CIM Best Paper

Our paper [1] presenting a framework for terminology mappings won one of two best paper awards at the First Workshop on Context, Interpretation and Meaning (CIM2014). The other award went to the paper by Amy Guy from the University of Edinburgh.

Kerstin Forsberg from AstraZeneca presented the paper. You can find her slides on slideshare and embedded below.

[1] S. Hussain, H. Sun, G. B. L. Erturkmen, M. Yuksel, C. Mead, A. J. G. Gray, and K. Forsberg, “A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings,” in Context. Interpret. Mean., Riva del Garda, Italy, 2014.
[Bibtex]
@inproceedings{Hussain2014CIM,
abstract = {Use of medical terminologies and mappings across them are consid- ered to be crucial pre-requisites for achieving interoperable eHealth applica- tions. However, experiences from several research projects have demonstrated that the mappings are not enough. Also the context of the mappings is needed to enable interpretation of the meaning of the mappings. Built upon these experi- ences, we introduce a semantic framework for representing, evaluating and uti- lizing terminology mappings together with the context in terms of the justifica- tions for, and the provenance of, the mappings. The framework offers a plat- form for i) performing various mappings strategies, ii) representing terminology mappings together with their provenance information, and iii) enabling termi- nology reasoning for inferring both new and erroneous mappings. We present the results of the introduced framework using the SALUS project where we evaluated the quality of both existing and inferred terminology mappings among standard terminologies.},
address = {Riva del Garda, Italy},
author = {Hussain, Sajjad and Sun, Hong and Erturkmen, Gokce Banu Laleci and Yuksel, Mustafa and Mead, Charles and Gray, Alasdair J G and Forsberg, Kerstin},
booktitle = {Context. Interpret. Mean.},
file = {:Users/Alasdair/Documents/Mendeley Desktop/2014/Hussain et al. - A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings.pdf:pdf},
title = {{A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings}},
year = {2014}
}

ISWC2014 In-use Paper

Slides for my ISWC2014 In-use track paper [1] are available below.

Paper abstract:

When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over the data with no way of varying the notion of equivalence to be applied.

In this paper, we present an approach to enable applications to choose the equivalence criteria to apply between datasets. Thus, supporting multiple dynamic views over the Linked Data. For chemical data, we show that multiple sets of links can be automatically generated according to different equivalence criteria and published with semantic descriptions capturing their context and interpretation. This approach has been applied within a large scale public-private data integration platform for drug discovery. To cater for different use cases, the platform allows the application of different lenses which vary the equivalence rules to be applied based on the context and interpretation of the links.

[1] [doi] C. R. Batchelor, C. Y. A. Brenninkmeijer, C. Chichester, M. Davies, D. Digles, I. Dunlop, C. T. A. Evelo, A. Gaulton, C. A. Goble, A. J. G. Gray, P. T. Groth, L. Harland, K. Karapetyan, A. Loizou, J. P. Overington, S. Pettifer, J. Steele, R. Stevens, V. Tkachenko, A. Waagmeester, A. J. Williams, and E. L. Willighagen, “Scientific Lenses to Support Multiple Views over Linked Chemistry Data,” in The Semantic Web – ISWC 2014 – 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part I, 2014, pp. 98-113.
[Bibtex]
@inproceedings{iswc2014,
author = {Colin R. Batchelor and
Christian Y. A. Brenninkmeijer and
Christine Chichester and
Mark Davies and
Daniela Digles and
Ian Dunlop and
Chris T. A. Evelo and
Anna Gaulton and
Carole A. Goble and
Alasdair J. G. Gray and
Paul T. Groth and
Lee Harland and
Karen Karapetyan and
Antonis Loizou and
John P. Overington and
Steve Pettifer and
Jon Steele and
Robert Stevens and
Valery Tkachenko and
Andra Waagmeester and
Antony J. Williams and
Egon L. Willighagen},
title = {Scientific Lenses to Support Multiple Views over Linked Chemistry
Data},
booktitle = {The Semantic Web - {ISWC} 2014 - 13th International Semantic Web Conference,
Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part {I}},
year = {2014},
pages = {98--113},
url = {http://dx.doi.org/10.1007/978-3-319-11964-9_7},
doi = {10.1007/978-3-319-11964-9_7},
}

ISWC 2014

ISWC 2014 is taking place on the shores of Lake Garda, Italy. However, I won’t have much time to relax on the lake. Look out for my tweets (@gray_alasdair).

My conference activities start on Sunday 19 October with the first workshop on Context, Interpretation and Meaning (CIM2014), which together with Harry Halpin (W3C) and Fiona McNeill (Heriot-Watt University) I am a chair. We have managed to put together an interesting selection of 5 papers – two focusing on the context of links, two on the interpretation of alignments and one on the meaning of mappings. I am a co-author on this final paper, but Kerstin Forsberg will be presenting the work [1]. We also have an exciting panel session in store with Aldo Gangemi (CNR), Paul Groth (VU University of Amsterdam) and Harry Halpin. 

Also taking place on Sunday is the Linked Science Workshop (LISC). Together with Simon Jupp and James Malone of the EBI we have a paper on modelling the provenance for linksets of convenience [2]. A linkset of convenience is one that does not model the underlying science correctly, but provides a convenient shortcut for linking data. An example from the world of biology is a linkset that directly links genes with their protein product. 

On Monday I will be working with the W3C RDF Stream Processing (RSP) Community Group. We have been having regular phone meetings for the last year and have made great progress towards defining a common community model for RDF streams and a query language for processing them. The group will largely be attending the Stream Ordering Workshop and the Semantic Sensor Networks Workshop.

Tuesday is the first day of ISWC, and it is going to be a busy one for me. In the morning I will be presenting the Open PHACTS paper on our work enabling scientific lenses for chemistry data [3]. In the evening I will be at the poster and demonstration session showing off the Open PHACTS VoID Editor [4].

Finally, I am organising the Lightning Talks session on the last day of the conference. This is a session where you can present late breaking results or responses to work presented in the conference. Talks will be 5 minutes each and abstracts can be submitted until 8.30 am on Thursday.

After ISWC I think I’m going to need a break.

[1] S. Hussain, H. Sun, G. B. L. Erturkmen, M. Yuksel, C. Mead, A. J. G. Gray, and K. Forsberg, “A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings,” in Context. Interpret. Mean., Riva del Garda, Italy, 2014.
[Bibtex]
@inproceedings{Hussain2014CIM,
abstract = {Use of medical terminologies and mappings across them are consid- ered to be crucial pre-requisites for achieving interoperable eHealth applica- tions. However, experiences from several research projects have demonstrated that the mappings are not enough. Also the context of the mappings is needed to enable interpretation of the meaning of the mappings. Built upon these experi- ences, we introduce a semantic framework for representing, evaluating and uti- lizing terminology mappings together with the context in terms of the justifica- tions for, and the provenance of, the mappings. The framework offers a plat- form for i) performing various mappings strategies, ii) representing terminology mappings together with their provenance information, and iii) enabling termi- nology reasoning for inferring both new and erroneous mappings. We present the results of the introduced framework using the SALUS project where we evaluated the quality of both existing and inferred terminology mappings among standard terminologies.},
address = {Riva del Garda, Italy},
author = {Hussain, Sajjad and Sun, Hong and Erturkmen, Gokce Banu Laleci and Yuksel, Mustafa and Mead, Charles and Gray, Alasdair J G and Forsberg, Kerstin},
booktitle = {Context. Interpret. Mean.},
file = {:Users/Alasdair/Documents/Mendeley Desktop/2014/Hussain et al. - A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings.pdf:pdf},
title = {{A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings}},
year = {2014}
}
[2] S. Jupp, J. Malone, and A. J. G. Gray, “Capturing Provenance for a Linkset of Convenience,” in Linked Sci., Riva del Garda, Italy, 2014, pp. 2-6.
[Bibtex]
@inproceedings{Jupp2014,
address = {Riva del Garda, Italy},
author = {Jupp, Simon and Malone, James and Gray, Alasdair J G},
booktitle = {Linked Sci.},
file = {:Users/Alasdair/Documents/Mendeley Desktop/2014/Jupp, Malone, Gray - Capturing Provenance for a Linkset of Convenience.pdf:pdf},
keywords = {data linking,provenance,void},
pages = {2--6},
title = {{Capturing Provenance for a Linkset of Convenience}},
year = {2014}
}
[3] [doi] C. R. Batchelor, C. Y. A. Brenninkmeijer, C. Chichester, M. Davies, D. Digles, I. Dunlop, C. T. A. Evelo, A. Gaulton, C. A. Goble, A. J. G. Gray, P. T. Groth, L. Harland, K. Karapetyan, A. Loizou, J. P. Overington, S. Pettifer, J. Steele, R. Stevens, V. Tkachenko, A. Waagmeester, A. J. Williams, and E. L. Willighagen, “Scientific Lenses to Support Multiple Views over Linked Chemistry Data,” in The Semantic Web – ISWC 2014 – 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part I, 2014, pp. 98-113.
[Bibtex]
@inproceedings{iswc2014,
author = {Colin R. Batchelor and
Christian Y. A. Brenninkmeijer and
Christine Chichester and
Mark Davies and
Daniela Digles and
Ian Dunlop and
Chris T. A. Evelo and
Anna Gaulton and
Carole A. Goble and
Alasdair J. G. Gray and
Paul T. Groth and
Lee Harland and
Karen Karapetyan and
Antonis Loizou and
John P. Overington and
Steve Pettifer and
Jon Steele and
Robert Stevens and
Valery Tkachenko and
Andra Waagmeester and
Antony J. Williams and
Egon L. Willighagen},
title = {Scientific Lenses to Support Multiple Views over Linked Chemistry
Data},
booktitle = {The Semantic Web - {ISWC} 2014 - 13th International Semantic Web Conference,
Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part {I}},
year = {2014},
pages = {98--113},
url = {http://dx.doi.org/10.1007/978-3-319-11964-9_7},
doi = {10.1007/978-3-319-11964-9_7},
}
[4] C. Goble, A. J. G. Gray, and E. Tatakis, “Help me describe my data: A demonstration of the Open PHACTS VoID Editor,” in ISWC 2014 – Poster Demos, Riva del Garda, Italy, 2014, pp. 1-4.
[Bibtex]
@inproceedings{Goble2014,
address = {Riva del Garda, Italy},
author = {Goble, Carole and Gray, Alasdair J G and Tatakis, Eleftherios},
booktitle = {ISWC 2014 – Poster Demos},
number = {July},
pages = {1--4},
title = {{Help me describe my data: A demonstration of the Open PHACTS VoID Editor}},
year = {2014}
}

Bolzano Research Visit

Before going to ISWC2014, I am taking a quick trip to visit Werner Nutt at the Free University of Bozen-Bolzano. Werner was my PhD supervisor where we developed techniques for integrating distributed data streams [1]. The work was inspired by the problem of monitoring the resources on a computational Grid [2, 3, 4, 5]. We will be exploring our common interests in stream processing, data integration and incompleteness.

As part of my visit, I’m giving a seminar on my work in the Open PHACTS project on using Scientific Lenses to support multiple views over linked data. You can see my slides below.

(more…)

[1] A. J. G. Gray, “Integrating Distributed Data Streams,” PhD Thesis, Edinburgh, UK, 2007.
[Bibtex]
@phdthesis{Gray2007Integrating-Dis,
Address = {Edinburgh, UK},
Author = {A.J.G. Gray},
School = {Heriot-Watt University},
Title = {Integrating Distributed Data Streams},
Url = {http://www.cs.man.ac.uk/~graya/Publications/thesis-final_web-copy.pdf},
Year = {2007},
Bdsk-Url-1 = {http://www.cs.man.ac.uk/~graya/Publications/thesis-final_web-copy.pdf}}
[2] A. W. Cooke, A. J. G. Gray, and W. Nutt, “Stream integration techniques for Grid monitoring,” Journal on Data Semantics, vol. 2800, pp. 136-175, 2005.
[Bibtex]
@article{Cooke2005Stream-integrat,
Author = {A. W. Cooke and A. J. G. Gray and W. Nutt},
Journal = {Journal on Data Semantics},
Note = {(Alphabetical authorship, equal responsibility)},
Pages = {136-175},
Publisher = {Springer},
Series = {LNCS},
Title = {Stream integration techniques for Grid monitoring},
Volume = {2800},
Year = {2005}}
[3] A. W. Cooke, A. J. G. Gray, W. Nutt, J. Magowan, M. Oevers, P. Taylor, R. Cordenonsi, R. Byrom, L. Cornwall, A. Djaoui, L. Field, S. Fisher, S. Hicks, J. Leake, R. Middleton, A. J. Wilson, X. Zhu, N. Podhorszki, B. A. Coghlan, S. Kenny, D. O’Callaghan, and J. Ryan, “The relational grid monitoring architecture: Mediating information about the grid,” Journal of Grid Computing, vol. 2, iss. 4, pp. 323-339, 2004.
[Bibtex]
@article{Cooke2004The-relational-,
Author = {A.W. Cooke and A.J.G. Gray and W. Nutt and J. Magowan and M. Oevers and P. Taylor and R. Cordenonsi and R. Byrom and L. Cornwall and A. Djaoui and L. Field and S. Fisher and S. Hicks and J. Leake and R. Middleton and A.J. Wilson and X. Zhu and N. Podhorszki and B.A. Coghlan and S. Kenny and D. O'Callaghan and J. Ryan},
Journal = {Journal of Grid Computing},
Note = {(Alphabetical authorship by site, Heriot-Watt authored paper)},
Number = {4},
Pages = {323-339},
Publisher = {Springer},
Title = {The relational grid monitoring architecture: {M}ediating information about the grid},
Volume = {2},
Year = {2004}}
[4] A. W. Cooke, A. J. G. Gray, L. Ma, W. Nutt, J. Magowan, M. Oevers, P. Taylor, R. Byrom, L. Field, S. Hicks, J. Leake, M. Soni, A. J. Wilson, R. Cordenonsi, L. Cornwall, A. Djaoui, S. Fisher, N. Podhorszki, B. A. Coghlan, S. Kenny, and D. O’Callaghan, “R-GMA: An information integration system for Grid monitoring,” in CoopIS/DOA/ODBASE 2003, Catania, Italy, 2003, pp. 462-481.
[Bibtex]
@inproceedings{Cooke2003R-GMA:-An-infor,
Address = {Catania, Italy},
Author = {A.W. Cooke and A.J.G. Gray and L. Ma and W. Nutt and J. Magowan and M. Oevers and P. Taylor and R. Byrom and L. Field and S. Hicks and J. Leake and M. Soni and A.J. Wilson and R. Cordenonsi and L. Cornwall and A. Djaoui and S. Fisher and N. Podhorszki and B.A. Coghlan and S. Kenny and D. O'Callaghan},
Booktitle = {CoopIS/DOA/ODBASE 2003},
Pages = {462-481},
Publisher = {Springer},
Series = {LNCS},
Title = {{R-GMA}: {A}n information integration system for Grid monitoring},
Volume = {2888},
Year = {2003}}
[5] A. J. G. Gray, W. Nutt, and M. H. Williams, “Answering queries over incomplete data stream histories,” International Journal of Web Information Systems, vol. 3, iss. 1/2, pp. 41-60, 2007.
[Bibtex]
@article{Gray2007Answering-queri,
Author = {A.J.G. Gray and W. Nutt and M.H. Williams},
Journal = {International Journal of Web Information Systems},
Number = {1/2},
Pages = {41-60},
Publisher = {Emerald},
Title = {Answering queries over incomplete data stream histories},
Volume = {3},
Year = {2007}}

EUON Talk on Dataset Descriptions

Tomorrow I will be talking at the 1st European Ontology Network meeting (EUON) about the work I have been doing in the W3C Health Care and Life Sciences (HCLS) Interest Group on creating a community profile for describing datasets.

The work on the HCLS Dataset Description Community Profile has been ongoing for two years now and is just about to reach fruition. Please do read the latest Editors’ Draft and provide feedback.

Medical Informatics Europe Conference

Kerstin Forsberg presenting at MIE 2014

Kerstin presenting at MIE 2014

The MIE conference is in full swing this week in Istanbul I thought it time to share our paper on mapping medical terminologies [1].

The paper was collaborative effort combining input from EU IMI funded projects EHR4CR, SALUS and Open PHACTS as well as the W3C Health Care and Life Sciences Interest Group (HCLS).

Below are Kerstin’s slides.
(more…)

[1] [doi] S. Hussain, H. Sun, A. Sinaci, G. B. L. Erturkmen, C. Mead, A. J. G. Gray, D. Mcguinness, E. Prud’hommeaux, C. Daniel, and K. Forsberg, “A framework for evaluating and utilizing medical terminology mappings,” in 25th Eur. Med. Informatics Conf. – MIE2014, Istanbul, Turkey, 2014, pp. 594-598.
[Bibtex]
@inproceedings{Hussain2014,
abstract = {Use of medical terminologies and mappings across them are considered to be crucial pre-requisites for achieving interoperable eHealth applications. Built upon the outcomes of several research projects, we introduce a framework for evaluating and utilizing terminology mappings that offers a platform for i) performing various mappings strategies, ii) representing terminology mappings together with their provenance information, and iii) enabling terminology reasoning for inferring both new and erroneous mappings. We present the results of the introduced framework from SALUS project where we evaluated the quality of both existing and inferred terminology mappings among standard terminologies.},
address = {Istanbul, Turkey},
author = {Hussain, Sajjad and Sun, Hong and Sinaci, Anil and Erturkmen, Gokce Banu Laleci and Mead, Charles and Gray, Alasdair J G and Mcguinness, Deborah and Prud'hommeaux, Eric and Daniel, Christel and Forsberg, Kerstin},
booktitle = {25th Eur. Med. Informatics Conf. - MIE2014},
doi = {10.3233/978-1-61499-432-9-594},
month = aug,
pages = {594--598},
title = {{A framework for evaluating and utilizing medical terminology mappings}},
url = {http://ebooks.iospress.nl/volumearticle/37557},
year = {2014}
}

SensorBench SICSA Presentation

SensorBench [1] is a benchmark suite for wireless sensor networks. The design of wireless sensor network systems sits within a multi-dimensional design space, where it can be difficult to understand the implications of specific decisions and to identify optimal solutions. SensorBench enables the systematic analysis and comparison of different techniques and platforms, enabling both development and user communities to make well informed choices. The benchmark identifies key variables and performance metrics, and specifies experiments that explore how different types of task perform under different metrics for the controlled variables. The benchmark is demonstrated by its application on representative platforms.

[1] [pdf] [doi] I. Galpin, A. B. Stokes, G. Valkanas, A. J. G. Gray, N. W. Paton, A. A. A. Fernandes, K. Sattler, and D. Gunopulos, “SensorBench: benchmarking approaches to processing wireless sensor network data,” in Proceedings of the 26th International Conference on Scientific and Statistical Database Management (SSDBM2014), 2014, p. 21.
[Bibtex]
@inproceedings{SensorBenchSSDBM2014,
abstract = {Wireless sensor networks enable cost-effective data collection for tasks such as precision agriculture and environment monitoring. However, the resource-constrained nature of sensor nodes, which often have both limited computational capabilities and battery lifetimes, means that applications that use them must make judicious use of these resources. Research that seeks to support data intensive sensor applications has explored a range of approaches and developed many different techniques, including bespoke algorithms for specific analyses and generic sensor network query processors. However, all such proposals sit within a multi-dimensional design space, where it can be difficult to understand the implications of specific decisions and to identify optimal solutions. This paper presents a benchmark that seeks to support the systematic analysis and comparison of different techniques and platforms, enabling both development and user communities to make well informed choices. The contributions of the paper include: (i) the identification of key variables and performance metrics; (ii) the specification of experiments that explore how different types of task perform under different metrics for the controlled variables; and (iii) an application of the benchmark to investigate the behavior of several representative platforms and techniques.},
author = {Ixent Galpin and
Alan B. Stokes and
George Valkanas and
Alasdair J. G. Gray and
Norman W. Paton and
Alvaro A. A. Fernandes and
Kai-Uwe Sattler and
Dimitrios Gunopulos},
title = {SensorBench: benchmarking approaches to processing wireless
sensor network data},
booktitle = {Proceedings of the 26th International Conference on Scientific and Statistical Database Management ({SSDBM2014})},
doi = {10.1145/2618243.2618252},
year = {2014},
pages = {21},
web = {http://doi.acm.org/10.1145/2618243.2618252},
}