Archive for the ‘ Ontology Interest Group Meetings ’ Category


Red Stag Deer Locking Horns
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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!


Second Meeting of the Ontology Interest Group, 28/01/09

Today we had the second meeting of the ontology interest group at the EBI. The programme was as follows:

Robert Hoehndorf: “What is an Ontology?”
Short use case 1: James Malone: “Ontologically Modeling Sample Variables in Gene Expression Data”

Short use case 2: Dietrich Rebholz-Schuhmann: “Extraction of GO terms from literature for the identification of gene-disease associations”

The meeting was very well attended with around 30 people. Robert’s talk gave a great overview over the various uses and usages of both the term and the tool/methodology/technology that “ontology” represents and the evolutuon of “ontology” as a discipline in both philosophy and computer science and artificial intelligence as well as the relationship between them. He has promised to write up his talk into a blog post soon. Until he does so, here are his slides:

“What is an ontology”

James then presented a use case, showing how  ontologies, such as the Experimental Factor Ontology could be used for sophisticated querying of resources such as Array Express Atlas and data integration.

Unfortunately, Dietrich didn’t get to present his talk as we ran out of time during the meeting: it will be the first item on the agenda for the next meeting in approximately 2 weeks.

During the meeting it became apparent, that we should talk about ways of formalizing ontologies, i.e. ontology languages next rather than to start with ontology development best practice. In particular, the group seemed to be interested in OWL. We will therefore aim to start with OWL in the next meeting.

There have also been suggestions from several members of the group to preserve the talks as videos and to make them publicly available, which is a great idea and we will look into this.

So far the rough summary of the meeting. As always, please comment, correct any mistakes, carry on the conversation in the comments section of the blog. I will send a link to a poll to determine the best time for the next meeting via the mailing list.


Announcing the next Meeting of the Ontology Reading Group

Dear All,

the next meeting of the  Cambridge Ontology Reading Group will take place on the 4th of February at 7:00 pm in the Kingston Arms, Kingston Street, Cambridge.

Please suggest reading material in the comments section of the blog. If we get too many suggestions, we can carry over to the next few months as well.

All the best,


Announcing the second meeting of the Ontology Interest Group at the EBI

Our next meeting will be held on the 28th of January at 11:00 in A2-33.

There is an exciting line-up of speakers, who will give short presentations about the topics we decided on in the last meeting:

Robert Hoehndorf: “What is an Ontology?”
Robert will discuss the origins and development of ontology in philosophy and the cross-over of the discipline into computer science, knowledge representation and AI. He will also address what “ontology” means to different group of people and what the relationship between philosophical ontology and ontology in CS is today. Philosophers have a direct impact on the work of biologists these days, as those of you who have come into contact with or participate in the OBO Foundry will appreciate. Therefore this talk is an important foundation for our future work.

Duncan Hull: “Protege and its Ecosystem”
Protege is arguably the most important tool for ontology engineering at the moment. As such it has eveolved a whole ecosystem of add-ons and functionality, which facilitate ontology construction and maintenance. Duncan will aim to provide us with a first overview over the Protege system. This is part of an ongoing series and in future talks we will look at other tools for collaborative development of ontologies, other ontology editors, reasoners etc…

Short use case 1: James Malone: “Ontologically Modeling Sample Variables in Gene Expression Data”
Short use case 2: Dietrich Rebhold-Schuhmann: “Extraction of GO terms from literature for the identification of gene-disease associations”

We should finish the meeting at 12:00 and after that there should be plenty of time for further discussion over lunch.

Looking forward to seeing you all there!