Correspondence

Muscle Research and Gene Ontology: New standards for improved data integration

Erika Feltrin¹ , Stefano Campanaro² , Alexander D Diehl³ , Elisabeth Ehler⁴ , Georgine Faulkner⁵ , Jennifer Fordham⁴ , Chiara Gardin¹ , Midori Harris⁶ , David Hill³ , Ralph Knoell⁷ , Paolo Laveder² , Lorenza Mittempergher¹ , Alessandra Nori⁸ , Carlo Reggiani⁹ , Vincenzo Sorrentino¹⁰ , Pompeo Volpe⁸ , Ivano Zara¹ , Giorgio Valle¹ and Jennifer Deegan née Clark⁶

¹CRIBI- Interdepartmental Biotechnology Center, University of Padua, Padua, Italy

²Department of Biology, University of Padua, Padua, Italy

³The Jackson Laboratory, Bar Harbor, ME, USA

⁴Randall Division of Cell & Molecular Biophysics, King's College, London, UK

⁵ICGEB, Trieste, Italy

⁶EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

⁷Heart Center, Georg August University, Goettingen, Germany

⁸Department of Experimental Biomedical Sciences, University of Padua, Padua, Italy

⁹Department of Anatomy and Physiology, University of Padua, Padua, Italy

¹⁰Department of Neuroscience, University of Siena, Siena, Italy

author email corresponding author email

BMC Medical Genomics 2009, 2:6doi:10.1186/1755-8794-2-6

Published:	29 January 2009

Abstract

Background

The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO) Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community.

Results

The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature.

Conclusion

The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology webcite.