Archive for the ‘ Ontologies ’ Category

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.



Blogging an Ontology Book

University of Manchester
Image via Wikipedia

I and fellow EBIers Duncan Hull and Helen Parkinson have just completed a two-day meeting at Manchester University titled “blogging a book”. The idea was the brain child of Phil Lord and was ran by Robert Stevens and David Shotton under the OntoGenesis Network. The aim of the meeting was to produce encyclopedic-like articles about ontology (particular ontologies in biology) which might be of use to those coming to the field from new (or perhaps just after a refresher or something to cite).

The articles produced include topics such as :

What is an Ontology?
Upper ontologies



Application and reference ontologies

Community dirven ontology development
Protege and Protege OWL
Semantic Integration in Life Sciences

As well as producing interesting and hopefully useful articles, a further motivation of the meeting was to see if the authoring and peer-review process could be duplicated in an online, blog-style framework.  Each blog article, following authoring, is submitted for review and will only be considered ‘published’ when it has passed reviews from 2 peers.  It exposed some interesting strengths and weaknesses of authoring technology such as blogs.

Perhaps the primary weakness of the approach was the lack of collaborative software for authoring an article between multiple collaborators, although this is generally not how blog articles are written. Perhaps this is an area that may be strengthened in future. A strength is that the articles were quickly published and that DOI will (eventually) be obtained for articles so that they are citeable and therefore credit can be assigned.

Perhaps a more debatable strength, is that reviews were posted alongside the finished article for all to see, including the reviewers names, rendering the process entirely transparent. It raises some interesting thoughts, not least, would a reviewer be more or less inclined to criticise a paper they were reviewing if their identity was revealed and if their review were to be made public? Would reviews be more thorough as a consequence, since they would, in essence, also be published and available for peer scrutiny?

James Malone

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,


First Meeting: Building Bridges

We have our first Ontology Interest Group planned for next week. My hope is that we use the time to better inform the various groups of other activities and to encourage interactions.

I wrote in a paper last year that good ontology work begins when bedroom ontology development ends and I still believe that is true. I intend to capture a bit of a snapshot of the work the attendees are doing across the campus and place that on a resource that is accessible to all. That way we have a reference if we want to know with whom we should speak regarding a particular area. I’ll probably blog it first, then set up a nice EBI web page later. I dislike designing web pages as they usually reflect my total lack of artistic ability 🙂