Today is the day of the Bio-Ontologies SIG meeting, which I have now co-organised for 4 years or so. It’s a surprisingly large amount of work to do, not least this year because we had 36 submissions. The organisation of this is a large part of the effort, but it has made for a strong programme; it’s gratifying to see that we have an audience of size to match.


We had a moment of worry when the first speaker didn’t register, but Mark Musen is a notable replacement, talking about representing OBO to OWL mappings.


Following Mark’s talk about using more rigourous models of OWL, Simon Jupp is talking about using the more light-weight semantics of SKOS, which turns out to be well suited for document navigation.


Lina Yip covers a familar problem — mapping between one resource and another: in this case MESH and Swissprot — to support the flow of knowledge from bioinformatics research toward medical practice.


The mapping theme continued (you’d almost think it was planned!) by Julie Chabalier who has mapped a number of resources to build a query warehouse.


Judy Blake has just spoke on annotation of GO and exactly what they mean. It’s good to see an increased formality to the relationships between a GO term and the entity that it is describing. This talk has generated the most questions so far, mostly asking for more details.


Mikel Arungen is now talking about design patterns, which are analogous to software design patterns. These should help to bridge the gap between the desire to write rigourous logical definitions, but the difficulties of doing this.


Daniel Schober is now describing efforts to standardise naming conventions, fitting with the theme of methods to help people produce interoperable and standardised ontologies.


Lunch, and nearly on time. Most of the lag was from coffee break, so I don’t feel that I, as timekeeper can be held responsible for this! Next for poster session, followed by the panel.


Well, the panel session has an element of self-indulgence about it. Robert has been doing this for much longer than I, but even for me it’s four years. After such a long span, it’a amasing that we have got to ten yeas. All of the speakers commented on how big the community has got, and that we are all a little surprised about this. The current religious themes running through bio-ontologies are also here, but so far fairly muted. A good panel all in all, and a nice marker for 10 years.

16:00 (ish)

Larisa Soldatova’s talk addressed the need for an tool enabling scientists to add additional semantics to their written work.


Catia Pesquita is talking about semantic similarity, which is a topic close to my heart. An interesting and careful body of work which covered the ground well, I thought.


Kieran O’Neil is not showing some interesting research, where he has been investigating novel techniques for query building over integrated databases.


Irena Spasic talked about some building term lists for metabolomics from literature mining. Once again she highlighted the need for access to full papers.


Daniel Faria took the graveyard slot, and discussed measure for protein clustering using sequence and GO information.


Overall a good day. It was great to have some many papers, and such a lively debate. This also marks the retirement of Robert as co-chair. His presence will be greatly missed — he’s taught my everything I know about being relaxed and not faffing too much while conference organising.

Onward till next year.

Originally published on my old blog site.