Archive for the ‘ Uncategorized ’ Category

UK Ontology Network: from Archipelago to Pangaea

At a meeting of minds at the KMI, Open University on Friday 30th April, 2010, it was decided the UK ontology community should attempt to coordinate its efforts in a slightly more structured (I hesitate to use the word ‘formal’ ) manner. The participants, including both myself and Janna Hastings from EBI, represented a variety of organisations, both inside and outside of academia, from areas including bioinformatics, health care, chemistry, formal ontology, ontology languages, geographical surveying, philosophy, engineering and computer science.

The topography of the UK
Image via Wikipedia

It appeared to me that there was a general consensus in the room that present ontology work in the UK appears as an archipelago; formed of multiple, disparate efforts, often without knowledge of things occurring in organizations up and down the land. The desire is to better coordinate and collaborate, as is the true spirit of ontology work; who coordinates the coordinators indeed. We need to connect these islands and form our pangaea.

The outcome of the meeting was the establishment of a UK Ontology Network, whose members are those working in ontology and ontology related projects based in the UK. As work continues on creating a more permanent web presence (this is one of my tasks so I can say with confidence it will be done ‘soon’), a mailing list has already been established. For those interested, please subscribe to the Google Group to join us in our efforts to give a stronger cross-domain community feel to the UK based ontology work that we all know goes on, though we may not know exactly what and where, or by whom. Hopefully we will know  soon.

JM

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The Fast and the Furious?

Dietrich Rebholz-Schuhmann gave a talk at the Ontology Interest Group today on using ontologies within the contact of text mining. It provided a lot of perspective and I think gave a strong and convincing use case as to how ontologies could be used. It also poses questions as to how amenable to such analysis ontologies are. For instance, those developed in upper ontologies which often use abstract terminology such as those seen in BFO do not reflect normal biological language. Relations such as has_quality for relating phenotypic information are unlikely to produce results used on current biomedical literature. There is also a suggestion that an increased number of more granular relationships can help to improve this analysis. Minimally, richer synoyms for both classes and relationships would help both text mining analysis and human understanding.

My favourite quote of the talk:
“Ontology: The Slow and the Furious”.

JM

BBC One-tology

There was a recent posting to the OntoGenesis network I thought it would be worth sharing. It highlights some of the work done at the BBC on wildlife linked data at the new Wildlife finder.

This work was done by Tom Scott and Leigh Dodds et al and can be found at http://purl.org/ontology/wo/

It appears the BBC are using the ontology to generate rather attractive web pages on various taxa, e.g. http://www.bbc.co.uk/nature/class/Amphibian

and by adding ‘.rdf’ to the end of each link, a dereferenceable rdf fragment is visible:
http://www.bbc.co.uk/nature/class/Amphibian.rdf

This is not the first time the BBC have looked into using ontologies, although it is clearly the most relevant to bioontologies. They have also spend time on developing a ‘programme ontology‘ which is also publicly available. The BBC are not alone in large organisations investing time into ontology usage. Last year, NASA announced it too had been using ontologies to perform automated data analysis and for organising earth and environmental terminology. Perhaps the kill aspp is on its way;  Google-ontology…

JM

ICBO 2011

Congo Buffalo
Image by Durotriges via Flickr

Barry Smith announced at the OBO Foundry workshop this week that the 2nd International Conference on Biomedical Ontologies will be held in Buffalo, New York, US on the July 29th-31st 2011. Note, this confirms that there will not be an ICBO 2010.

JM

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Summary of the First Meeting of the Ontlogy Interest Group

The first meeting of the ontology interest group at the EBI took place today. As James phrased so aptly in his last post, we used the meeting to build bridges. The agenda was as follows:

  • Introductions – What are we all working on and why did we come to the meeting?
  • Topics – What are we interested in, what would we like to see the group do and which activities might be interesting to the members?
  • Timings – When would be an appropriate time for the meeting? What frequency?
  • Blogging – Who would like to contribute to this blog to keep the ontology conversation going?
  • Any other business.

Here is a summary of the answers to some of the questions:

Introductions

The meeting was attended by a diverse set of people, both in terms of the groups who were represented (diverse groups from the EBI and members of the Sanger) and in terms of their interest in ontologies: some of us were ontology developers and maintainers, others consumers of ontologies and yet others usability and interface experts and those who were curious about ontologies and wanted to learn more about ontologies/ontology technology and understand how they could leverage these in their own work.

Topics

The diversity of the attendees was also reflected in the diversity of the topics they felt the interest group should address. The following topics were raised:

  • Understanding the use of ontologies – how to annotate data?
  • Once you have annotated data – how do you build a query system? Data retrieval?
  • Ontology visualisation/interaction of different user groups/user types with ontologies. Visualisation, visualisation, visualisation – how does one visualise complexity/complex ontologies?
  • How does an ontology project identify/communicate/interact with its users?
  • How do you develop ontologies? Best practices? How do you interact with the existing ontologies/ontology groups/OBO Foundry….the politics of ontology development.
  • Ontology mapping/integration – how to deal with context dependence.
  • From terminology/dictionary to taxonomy to ontology.
  • Reasoning over ontologies: how to go about it? How useful is it? What are the technical issues? What are the scientific issues? How many people actually do it “in anger”?
  • Ontologies in the context of semantic web? Repository technology? Data in RDF with ontological support?
  • Formal Ontology – the philosophical foundation/basis of ontology…what are functions?
  • Application examples of ontologies/ ontologies in production systems? Data standards/formats – interaction with ontology

As a group we agreed that, during our first meetings, we should step back and aim to get an overview over the various meanings the term “ontology” can have for different groups and to understand the evolution of the discipline and the interaction/cross-over between philosophy and computer science. Furthermore, we should try to get an overview over some of the tools currently used in the area of ontological engineering and look at some use cases which illustrate the potential use of ontologies in research or information systems. In the meeting following this, we would like to start looking at how to develop an ontology, best practice, etc…

Timings

The group agreed, that regular meetings  are essential for maintaining momentum and that, at least for the first several meetings, we should aim to meet every fortnight. However, it was also felt that the exact date an time would best be determined by doodle poll. Furthermore, we all agreed that extra activities would always be welcome. Extra activities could, for example, include a reading group in formal ontology, tutorial style activities etc…

Blogging

We decided that a combination of blog and mailinglist would be the most appropriate form of communication for now. There have been no volunteers so far wishing to contribute blog posts, but we hope that that will change in the future.

Any other business

There was no further business to discuss.

I hope that this is a fair summery of the first meeting of the Ontology Interest Group. Please add anything, which I have omitted, iswrong or which you would like to see discussed further in the comments section of this post! I will send round a link to a doodle poll for the next meeting via the internal ontology mailing list.

Nico