SICSA Databases for the Environmental and Social Sciences

Today I attended the SICSA Databases for the Environmental and Social Sciences event hosted by Andy Cobley from the University of Dundee. I gave the below talk on the challenges of linking data. Many areas of scientific discovery rely on combining data from multiples data sources. However there are many challenges in linking data. This […]

Today I attended the SICSA Databases for the Environmental and Social Sciences event hosted by Andy Cobley from the University of Dundee. I gave the below talk on the challenges of linking data.

Many areas of scientific discovery rely on combining data from multiples data sources. However there are many challenges in linking data. This presentation highlights these challenges in the context of using Linked Data for environmental and social science databases.

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. A […]

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 […]

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}},
month = oct,
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},
}

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 […]

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.

[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 […]

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.