Retrieved January 27, 2005, from: http://www.reciprocalnet.org/
• 58: Smart Tea project. Retrieved January 27, 2005, from: http://www.smarttea.org/
• 59: UK Data Archive. Retrieved January 27, 2005, from: http://www.data-archive.ac.uk/
• 60: University of Southampton, Crystal Structure Report Archive. Retrieved January 27, 2005, from: http://ecrystals.chem.soton.ac.uk/
• 61: Van de Sompel, H., Nelson, M. L., Lagoze, C. and Warner, S. Resource harvesting within the OAI-PMH framework. D-Lib Magazine, 10, 12 (December 2004). doi:10.1045/december2004-vandesompel
• 62: XML Data Dictionaries in Chemistry. Retrieved January 27, 2005, from: http://www.iupac.org./projects/2002/2002-022-1-024.html.

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.7 Digital Libraries
          Subjects: Collection

Additional Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.7 Digital Libraries
          Subjects: Dissemination; User issues; Standards

General Terms:
Experimentation, Standardization

Keywords:
Eprints.org, OAI-PMH, crystallography, dublin core, institutional repositories, metadata, scholarly communication