OWL research at the University of Manchester

Joint research by members of the Information Management Group and the Bio-Health Informatics Group.

May 26, 2014
by Nico Matentzoglu
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New Tutorial: Introduction to Implementing Ontologies in the Web Ontology Language (OWL)

The school of Computer Science at the University of Manchester are pleased to invite you to participate in their internationally renowned OWL Ontology tutorials.

 It is to be hosted at the University of Manchester on 01 and 02 July 2014.

 Abstract

This two-day introductory ‘hands-on’ workshop aims to provide attendees with both the theoretical foundations and practical experience to begin building OWL ontologies using the latest version of the Protégé-OWL tools (Protege4.3).  It is based on Manchester’s well-known “Pizza tutorial” (see http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/).

 This tutorial will cover the main conceptual parts of the Web Ontology Language (OWL) through the hands-on building of an ontology focusing on pizzas and their ingredients. A series of practical exercises take attenders through the process of conceptualizing the toppings found on a pizza; the entry of this classification into the Protégé environment; the description of many types of pizza. All this is set in the context of using automated reasoning to check the consistency of the growing ontology and to use the reasoner to make queries about pizzas.

 Since 2003 this tutorial, in various forms, has been given over 30 times and been attended by hundreds of budding ontologists.

 Aims

The aims of this tutorial are to:

- understand the use of ontologies

- understand statements written in OWL;

- understand the role of automated reasoning in ontology building;

- build an ontology and use a reasoner to draw inferences based on that ontology;

- gain experience in the Protégé 4 ontology building environment;

- gain insight into how OWL can play a role in semantic metadata.

 Speakers

Robert Stevens is a Professor of computer science in the Bio and Health Informatics Group at the University of Manchester.  His main areas of research include: (1) the development and use of ontologies to describe biology and to make knowledge about molecular biology computationally useful; (2) communal building of ontologies — enabling domain experts to use the power of formal, expressive languages, such as the Web Ontology Language (OWL); and (3) semantic description of content through ontologies in e-Science research.

Dr. Georgina Moulton is an Education and Development Fellow with over 7 years experience delivering education and development programmes in the bio-and health informatics sectors.  She has focussed on the comprehension and use of ontologies and has delivered tutorials in this field across the UK.

Number of Places and Cost

In total there are 15 places.  The cost of the course is £250 per day.

 Registration and Further Information

To register, please email Kieran O’Malley (kieran.omalley@manchester.ac.uk) prior to June 23rd 2014.   Payment options will be returned to you following reservation.

April 17, 2014
by Nico Matentzoglu
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Hard subsets in OWL ontologies

Very expressive Description Logics in the SH family have worst case complexity ranging from EXPTIME to double NEXPTIME. In spite of this, they are very popular with modellers and serve as the foundation of the Web Ontology Language (OWL), a W3C standard. Highly optimised reasoners handle a wide range of naturally occurring ontologies with relative ease, albeit with some pathological cases. A recent optimisation trend has been modular reasoning, that is, breaking the ontology into hopefully easier subsets with a hopefully smaller overall reasoning time (see MORe and Chainsaw for prominent examples).

However, it has been demonstrated that subsets of an OWL ontology may be harder — even much harder — than the whole ontology. This introduces the risk that modular approaches might have even more severe pathological cases than the normal monolithic ones.

In our submission to DL 2014, we analyse a number of ontologies from the BioPortal repository in order to isolate cases where random subsets are harder than the whole. For such cases, we then examine whether the module nearest to the random subset also exhibits the pathological behaviour.

Data
Experiment Data (Ontologies, subsets and their corresponding modules)
Spreadsheets

April 15, 2014
by Nico Matentzoglu
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Whatif: Understanding the Ontology Authoring Process

Despite various gross ontology engineering methods, philosophical principles and work on design patterns, there is no work that informs us about the ontology authoring process at the level of addition of axioms. Logic based ontologies, such as those written in OWL, can be complex systems of axioms where a single change can have ramifications across the ontology.

Authors can call upon a reasoner to ‘check’ their ontology and re-organise it according to the implications of the added axioms. This is, however, a post hoc activity; an ontology author lacks the means of undertaking ‘test driven development’ (apart from issuing queries against the reasoned ontology). Our hypothesis is that by allowing an author to pose ‘what if…?’ questions to an ontology prior to the addition of axioms, then the authoring process will run in a more informed manner. In order to test this view, we need to understand ontology authoring at the axiom level to find out how users decide upon the addition of axioms; that is, the dialogue they have with the system.

Software

Protégé4US – Protégé for User Studies (version 0.1, available soon)

Data repositories

Emergent behavioral patterns of ontology authoring tasks

Identifying ontology authoring patterns

January 28, 2014
by Nico Matentzoglu
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Manchester Family History Advanced OWL Tutorial in February

Manchester Family History Advanced OWL Tutorial

Dates: 27th/28th February 2014

Time: 10am – 5pm

Location: Room G306a Jean McFarlane Building, University of Manchester.

The Bio-Health Informatics Group at The University of Manchester invites you to participate in a newly developed OWL Ontology that covers more advanced language concepts for OWL.

The overall goal for this tutorial is to introduce the more advanced language concepts for OWL. This new tutorial builds on the world-famous Manchester Pizza Tutorial, by exploring OWL concepts in greater depth, concentrating on properties, property hierarchies, property features and individuals. The topic of family history is used to take the tutee through various modelling issues and, in doing so, using many features of OWL 2 to build a Family History Knowledgebase (FHKB). The exercises involving the FHKB are designed to maximise inference about family history through use of an automated reasoner on an OWL knowledgebase (KB) containing many members of the Stevens family.  The aim, therefore, is to enable people to learn advanced features of OWL 2 in a setting that involves both classes and individuals, while attempting to maximise the use of inference within the FHKB.

 

By the end of the tutorial you will be able to:

  1. Know about the separation of entities into TBox and ABox;
  2. Use classes and individuals in modelling;
  3. Write detailed class expressions;
  4. Assert facts about individuals;
  5. Use the effects of property hierarchies, property characteristics, domain/range constraints to drive inference;
  6. Use property characteristics and subproperty chains on inferences about individuals
  7. Understand and manage the consequences of the open world assumption in the TBox and ABox;
  8. Use nominals in class expressions;
  9. Appreciate some of the limits of OWL 2.

 

Supplementary material for the tutorial can be found at: http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/fhkbtutorial/

The cost of the course is £250 per day.

 

Registration and Further Information

To register, please email Kieran O’Malley

(kieran.omalley@manchester.ac.uk) prior to February 21st 2014. Payment options will be returned to you following reservation. For further information please visit the website at:

http://owl.cs.manchester.ac.uk/

October 11, 2013
by Samantha Bail
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Web page move

We finally completed the move of owl.cs to a new web server which is hosted by the university’s IT services team. Some things might have gotten jumbled up a little – please contact us if you come across any broken links or missing resources.

June 8, 2013
by Samantha Bail
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Web services update

We have been providing several different OWL related web services, such as the OWL syntax converter and the ontology browser,  for a few years now. It seems our current hosting solution can no longer cope with some of the larger and more complex ontologies that are uploaded, so we’ve been seeing a few server hiccups lately.

In order to deal with this problem, we’re currently in the process of moving the applications to more stable server infrastructure. In addition, we will also be providing downloads for the tools, which means that anyone wanting to modularise a large ontology can do that locally on their own machine rather than having to deal with long upload times and possible server outage.

While we’re moving the applications, this owl.cs site will also find a new home on a university server rather than our good ol’ Mac Mini, which can will improve uptime drastically. The overhaul should be completed by the end of June 2013. We will keep you updated on this.

May 27, 2012
by Bijan Parsia
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An OWLED W3C Community Group?

At OWLED today, I proposed that we form a W3C Community Group. They goal is to support the activist part of the OWLED mission.

OWLED was founded in order to push OWL forward. The subtitle is Experiences (what we’ve learned) and Directions (where we want to go). We founded it because there was a bit of “OWL fatigue” at the W3C and we didn’t want OWL 1 to be the last word on OWL.

Also, at the time, the W3C wasn’t well set up to do the kind of nurturing of the infrastructure and state of deployed art we wanted to do. Formal standards aren’t the last word in any technical community: We can have rough, bottom up, effective, de facto standardization if we set up the right incentive structures.

The room was receptive so I pushed the button and we now have a proposed group! We need 4 more people with W3C accounts to push the button and then the group is ago.

As[While] I cannot coerce WordPress to embed a PDF, I’ll just also provide a link to my pitch talk for the CG.

We’ll be talking about possible projects over the next 1.5 days. Feel free to drop me a line if you have an idea!

Update: We now have 6 supporters, so the group will be created! Hurray!

June 2, 2011
by admin
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Event announcement: Introduction to Implementing Ontologies in OWL

11 & 12 July 2011, Manchester

This two-day introductory ‘hands-on’ workshop aims to provide attendees with both the theoretical foundations and practical experience to begin building OWL ontologies using the latest version of the Protégé-OWL tools (Protege4). It is based on Manchester’s well-known “Pizza tutorial” (see http://www.co-ode.org).
More information can be found on NorthWest e-Health.

March 3, 2011
by Bijan Parsia
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The great owl.cs reboot

The website for OWL at Manchester was looking a little creaky, so we banded together to do a complete overhaul. The first good move was to migrate to a content management system (in our case, WordPress). The second good move was to update all our WebApps to the latest OWL API. A bit of reorg and writing and you have the lovely site you see before you.