SO progress report for October 2008 meetings

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Progress update for Sequence Ontology from February to September 2008


FTE: Karen Eilbeck (60%) University of Utah, Salt Lake City.

Ontology Development

Number of terms in SO: 1573 84 % of terms are defined, 44 % have at least 1 synonym, with 1170 synonyms total. 118 terms originated from the Biosapiens protein feature collaboration. 199 terms are internal cross products. 39 term request tracker items submitted since the grant period began.

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

Significant changes

  • Core terms and relationships. SO is working with the community to further develop the core structure of the ontology incorporating new better defined relationships that describe the topology and biology of the genome.
  • The region terms in SO have been organized based on whether they represent a biological entity or the result of an experiment or procedure.


  • Bioisapiens. SO continued to work with the Biosapiens Consortium on the development of protein features. Their curator Gabby Reeves has been replaced by Sandra Orchard.
  • 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 SO to their annual consortium meeting.


Release 2.3 occurred in January. Release 2.4 expected in September. Incremental daily revisions are still available from the cvs repository and the miSO browser allows the user to chose the latest release or revision.


  • “SO and the RNAO” was presented at the RNA Ontology Consortium meeting - Berlin, July 2008 by Colin Batchelor. Colin also presented a talk by Karen Eilbeck entitled “Ontological Relations for Sequences at DNA, RNA and Protein levels” as she was unable to attend in person due to advanced stage of pregnancy.
  • “Recent developments in the Sequence Ontology” was presented at the OBO foundary workshop in Hinxton in July 2008 by Colin Batchelor from the RSC.
  • “Annotator consistency when classifying sequence attributes” was presented at the GOC meeting in Salt Lake City in March 2007.


SO and RNAO held a joint workshop in April 2008 in Salt Lake City, funded by the NSF, entitled: Ontological Relations for Sequences at DNA, RNA and Protein levels. The aim of this workshop was to build a common infrastructure to annotate both the features and 2 and 3 dimensional structure of sequence. The end product of this work will be a description Logic representation of the core terms and relationships in SO.


“The Protein Feature Ontology: a controlled vocabulary for protein feature annotations.” This paper describing the protein features in biosapiens and SO has been submitted and is under review.