Category: Presentation

Smart Descriptions & Smarter Vocabularies (SDSVoc) Report

In December 2016 I presented at the Smart Descriptions and Smarter Vocabularies workshop on the Health Care and Life Sciences Community Profile for describing datasets, and our validation tool (Validata). Presentations included below. The purpose of the workshop was to understand current practice in describing datasets and where the DCAT vocabulary needs improvement. Phil Archer has written a very […]

In December 2016 I presented at the Smart Descriptions and Smarter Vocabularies workshop on the Health Care and Life Sciences Community Profile for describing datasets, and our validation tool (Validata). Presentations included below.

The purpose of the workshop was to understand current practice in describing datasets and where the DCAT vocabulary needs improvement. Phil Archer has written a very comprehensive report covering the workshop. A charter is being drawn up for a W3C working group to develop the next iteration of the DCAT vocabulary.

HCLS Tutorial at SWAT4LS 2016

On 5 December 2016 I presented a tutorial [1] on the Heath Care and Life Sciences Community Profile (HCLS Datasets) at the 9th International Semantic Web Applications and Tools for the Life Sciences Conference (SWAT4LS 2016). Below you can find the slides I presented. The 61 metadata properties from 18 vocabularies reused in the HCLS Community […]

On 5 December 2016 I presented a tutorial [1] on the Heath Care and Life Sciences Community Profile (HCLS Datasets) at the 9th International Semantic Web Applications and Tools for the Life Sciences Conference (SWAT4LS 2016). Below you can find the slides I presented.

The 61 metadata properties from 18 vocabularies reused in the HCLS Community Profile are available in this spreadsheet (.ods).

[1] M. Dumontier, A. J. G. Gray, and S. M. Marshall, “Describing Datasets with the Health Care and Life Sciences Community Profile,” in Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016), Amsterdam, The Netherlands, 2016.
[Bibtex]
@InProceedings{Gray2016SWAT4LSTutorial,
abstract = {Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting HCLS community profile covers elements of description, identification, attribution, versioning, provenance, and content summarization. The HCLS community profile reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. The goal of this tutorial is to explain elements of the HCLS community profile and to enable users to craft and validate descriptions for datasets of interest.},
author = {Michel Dumontier and Alasdair J. G. Gray and M. Scott Marshall},
title = {Describing Datasets with the Health Care and Life Sciences Community Profile},
OPTcrossref = {},
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booktitle = {Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016)},
year = {2016},
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month = dec,
address = {Amsterdam, The Netherlands},
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note = {(Tutorial)},
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HCLS Tutorial at SWAT4LS 2016

On 5 December 2016 I presented a tutorial [1] on the Heath Care and Life Sciences Community Profile (HCLS Datasets) at the 9th International Semantic Web Applications and Tools for the Life Sciences Conference (SWAT4LS 2016). Below you can find the slides I presented. The 61 metadata properties from 18 vocabularies reused in the HCLS Community […]

On 5 December 2016 I presented a tutorial [1] on the Heath Care and Life Sciences Community Profile (HCLS Datasets) at the 9th International Semantic Web Applications and Tools for the Life Sciences Conference (SWAT4LS 2016). Below you can find the slides I presented.

The 61 metadata properties from 18 vocabularies reused in the HCLS Community Profile are available in this spreadsheet (.ods).

[1] M. Dumontier, A. J. G. Gray, and S. M. Marshall, “Describing Datasets with the Health Care and Life Sciences Community Profile,” in Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016), Amsterdam, The Netherlands, 2016.
[Bibtex]
@InProceedings{Gray2016SWAT4LSTutorial,
abstract = {Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting HCLS community profile covers elements of description, identification, attribution, versioning, provenance, and content summarization. The HCLS community profile reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. The goal of this tutorial is to explain elements of the HCLS community profile and to enable users to craft and validate descriptions for datasets of interest.},
author = {Michel Dumontier and Alasdair J. G. Gray and M. Scott Marshall},
title = {Describing Datasets with the Health Care and Life Sciences Community Profile},
OPTcrossref = {},
OPTkey = {},
booktitle = {Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016)},
year = {2016},
OPTeditor = {},
OPTvolume = {},
OPTnumber = {},
OPTseries = {},
OPTpages = {},
month = dec,
address = {Amsterdam, The Netherlands},
OPTorganization = {},
OPTpublisher = {},
note = {(Tutorial)},
url = {http://www.swat4ls.org/workshops/amsterdam2016/tutorials/t2/},
OPTannote = {}
}

Seminar: Managing Domain-Aware Lexical Knowledge

Date: 11:15, 10 October 2016

Venue: F.17. Colin Maclaurin Building, Heriot-Watt University

Title: Managing Domain-Aware Lexical Knowledge

Speaker: David Leoni, Heriot-Watt University

Abstract: The talk will describe the implementation of Diversicon, a new open source system for extending and integrating terminologies as found in Wordnet databases. Issues on knowledge formats, standards, and open source development will be discussed. As a practical use case, we connected Diversicon to the the S-Match semantic matcher tool in order to support domain-aware semantic matching (http://semanticmatching.org).

Seminar: Language-integrated Provenance

Wher ProvenanceDate: 11:15, 3 October 2016

Venue: F.17. Colin Maclaurin Building, Heriot-Watt University

Title: Language-integrated Provenance

Speaker: Stefan Fehrenbach,  Informatics, University of Edinburgh

Abstract: Provenance, or information about the origin or derivation of data, is important for assessing the trustworthiness of data and identifying and correcting mistakes. Most prior implementations of data provenance have involved heavyweight modifications to database systems and little attention has been paid to how the provenance data can be used outside such a system. We present extensions to the Links programming language that build on its support for language-integrated query to support provenance queries by rewriting and normalizing monadic comprehensions and extending the type system to distinguish provenance metadata from normal data. We show that the two most common forms of provenance can be implemented efficiently and used safely as a programming language feature with no changes to the database system.

Bio: Stefan is a second year PhD student at the University of Edinburgh where he works with James Cheney on language support for provenance.

Seminar: Data Integration Support for Offshore Decommissioning Waste Management

Oli RigDate: 11:15, 26 September 2016

Venue: F.17. Colin Maclaurin Building, Heriot-Watt University

Title: Data Integration Support for Offshore Decommissioning Waste Management

Speaker: Abiodun Akinyemi, School of Energy, Geoscience, Infrastructure and Society (EGIS), Heriot-Watt University

Abstract: Offshore decommissioning activities represent a significant business opportunity for UK contracting and consulting companies, albeit they constitute liability to the owners of the assets – because of the cost – and UK government – because of tax relief. The silver lining is that waste reuse can bring some reprieve as savings from the sales of decommissioned facility items can reduce the overall removal cost to an asset owner. However, characterizing an asset inventory to determine which decommissioned facility items can be reused is prone to errors because of the difficulty involved in integrating asset data from different sources in a meaningful way. This research investigates a data integration framework, which enables rapid assessment of items to be decommissioned, to inform circular economy principles. It evaluates existing practices in the domain and devises a mechanisms for higher productivity using the semantic web and ISO 15926.

Bio: Abiodun Akinyemi is a PhD student at the School of Energy, Geoscience, Infrastructure and Society at Heriot-Watt University. He has an MPhil in Engineering from the University of Cambridge and has worked on Asset Information Management in the oil and gas industry for over 8 years.

Open PHACTS Closing Symposium

For the last 5 years I have had the pleasure of working with the Open PHACTS project. Sadly, the project is now at an end. To celebrate we are having a two day symposium to look over the contributions of the project and its future legacy. The project has been hugely successful in developing an […]

For the last 5 years I have had the pleasure of working with the Open PHACTS project. Sadly, the project is now at an end. To celebrate we are having a two day symposium to look over the contributions of the project and its future legacy.

The project has been hugely successful in developing an integrated data platform to enable drug discovery research (see a future post for details to support this claim). The result of the project is the Open PHACTS Foundation which will now own the drug discovery platform and sustain its development into the future.

Here are my slides on the state of the data in the Open PHACTS 2.0 platform.

MACS Christmas Conference

I was asked to speak at the School (Faculty) of Mathematical and Computer Sciences (MACS) Christmas conference. I decided I would have some fun with the presentation. Title: Project X Abstract: For the last 11 months I have been working on a top secret project with a world renowned Scandinavian industry partner. We are now […]

I was asked to speak at the School (Faculty) of Mathematical and Computer Sciences (MACS) Christmas conference. I decided I would have some fun with the presentation.

Title: Project X

Abstract: For the last 11 months I have been working on a top secret project with a world renowned Scandinavian industry partner. We are now moving into the exciting operational phase of this project. I have been granted an early lifting of the embargo that has stopped me talking about this work up until now. I will talk about the data science behind this big data project and how semantic web technology has enabled the delivery of Project X.

You can find more details of flood defence work in this paper.

Crusade for Big Data Keynote

Today I gave the keynote presentation (slides below) at the Crusade for Big Data in the AAL domain workshop as part of the EU Ambient Assisted Living Forum. I gave an overview of the way that the Open PHACTS project has overcome various Big Data challenges to provide a production quality data integration platform that is […]

Today I gave the keynote presentation (slides below) at the Crusade for Big Data in the AAL domain workshop as part of the EU Ambient Assisted Living Forum. I gave an overview of the way that the Open PHACTS project has overcome various Big Data challenges to provide a production quality data integration platform that is being used to answer real pharmacology business questions.

The workshop then broke out into five breakout groups to discuss open challenges facing the AAL community that are posed by Big Data. The breakout groups were:

  1. Privacy and Ethics
  2. Business models for sustainability
  3. Data reuse and interoperability
  4. Data quality
  5. Feedback to the users

The organisers of the workshop (Femke Ongenae and Femke De Backere) will be sharing the outcomes of the brainstorming by proposing several working groups to focus on the issues in the area of AAL.

Data Integration in a Big Data Context

Today I had the pleasure of visiting the Urban Big Data Centre (UDBC) to give a seminar on Data Integration in a Big Data context (slides below). The idea for the seminar came about due to my collaboration with Nick Bailey (Associate Director of the UBDC) in the Administrative Research Data Centre for Scotland (ADRC-S). In […]

Today I had the pleasure of visiting the Urban Big Data Centre (UDBC) to give a seminar on Data Integration in a Big Data context (slides below). The idea for the seminar came about due to my collaboration with Nick Bailey (Associate Director of the UBDC) in the Administrative Research Data Centre for Scotland (ADRC-S).

In the seminar I wanted to highlight the challenges of data integration that arise in a Big Data context and show examples from my past work that would be relevant to those in the UBDC. In the presentation, I argue that RDF provides a good approach for data integration but it does not solve the basic challenges of messy data and generating mappings between datasets. It does however lay these challenges bare on the table, as Frank van Harmelen highlighted in his SWAT4LS keynote in 2013.

The first use case is drawn from my work on the EU SemSorGrid4Env project where we were developing an integrated view for emergency response planning. The particular use case shown is that of coastal flooding on the south coast of England. Although this project finished in 2011, I am still involved with developing RDF and SPARQL continuous data extensions; see the W3C RDF Stream Processing Community Group for details.

The second use case is drawn from my work on the EU Open PHACTS project. I showed the approach we developed for supporting user controlled views of the integrated data through Scientific Lenses. However, I also talked about the successes of the project and the fact that is currently being actively used for pharmacology research and receiving over 20million hits a month.

I finished the talk with an overview of the Administrative Data Research Centre for Scotland (ADRC-S) and my work on linking birth, marriage, and death records. I am hoping that we can adopt the lenses approach together with incorporating feedback on the linkages from the researchers who will use the integrated views.

In the discussions following the talk, the notion of FAIR data came up. This is the idea that data should be Findable, Accessible, Interoperable, and Reusable by both humans and machines. RDF is one approach that could lead to this. The other area of discussion was around community initiatives for converting existing open datasets into an RDF format. I advocated adopting the approach followed by the Bio2RDF community who share the tasks of creating and maintaining such scripts for biological datasets. An important part of this jigsaw is tracking the provenance of the datasets, for which the W3C Health Care and Life Sciences Community Profile for Dataset Descriptions could be beneficial (there is nothing specific to the HCLS community in the profile).