First steps with Jupyter Notebooks

At the 2nd Workshop on Enabling Open Semantic Sciences (SemSci2018), colocated at ISWC2018, I presented the following paper (slides at end of this post): Title: Using a Jupyter Notebook to perform a reproducible scientific analysis over semantic web sources Abstract: In recent years there has been a reproducibility crisis in science. Computational notebooks, such as […]

At the 2nd Workshop on Enabling Open Semantic Sciences (SemSci2018), colocated at ISWC2018, I presented the following paper (slides at end of this post):

Title: Using a Jupyter Notebook to perform a reproducible scientific analysis over semantic web sources

Abstract: In recent years there has been a reproducibility crisis in science. Computational notebooks, such as Jupyter, have been touted as one solution to this problem. However, when executing analyses over live SPARQL endpoints, we get different answers depending upon when the analysis in the notebook was executed. In this paper, we identify some of the issues discovered in trying to develop a reproducible analysis over a collection of biomedical data sources and suggest some best practice to overcome these issues.

The paper covers my first attempt at using a computational notebook to publish a data analysis for reproducibility. The paper provokes more questions than it answers and this was the case in the workshop too.

One of the really great things about the paper is that you can launch the notebook, without installing any software, by clicking on the binder button below. You can then rerun the entire notebook and see whether you get the same results that I did when I ran the analysis over the various datasets.

Summer of Good News

This has been a good summer, not just because the British weather has been somewhat more summery than usual. Qianru’s Graduation In June, my first PhD student graduated. Dr Qianru Zhou investigated the use of an ontology to enable a software defined network. Her PhD thesis is “Ontology-driven knowledge based autonomic management for telecommunication networks: Theory, […]

Picture of Qianru on her graduation day

This has been a good summer, not just because the British weather has been somewhat more summery than usual.

Qianru’s Graduation

In June, my first PhD student graduated. Dr Qianru Zhou investigated the use of an ontology to enable a software defined network. Her PhD thesis is “Ontology-driven knowledge based autonomic management for telecommunication networks: Theory, implementation and applications”,

Promotion

As of today (1 August 2018), I am now an Associate Professor (equivalent to Senior Lecturer in traditional British universities).

Grant Success

Today saw the start of a collaboration with VisionWare, a company based in Glasgow who specialise in record linkage, and is funded as an Interface Voucher. We are investigating combining the data corruption framework that Ahmad has been developing with the synthetic data that VisionWare have been generating. The purpose is to enable us to evaluate, and thus improve, record linkage.

 

Report on the 6th Scottish Linked Data Interest Group Workshop

On 29 May, the Heriot-Watt Semantic Web Lab hosted the sixth Scottish Linked Data Interest Group workshop (SLiDinG6), sponsored by the SICSA Data Science theme. There were 30 attendees from academia, government, and industry.

The main focus of the day was to share interests and knowledge around Semantic Web and Linked Data research and use across Scotland, with a view to fostering collaboration and interaction.  We asked all attendees to fill out a well-sorted form two weeks prior to the event.  Well Sorted allows attendees of events to put in titles and short descriptions of their interests.  Once these are all received, attendees group them according to their own view of how they interact. The Well Sorted algorithm then takes all sortings and creates themed groups.  Attendees were allowed to submit up to two responses. We received 17 responses, which were sorted into three groups as shown in the figure below. The full well-sorted results can be found here.

The full schedule for the day can be found on the event webpage.  We began with lightning talks – 17 in total – to give attendees a feel for the breadth and focus of interest across the group.  After lunch we had the first group session, based on the well-sorted groups. All attendees could see the topics in each group and attend whichever they felt suited them best.  The groups discussed the first three questions outlined on the event webpage, with a focus on their interests within their particular group:

  1. What are the killer apps of the Semantic Web?
  2. What are the challenges from industry and government?
  3. Where are the synergies in Semantic Web research in Scotland?

Feedback was given by each group before the coffee break, and on this basis some attendees moved between groups.

After the coffee break, group discussions continued, with more focus on using the outcome of the earlier session to discuss the fourth question:

  1. Can we identify projects to push forward for funding?

At the end of the day, we summarised across the meeting what had come out of these groups, and various potential avenues which could be developed further were identified.

We discussed when we would like to hold the next event and agreed that holding SLiDInG events more often would be preferable.  We agreed that the next one would be held around Easter next year (10 months away), possibly in conjunction with the UK Ontology Network Meeting, venue to be confirmed.

Throughout the day attendees were encouraged to contribute to the live blog of the meeting, which can be found here.  This gives a much more thorough overview of the discussion of the day.

We are very grateful to SICSA for the support, which enabled this useful event to take place.

SLiDInG 6

Today, the Semantic Web Lab hosted the 6th Scottish Linked Data Interest Group workshop at Heriot-Watt University. The event was sponsored by the SICSA Data Science Theme. The event was well attended with 30 researchers from across Scotland (and Newcastle) coming together for a day of flash talks and discussions. Live minutes were captured during the […]

Today, the Semantic Web Lab hosted the 6th Scottish Linked Data Interest Group workshop at Heriot-Watt University. The event was sponsored by the SICSA Data Science Theme. The event was well attended with 30 researchers from across Scotland (and Newcastle) coming together for a day of flash talks and discussions. Live minutes were captured during the day and can be found here.

I gave a talk on the successes and challenges of FAIR data. My slides are embedded below.

Seminar: Using Interactive Visualisations to Analyse the Structure and Treatment of Topics in Learning Materials

Title: Using Interactive Visualisations to Analyse the Structure and Treatment of Topics in Learning Materials

Speaker: Tanya Howden, Heriot-Watt University

Date: 11:30 on 14 May 2018

Location: CM F.17, Heriot-Watt University

Abstract: With the amount of information available online growing, it is becoming more and more difficult to find what you are looking for, particularly when you’re in an area that you have very little background in. For example, if you were learning about neural networks for the first time, the number of responses you get from a simple Google search can be overwhelming – how do you know where to start?! This is only one of the many challenges faced when searching for appropriate learning materials.

In this talk, I will be discussing the motivations behind my research interests before introducing and demonstrating a prototype that has been created with the aim to give learners a more engaging environment with unified organisation and access to different materials on one subject.

Congratulations Qianru Zhou

This morning Qianru Zhou successfully her PhD thesis “Ontology-driven knowledge based autonomic management for telecommunication networks: Theory, implementation and applications”, receiving minor corrections. Congratulations!
Supervisors: …

This morning Qianru Zhou successfully her PhD thesis “Ontology-driven knowledge based autonomic management for telecommunication networks: Theory, implementation and applications”, receiving minor corrections. Congratulations!

Supervisors:

External examiner: James Irvine (University of Strathclyde)

Internal examiner: Mauro Dragone (Engineering and Physical Sciences)

 

UK Ontology Network 2018

This week I went to the UK Ontology Network meeting hosted at Keele University. There was an interesting array of talks in the programme showing the breadth of work going on in the UK. I gave a talk on the Bioschemas Community  (slides below) and Leyla Garcia presented a poster providing more details of the […]

This week I went to the UK Ontology Network meeting hosted at Keele University. There was an interesting array of talks in the programme showing the breadth of work going on in the UK.

I gave a talk on the Bioschemas Community  (slides below) and Leyla Garcia presented a poster providing more details of the current Bioschema Profiles.

The UK Ontology Network is going through a reflection phase and would like interested parties to complete the following online survey.

 

Bioschemas Samples Hackathon

Last week the Bioschemas Community hosted a workshop. The focus of the meeting was to get web resources describing biological samples to embed Schema.org mark up in their pages. The embedded mark up will enable the web resources to become more discoverable, and therefore the biological samples also. I was not able to attend the […]

Last week the Bioschemas Community hosted a workshop. The focus of the meeting was to get web resources describing biological samples to embed Schema.org mark up in their pages. The embedded mark up will enable the web resources to become more discoverable, and therefore the biological samples also.

I was not able to attend the event but Justin Clark-Casey has written this blog post summarising the event.

NAR Database Paper

The new year started with a new publication, an article in the 2018 NAR Database issue about the IUPHAR Guide to Pharmacology Database. Simon D. Harding, Joanna L. Sharman, Elena Faccenda, Chris Southan, Adam J. Pawson, Sam Ireland, Alasdair J. G. Gray, Liam Bruce, Stephen P. H. Alexander, Stephen Anderton, Clare Bryant, Anthony P. Davenport, […]

The new year started with a new publication, an article in the 2018 NAR Database issue about the IUPHAR Guide to Pharmacology Database.

  • Simon D. Harding, Joanna L. Sharman, Elena Faccenda, Chris Southan, Adam J. Pawson, Sam Ireland, Alasdair J. G. Gray, Liam Bruce, Stephen P. H. Alexander, Stephen Anderton, Clare Bryant, Anthony P. Davenport, Christian Doerig, Doriano Fabbro, Francesca Levi-Schaffer, Michael Spedding, Jamie A. Davies, and {NC-IUPHAR}. The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. Nucleic Acids Research, 46(D1):D1091-D1106, 2018. doi:10.1093/nar/gkx1121
    [BibTeX] [Abstract] [Download PDF]

    The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been ‘forked’ from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.

    @Article{Harding2018-GTP,
    abstract = {The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been ‘forked’ from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.},
    author = {Harding, Simon D and Sharman, Joanna L and Faccenda, Elena and Southan, Chris and Pawson, Adam J and Ireland, Sam and Gray, Alasdair J G and Bruce, Liam and Alexander, Stephen P H and Anderton, Stephen and Bryant, Clare and Davenport, Anthony P and Doerig, Christian and Fabbro, Doriano and Levi-Schaffer, Francesca and Spedding, Michael and Davies, Jamie A and , {NC-IUPHAR}},
    title = {The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY},
    journal = {Nucleic Acids Research},
    year = {2018},
    volume = {46},
    number = {D1},
    pages = {D1091-D1106},
    month = jan,
    OPTnote = {},
    OPTannote = {},
    url = {http://dx.doi.org/10.1093/nar/gkx1121},
    doi = {10.1093/nar/gkx1121}
    }

My involvement came from Liam Bruce’s honours project. Liam developed the RDB2RDF mappings that convert the existing relational content into an RDF representation. The mappings are executed using the Morph-RDB R2RML engine.

To ensure that we abide by the FAIR data principles, we also generate machine processable metadata descriptions of the data that conform to the HCLS Community Profile.

Below is an altmetric donut so you can see what people are saying about the paper.