Announcing the First Meeting of the Ontology Reading Group

The  first Reading Group meeting will take place next thursday at 7pm at the Kingston Arms.

For reading material, let’s all read these two papers, which have similar topics:

Integrating phenotype ontologies across multiple species. Genome Biology

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype
Annotation. PLoS Biol 7(11): e1000247.

*beforehand* please ;-).

The third suggested paper we’ll carry over to our meeting next month.

All the best,


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,


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!


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:


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.


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…


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…


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.


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 🙂