This paper presents an overview of the changing landscape of scholarly communication and describes outcomes from the innovative eBank UK project, which seeks to build links from e-research through to e-learning. As introduction, the scholarly knowledge cycle is described and the role of digital repositories and aggregator services in linking datasets from Grid-enabled projects to e-prints through to peer-reviewed articles as resources in portals and Learning Management Systems, are assessed. The development outcomes from the eBank UK project are presented including the distributed information architecture, requirements for common ontologies, data models, metadata schema, open linking technologies, provenance and workflows. Some emerging challenges for the future are presented in conclusion

Carr, Les

Coles, Simon

De Roure, Dave

Duke, Monica

Frey, Jeremy

Gutteridge, Christopher

Heery, Rachel

Hursthouse, Mike

Lyon, Liz

English

Southampton (e-Prints Soton)

eBank UK Linking Research Data, ScholarlyCommunication and LearningDr Liz Lyon1, Dr Simon Coles2, Dr Les Carr3, Rachel Heery1, Prof MikeHursthouse2, Christopher Gutteridge3, Monica Duke1, Dr. Jeremy Frey2, andProf Dave De Roure31 UKOLN, University of Bath, UK2 School of Chemistry, University of Southampton, UK3 School of Electonics and Computer Science, University of Southampton, UKAbstract. This paper presents an overview of the changing landscapeof scholarly communication and describes outcomes from the innovativeeBank UK project, which seeks to build links from e-research throughto e-learning. As introduction, the scholarly knowledge cycle is describedand the role of digital repositories and aggregator services in linking data-sets from Grid-enabled projects to e-prints through to peer-reviewed ar-ticles as resources in portals and Learning Management Systems, areassessed. The development outcomes from the eBank UK project are pre-sented including the distributed information architecture, requirementsfor common ontologies, data models, metadata schema, open linkingtechnologies, provenance and workﬂows. Some emerging challenges forthe future are presented in conclusion.1 Introduction and context the scholarly knowledge cycleThe eBank project is predicated on the concept that research and learning pro-cesses are cyclical in nature, and that subsequent outputs which contribute toknowledge, are based on the continuous use and reuse of data and information[1]. We can start by examining the creation of original data, (which may be, forexample, numerical data generated by an experiment or a survey, or alterna-tively images captured as part of a clinical study). This initial process is usuallyfollowed by one or more additional processes which might include aggregation ofexperimental data, selection of a particular data subset, repetition of a labora-tory experiment, statistical analysis or modelling of a set of data, manipulationof a molecular structure, annotation of a diagram or editing of a digital image,and which in turn generate modiﬁed datasets. This newly-derived data is relatedto the original data and can be re-purposed through publication in a database, ina pre-print or in a peer-reviewed article. These secondary items may themselvesbe reused through a citation in a related paper, by a reference in a reading list oras an element within modular materials which form part of an undergraduate orpostgraduate course. Clearly it will not always be appropriate to re-purpose theoriginal data from an experiment or study, but it is evident that much researchactivity is derivative in nature.The impact of Grid technologies and the huge amounts of data generatedby Grid-enabled applications, suggest that in the future, (e-)science will beincreasingly data-intensive and collaborative. This is exempliﬁed in the bio-sciences where the growing outputs from genome sequencing work are storedin databases such as GenBank but require advanced computing tools for datamining and analysis. The UK Biotechnology and Biological Sciences ResearchCouncil (BBSRC) recently published a Ten Year Vision which describes thistrend as ”Towards predictive biology” and proposes that in the 21st Century,biology is becoming a more data-rich and quantitative science. The trend hasclear implications for data/information management and curation procedures,and we can examine these further by returning to the concept of a scholarlyknowledge cycle, ﬁgure 1.Fig.1. Illustration of the scholarly knowledge cycle for research and teachingA complete cycle may be implemented in either direction so for example,discrete research data could (ultimately) be explicitly referenced in some formof electronic learning and teaching materials. Alternatively, a student mightwish to ”rollback” to the original research data from a secondary informationresource such as a published article or from an element within an online coursedelivered via a Learning Management System. In order to achieve this, a numberof assumptions must be made which relate largely to the discovery process butare also closely linked to the requirement for essential data curation procedures.The assumptions are:– The integrity of the original data is maintained– There is a shared understanding of the concept of provenance– The original dataset is adequately described using a metadata descriptionframework based on agreed standards– A common ontology for the domain is understood– Each dataset and derived data and information are uniquely identiﬁed (ﬁg.2)– Open linking technology is applied to the original dataset and the deriveddata and informationIn addition to the Grid computing context, these requirements relate directlyto the vision of the Semantic Web, and Semantic Web technologies can be used toexpress the necessary relationships between objects. The application of SemanticWeb technologies within the e-Science and Grid computing context places thissresearch in the arena of the Semantic Grid [2].2 The eBank UK Project - outcomes to dateThe eBank UK project is addressing this challenge by investigating the roleof aggregator services in linking data-sets from Grid-enabled projects to opendata archives contained in digital repositories through to peer-reviewed articlesas resources in portals. This innovative JISC-funded project which is led byUKOLN in partnership with the Universities of Southampton and Manchester,is seeking to build the links between e-research data, scholarly communicationand other on-line sources. It is working in the chemistry domain with the EPSRCfunded eScience testbed CombeChem [3], which is a pilot project that seeks toapply the Grid philosophy to integrate existing structure and property datasources into an information and knowledge environment.The speciﬁc examplar chosen from this subject area is that of crystallog-raphy as it has a strict workﬂow and produces data that is rigidly formattedto an internationally accepted standard. The EPSRC National CrystallographyService (NCS) is housed in the School of Chemistry, University of Southamp-ton, and is an ideal case study due to its high sample throughput, state ofthe art instrumentation, expert personnel and proﬁle in the academic chemistrycommunity. Moreover, recent advances in crystallographic technology and com-putational resources have caused an explosion of crystallographic data, as shownby the recent exponential growth of the Crystal Structure Database (CSD) seeCambridge Crystallographic Data Centre. However, despite this rise it is com-monly recognized that approximately only 20reaching the public domain. Thissituation is even worse in the high throughput NCS scenario where approxi-mately 15disseminated, despite producing ¿60 peer reviewed journal articles perannum. With the imminent advent of the eScience environment, this problemcan only get more severe.A schema for the crystallographic experiment has been devised that detailscrystallographic metadata items and is built on a generic schema for scientiﬁcexperiments, ﬁgure 2. During the deposition of data in a Crystallographic EPrintmetadata items are seamlessly extracted and indexed for searching at the localarchive level. The top level document includes ’Dublin Core bibliographic’ and’chemical identiﬁer’ metadata elements in an Open Archives Initiative Protocolfor Metadata Harvesting (OAI-PMH) compliant form, which allow access to asecondary level of searchable crystallographic metadata items, which are in turndirectly linked to the associated archived data. In this manner the output froma crystallographic experiment may be disseminated as ’data’ in such a way thataggregator services and researchers may add value to it and transform it intoknowledge and the publication ’bottleneck’ problem can be addressed.The metadata about datasets made available in the repository will be har-vested into a central database using the OAI-PMH. This metadata will thenbe indexed together with any other available metadata about research publi-cations. A searchable interface will enable users to discover datasets as well asrelated literature. The metadata contains links back to the datasets which theuser will be able to follow in order to obtain access to the original data, whenthis is available. Harvested metadata from diﬀerent repositories not only pro-vides a common entry point to potentially disparate resources (such as datasetsin dataset repositories and published literature which may reside elsewhere) butalso oﬀers the potential of enhancement of the metadata such as the addition ofsubject keywords to research datasets based on the knowledge of subject classiﬁ-cation terms assigned to related publications. A further area of work investigatesthe embedding of the search interface within web sites, adopting their look-and-feel. PSIgate (http://www.psigate.ac.uk/) will be used to pilot these embeddingtechniques based on CGI-mechanisms and portal-related standards.The concept we have implemented within the Southampton e-print archivesystem is Data Publication@Source [4]. Crystallographic EPrints use the OAIconcept to make available ALL the data generated during the course of a struc-ture determination experiment. That is the publishable output is constructedfrom all the raw, results and derived data that is generated during the courseof the experiment. This presents the data in a searchable and hierarchical sys-tem that relates to the workﬂow of the experiment. This metadata includesbibliographic and chemical identiﬁer items which are above a secondary levelof searchable crystallographic items which are directly linked to the associatedarchived data. The table below depicts the schema and shows the hierarchicalmanner in which the open archive report is constructed in the ﬁgure below.Hence the results of a crystal structure determination may be disseminatedin a manner that anyone wishing to utilise the information may access the entirearchive of data related to it and assess its validity and worth. In the future anotiﬁcation, or bulletin board type system, (much like Amazons reviewers com-ments) could be added to create in eﬀect a new type of peer reviewed publication.Name Files associated with this stage Metadata associated with this stageFile Type Description Name Data TypeInitialisation .htm HTML Metadata for crystallography expt Morphology *STRING (SET)i*.kcd BINARY Unit cell determination images Solvent *STRINGUnit cell Sample image .JPGCollection s*.kcd BINARY Diffraction images Instrument Type *STRING*scan*.jpg JPG Visual version of .kcd file Temperature *INTEGERCrystal image .JPGSoftware Name STRINGSoftware Version INTEGERProcessing scale all.in ASCII Result of processing Cell a *NUMBERscale all.out ASCII Result of correction on processed data Cell b *NUMBER.hkl ASCII Derived data set Cell c *NUMBER.htm HTML Report file Cell alpha *NUMBERCell beta *NUMBERCell gamma *NUMBERCrystal system *STRING (SET)Completeness *INTEGER (%)Software Name STRINGSoftware Version INTEGERSolution .prp ASCII Symmetry file, log of process Space group *STRING (SET)xs.lst ASCII Solution log file Figure of merit *NUMBERSoftware Name STRINGSoftware Version INTEGERRefinement xl.lst ASCII Final refinement listing R1 obs *NUMBER.res ASCII Output coordinates wR2 obs *NUMBERR1 all *NUMBERwR2 all *NUMBERSoftware Name STRINGSoftware Version INTEGERCIF .cif ASCII Final results Formula moiety *STRINGcheckcif.htm HTML Automatic validation results CIF check *STRINGReport .html .HTML Publication format EPrint type *CRYSTAL(HTML/XHTML) STRUCTUREAuthors *STRINGAffiliations *STRINGFormula empirical *STRINGCompound name *STRINGCCDC Code *STRINGCompound class *STRING (SET)Keywords *STRING (SET)Available data *STRING (SET)Related publications STRINGFig.2. The draft version of the schema details for the crystallographic data show-ing the main data types and associated ﬁle names generated in a crystal structuredetermination.Fig.3. A summary of the diﬀerent screens available from the basic e-data report show-ing how the data and metadata described in the basic schema of ﬁgure 2 are displayed.3 Conclusions - issues and challenges for the futureWhile only test versions of the e-crystal-data-report have been produced so farthey have been populated with real crystallographic data sets produced at theNational Crystallography Service (NCS). The lessons learnt so far fall in to threemain areas. First, the ease of use in inputting the data to the system and ensuringthat suﬃcient information about the materials, the experiment and the natureof the data is being entered. Some of the input styling is taken over directly fromthe current e-print system which of course allows for ﬁles of diﬀerent types to beup loaded. However the issue of ﬁle types becomes more complex with the adventof data. In this regard the conformity of the crystallography community is anadvantage, with common ﬁle types with well-understood extensions. Never theless some standardization is imposed following the NCS practice at this stage.Conversion between diﬀerent ﬁle types for the higher-level data elements (e.g.the molecular structure ﬁles) can be done automatically, with a high degreeof ﬁdelity, and this is necessary to provide suitable data for the visualizationprograms built in to the viewing interface.This brings us on to the second main area, the viewing of this informationdirectly from the e-print system. Once an entry is located then the information ispresented on a web interface with the major details about the molecule available,including a visual, rotateable image. The conversion of the crystallographic CIFﬁle to other formats (e.g. MOL ﬁle) is necessary for this. Similarly the newlydeﬁne unique chemical identiﬁer (INCHI) is also calculated by converting the CIFﬁle via these stages to a CML ﬁle. The required conversions are implemented (orsoon will be) as web services to allow updates independently of the main e-printsoftware system.The ﬁnal issues revolve around ﬁnding the existence of the data on the e-print system. As indicated above the data schema that provides the outline forthe arrangement of the data highlights the signiﬁcant data that a chemist wouldwish to search on. This is made available via an OIA interface to harvestingprograms, which can then provide additional functionality to enable a multi-parameter search. This side of the system is less tested and does present someproblems for us as many of the current search systems allow for searches onchemical structures (drawn in 2 or 3D) using proprietary algorithms, especiallyfor the sub-structure search. We are thus not able to implement this type ofsearch but can demonstrate that the data needed for such searches can be madeavailable to data aggregators.The test experiments have proved very successful and have engaged the in-terest of several of the traditional suppliers of crystallographic information, whowish in eﬀect to move up market in the information supply chain. In the academiccommunity there is a growing word wide interest. The system of separating thearchiving of the data, including all the raw and background information, fromthe aggregated higher level structural data which is to be curated over a muchlonger term, looks to be very successful.We should stress that the e-experiment-data-reports are not restricted tocrystallographic data. These data sets were chosen as an ideal test case due totheir relative uniformity, community agreement and availability of diagnosticsto enable the user to assess the quality of the data. We are now extending thesystem to cover spectroscopic data, for which again the issue of the lack ofextensive libraries of even common molecules is a major hindrance to eﬃcientresearch. We are applying the principle to Raman spectra are working with oneof the spectrometer supplies from the start to ensure that the links to the e-printsystem can be built in to the spectrometer software, further simplifying the taskof disseminating the data.One aspect that may need further consideration if the automated processesare enhanced, is ﬁner control over access to the data by diﬀerent groups atdiﬀerent times. This will of course overlap with security concerns.References1. Lyon, L.: Developing Information Architectures - to support Research, Learningand Teaching. In: UCISA Conference. (2002)2. De Roure, D., Jennings, N.R., Shadbolt, N.R.: The Semantic Grid: A future e-Science infrastructure. In: Grid Computing - Making the Global Infrastructure aReality. John Wiley and Sons Ltd (2003) 437–4703. Frey, J.G., Bradley, M., Essex, J.W., Hursthouse, M.B., Lewis, S.M., Luck, M.M.,Moreau, L., De Roure, D.C., Surridge, M., Welsh, A.: Combinatorial chemistry andthe Grid. In: Grid Computing - Making the Global Infrastructure a Reality. JohnWiley and Sons Ltd (2003) 945–9624. Frey, J., De Roure, D., Carr, L.: Publishing at Source: Scientiﬁc Publication froma Web to a Data Grid. In: EuroWeb 2002 Conference, Oxford (2002)5. Bearman, D., Lytle, R.: The Power of the Principle of Provenance. Archivaria (21)14–276. Hitchcock, S., Brody, T., Gutteridge, C., Carr, L., Hall, W., Harnad, S., Bergmark,D., Lagoze, C.: Open Citation Linking: The Way Forward. D-Lib Magazine 8 (2002)

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eBank UK linking research data, scholarly communication and learning

This paper includes an overview of the changing landscape of scholarly communication and describes outcomes from the innovative eBank UK project, which seeks to build links from e-research through to e-learning. As introduction, the scholarly knowledge cycle is described and the role of digital repositories and aggregator services in linking data-sets from Grid-enabled projects to e-prints through to peer-reviewed articles as resources in portals and Learning Management Systems, are assessed. The development outcomes from the eBank UK project are presented including the distributed information architecture, requirements for common ontologies, data models, metadata schema, open linking technologies, provenance and workflows. Some emerging challenges for the future are presented in conclusion

eBank UK linking research data, scholarly communication and learning

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