Open PHACTS

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] Sajjad Hussain, Hong Sun, Gokce Banu Laleci Erturkmen, Mustafa Yuksel, Charles Mead, Alasdair J. G. Gray, and Kerstin Forsberg. A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings. In Context Interpretation and Meaning, Riva del Garda, Italy, oct 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 Interpretation and Meaning},
Title = {{A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings}},
url = {http://www.macs.hw.ac.uk/~fm206/cim14/cim20140_submission_2.pdf},
Month = oct,
Year = {2014}
}
[2] Unknown bibtex entry with key [Jupp2014]
[Bibtex]
[3] Unknown bibtex entry with key [iswc2014]
[Bibtex]
[4] Unknown bibtex entry with key [Goble2014]
[Bibtex]

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.

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[1] Alasdair J. G. Gray. Integrating Distributed Data Streams. PhD thesis, Heriot-Watt University, Edinburgh, UK, 2007.
[Bibtex]
@phdthesis{Gray2007Integrating-Dis,
Abstract = {  There is an increasing amount of information being made available as data streams, e.g. stock tickers, data from sensor networks, smart homes, monitoring data, etc.
In many cases, this data is generated by distributed sources under the control of many different organisations.
Users would like to seamlessly query such data without prior knowledge of where it is located or how it is published.
This is similar to the problem of integrating data residing in multiple heterogeneous stored data sources.
However, the techniques developed for stored data are not applicable due to the continuous and long-lived nature of queries over data streams.
This thesis proposes an architecture for a stream integration system.
A key feature of the architecture is a republisher component that collects together distributed streams and makes the merged stream available for querying.
A formal model for the system has been developed and is used to generate plans for executing continuous queries which exploit the redundancy introduced by the republishers.
Additionally, due to the long-lived nature of continuous queries, mechanisms for maintaining the plans whenever there is a change in the set of data sources have been developed.
A prototype of the system has been implemented and performance measures made.
The work of this thesis has been motivated by the problem of retrieving monitoring information about Grid resources.
However, the techniques developed are general and can be applied wherever there is a need to publish and query distributed data involving data streams.
},
Address = {Edinburgh, UK},
Author = {Alasdair J.G. Gray},
School = {Heriot-Watt University},
Title = {Integrating Distributed Data Streams},
Url = {http://AlasdairGray.github.io/publications/thesis-final_web-copy.pdf},
Year = {2007},
}
[2] Unknown bibtex entry with key [Cooke2005Stream-integrat]
[Bibtex]
[3] Unknown bibtex entry with key [Cooke2004The-relational-]
[Bibtex]
[4] Unknown bibtex entry with key [Cooke2003R-GMA:-An-infor]
[Bibtex]
[5] Unknown bibtex entry with key [Gray2007Answering-queri]
[Bibtex]

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.
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[1] Unknown bibtex entry with key [Hussain2014]
[Bibtex]