| Author | Title | Year | Journal/Proceedings | Reftype | DOI/URL |
|---|---|---|---|---|---|
| schraefel, m., Carr, L., De Roure, D. & Hall, W. | You've Got Hypertext | 2004 | Journal of Digital Information | article | URL |
| Abstract: The paper considers possible "future everyday hypertext systems". To ground the discussion, we look first at the functional and conceptual definitions of hypertext that have evolved in the hypertext research community. We then consider these definitions against the Web, the best known current everyday hypertext, but one that the hypertext community has regarded as only partially a hypertext system at best. We propose, however, that a full, rich hypertext is alive and well and living in an equally successful everyday system: that system is email. We look at how email meets the criteria, both functionally and conceptually, for rich hypertext. We then use email-as-hypertext as our touchstone for assessing future hypertext systems. In particular, we consider the newest system on the Web event horizon, the Semantic Web, and show how the potential hypertextness of the Semantic Web has been anticipated by pre- and co-Web hypertext research systems. We consider how, if informed by the attributes of our email model, the Semantic Web may be able to break away from the limited hypertext model of the Web to become a rich, everyday hypertext system like email. We present three current hypertext research efforts that use the Semantic Web platform to show how these may be seen to embody such email-like hypertext qualities. | |||||
BibTeX:
@article{2004,
author = {schraefel, m.c. and Carr, Leslie and De Roure, David and Hall, Wendy},
title = {You've Got Hypertext},
journal = {Journal of Digital Information},
year = {2004},
volume = {5},
number = {1},
note = {ISSN 1368-7506},
url = {http://jodi.tamu.edu/Articles/v05/i01/schraefel/}
}
|
|||||
| Addis, M. | Creating, searching and navigating collections of 3D models [BibTeX] |
2005 | London 3D Imaging Technology Conference | inproceedings | URL |
BibTeX:
@inproceedings{Addis2005,
author = {Addis, Matthew},
title = {Creating, searching and navigating collections of 3D models},
booktitle = {London 3D Imaging Technology Conference},
year = {2005},
url = {http://eprints.ecs.soton.ac.uk/12218/}
}
|
|||||
| Addis, M. | Distributed stochastic analysis using remote service providers [BibTeX] |
2003 | 2nd ESA Space Systems Design, Verification and AIT Workshop | inproceedings | URL |
BibTeX:
@inproceedings{Addis2003,
author = {Addis, Matthew},
title = {Distributed stochastic analysis using remote service providers},
booktitle = {2nd ESA Space Systems Design, Verification and AIT Workshop},
year = {2003},
url = {http://eprints.ecs.soton.ac.uk/8912/}
}
|
|||||
| Addis, M. | myGrid: An Open Platform for Data-intensive Post-Genomic Functional Analysis [BibTeX] |
2002 | The Grid in Bioinformatics and Materials Science | inproceedings | URL |
BibTeX:
@inproceedings{Addis2002,
author = {Addis, Matthew},
title = {myGrid: An Open Platform for Data-intensive Post-Genomic Functional Analysis},
booktitle = {The Grid in Bioinformatics and Materials Science},
year = {2002},
url = {http://eprints.ecs.soton.ac.uk/9030/}
}
|
|||||
| Addis, M., Allen, P. & Surridge, M. | Simulation on Demand | 2000 | E-business: Key Issues, Applications, TechnologiesE-business: Key Issues, Applications and Technologies. IOS Press. | article | URL |
| Abstract: The use of engineering meta-applications for activities such as design optimisation and sensitivity analysis can provide substantial business benefits, but require significant computing resources. However, they can be made financially viable through the exploitation of software and hardware on demand business models, supported by an electronic marketplace. This paper presents an agent-based business-to-business e-commerce system that enables large-scale distributed engineering simulations using third-party resources. The system has wide applicability and can form an e-business framework for many resource-intensive applications provided by the emerging application service provision (ASP) market. | |||||
BibTeX:
@article{Addis2000,
author = {Addis, Matthew and Allen, P. and Surridge, M.},
title = {Simulation on Demand},
booktitle = {E-business: Key Issues, Applications and Technologies. IOS Press.},
journal = {E-business: Key Issues, Applications, Technologies},
publisher = {IOS Press},
year = {2000},
pages = {906--912},
url = {http://eprints.ecs.soton.ac.uk/4226/}
}
|
|||||
| Addis, M., Allen, P. & Surridge, M. | Negotiating for Software Services | 2000 | Eleventh International Workshop on Database and Expert Systems Applications (DEXA 2000) | inproceedings | URL |
| Abstract: We are investigating how the routine use of engineering meta-applications can be made financially viable by using a software and hardware on-demand business model supported by an agent based electronic marketplace. This paper presents how our work has combined Web, agent and security technologies to create a robust and secure Internet based marketplace in which a trusted third party provides negotiation services between software application users and third party hardware and software service providers. | |||||
BibTeX:
@inproceedings{Addis2000a,
author = {Addis, Matthew and Allen, P. and Surridge, M.},
title = {Negotiating for Software Services},
booktitle = {Eleventh International Workshop on Database and Expert Systems Applications (DEXA 2000)},
publisher = {IEEE Computer Society},
year = {2000},
pages = {1039--1043},
note = {ISBN: 0-7695-0680-1},
url = {http://eprints.ecs.soton.ac.uk/4225/}
}
|
|||||
| Addis, M., Allen, P., Y., C., De Roure, D., Hall, M. & Hall, W. | Making WWW applications weather proof: adaptive use of Internet bandwidth [BibTeX] |
1999 | 8th International World Wide Web Conference (WWW8) | inproceedings | URL |
BibTeX:
@inproceedings{Addis1999,
author = {Addis, Matthew and Allen, P. and Cheng. Y. and De Roure, David and Hall, M. and Hall, W.},
title = {Making WWW applications weather proof: adaptive use of Internet bandwidth},
booktitle = {8th International World Wide Web Conference (WWW8)},
publisher = {Elsevier Science},
year = {1999},
pages = {164--165},
note = {Poster proceedings},
url = {http://eprints.ecs.soton.ac.uk/2569/}
}
|
|||||
| Addis, M., Boniface, M., Goodall, S., Grimwood, P., Kim, S., Lewis, P., Martinez, K. & Stevenson, A. | SCULPTEUR: Towards a New Paradigm for Multimedia Museum Information Handling | 2003 | Semantic Web ISWC | inproceedings | URL |
| Abstract: This paper describes the design and prototype implementation of a novel architecture for integrated concept, metadata and content based browsing and retrieval of museum information. The work is part of a European project involving several major galleries and the aim is to provide more versatile access to digital collections of museum artefacts, including 2-D images, 3-D models and other multimedia representations. An ontology for the museum domain, based on the CIDOC Conceptual Reference Model, is being developed as a semantic layer with references to the digital collection as instance information. A graphical concept browser is an integral component in the user interface, allowing navigation through the semantic layer, display of thumbnails, or full representations of artefacts and textual information in appropriate viewers and the invocation of conventional content based searching or combined querying. Semantic Web technologies are used in system integration to describe how tools for analysis and visualisation can be applied to different data types and sources. This supports flexible and managed formulation, execution and interpretation of the results of distributed multimedia queries. Combined searches using concepts, content and metadata can be initiated from a single user interface. | |||||
BibTeX:
@inproceedings{Addis2003a,
author = {Addis, Matthew and Boniface, Mike and Goodall, Simon and Paul Grimwood and Sanghee Kim and Lewis, Paul and Martinez, Kirk and Stevenson, Alison},
title = {SCULPTEUR: Towards a New Paradigm for Multimedia Museum Information Handling},
booktitle = {Semantic Web ISWC},
publisher = {Springer},
year = {2003},
volume = {2870},
pages = {582 --596},
url = {http://eprints.ecs.soton.ac.uk/8593/}
}
|
|||||
| Addis, M., Boniface, M., Goodall, S., Paul, G., Kim, S., Lewis, P., Martinez, K. & Stevenson, A. | Integrated image content and metadata search and retrieval across multiple databases. | 2003 | Second International Conference on Image and Video Retrieval 2003 | inproceedings | URL |
| Abstract: Abstract. This paper presents an updated technical overview of an integrated content and metadata-based image retrieval system used by several major art galleries in Europe including the Louvre in Paris, the Victoria and Albert Museum in London, the Uffizi Gallery in Florence and the National Gallery in London. In our approach, the subjects of a query (e.g. images, textual metadata attributes), the operators used in a query (e.g. SimilarTo, Contains, Equals) and the rules that constrain the query (e.g. SimilarTo can only be applied to Images) are all explicitly defined and published for each gallery collection. In this way, cross-collection queries are dynamically constructed and executed in a way that is automatically constrained to the capabilities of the particular image collections being searched. The application of existing, standards based, technology to integrate metadata and content based queries underpins an open standards approach to extending interoperability across multiple image databases. | |||||
BibTeX:
@inproceedings{Addis2003b,
author = {Addis, Matthew and Boniface, M. and Goodall, Simon and Grimwood. Paul and Kim, Sanghee and Lewis, Paul and Martinez, Kirk and Stevenson, Alison},
title = {Integrated image content and metadata search and retrieval across multiple databases.},
booktitle = {Second International Conference on Image and Video Retrieval 2003},
publisher = {Springer LNCS 2728},
year = {2003},
pages = {91--100},
url = {http://eprints.ecs.soton.ac.uk/8915/}
}
|
|||||
| Addis, M., Choi, F. & Miller, A. | Planning the digitisation, storage and access of large scale audiovisual archives | 2005 | Ensuring Long-term Preservation and Adding Value to Scientific and Technical data (PV 2005) | inproceedings | URL |
| Abstract: This paper presents ongoing work in PrestoSpace on how broadcast archives can plan large-scale, long-term digitization and storage projects. In our approach, carrier decay, technical obsolescence, and rapidly falling costs of mass storage are represented as a series of statistical and predictive models. The models include ongoing migration within a digital archive. The objective is to allow archive managers to investigate the trade-offs between how many items to transfer, the cost of transfer and storage, how long it will take, what quality can be achieved, how much will be lost, and what digital storage solutions to adopt over time. The process and models are based on digitization projects conducted by large broadcast archives that are currently migrating their collections into digital form. Whilst our focus is on broadcast archives, our findings should be readily transferable to other scenarios where there is a need to store large volumes of digital data over long periods of time. | |||||
BibTeX:
@inproceedings{Addis2005c,
author = {Addis, Matthew and Choi, Freddy and Miller, A.},
title = {Planning the digitisation, storage and access of large scale audiovisual archives},
booktitle = {Ensuring Long-term Preservation and Adding Value to Scientific and Technical data (PV 2005)},
year = {2005},
url = {http://eprints.ecs.soton.ac.uk/12231/}
}
|
|||||
| Addis, M., Ferris, J., Greenwood, M., Li, P., Marvin, D., Oinn, T. & Wipat, A. | Experiences with e-Science workflow specification and enactment in bioinformatics | 2003 | All Hands Meeting | inproceedings | URL |
| Abstract: Workflow techniques form an important part of in-silico experimentation within the bioinformatics domain and potentially allow the eScientist to describe and enact their experimental processes in a structured, repeatable and verifiable way. Bioinformaticians routinely use Web-based resources within their in-silico experiments. However, the use of current web service orchestration techniques is problematic, and represents a significant barrier to take-up by the bioinformatics community, due to the rapidly evolving and competing standards, a lack of freely available tools, limited support for interaction with stateful services, and inappropriate levels of abstraction for the bioinformatics domain. As a result, the EPSRC funded myGrid[11] project has, in collaboration with the European Bioinformatics Institute and the Human Genome Mapping Project, developed a graphical toolset and workflow enactor which uses its own high level representation of a process flow, including specification of processing units, data transfers and execution constraints | |||||
BibTeX:
@inproceedings{Addis2003c,
author = {Addis, Matthew and Ferris, Justin and Greenwood, Mark and Li, Peter and Marvin, Darren and Oinn, Thomas and Wipat, Anil},
title = {Experiences with e-Science workflow specification and enactment in bioinformatics},
booktitle = {All Hands Meeting},
year = {2003},
url = {http://www.nesc.ac.uk/events/ahm2003/AHMCD/pdf/108.pdf}
}
|
|||||
| Addis, M., Giorgini, F., Lewis, P. & Martinez, K. | Content and concept-based retrieval and navigation tools in Sculpteur [BibTeX] |
2003 | EVA London 2003 | inproceedings | URL |
BibTeX:
@inproceedings{Addis2003d,
author = {Addis, Matthew and Giorgini, Fabrizio and Lewis, Paul and Martinez, Kirk},
title = {Content and concept-based retrieval and navigation tools in Sculpteur},
booktitle = {EVA London 2003},
year = {2003},
url = {http://eprints.ecs.soton.ac.uk/8891/}
}
|
|||||
| Addis, M., Giorgini, F., Stevenson, J. & Sinclair, P. | New Methods for Digitising, Searching, and Accessing Cultural Heritage Collections
|
2004 | Research and Advanced Technology for Digital Libraries: 8th European Conference, ECDL 2004 | inproceedings | URL |
| Abstract: The first session will describe the processes, tools and techniques that are used for digitising, cataloguing, searching, and accessing multimedia representations of works of art in a range of cultural heritage institutions from across Europe. Particular attention will be made to 3D content acquisition, advanced searching methodologies, and the use of digital content in eLearning applications. Practical issues such as fit with infrastructure (people, processes, culture, systems) and ease of use (training, deployment and operation) will also be discussed. The second session will present practical guidelines on how to use cultural heritage ontologies (specifically the CIDOC CRM) to structure, integrate and improve access to multimedia museum and gallery information. We will present both the challenges and benefits of using the CIDOC CRM and Semantic Web techniques to improve the understandability and navigation of large digital collections. We will discuss how mapping museum and gallery legacy systems to a common ontological model can facilitate interoperability and improve accessibility. Both sessions will focus on the IST FP5 supported Sculpteur project (http://www.sculpteurweb.org) as a case study and will include the wider experiences of the partners involved. Experiences will be presented from a range of museums and galleries that include the Victoria and Albert Museum and National Gallery in London, the Uffizi in Italy, and the Musee de Cherbourg and the Centre de Recherche et de Restauration des Musees de France (C2RMF). Facilities will be provided for hands-on access to the technology and techniques used in Sculpteur, including 3D content. |
|||||
BibTeX:
@inproceedings{Addis2004,
author = {Addis, Matthew and Giorgini, Fabrizio and Stevenson, James and Sinclair, Patrick},
title = {New Methods for Digitising, Searching, and Accessing Cultural Heritage Collections |
|||||
| Addis, M., Goodall, S., Lewis, P., Martinez, K., Sinclair, P., Giorgini, F., Lahanier, C., Stevenson, J., Cappellini, M., Serni, L. & Rimaboschi, R. | SEARCHING AND EXPLORING MULTIMEDIA MUSEUM COLLECTIONS OVER THE WEB [BibTeX] |
2005 | EVA 2005 | inproceedings | URL |
BibTeX:
@inproceedings{Addis2005d,
author = {Addis, Matthew and Goodall, Simon and Lewis, Paul and Martinez, Kirk and Sinclair, Patrick and Giorgini, Fabrizio and Lahanier, Christian and Stevenson, James and Cappellini, M. and Serni, L. and Rimaboschi, R.},
title = {SEARCHING AND EXPLORING MULTIMEDIA MUSEUM COLLECTIONS OVER THE WEB},
booktitle = {EVA 2005},
year = {2005},
url = {http://eprints.ecs.soton.ac.uk/10911/}
}
|
|||||
| Addis, M., Hafeez, S., Prideaux, D., Lowe, R., Lewis, P., Martinez, K. & Sinclair, P. | The eCHASE System for Cross-border Use of European Multimedia Cultural Heritage Content in Education and Publishing | 2006 | AXMEDIS 2006: 2nd International Conference on Automated Production of Cross Media Content for Multi-channel Distribution | inproceedings | URL |
| Abstract: Europe?s digital cultural heritage content has tremendous exploitation potential in applications such as Education, Publishing, e-Commerce, Public-Access and Tourism. Value is hugely amplified if the content can be aggregated repurposed and distributed at a European level. The eCHASE project seeks to demonstrate that public-private partnerships between content holders and commercial service providers can create new services and a sustainable business based on access and exploitation of digital cultural heritage content. This paper describes the eCHASE demonstrator from a technical perspective, briefly detailing the tools and components which make up the system and the use of open standards. | |||||
BibTeX:
@inproceedings{Addis2006,
author = {Addis, Matthew and Hafeez, S. and Prideaux, D. and Lowe, R. and Lewis, P. and Martinez, K. and Sinclair, P.},
title = {The eCHASE System for Cross-border Use of European Multimedia Cultural Heritage Content in Education and Publishing},
booktitle = {AXMEDIS 2006: 2nd International Conference on Automated Production of Cross Media Content for Multi-channel Distribution},
year = {2006},
url = {http://eprints.ecs.soton.ac.uk/14265/}
}
|
|||||
| Addis, M., Lewis, P. & Martinez, K. | ARTISTE image retrieval system puts European galleries in the picture | 2002 | Cultivate Interactive | article | URL |
| Abstract: ARTISTE is a European Commission-funded collaboration, investigating the use of integrated content and metadata-based image retrieval across disparate databases in several major art galleries across Europe. Collaborating galleries include the Louvre in Paris, the Victoria and Albert Museum in London, the Uffizi Gallery in Florence and the National Gallery in London. Museums and galleries often have several digital collections ranging from public access images to specialised scientific images used for conservation purposes. Direct access from one gallery to another is currently uncommon for textual data and almost unheard of in terms of image-based search and retrieval. Cross-collection access is recognised as important, however, for example to compare the treatments and conditions of Europe's paintings, which form a core part of our cultural heritage. A key aim of ARTISTE is to provide an image retrieval system that can provide integrated cross-collection searching. Whilst ARTISTE is primarily designed for inter-museum searching and as a building block for public access systems, it could equally be applied to museum intranets. An article on ARTISTE in the first issue of Cultivate presented the project objectives and technical approach. Now that ARTISTE is nearing completion, this article looks at how those objectives have been fulfilled and discusses future work to continue and build upon the achievements of the project. |
|||||
BibTeX:
@article{Addis2002a,
author = {Addis, Matthew and Lewis, Paul and Martinez, Kirk},
title = {ARTISTE image retrieval system puts European galleries in the picture},
journal = {Cultivate Interactive},
publisher = {UKOLN},
year = {2002},
url = {http://eprints.ecs.soton.ac.uk/7413/}
}
|
|||||
| Addis, M., Martinez, K., Lewis, P., Stevenson, J. & Giorgini, F. | New Ways to Search, Navigate and Use Multimedia Museum Collections over the Web | 2005 | Museums and the Web 2005 | inproceedings | URL |
| Abstract: Museums and galleries are becoming increasing rich in digital information. This is often created for internal activities such as cataloguing, curation, conservation and restoration, but also has many additional uses including gallery terminals, Web access, educational, scientific, and commercial licensing. New forms of multimedia content such as 3D models and virtual spaces have huge potential for enhancing the way people interact with museum collections; for example, in structured eLearning environments. Despite drivers for increased integration of information sources within the museum or gallery, and for improved Web accessibility for external users, this content is often hard to access and is held in multiple internal systems with non-standard schemas and descriptions. Providing information to external users or applications in a structured and machine-readable form is particularly difficult due to a lack of tools and standards. This makes it difficult to expose this rich source of information so it can be used over the Web in external applications. Over the past three years, the European Commission IST supported SCULPTEUR project has been addressing these problems by developing new ways to create, search, navigate, access, share, repurpose and use multimedia content over the Web for professional users. This paper describes the tools and techniques developed in the project. | |||||
BibTeX:
@inproceedings{Addis2005e,
author = {Addis, Matthew and Martinez, Kirk and Lewis, Paul and Stevenson, James and Giorgini, Fabrizio},
title = {New Ways to Search, Navigate and Use Multimedia Museum Collections over the Web},
booktitle = {Museums and the Web 2005},
year = {2005},
volume = {7},
number = {797},
note = {Semantic Web, 3D models, CIDOC CRM, Search and Retrieval, eLearning},
url = {http://eprints.ecs.soton.ac.uk/10909/}
}
|
|||||
| Addis, M., Rana, O., Bunford-Jones, D., Walker, D., Harwick, K. & Surridge, M. | Agent Based Resource Discovery for Dynamic Clusters [BibTeX] |
2000 | IEEE International Conference on Cluster Computing | inproceedings | URL |
BibTeX:
@inproceedings{Addis2000b,
author = {Addis, Matthew and Rana, Omer and Bunford-Jones, Daniel and Walker, David and Harwick, K. and Surridge, M.},
title = {Agent Based Resource Discovery for Dynamic Clusters},
booktitle = {IEEE International Conference on Cluster Computing},
year = {2000},
note = {poster},
url = {http://eprints.ecs.soton.ac.uk/4227/}
}
|
|||||
| Addis, M. J., Allen, P. J., Cheng, Y., Hall, M., Stairmand, M., Hall, W. & De Roure, D. | Spending less time in Internet traffic jams [BibTeX] |
1999 | Fourth International Conference on the Practical Application of Intelligent Agents and Multi-Agents (PAAM99) | inproceedings | URL |
BibTeX:
@inproceedings{Addis1999a,
author = {M J Addis and P J Allen and Y Cheng and M Hall and M Stairmand and W Hall and De Roure, David},
title = {Spending less time in Internet traffic jams},
booktitle = {Fourth International Conference on the Practical Application of Intelligent Agents and Multi-Agents (PAAM99)},
publisher = {The Practical Application Company Ltd.},
year = {1999},
pages = {193--209},
url = {http://eprints.ecs.soton.ac.uk/2570/}
}
|
|||||
| Ainsworth, J., Harper, R., Juma, I. & Buchan, I. | PsyGrid: Applying e-Science to Epidemiology | 2006 | Computer-Based Medical Systems, 2006. CBMS 2006. 19th IEEE International Symposium on | inproceedings | DOI |
| Abstract: The process of hypothesis-driven epidemiological research has three phases - the establishment and characterisation of a large, representative cohort from a geographically distributed population; the integration of the cohort data with other data sources to provide additional characterisation; the formulation of a hypothesis and generation of the corresponding predictions. Grid-computing technologies make possible secure, distributed collaboration, and the ability to share data sources, computational resources and storage resources across administrative boundaries. PsyGrid is an e-science project established to apply grid-computing technologies to each of the three phases, with the aim of eliminating the obstacles that hinder epidemiological research. We describe a system for distributed cohort characterisation, and the first application to the study of first episode psychosis | |||||
BibTeX:
@inproceedings{Ainsworth2006,
author = {Ainsworth, John and Harper, Rob and Juma, Ismael and Buchan, Iain },
title = {PsyGrid: Applying e-Science to Epidemiology},
booktitle = {Computer-Based Medical Systems, 2006. CBMS 2006. 19th IEEE International Symposium on},
year = {2006},
pages = {727--732},
doi = {http://dx.doi.org/10.1109/CBMS.2006.135}
}
|
|||||
| Akhtar, M., Fernandes, A. & Paton, N. | MOVIE: An incremental maintenance system for materialized object views | 2003 | Data and Knowledge Engineering | article | DOI |
| Abstract: View materialization is an important technique for high performance query processing, data integration and replication. Solutions to the problem of incrementally maintaining materialized views are very relevant. So far, most work on this problem has been confined to relational settings and solutions have not been comprehensively evaluated. This paper describes MOVIE, a complete, implemented and evaluated solution to the problem of incrementally maintaining materialized OQL views in ODMG-compliant object databases. The evaluation throws light into how the effectiveness of incremental maintenance is affected by issues such as database size, and the complexity and selectivity of views. | |||||
BibTeX:
@article{Akhtar2003,
author = {Akhtar, M. and Fernandes, Alvaro and Paton, Norman },
title = {MOVIE: An incremental maintenance system for materialized object views},
journal = {Data and Knowledge Engineering},
year = {2003},
volume = {47},
number = {2},
pages = {131--166},
doi = {http://dx.doi.org/10.1016/S0169-023X(03)00048-X}
}
|
|||||
| Alam, I., Cornell, M., Soanes, D., Hedeler, C., Wong, H., Rattray, M., Hubbard, S., Talbot, N., Oliver, S. & Paton, N. | A Methodology for Comparative Functional Genomics | 2007 | Journal of Integrative Bioinformatics | article | DOI |
| Abstract: The continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value that can be obtained from sequenced genomes. The principal result of the paper is a methodology, in which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse. | |||||
BibTeX:
@article{Alam2007,
author = {Alam, Intikhab and Cornell, Michael and Soanes, Darren and Hedeler, Cornerlia and Wong, Han and Rattray, Magnus and Hubbard, Simon and Talbot, Nicholas and Oliver, Stephen and Paton, Norman},
title = {A Methodology for Comparative Functional Genomics},
journal = {Journal of Integrative Bioinformatics},
year = {2007},
volume = {4},
number = {3},
doi = {http://dx.doi.org/10.2390/biecoll-jib-2007-69}
}
|
|||||
| Albeck, S., Alzari, P., Andreini, C., Banci, L., Berry, I. M., Bertini, I., Cambillau, C., Canard, B., Carter, L., Cohen, S. X., Diprose, J. M., Dym, O., Esnouf, R. M., Felder, C., Ferron, F., Guillemot, F., Hamer, R., Ben Jelloul, M., Laskowski, R. A., Laurent, T., Longhi, S., Lopez, R., Luchinat, C., Malet, H., Mochel, T., Morris, R. J., Moulinier, L., Oinn, T., Pajon, A., Peleg, Y., Perrakis, A., Poch, O., Prilusky, J., Rachedi, A., Ripp, R., Rosato, A., Silman, I., Stuart, D. I., Sussman, J. L., Thierry, J., Thompson, J. D., Thornton, J. M., Unger, T., Vaughan, B., Vranken, W., Watson, J. D., Whamond, G. & Henrick, K. | SPINE bioinformatics and data-management aspects of high-throughput structural biology | 2006 | Acta Crystallographica Section D | article | DOI |
| Abstract: SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited. | |||||
BibTeX:
@article{Albeck2006,
author = {Albeck, S. and Alzari, P. and Andreini, C. and Banci, L. and Berry, I. M. and Bertini, I. and Cambillau, C. and Canard, B. and Carter, L. and Cohen, S. X. and Diprose, J. M. and Dym, O. and Esnouf, R. M. and Felder, C. and Ferron, F. and Guillemot, F. and Hamer, R. and Ben Jelloul, M. and Laskowski, R. A. and Laurent, T. and Longhi, S. and Lopez, Rodrigo and Luchinat, C. and Malet, H. and Mochel, T. and Morris, R. J. and Moulinier, L. and Oinn, Thomas and Pajon, A. and Peleg, Y. and Perrakis, A. and Poch, O. and Prilusky, J. and Rachedi, A. and Ripp, R. and Rosato, A. and Silman, I. and Stuart, D. I. and Sussman, J. L. and Thierry, J.-C. and Thompson, J. D. and Thornton, J. M. and Unger, T. and Vaughan, B. and Vranken, W. and Watson, J. D. and Whamond, G. and Henrick, K.},
title = {SPINE bioinformatics and data-management aspects of high-throughput structural biology},
journal = {Acta Crystallographica Section D},
year = {2006},
volume = {62},
number = {10},
pages = {1184--1195},
doi = {http://dx.doi.org/10.1107/S090744490602991X}
}
|
|||||
| Ali, M., Fernandes, A. & Paton, N. | Incremental maintenance of materialized OQL views [BibTeX] |
2000 | DOLAP '00: Proceedings of the 3rd ACM international workshop on Data warehousing and OLAP | inproceedings | DOI |
BibTeX:
@inproceedings{Ali2000,
author = {Ali, M. and Fernandes, Alvaro and Paton, Norman},
title = {Incremental maintenance of materialized OQL views},
booktitle = {DOLAP '00: Proceedings of the 3rd ACM international workshop on Data warehousing and OLAP},
publisher = {ACM},
year = {2000},
pages = {41--48},
doi = {http://dx.doi.org/10.1145/355068.355314}
}
|
|||||
| Ali, M., Paton, N. & Fernandes, A. | An Experimental Performance Evaluation of Incremental Materialized View Maintenance in Object Databases | 2001 | Data Warehousing and Knowledge Discovery Third International Conference, DaWaK 2001 Munich, Germany, September 5Ð7, 2001 Proceedings | inproceedings | DOI |
| Abstract: The development of techniques for supporting incremental maintenance of materialized views has been an active research area for over twenty years. However, although there has been much research on methods and algorithms, there are surprisingly few systematic studies on the performance of different approaches. As a result, understanding of the circumstances in which materialized views are beneficial (or not) can be seen to lag behind research on incremental maintenance techniques. This paper presents the results of an experimental performance analysis carried out in a system that incrementally maintains OQL views in an ODMG compliant object database. The results indicate how the effectiveness of incremental maintenance is affected by issues such as database size, and the complexity and selectivity of views. | |||||
BibTeX:
@inproceedings{Ali2001,
author = {Ali, M. and Paton, Norman and Fernandes, Alvaro },
title = {An Experimental Performance Evaluation of Incremental Materialized View Maintenance in Object Databases},
booktitle = {Data Warehousing and Knowledge Discovery Third International Conference, DaWaK 2001 Munich, Germany, September 5Ð7, 2001 Proceedings},
publisher = {Springer Berlin / Heidelberg},
year = {2001},
volume = {2114},
pages = {240--253},
doi = {http://dx.doi.org/10.1007/3-540-44801-2_24}
}
|
|||||
| Allenby, N., O'Connor, N., Pragai, Z., Carter, N., Miethke, M., Engelmann, S., Hecker, M., Wipat, A., Ward, A. & Harwood, C. | Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter | 2004 | Microbiology | article | DOI |
| Abstract: During phosphate starvation, Bacillus subtilis regulates genes in the PhoP regulon to reduce the cell's requirement for this essential substrate and to facilitate the recovery of inorganic phosphate from organic sources such as teichoic and nucleic acids. Among the proteins that are highly induced under these conditions is PstS, the phosphate-binding lipoprotein component of a high-affinity ABC-type phosphate transporter. PstS is encoded by the first gene in the pst operon, the other four members of which encode the integral membrane and cytoplasmic components of the transporter. The transcription of the pst operon was analysed using a combination of methods, including transcriptional reporter gene technology, Northern blotting and DNA arrays. It is shown that the primary transcript of the pst operon is processed differentially to maintain higher concentrations of PstS relative to other components of the transporter. The comparative studies have revealed limitations in the use of reporter gene technology for analysing the transcription of operons in which the messenger RNA transcript is differentially processed. 10.1099/mic.0.27126-0 | |||||
BibTeX:
@article{Allenby2004,
author = {Allenby, Nicholas and O'Connor, Nicola and Pragai, Zoltan and Carter, Noel and Miethke, Marcus and Engelmann, Susanne and Hecker, Michael and Wipat, Anil and Ward, Alan and Harwood, Colin },
title = {Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter},
journal = {Microbiology},
year = {2004},
volume = {150},
number = {8},
pages = {2619--2628},
doi = {http://dx.doi.org/10.1099/mic.0.27126-0}
}
|
|||||
| Allenby, N., O'Connor, N., Pragai, Z., Ward, A., Wipat, A. & Harwood, C. | Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis. | 2005 | Journal of Bacteriology | article | DOI |
| Abstract: Bacillus subtilis responds to phosphate starvation stress by inducing the PhoP and SigB regulons. While the PhoP regulon provides a specific response to phosphate starvation stress, maximizing the acquisition of phosphate (P(i)) from the environment and reducing the cellular requirement for this essential nutrient, the SigB regulon provides nonspecific resistance to stress by protecting essential cellular components, such as DNA and membranes. We have characterized the phosphate starvation stress response of B. subtilis at a genome-wide level using DNA macroarrays. A combination of outlier and cluster analyses identified putative new members of the PhoP regulon, namely, yfkN (2',3' cyclic nucleotide 2'-phosphodiesterase), yurI (RNase), yjdB (unknown), and vpr (extracellular serine protease). YurI is thought to be responsible for the nonspecific degradation of RNA, while the activity of YfkN on various nucleotide phosphates suggests that it could act on substrates liberated by YurI, which produces 3' or 5' phosphoribonucleotides. The putative new PhoP regulon members are either known or predicted to be secreted and are likely to be important for the recovery of inorganic phosphate from a variety of organic sources of phosphate in the environment. | |||||
BibTeX:
@article{Allenby2005,
author = {Allenby, N. and O'Connor, N. and Pragai, Z. and Ward, A. and Wipat, Anil and Harwood, C. },
title = {Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis.},
journal = {Journal of Bacteriology},
year = {2005},
volume = {187},
number = {23},
pages = {8063--8080},
doi = {http://dx.doi.org/10.1128/JB.187.23.8063-8080.2005}
}
|
|||||
| Allenby, N., Watts, C., Homuth, G., Pragai, Z., Wipat, A., Ward, A. & Harwood, C. | Phosphate Starvation Induces the Sporulation Killing Factor of Bacillus subtilis | 2006 | Journal of Bacteriology | article | DOI |
| Abstract: Bacillus subtilis produces and exports a peptide sporulation killing factor (SkfA) that induces lysis of sibling cells. skfA is part of the skf operon (skfA-H), which is responsible for immunity to SkfA, as well as for production and export of SkfA. Here we report that transcription of skfA is markedly induced when cells of B. subtilis are subjected to phosphate starvation. The role of PhoP in regulation of the skf operon was confirmed by in vitro gel shift assays, which showed that this operon is a new member of the PhoP regulon. A putative stem-loop structure in the skfA-skfB intergenic region is proposed to act as a stabilizer of an skfA-specific transcript. 10.1128/JB.00084-06 | |||||
BibTeX:
@article{Allenby2006,
author = {Allenby, Nicholas and Watts, Carys and Homuth, Georg and Pragai, Zoltan and Wipat, Anil and Ward, Alan and Harwood, Colin },
title = {Phosphate Starvation Induces the Sporulation Killing Factor of Bacillus subtilis},
journal = {Journal of Bacteriology},
year = {2006},
volume = {188},
number = {14},
pages = {5299--5303},
doi = {http://dx.doi.org/10.1128/JB.00084-06}
}
|
|||||
| Alonso, E., Colton, S., Kodenko, D., Moreau, L., Schroeder, M. & Stathis, K. | Special Issue on Agents [BibTeX] |
2001 | Journal of the Society for Artificial Intelligence and Social Behaviour | article | URL |
BibTeX:
@article{Alonso2001,
author = {Alonso, Eduardo and Colton, Simon and Kodenko, Daniel and Moreau, Luc and Schroeder, Michael and Stathis, Kostas},
title = {Special Issue on Agents},
journal = {Journal of the Society for Artificial Intelligence and Social Behaviour},
year = {2001},
volume = {1},
number = {1},
url = {http://eprints.ecs.soton.ac.uk/7663/}
}
|
|||||
| Alpdemir, N., Gounaris, A., Mukherjee, A., Fitzgerald, D., Paton, N., Watson, P., Fernandes, A. & Smith, J. | Experience on Performance Evaluation with OGSA-DQP | 2005 | All Hands Meeting | inproceedings | URL |
| Abstract: OGSA-DQP is an open source service-based Distributed Query Processor; as such, it supports the evaluation of queries over collections of potentially remote data access and analysis services. As it operates over several layers of service-oriented infrastructure, one particular need (both among the developer team and the relevant community) has been to investigate the impact of the infrastructure layers, understand performance issues, identify bottlenecks and improve the response times of queries where possible. This paper conveys experiences gained in doing so, by describing the experiments carried out and presenting the results obtained. |
|||||
BibTeX:
@inproceedings{Alpdemir2005,
author = {Alpdemir, Nedim and Gounaris, Anastasios and Mukherjee, Arijit and Fitzgerald, Desmond and Paton, Norman and Watson, Paul and Fernandes, Alvaro and Smith, Jim},
title = {Experience on Performance Evaluation with OGSA-DQP},
booktitle = {All Hands Meeting},
year = {2005},
url = {http://www.allhands.org.uk/2005/proceedings/papers/453.pdf}
}
|
|||||
| Alpdemir, N., Mukherjee, A., Gounaris, A., Paton, N., Fernandes, A., Sakellariou, R., Watson, P. & Li, P. | Using OGSA-DQP to Support Scientific Applications for the Grid | 2005 | Scientific Applications of Grid Computing - First International Workshop, SAG 2004, Beijing, China, September 20-24, 2004, Revised Selected and Invited Papers | inproceedings | DOI |
| Abstract: The data management problems in grid computing are often challenging in many aspects such as data volumes, heterogeneity, structural complexity and semantic content. Thus, e-Scientists and scientific application developers stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources. This paper describes OGSA-DQP, a high level data integration tool for service-based grids, and illustrates how it can be used to support grid users, via an example scientific study in bioinformatics. The paper also discusses various options for employing OGSA-DQP to handle data integration tasks as service orchestrations involving both data and analysis services. | |||||
BibTeX:
@inproceedings{Alpdemir2005a,
author = {Alpdemir, Nedim and Mukherjee, Arijit and Gounaris, Anastasios and Paton, Norman and Fernandes, Alvaro and Sakellariou, Rizos and Watson, Paul and Li, Peter},
title = {Using OGSA-DQP to Support Scientific Applications for the Grid},
booktitle = {Scientific Applications of Grid Computing - First International Workshop, SAG 2004, Beijing, China, September 20-24, 2004, Revised Selected and Invited Papers},
publisher = {Springer Berlin / Heidelberg},
year = {2005},
volume = {3458},
pages = {13--24},
doi = {http://dx.doi.org/10.1007/11423287_2}
}
|
|||||
| Alpdemir, N., Mukherjee, A., Gounaris, A., Paton, N., Watson, P., Fernandes, A. & Fitzgerald, D. | OGSA-DQP: A Service for Distributed Querying on the Grid | 2004 | Advances in Database Technology - EDBT 2004 - 9th International Conference on Extending Database Technology, Heraklion, Crete, Greece, March 14-18, 2004 | inproceedings | DOI |
| Abstract: OGSA-DQP is a distributed query processor exposed to users as an Open Grid Services Architecture (OGSA)-compliant Grid service. This service supports the compilation and evaluation of queries that combine data obtained from multiple services on the Grid, including Grid Database Services (GDSs) and computational web services. Not only does OGSA-DQP support integrated access to multiple Grid services, it is itself implemented as a collection of interacting Grid services. OGSA-DQP illustrates how Grid service orchestrations can be used to perform complex, data-intensive parallel computations. The OGSA-DQP prototype is downloadable from www.ogsadai.org.uk/dqp/. This demonstration aims to illustrate the capabilities of OGSA-DQP prototype via a GUI Client over a collection of bioinformatics databases and analysis tools. | |||||
BibTeX:
@inproceedings{Alpdemir2004,
author = {Alpdemir, Nedim and Mukherjee, Arijit and Gounaris, Anastasios and Paton, Norman and Watson, Paul and Fernandes, Alvaro and Fitzgerald, Desmond},
title = {OGSA-DQP: A Service for Distributed Querying on the Grid},
booktitle = {Advances in Database Technology - EDBT 2004 - 9th International Conference on Extending Database Technology, Heraklion, Crete, Greece, March 14-18, 2004},
publisher = {Springer Berlin / Heidelberg},
year = {2004},
volume = {2992},
pages = {858--861},
doi = {http://dx.doi.org/10.1007/b95855}
}
|
|||||
| Alpdemir, N., Mukherjee, A., Gounaris, A., Paton, N., Watson, P., Fernandes, A. & Smith, J. | OGSA-DQP: A Service-Based Distributed Query Processor for the Grid |
2003 | All Hands Meeting | inproceedings | URL |
| Abstract: The Grid is an emerging infrastructure that supports the discovery, access and use of distributed computational resources. The emergence of a serviceoriented view of hardware and software resources on the grid raises the question as to how database management systems and technologies can best be deployed or adapted for use in such an environment. We argue that distributed query processing (DQP) can provide effective declarative support for service orchestration, and we describe an approach to service-based DQP (OGSA-DQP) on the Grid that supports queries over Grid Data Services (GDS)s provided by OGSA-DAI project, and over other services available on the Grid, thereby combining data access with analysis; uses the facilities of the OGSA to dynamically obtain the resources necessary for ef- cient evaluation of a distributed query; adapts techniques from parallel databases to provide implicit parallelism for complex data-intensive requests; and uses the emerging standard for GDSs to provide consistent access to database metadata and to interact with databases on the Grid. The service-based Distributed Query Processor is itself cast as a service referred to here as Grid Distributed Query Service (GDQS). In addition, OGSADQP employs another service for query evaluation referred to here as Grid Query Evaluation Service (GQES). As such, OGSA-DQP implements a service orchestration framework in two sense: both in terms of the way its internal architecture handles the construction and execution of distributed query plans and in terms of being able to query over data and analysis resources made available as services. |
|||||
BibTeX:
@inproceedings{Alpdemir2003,
author = {Alpdemir, Nedim and Mukherjee, Arijit and Gounaris, Anastasios and Paton, Norman and Watson, Paul and Fernandes, Alvaro and Smith, Jim},
title = {OGSA-DQP: A Service-Based Distributed Query Processor |
|||||
| Alpdemir, N., Mukherjee, A., Paton, N., Fernandes, A., Gounaris, A. & Smith, J. | An Experience Report on Designing and Building OGSA-DQP: A Service Based Distributed Query Processor for the Grid | 2003 | Global Grid Forum Workshop on Designing and Building Grid Services | inproceedings | URL |
| Abstract: OGSA-DQP is a distributed query processor exposed to users as an OGSA-compliant Grid service. This service supports the compilation and evaluation of queries that combine data obtained from multiple services on the Grid, including Grid Database Services (GDSs) provided by OGSA-DAI project. Not only does OGSA-DQP support integrated access to multiple Grid services, it is itself implemented as a collection of interacting Grid services. Thus, OGSA-DQP is an example of a Grid service with a signi cant amount of aggregated functionality that, in addition, illustrates how Grid service orchestrations can be used to perform reasonably complex, data-intensive parallel computations. OGSA-DQP prototype has been released and it is downloadable from www.ogsadai.org.uk/dqp/. This paper contributes an experience report on the design of OGSA-DQP, with a particular emphasis on the issues, challenges and trade-o s that the OGSA-DQP development team have had to contend with. |
|||||
BibTeX:
@inproceedings{Alpdemir2003a,
author = {Alpdemir, Nedim and Mukherjee, Arijit and Paton, Norman and Fernandes, Alvaro and Gounaris, Anastasios and Smith, Jim},
title = {An Experience Report on Designing and Building OGSA-DQP: A Service Based Distributed Query Processor for the Grid},
booktitle = {Global Grid Forum Workshop on Designing and Building Grid Services},
year = {2003},
url = {http://www.cs.man.ac.uk/~alpdemim/publications/ggf9-workshop.pdf}
}
|
|||||
| Alpdemir, N., Mukherjee, A., Paton, N., Fernandes, A., Watson, P., Glover, K., Greenhalgh, C., Oinn, T. & Tipney, H. | Contextualised Workflow Execution in MyGrid | 2005 | Advances in Grid Computing - EGC 2005 - European Grid Conference, Amsterdam, The Netherlands, February 14-16, 2005, Revised Selected Papers | inproceedings | DOI |
| Abstract: e-Scientists stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources that might be used as part of an in silico experiment. This paper illustrates the benefits that derive from the provision of integrated access to contextual information that links the phases of a problem-solving activity, so that the steps of a solution do not happen in isolation, but rather as the components of a coherent whole. Experiences with myGrid workflow execution environment (Taverna) are presented, where an information model provides the conceptual basis for contextualisation. This information model describes key characteristics that are shared by many e-Science activities, and is used both to organise the scientist‰Ûªs personal data resources, and to support data sharing and capture within the myGrid environment. | |||||
BibTeX:
@inproceedings{Alpdemir2005b,
author = {Alpdemir, Nedim and Mukherjee, Arijit and Paton, Norman and Fernandes, Alvaro and Watson, Paul and Glover, Kevin and Greenhalgh, Christopher and Oinn, Thomas and Tipney, Hannah},
title = {Contextualised Workflow Execution in MyGrid},
booktitle = {Advances in Grid Computing - EGC 2005 - European Grid Conference, Amsterdam, The Netherlands, February 14-16, 2005, Revised Selected Papers},
publisher = {Springer Berlin / Heidelberg},
year = {2005},
volume = {3470},
pages = {444--453},
doi = {http://dx.doi.org/10.1007/11508380_46}
}
|
|||||
| Alpdemir, N., Mukherjee, A., Paton, N., Watson, P., Fernandes, A., Gounaris, A. & Smith, J. | Service-Based Distributed Querying on the Grid | 2003 | Grid Computing Ñ GRID 2002 | inproceedings | DOI |
| Abstract: Service-based approaches (such as Web Services and the Open Grid Services Architecture) have gained considerable attention recently for supporting distributed application development in e-business and e-science. The emergence of a service-oriented view of hardware and software resources raises the question as to how database management systems and technologies can best be deployed or adapted for use in such an environment. This paper explores one aspect of service-based computing and data management, viz., how to integrate query processing technology with a service-based Grid. The paper describes in detail the design and implementation of a service-based distributed query processor for the Grid. The query processor is service-based in two orthogonal senses: firstly, it supports querying over data storage and analysis resources that are made available as services, and, secondly, its internal architecture factors out as services the functionalities related to the construction of distributed query plans on the one hand, and to their execution over the Grid on the other. The resulting system both provides a declarative approach to service orchestration in the Grid, and demonstrates how query processing can benefit from dynamic access to computational resources on the Grid. | |||||
BibTeX:
@inproceedings{Alpdemir2003b,
author = {Alpdemir, Nedim and Mukherjee, Arijit and Paton, Norman and Watson, Paul and Fernandes, Alvaro and Gounaris, Anastasios and Smith, Jim},
title = {Service-Based Distributed Querying on the Grid},
booktitle = {Grid Computing Ñ GRID 2002},
publisher = {Springer Berlin / Heidelberg},
year = {2003},
pages = {467--482},
doi = {http://dx.doi.org/10.1007/3-540-36133-2_26}
}
|
|||||
| Alper, P., Corcho, O. & Goble, C. | Understanding Semantic Aware Grid Middleware for e-Science | 2008 | Computing and Informatics | article | |
| Abstract: In this paper we analyze several semantic-aware Grid middleware services used in e-Science applications. We describe them according to a common analysis framework, so as to find their commonalities and their distinguishing features. As a result of this analysis we categorize these services into three groups: information services, data access services and decision support services. We make comparisons and provide additional conclusions that are useful to understand better how these services have been developed and deployed, and how similar services would be developed in the future, mainly in the context of e-Science applications. | |||||
BibTeX:
@article{Alper2008,
author = {Alper, Pinar and Corcho, Oscar and Goble, Carole},
title = {Understanding Semantic Aware Grid Middleware for e-Science},
journal = {Computing and Informatics},
year = {2008},
volume = {27},
pages = {93-118}
}
|
|||||
| Altintas, I., Barney, O. & Jaeger-Frank, E. | Provenance Collection Support in the Kepler Scientific Workflow System | 2006 | Provenance and Annotation of Data International Provenance and Annotation Workshop, IPAW 2006, Chicago, IL, USA, May 3-5, 2006, Revised Selected Papers | inproceedings | DOI |
| Abstract: In many data-driven applications, analysis needs to be performed on scientific information obtained from several sources and generated by computations on distributed resources. Systematic analysis of this scientific information unleashes a growing need for automated data-driven applications that also can keep track of the provenance of the data and processes with little user interaction and overhead. Such data analysis can be facilitated by the recent advancements in scientific workflow systems. A major profit when using scientific workflow systems is the ability to make provenance collection a part of the workflow. Specifically, provenance should include not only the standard data lineage information but also information about the context in which the workflow was used, execution that processed the data, and the evolution of the workflow design. In this paper we describe a complete framework for data and process provenance in the Kepler Scientific Workflow System. We outline the requirements and issues related to data and workflow provenance in a multi-disciplinary workflow system and introduce how generic provenance capture can be facilitated in KeplerÕs actor-oriented workflow environment. We also describe the usage of the stored provenance information for efficient rerun of scientific workflows. | |||||
BibTeX:
@inproceedings{Altintas2006,
author = {Altintas, Ilkay and Barney, Oscar and Jaeger-Frank, Efrat},
title = {Provenance Collection Support in the Kepler Scientific Workflow System},
booktitle = {Provenance and Annotation of Data International Provenance and Annotation Workshop, IPAW 2006, Chicago, IL, USA, May 3-5, 2006, Revised Selected Papers},
publisher = {Springer Berlin / Heidelberg},
year = {2006},
pages = {118--132},
doi = {http://dx.doi.org/10.1007/11890850_14}
}
|
|||||
| Anagnostopoulos, V., Chatzis, S., Lalos, C., Doulamis, A., Kosmopoulos, D., Varvarigou, T., Neuschmied, H., Thallinger, G., Middleton, S., Addis, M., Bustos, E. & Giorgini, F. | A Cross Media Platform for Personalized Leisure and Entertainment: The POLYMNIA Approach | 2006 | AXMEDIS 2006: 2nd International Conference on Automated Production of Cross Media Content for Multi-channel Distribution | inproceedings | DOIURL |
| Abstract: The POLYMNIA project aims to develop an intelligent cross-media platform for personalised leisure and entertainment in thematic parks or venues. The system allows the visitors to be the real protagonist in the venue. Towards this goal, POLYMNIA platform is equipped with innovative imaging technologies for real time detection, localisation and tracking of "human content", i.e., the human visitor within the recoding being made in real-time by the system. No constraints are imposed on the variation of the environment. New, content-based media representation and organisation schemes will be developed to provide scalable, efficient and user-oriented description of the ?human content?, enabling efficient retrieval, access, and delivery across heterogeneous media platforms. In addition, adaptive mechanisms are employed to update the system response to the current user's information needs and preferences. | |||||
BibTeX:
@inproceedings{Anagnostopoulos2006,
author = {Anagnostopoulos, Vasilios and Chatzis, Sotiris and Lalos, Constantinos and Doulamis, Anastasios and Kosmopoulos, Dimitrios and Varvarigou, Theodora and Neuschmied, Helmut and Thallinger, Georg and Middleton, Stuart and Addis, Matthew and Bustos, Eduardo and Giorgini, Fabrizio},
title = {A Cross Media Platform for Personalized Leisure and Entertainment: The POLYMNIA Approach},
booktitle = {AXMEDIS 2006: 2nd International Conference on Automated Production of Cross Media Content for Multi-channel Distribution},
year = {2006},
note = {ISBN: 0-7695-2625-X},
url = {http://eprints.ecs.soton.ac.uk/14269/},
doi = {http://dx.doi.org/10.1109/AXMEDIS.2006.3}
}
|
|||||
| Ananiadou, S., Kell, D. & Tsujii, J. | Text mining and its potential applications in systems biology. | 2006 | Trends in Biotechnology | article | DOI |
| Abstract: With biomedical literature increasing at a rate of several thousand papers per week, it is impossible to keep abreast of all developments; therefore, automated means to manage the information overload are required. Text mining techniques, which involve the processes of information retrieval, information extraction and data mining, provide a means of solving this. By adding meaning to text, these techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models. | |||||
BibTeX:
@article{Ananiadou2006,
author = {Ananiadou, Sophia and Kell, Douglas and Tsujii, Jun-Ichi},
title = {Text mining and its potential applications in systems biology.},
journal = {Trends in Biotechnology},
year = {2006},
volume = {24},
pages = {571-579},
doi = {http://dx.doi.org/10.1016/j.tibtech.2006.10.002}
}
|
|||||
| Antonioletti, M., Atkinson, M., Baxter, R., Borley, A., Chue Hong, N., Collins, B., Hardman, N., Hume, A., Knox, A., Jackson, M., Krause, A., Laws, S., Magowan, J., Paton, N., Pearson, D., Sugden, T., Watson, P. & Westhead, M. | The design and implementation of Grid database services in OGSA-DAI: Research Articles | 2005 | Concurrency and Computation: Practice and Experience | article | DOI |
| Abstract: Initially, Grid technologies were principally associated with supercomputer centres and large-scale scientific applications in physics and astronomy. They are now increasingly seen as being relevant to many areas of e-Science and e-Business. The emergence of the Open Grid Services Architecture (OGSA), to complement the ongoing activity on Web Services standards, promises to provide a service-based platform that can meet the needs of both business and scientific applications. Early Grid applications focused principally on the storage, replication and movement of file-based data. Now the need for the full integration of database technologies with Grid middleware is widely recognized. Not only do many Grid applications already use databases for managing metadata, but increasingly many are associated with large databases of domain-specific information (e.g. biological or astronomical data). This paper describes the design and implementation of OGSA-DAI, a service-based architecture for database access over the Grid. The approach involves the design of Grid Data Services that allow consumers to discover the properties of structured data stores and to access their contents. The initial focus has been on support for access to Relational and XML data, but the overall architecture has been designed to be extensible to accommodate different storage paradigms. The paper describes and motivates the design decisions that have been taken, and illustrates how the approach supports a range of application scenarios. The OGSA-DAI software is freely available from . Copyright © 2005 John Wiley and Sons, Ltd. | |||||
BibTeX:
@article{Antonioletti2005,
author = {Antonioletti, Mario and Atkinson, Malcolm and Baxter, Rob and Borley, Andrew and Chue Hong, Neil and Collins, Brian and Hardman, Neil and Hume, Alastair and Knox, Alan and Jackson, Mike and Krause, Amy and Laws, Simon and Magowan, James and Paton, Norman and Pearson, Dave and Sugden, Tom and Watson, Paul and Westhead, Martin },
title = {The design and implementation of Grid database services in OGSA-DAI: Research Articles},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley and Sons Ltd.},
year = {2005},
volume = {17},
number = {2-4},
pages = {357--376},
doi = {http://dx.doi.org/10.1002/cpe.v17:2/4}
}
|
|||||
| Antonioletti, M., Krause, A. & Paton, N. | An Outline of the Global Grid Forum Data Access and Integration Service Specifications | 2006 | Data Management in Grids - First VLDB Workshop, DMG 2005, Trondheim, Norway, September 2-3, 2005, Revised Selected Papers | inproceedings | DOI |
| Abstract: Grid computing concerns itself with building the infrastructure to facilitate the sharing of computational and data resources to enable collaboration within virtual organisations. The Global Grid Forum (GGF) provides a framework for users, developers and vendors to come together to develop standards to ensure interoperability between middleware from different service providers. Central to this effort is the Open Grid Services Architecture (OGSA), and its associated specifications. These define consistent interfaces, generally couched as web services, and the components required to construct grid infrastructures. Both the web service and grid communities stand to benefit from the provision of consistent and agreed web service interfaces for data resources and the systems that manage them. This paper describes, motivates and presents the context for the work that has been undertaken by the GGF Data Access and Integration Services Working Group (DAIS-WG). The group has defined a set of data access and integration interfaces that are consistent with the OGSA vision. A brief overview of the current family of DAIS specifications is given: WS-DAI specifies a collection of generic data resource properties and messages that are specialised by WS-DAIR and WS-DAIX for use with relational and XML data resources, respectively. The WS-DAI specifications can be applied in regular web services environments or as part of a grid fabric. | |||||
BibTeX:
@inproceedings{Antonioletti2006,
author = {Antonioletti, Mario and Krause, Amy and Paton, Norman },
title = {An Outline of the Global Grid Forum Data Access and Integration Service Specifications},
booktitle = {Data Management in Grids - First VLDB Workshop, DMG 2005, Trondheim, Norway, September 2-3, 2005, Revised Selected Papers},
publisher = {Springer Berlin / Heidelberg},
year = {2006},
volume = {3836},
pages = {71--84},
note = {ISBN 978-3-540-31212-3},
doi = {http://dx.doi.org/10.1007/11611950_7}
}
|
|||||
| Antonioletti, M., Krause, A., Paton, N., Eisenberg, A., Laws, S., Malaika, S., Melton, J. & Pearson, D. | The WS-DAI family of specifications for web service data access and integration | 2006 | ACM SIGMOD Record | article | DOI |
| Abstract: This month, we are pleased to provide to our readers a column that addresses an important aspect of grid computing: data access. Grid computing is important and relevant because it provides middleware that supports secure and managed sharing of networked computational resources. This is valuable because many activities involve collaborations that stand to benefit from more efficient and systematic access to computational and data resources across management domains. The GGF is important because the development of grids depends on shared abstractions and consistent interfaces; the GGF is the principal standards body for grid computing. For the most part, the GGF is developiong web service standards for resource management and use that can be used relatively independently or as part of a wider service-based architecture. The authors of the note belong to two overlapping groups: the chairs of the GGF Data Access and Integration Services Working Group, and the members of the Design Team that was responsible for writing the specificationsm and for evolving them in the light of input from other members of the working group and the wider community. | |||||
BibTeX:
@article{Antonioletti2006a,
author = {Antonioletti, Mario and Krause, Amy and Paton, Norman and Eisenberg, Andrew and Laws, Simon and Malaika, Susan and Melton, Jim and Pearson, Dave},
title = {The WS-DAI family of specifications for web service data access and integration},
journal = {ACM SIGMOD Record},
publisher = {ACM},
year = {2006},
volume = {35},
number = {1},
pages = {48--55},
doi = {http://dx.doi.org/10.1145/1121995.1122006}
}
|
|||||
| Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M. D. R., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N. J., Oinn, T., Pagni, M., Servant, F., Sigrist, C. J. A. & Zdobnov, E. M. | The InterPro database, an integrated documentation resource for protein families, domains and functional sites | 2001 | Nucleic Acids Research | article | DOI |
| Abstract: Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk. 10.1093/nar/29.1.37 | |||||
BibTeX:
@article{Apweiler2001,
author = {Apweiler, R. and Attwood, T. K. and Bairoch, A. and Bateman, A. and Birney, E. and Biswas, M. and Bucher, P. and Cerutti, L. and Corpet, F. and Croning, M. D. R. and Durbin, R. and Falquet, L. and Fleischmann, W. and Gouzy, J. and Hermjakob, H. and Hulo, N. and Jonassen, I. and Kahn, D. and Kanapin, A. and Karavidopoulou, Y. and Lopez, R. and Marx, B. and Mulder, N. J. and Oinn, Thomas and Pagni, M. and Servant, F. and Sigrist, C. J. A. and Zdobnov, E. M. },
title = {The InterPro database, an integrated documentation resource for protein families, domains and functional sites},
journal = {Nucleic Acids Research},
year = {2001},
volume = {29},
number = {1},
pages = {37--40},
doi = {http://dx.doi.org/10.1093/nar/29.1.37}
}
|
|||||
| Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M. D. R., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N. J., Oinn, T., Pagni, M., Servant, F., Sigrist, C. J. A. & Zdobnov, E. M. | InterPro--an integrated documentation resource for protein families, domains and functional sites | 2000 | Bioinformatics | article | DOIURL |
| Abstract: Motivation: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Results: Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL). Availability: The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Contact: Interhelp@ebi.ac.uk 10.1093/bioinformatics/16.12.1145 | |||||
BibTeX:
@article{Apweiler2000,
author = {Apweiler, R. and Attwood, T. K. and Bairoch, A. and Bateman, A. and Birney, E. and Biswas, M. and Bucher, P. and Cerutti, L. and Corpet, F. and Croning, M. D. R. and Durbin, R. and Falquet, L. and Fleischmann, W. and Gouzy, J. and Hermjakob, H. and Hulo, N. and Jonassen, I. and Kahn, D. and Kanapin, A. and Karavidopoulou, Y. and Lopez, R. and Marx, B. and Mulder, N. J. and Oinn, Thomas and Pagni, M. and Servant, F. and Sigrist, C. J. A. and Zdobnov, E. M. },
title = {InterPro--an integrated documentation resource for protein families, domains and functional sites},
journal = {Bioinformatics},
year = {2000},
volume = {16},
number = {12},
pages = {1145--1150},
url = {http://dx.doi.org/10.1093/bioinformatics/16.12.1145},
doi = {http://dx.doi.org/10.1093/bioinformatics/16.12.1145}
}
|
|||||
| Aragao, V., Fernandes, A. & Goble, C. | Towards an Architecture for Personalization and Adaptivity in the Semantic Web [BibTeX] |
2001 | Proc. 3rd. Intl. Conf. on Information Integration and Web-Based Applications and Service, iiWAS 2001 | inproceedings | |
BibTeX:
@inproceedings{Aragao2001,
author = {Aragao, V. and Fernandes, Alvaro and Goble, Carole},
title = {Towards an Architecture for Personalization and Adaptivity in the Semantic Web},
booktitle = {Proc. 3rd. Intl. Conf. on Information Integration and Web-Based Applications and Service, iiWAS 2001},
year = {2001},
pages = {139-149},
note = {ISBN 3-85403-150-5}
}
|
|||||
| Aranguren, M., Antezana, E., Kuiper, M. & Stevens, R. | Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. | 2008 | BMC bioinformatics | article | DOI |
| Abstract: BACKGROUND: Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training. RESULTS: Analogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (http://odps.sourceforge.net/). CONCLUSIONS: Ontology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term. | |||||
BibTeX:
@article{Aranguren2008,
author = {Aranguren, Mikel and Antezana, E. and Kuiper, M. and Stevens, Robert},
title = {Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.},
journal = {BMC bioinformatics},
year = {2008},
volume = {9 Suppl 5},
pages = {S1},
doi = {http://dx.doi.org/10.1186/1471-2105-9-S5-S1}
}
|
|||||
| Aranguren, M., Bechoffer, S., Lord, P., Sattler, U. & Stevens, R. | Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL | 2007 | BMC Bioinformatics | article | DOI |
| Abstract: The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community. | |||||
BibTeX:
@article{Aranguren2007,
author = {Aranguren, Mikel and Bechoffer, Sean and Lord, Phillip and Sattler, Ulrike and Stevens, Robert},
title = {Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL},
journal = {BMC Bioinformatics},
year = {2007},
volume = {8},
pages = {57+},
doi = {http://dx.doi.org/10.1186/1471-2105-8-57}
}
|
|||||
| Aranguren, M., Wroe, C., Goble, C. & Stevens, R. | In situ migration of handcrafted ontologies to reason-able forms | 2008 | Data and Knowledge Engineering | article | DOI |
| Abstract: A methodology for in situ migration of a handcrafted Directed Acyclic Graph (DAG), to a formal and expressive OWL version is presented. Well-known untangling methodologies recommend wholesale re-coding. Unable to do this, we have tackled portions of the DAG, lexically dissecting term names to property-based descriptions in OWL. The different levels of expressivity are presented in a model called the "feature escalator", where the user can choose the level needed for the application and the expressivity that delivers requirement. The results of applying the methodology to some areas of the gene ontology (GO) demonstrate the validity of the methodology. | |||||
BibTeX:
@article{Aranguren2008a,
author = {Aranguren, Mikel and Wroe, Christopher and Goble, Carole and Stevens, Robert},
title = {In situ migration of handcrafted ontologies to reason-able forms},
journal = {Data and Knowledge Engineering},
year = {2008},
volume = {In Press, Corrected Proof},
pages = {--},
doi = {http://dx.doi.org/10.1016/j.datak.2008.02.002}
}
|
|||||
| Arnold, P., Farrell, M. & Pettifer, S. | Transfer of Spatial Learning from Virtual To Real Environments [BibTeX] |
2002 | Proceedings of Human Factors and Ergonomics Europe 2002 | inproceedings | |
BibTeX:
@inproceedings{Arnold2002,
author = {Arnold, P. and Farrell, M. and Pettifer, Stephen},
title = {Transfer of Spatial Learning from Virtual To Real Environments},
booktitle = {Proceedings of Human Factors and Ergonomics Europe 2002},
year = {2002},
note = {Dortmund, Germany}
}
|
|||||
| Arnold, P., Farrell, M., Pettifer, S. & West, A. | Performance of a skilled motor task in virtual and real environments. | 2002 | Ergonomics | article | DOI |
| Abstract: Three experiments compared the performances of adult participants (three groups of 10) on a perceptuo-motor task in both real world (RW) and virtual environments (VEs). The task involved passing a hoop over a bent wire course, and three versions of the task were used: a 3-D wire course with no background, a flattened version of the 3-D course (2(1/2)-D course) with no background, and the 2(1/2)-D course with added background to provide spatial context. In all three experiments the participants had to prevent the hoop from touching the wire as they moved it. In the first experiment, the VE condition produced about 18 times more errors than the RW task. The VE 2(1/2)-D task was found to be as difficult as the 3-D, and the 2(1/2)-D with the added background produced more errors than the other two experiments. Taken together, the experiments demonstrate the difficulty of performing fine motor tasks in VEs, a phenomenon that has not been given due attention in many previous studies of motor control in VEs. | |||||
BibTeX:
@article{Arnold2002a,
author = {Arnold, P. and Farrell, M. and Pettifer, Stephen and West, Adrian },
title = {Performance of a skilled motor task in virtual and real environments.},
journal = {Ergonomics},
year = {2002},
volume = {45},
number = {5},
pages = {348--361},
doi = {http://dx.doi.org/10.1080/00140130110120510}
}
|
|||||
| Ashish, N., Goble, C. & Sheth, A. | Introduction [BibTeX] |
2005 | International Journal of Digital Libraries | article | DOI |
BibTeX:
@article{Goble2004,
author = {Ashish, Naveen and Goble, Carole and Sheth, Amit},
title = {Introduction},
journal = {International Journal of Digital Libraries},
year = {2005},
volume = {5},
number = {2},
pages = {71},
doi = {http://dx.doi.org/10.1007/s00799-004-0084-x}
}
|
|||||
| Atkinson, M., Chervenak, A., Kunszt, P., Narang, I., Paton, N., Pearson, D., Shoshani, A. & Watson, P. | Data Access, Integration and Management [BibTeX] |
2003 | The Grid 2: Blueprint for a New Computing Infrastructure | inbook | |
BibTeX:
@inbook{Atkinson2003,
author = {Atkinson, Malcolm and Chervenak, A. and Kunszt, P. and Narang, I. and Paton, Norman and Pearson, D. and Shoshani, A. and Watson, Paul},
title = {Data Access, Integration and Management},
booktitle = {The Grid 2: Blueprint for a New Computing Infrastructure},
publisher = {Morgan Kaufmann},
year = {2003},
pages = {391-429}
}
|
|||||
| Atkinson, M., De Roure, D., Dunlop, A., Fox, G., Henderson, P., Hey, T., Paton, N., Newhouse, S., Parastatidis, S., Trefethen, A., Watson, P. & Webber, J. | Web Service Grids: an evolutionary approach: Research Articles | 2005 | Concurrency and Computation: Practice and Experience | article | DOI |
| Abstract: The U.K. e-Science Programme is a £250 million, five-year initiative which has funded over 100 projects. These application-led projects are underpinned by an emerging set of core middleware services that allow the coordinated, collaborative use of distributed resources. This set of middleware services runs on top of the research network and beneath the applications we call the ÔGridÕ. Grid middleware is currently in transition from pre-Web Service versions to a new version based on Web Services. Unfortunately, only a very basic set of Web Services embodied in the Web Services Interoperability proposal, WS-I, are agreed by most IT companies. IBM and others have submitted proposals for Web Services for GridsÑthe Web Services ResourceFramework and Web Services Notification specificationsÑto the OASIS organization for standardization. This process could take up to 12 months from March 2004 and the specifications are subject to debate and potentially significant changes. Since several significant U.K. e-Science projects come to an end before the end of this process, the U.K. needs to develop a strategy that will protect the U.K.'s investment in Grid middleware by informing the Open Middleware Infrastructure Institute's (OMII) roadmap and U.K. middleware repository in Southampton. This paper sets out an evolutionary roadmap that will allow us to capture generic middleware components from projects in a form that will facilitate migration or interoperability with the emerging Grid Web Services standards and with ongoing OGSA developments. In this paper we therefore define a set of Web Services specifications, which we call ÔWS-I+Õ to reflect the fact that this is a larger set than currently accepted by WS-I, that we believe will enable us to achieve the twin goals of capturing these components and facilitating migration to future standards. We believe that the extra Web Services specifications we have included in WS-I+ are both helpful in building e-Science Grids and likely to be widely accepted. | |||||
BibTeX:
@article{Atkinson2005,
author = {Atkinson, Malcolm and De Roure, David and Dunlop, Alistair and Fox, Geoffrey and Henderson, Peter and Hey, Tony and Paton, Norman and Newhouse, Steven and Parastatidis, Savas and Trefethen, Anne and Watson, Paul and Webber, Jim},
title = {Web Service Grids: an evolutionary approach: Research Articles},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley and Sons Ltd.},
year = {2005},
volume = {17},
number = {2-4},
pages = {377--389},
doi = {http://dx.doi.org/10.1002/cpe.v17:2/4}
}
|
|||||
| Bachler, M., Shum, S., Chen-Burger, J., Dalton, J., De Roure, D., Eisenstadt, M., Komzak, J., Michaelides, D., Page, K., Potter, S., Shadbolt, N. & Tate, A. | Collaborative Tools in the Semantic Grid | 2004 | GGF11 Semantic Grid Applications Workshop | inproceedings | URL |
| Abstract: The CoAKTinG project aims to advance the state of the art in collaborative mediated spaces for distributed e-Science. The project is integrating several knowledge based and hypertext tools into existing collaborative environments, and through use of a shared ontology to exchange structure, promotes enhanced process tracking and navigation of resources before, after, and while a meeting occurs. This paper provides an overview of the CoAKTinG tools, the ontology that connects them, and current research activities. | |||||
BibTeX:
@inproceedings{Bachler2004,
author = {Bachler, Michelle and Shum, Simon and Chen-Burger, Jessica and Dalton, Jeff and De Roure, David and Eisenstadt, Marc and Komzak, Jiri and Michaelides, Danius and Page, Kevin and Potter, Stephen and Shadbolt, Nigel and Tate, Austin},
title = {Collaborative Tools in the Semantic Grid},
booktitle = {GGF11 Semantic Grid Applications Workshop},
year = {2004},
url = {http://eprints.ecs.soton.ac.uk/9439/}
}
|
|||||
| Bachler, M., Shum, S., Chen-Burger, J., Dalton, J., De Roure, D., Eisenstadt, M., Komzak, J., Michaelides, D., Page, K., Potter, S., Shadbolt, N. & Tate, A. | Collaboration in the Semantic Grid: a Basis for e-Learning | 2004 | Grid Learning Services workshop (GLS 2004) at the 7th International Conference on Intelligent Tutoring Systems (ITS 2004) | inproceedings | URL |
| Abstract: The CoAKTinG project aims to advance the state of the art in collaborative mediated spaces for the Semantic Grid. This paper presents an overview of the hypertext and knowledge based tools which have been deployed to augment existing collaborative environments, and the ontology which is used to exchange structure, promote enhanced process tracking, and aid navigation of resources before, after, and while a collaboration occurs. While the primary focus of the pro ject has been supporting e-science, this paper also explores the similarities and application of CoAKTinG technologies as part of a human-centred design approach to e-Learning. | |||||
BibTeX:
@inproceedings{Bachler2004a,
author = {Bachler, Michelle and Shum, Simon and Chen-Burger, Jessica and Dalton, Jeff and De Roure, David and Eisenstadt, Marc and Komzak, Jiri and Michaelides, Danius and Page, Kevin and Potter, Stephen and Shadbolt, Nigel and Tate, Austin},
title = {Collaboration in the Semantic Grid: a Basis for e-Learning},
booktitle = {Grid Learning Services workshop (GLS 2004) at the 7th International Conference on Intelligent Tutoring Systems (ITS 2004)},
publisher = {Eficiencia, Porto Alegre},
year = {2004},
pages = {1--12},
url = {http://eprints.ecs.soton.ac.uk/11164/}
}
|
|||||
| Bachler, M., Shum, S., De Roure, D., Michaelides, D. & Page, K. | Ontological Mediation of Meeting Structure: Argumentation, Annotation, and Navigation | 2003 | 1st International Workshop on Hypermedia and the Semantic Web (HTSW2003) | inproceedings | URL |
| Abstract: Compendium, a graphical hypertext system, can be used to gather a semantic group memory when used in a meeting scenario. By way of a specifically designed ontology, this structure is applied as annotation to other forms of meeting capture, such as audio and video recordings, and further employed to navigate between and through these resources. | |||||
BibTeX:
@inproceedings{Bachler2003,
author = {Bachler, Michelle and Shum, Simon and De Roure, David and Michaelides, Danius and Page, Kevin},
title = {Ontological Mediation of Meeting Structure: Argumentation, Annotation, and Navigation},
booktitle = {1st International Workshop on Hypermedia and the Semantic Web (HTSW2003)},
year = {2003},
url = {http://eprints.ecs.soton.ac.uk/8745/}
}
|
|||||
| Bada, M., McEntire, R., Wroe, C. & Stevens, R. | GOAT: The Gene Ontology Annotation Tool | 2003 | All Hands Meeting | inproceedings | URL |
| Abstract: The Gene Ontology (GO), a structured controlled vocabulary of over 15,000 terms, is becoming the de facto standard for describing gene products in terms of their molecular functions, biological processes in which they participate, and the cellular locations in which they are active. However, current annotation editors do not constrain the choice of GO terms users may enter, potentially resulting in inconsistent or even nonsensical descriptions of gene products. Relying upon a DAML+OIL version of GO, including mined GO-term-to-gene-product-type and GO-term-to-GO-term associations, and the FaCT reasoner, GOAT aims to guide the user in the annotation of gene products with GO terms by displaying those field values that are appropriate based on previously entered terms. This will result in annotations of a higher quality, which in turn will facilitate biomedical e-Science. | |||||
BibTeX:
@inproceedings{Bada2003,
author = {Bada, Michael and McEntire, Robin and Wroe, Christopher and Stevens, Robert},
title = {GOAT: The Gene Ontology Annotation Tool},
booktitle = {All Hands Meeting},
year = {2003},
url = {http://www.nesc.ac.uk/events/ahm2003/AHMCD/pdf/155.pdf}
}
|
|||||
| Bada, M., Stevens, R., Goble, C., Gil, Y., Ashburner, M., Blake, J. A., Cherry, J. M., Harris, M. & Lewis, S. | A short study on the success of the Gene Ontology | 2004 | Web Semantics: Science, Services and Agents on the World Wide Web2003 World Wide Web Conference | article | DOI |
| Abstract: While most ontologies have been used only by the groups who created them and for their initially defined purposes, the Gene Ontology (GO), an evolving structured controlled vocabulary of nearly 16,000 terms in the domain of biological functionality, has been widely used for annotation of biological-database entries and in biomedical research. As a set of learned lessons offered to other ontology developers, we list and briefly discuss the characteristics of GO that we believe are most responsible for its success: community involvement; clear goals; limited scope; simple, intuitive structure; continuous evolution; active curation; and early use. | |||||
BibTeX:
@article{Bada2004,
author = {Bada, Michael and Stevens, Robert and Goble, Carole and Gil, Yolanda and Ashburner, Michael and Blake, Judith A. and Cherry, J. Michael and Harris, Midori and Lewis, Suzanna},
title = {A short study on the success of the Gene Ontology},
booktitle = {2003 World Wide Web Conference},
journal = {Web Semantics: Science, Services and Agents on the World Wide Web},
year = {2004},
volume = {1},
number = {2},
pages = {235--240},
doi = {http://dx.doi.org/10.1016/j.websem.2003.12.003}
}
|
|||||
| Bada, M., Turi, D., Mcentire, R. & Stevens, R. | Using reasoning to guide annotation with gene ontology terms in GOAT | 2004 | ACM SIGMOD Record | article | DOI |
| Abstract: High-quality annotation of biological data is central to bioinformatics. Annotation using terms from ontologies provides reliable computational access to data. The Gene Ontology (GO), a structured controlled vocabulary of nearly 17,000 terms, is becoming the de facto standard for describing the functionality of gene products. Many prominent biomedical databases use GO as a source of terms for functional annotation of their gene-product entries to promote consistent querying and interoperability. However, current annotation editors do not constrain the choice of GO terms users may enter for a given gene product, potentially resulting in an inconsistent or even nonsensical description. Furthermore, the process of annotation is largely an unguided one in which the user must wade through large GO subtrees in search of terms. Relying upon a reasoner loaded with a DAML+OIL version of GO and an instance store of mined GO-term-to-GO-term associations, GOAT aims to aid the user in the annotation of gene products with GO terms by displaying those field values that are most likely to be appropriate based on previously entered terms. This can result in a reduction in biologically inconsistent combinations of GO terms and a less tedious annotation process on the part of the user. | |||||
BibTeX:
@article{Bada2004a,
author = {Bada, Michael and Turi, Daniele and Mcentire, Robin and Stevens, Robert},
title = {Using reasoning to guide annotation with gene ontology terms in GOAT},
journal = {ACM SIGMOD Record},
publisher = {ACM},
year = {2004},
volume = {33},
number = {2},
pages = {27--32},
doi = {http://dx.doi.org/10.1145/1024694.1024699}
}
|
|||||
| Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N. & Yeh, L. L. | The Universal Protein Resource (UniProt). | 2005 | Nucleic Acids Research | article | DOIURL |
| Abstract: The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, | |||||