Sequence Ontology Progress Report December 2009

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Sequence Ontology December 2009

  • Staff working on GOC tasks

Karen Eilbeck 0.6

Graduate student 0.2

The total number of FTE working on GOC tasks is 1.0

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.

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

The ontology is is_a complete. A release is made of the ontology every 2 months and daily revisions are checked into CVS.

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 many new terms to describe parts of sequence such as gene silencing, modified base sites, polypeptide regions.
    • Added dbxrefs to wikipedia.
    • Created new relations for transformations of sequence and also for topology. These relations are outlined in the ICBO paper. 20 new relations have been added to SO.
    • The kinds of biological sequence have been arranged to mirror OBI: biological_region, experimental_feature and biomaterial_region
    • SO has been harmonized with the Basic Formal Ontology to provide better interoperability between OBO ontologies. The root terms have been categorized according to BFO. For example sequence_feature is_a generic dependent continuant.


    • 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. A manuscript detailing this work is being submitted to ‘Applied Ontology’.
    • MHC working group. The SO has been part of a group discussing representation of MHC alleles. This work was initiated in a SO workshop and a paper detailing the development of a system for defining MHC alleles in Systemic Sclerosis has been accepted by ‘Human Molecular Genetics’.
    • Synthetic Biology. SO is in collaboration with a synthetic biology group at Virginia Tech, to type the genetic parts in their software.

Papers and Presentations (talks/tutorials) GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources

Other developments

    • Sequence Ontology: Molecules (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.