Archive for the ‘ Administrative ’ Category

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!



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 🙂


Welcome to the Bioontologies Blog!

As part of the new bioontology interest group , this blog will represent a place to gather opinion, collect thoughts and mine gems from the bioontology community based at the EBI, Cambridge. There are currently numerous projects in which bioontologies play a role and the number of ontologists within the field has steadily grown over the last few years. We believe the time is right to give a forum to these people and allow the useful sharing of tips, tricks and tweets.

We welcome any thoughts from people involved in developing, using, consuming or just generally interested in bioontologies from the wider bioinformatics community.

On behalf of the Bioontology Interest Group, have fun!