WS1: Gene Ontology: where are we now and what’s next?


Christophe Dessimoz (UNIL & SIB)

Workshop Summary:

The Gene Ontology (GO) is the undisputed standard for gene function annotation. As such, it is an indispensable part of a bioinformatician’s toolbox. At the same time, the complex, multifaceted, and rapidly developing nature of the GO can be daunting and a frequent source of misunderstandings for both novice and advanced users.

The recent publication of The Gene Ontology Handbook (Springer 2017), edited by the organiser of this workshop, provides an opportunity to reflect on recent advances and open challenges of the GO, such as computational inference, benchmarking, statistical analyses, visualisation, modelling of functional modules, or integration with other ontologies and controlled vocabularies.

The workshop will consist of short presentations by researchers directly involved in the development and maintenance of GO, as well as expert GO users and contributors. The invited speakers are chapter authors of the handbook, but there will be several slots available for contributed talks on the basis of submitted abstracts.

Workshop Agenda:

Tuesday, September 12, 2017
Venue: Kollegienhaus, University of Basel

9:00 Christophe Dessimoz: Welcome
9:05 - 10:30

Session I

Paul Thomas The Gene Ontology and the meaning of biological function
Pascale Gaudet Translating research data into Gene Ontology annotations
Domenico Cozzetto De novo protein function prediction using biophysical attributes
Gemma Holliday Enzymes: the space between chemistry and biology
10:30 - 11:00 Coffee break
11:00 - 12:15

Session II

Ruth Lovering Gene Ontology - annotation extensions
Fran Supek Visualizing Gene Ontology Annotations
Christophe Dessimoz Biases, Pitfalls & Remedies
12:15 - 13:45 Lunch break
13:45 - 15:00

Session III

Patrick Ruch Text Mining to Support Gene Ontology Curation and Vice Versa
Fabio Rinaldi Terminologies and Ontologies in Information Extraction
Alex Warwick Vesztrocy Metabolic QTL: Using GO to narrow down the causal gene
15:00 - 15:30 Coffee break
15:30 - 16:45

Session IV

Nick Furnham Complementary Sources Of Protein Functional Information: The Far Side Of GO
Spiros Denaxas Integrating Bio-ontologies and Controlled Clinical Terminologies: From Base Pairs to Bedside Phenotypes
Suzanna Lewis GO as a biological systems model
16:50 Christophe Dessimoz: Concluding remarks

Invited Speakers:

Spiros Denaxas, UCL, UK
Christophe Dessimoz, UNIL & SIB, Switzerland
Nick Furnham, London School of Hygiene and Tropical Medicine, UK
Pascale Gaudet, neXtProt group, Switzerland
Gemma Holliday, UCSF, USA
Suzanna Lewis, Berkeley Labs, USA
Ruth Lovering, UCL, UK
Fabio Rinaldi, Institute of Computational Linguistics, University of Zurich & SIB, Switzerland
Patrick Ruch, HES-SO & SIB, Switzerland
Fran Supek, CRG Barcelona, Spain
Paul Thomas, University of Southern California, USA
Domenico Cozzetto, University College London
Alex Warwick Vesztrocy, University College London

Workshop sponsor:

EMBO logo.gif