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.


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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”.


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

It appears the BBC are using the ontology to generate rather attractive web pages on various taxa, e.g.

and by adding ‘.rdf’ to the end of each link, a dereferenceable rdf fragment is visible:

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…


Next Meeting of the Cambridge Ontology Reading Group

The next meeting of the Ontology Reading Group will take place on the 11th of March at 8pm in the Kingston Arms (Kingston Street).

Please post suggestions for reading material either to the mailing list or as comments to the blog. I’ll circulate a final agenda a week before the meeting, and as mentioned before, we won’t expect much in terms of advance preparation.

We can also try to use the opportunity to informally discuss potentials for expanding our local collaborations?

Cheers, Janna

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.


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Red Stag Deer Locking Horns
Image by ifijay via Flickr

Thanks to Duncan Hull and Midori Harris for their talks today on OWL language and OBO format. The merits of both have been discussed, argued and fought over previously on several other online fora so it is probably not worth me recapitulating all of these. Instead I will point to some useful pages online and leave it to others to detail. From my own personal perspective, and without revealing any preferences, I would say that it is my belief the OWL specification driven approach has greatly benefited from the OBO format user driven approach and vice versa. It is also clear to me we are still learning from each other even now.

Phil Lord: OBO Format to Manchester Syntax

Carole Goble and Chris Wroe (2004). The Montagues and the Capulets Comparative and Functional Genomics, 5 (8), 623-632 DOI: 10.1002/cfg.442

Allyson Lister: OBO to OWL and back again

(please add others as comments to this blog)


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Announcing the Third Meeting of the Ontology Interest Group @EBI

The next meeting of the EBI ontology interest group will take place on Thursday, 11 Feb at 11:00 am in A2-33. During the meeting we will talk about ontology languages:

  • Duncan Hull (Chemoinformatics and Metabolism Team) will give an overview over the Web Ontology Language
  • Midori Harris (GO Team) will do the same for the OBO Language, comparing and contrasting the two.

Looking forward to seeing you all there!