Sequence Ontology

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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.

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.

9 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:

  • SO has added terminology to cope with the new sequencing technology.
  • SO has developed subtypes of amino acid.
  • There has been more work on the synonyms in the ontology, with the addition of over 300, new synonyms, and 3 new synonym classes. The classes, such as biosapiens synonym aid NLP by refining the context of the phrase.
  • SO is also developing new relations to better define the relation between sequence features and biology. A ICBO conference paper detailing this work has been accepted.


  • Royal Society of Chemistry. Colin Batchelor PhD. continues to work with the SO and has given several presentations on this work.
  • 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.


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: The evolution of the Sequence Ontology – to be presented in July.