School of CS newsletter

We’re approaching the end of the academic year. We’ve all been working hard and I hope everyone manages to take some time off. There is a lot of change, both within the university and from outside as universities are under increasing scrutiny. Thus we live in interesting times and I’m sure that the School will remain the splendid place it is – due to the staff and the students in the School. I’d like to thank everyone for all their hard work over the year.

This will be the last School Newsletter and the Newsletter will return in September.

Robert.

Tai Chi for Wellbeing

The Confucius Institute is offering two drop-in sessions of Tai Chi in July. The dates are Friday 5^th and 19 July. They take place at the courtyard outside the Lime Cafe, Samuel Alexander Building at 1 pm and lasts 30-40 minutes.

Tai Chi revolves around a series of movements called forms. Although there are videos available for learners, it is better to learn with experts known as “masters” with years of experience. In each session, you will learn the basic movements and deep breathing. It is widely acknowledged that tai chi has the benefits of reducing stress, improving posture, balance and general mobility, and increasing muscle strength in the legs.

No special clothing is required and it is recommended you wear comfortable clothes. All are welcome.

Speaker: Nicolas Matentzoglu

Host: Ulrike Sattler

The Unified Phenotype Ontology (uPheno) framework for standardised representation of phenotypes across domains

The Monarch Initiative is an international consortium to integrate, align, and re-distribute cross-species gene, genotype, variant, disease, and phenotype data and is best known for its flagship projects, the Human Phenotype Ontology, the Unified Phenotype Ontology (uPheno) and the disease variant prioritisation tool Exomiser. The uPheno project in particular aims to unify the annotation of phenotypes across domains in a manner analogous to the unification of gene function annotation by the Gene Ontology. uPheno 2.0 builds on earlier efforts with a new strategy that directly leverages the work of the phenotype ontology development community and incorporates phenotypes from a much wider range of domains. We have organised a collaborative community effort, including representatives of all major model organism databases, to document and align formal design patterns for representing phenotypes and further develop reference ontologies, such as PATO, which are used in these patterns. A common development infrastructure makes it easy to use these design patterns to generate both domain-specific ontologies and a domain-independent layer that subsumes them.

The resulting community-curated ontology for the representation and integration of phenotypes across domains serves two general purposes:

Providing a community-developed framework for ontology editors to bootstrap, maintain and extend their phenotype ontologies in a scalable and standardised manner.

Facilitating the retrieval and comparative analysis of domain-specific phenotypes through a deep layer of domain-independent phenotypes.

Here we present the general uPheno 2.0 framework, in particular how we leverage OWL, definition-oriented development, reasoning, semantic similarity and pattern-based development to integrate phenotypes across domains.

Biography:

Nico finished his PhD on OWL reasoning and modularity in 2015 in the school of computer science, supervised by Bijan Parsia and Uli Sattler. Since then, he has completed two postdocs with Bijan and Robert Stevens, in areas involving clinical information systems, ontology-based question generation and ontology engineering methodologies. In January 2018, he joined the Samples, Phenotypes and Ontologies team (SPOT) at the European Bioinformatics Institute (EMBL-EBI), charged with coordinating an international effort to reconcile phenotype ontologies to enable cross-domain inference. His current and favourite projects are developing resilient ontology engineering systems, evangelizing the use of OWL in knowledge-based systems, the Parsia Design Triangle (Q30) and inter-disciplinary collaborative ontology engineering.

Emmeline’s Pantry Foodbank

Donations needed

With school out for summer, many children face going hungry with no access to school meals over the holidays. Please help if you can.

Items urgently needed:

• Tinned foods, cereals, jams and spreads

• Teas (normal & herbal), coffee, sugar

• Biscuits, crisps & treats

• Cooking oil, rice & pasta

• Clothes detergent, softener,

• Washing up liquid

• Toiletries (all ages)

  Please drop off donations at ACSO with Mel or Karon.