Sequence Ontology, September 09

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Sequence Ontology March 2009 / WORKING VERSION, NOT FINAL VERSION

1. Staff working on GOC tasks

Karen Eilbeck

The total number of FTE working on GOC tasks is 0.6

Graduate student 0.2

Ontology Development

Number of terms in SO: 1620

83 % of terms are defined, 94% have at least 1 synonym, with 1520 synonyms total.

118 terms originated from the Biosapiens protein feature collaboration.

195 terms are internal cross products.

22 term request tracker items submitted since the beginning of the year.

The ontology is is_a complete.

The SO has continued to grow and develop with the considerable input from external experts.

Significant changes:

  • Created synonym categories for amino acid and polypeptide terms. These categories help to organize synonyms, especially if there are multiple contexts.
  • Added dbxrefs to wikipedia.
  • Created new relations for transformations of sequence and also for topology. These relations are outlined in the ICBO paper.
  • The kinds of biological sequence have been arranged to mirror OBI: biological_region, experimental_feature and biomaterial_region


  • Royal Society of Chemistry. Colin Batchelor PhD. continues to work with the SO and has given several presentations on this work, including to the OBO foundry workshops.
  • RNA Ontology. The RNA Ontology consortium has strengthened its link to SO by funding a workshop and presentations by including SO in their consortium meetings.

Presentations (talks/tutorials)

SO was represented by KE and CJM at the January RNAO content meeting in Cambridge. The division of labor between SO and RNAO was worked out.

ICBO Buffalo July– conference paper about evolution of SO terms and relationships presented.

Invitation to present SO at Idaho State University Bioinformatics Conference, October 2009

Invitation to present SO at Department of Biomedical Informatics, University of Utah, seminar series Oct 2009


Methodology article: Quantitative measures for the management and comparison of annotated genomes. Karen Eilbeck , Barry Moore , Carson Holt and Mark Yandell. BMC Bioinformatics 2009, 10:67doi:10.1186/1471-2105-10-67

Conference paper for ICBO accepted and available from nature Preceedings: The Evolution of the Sequence Ontology

Invitation to submit updated ICBO conference paper to the Journal of Biomedical Informatics. Manuscript in preparation.

Other developments

  • SOM – a small ontology of genome derived molecules, not present in chEBI is being generated from SO, to provide the right terms for cross product generation with other ontologies.
  • Graduate project to better define the terms and relations involved with the immunological aspects of SO such as VDJ recombination.