Sequence Ontology Publications

Intelligently Designed Ontology Alignment: A Case Study from the Sequence Ontology

Michael Sinclair, Michael Bada, and Karen Eilbeck

ISMB Bio-ontologies track conference proceeding 2018

Efforts toward a More Consistent and Interoperable Sequence Ontology

Michael Bada and Karen Eilbeck

Conference Proceeding ICBO 2012

 

Toward a Richer Representation of Sequence Variation in the Sequence Ontology

Michael Bada and Karen Eilbeck

Annotation, Interpretation and Management of Mutations. A workshop at ECCB10.


A standard variation file format for human genome sequences

Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K
 Genome Biology 2010, 11:R88


SOBA: sequence ontology bioinformatics analysis

Moore B, Fan G, Eilbeck K
Nucl Acids Res 2010, 38(suppl 2)


Evolution of the Sequence Ontology terms and relationships

Mungall, C. J. Batchelor C. Eilbeck K.
J Biomed Inform. 2010 Mar 10


Quantitative Measures for the Management and Comparison of Annotated Genomes.

Eilbeck K., Moore B., Holt C., Yandell M.
BMC Bioinformatics 2009, 10:67


The Protein Feature Ontology: a tool for the unification of
protein feature annotations.

Reeves G.A., Eilbeck K., Magrane M., O’Donovan C.,
Montecchi-Palazzi L., Harris M.A., Orchard S., Jimenez R.C., Prlic
A., Hubbard T.J., Hermjakob H., Thornton J.M.
Bioinformatics. 2008 Dec 1; 24(23):2767-72


A Chado case study: an ontology-based modular schema for
representing genome-associated biological information

Christopher J. Mungall 1, David B. Emmert, and The FlyBase Consortium.
Bioinformatics 2007 23(13):i337-i346


The Sequence Ontology: A tool for the unification of genome
annotations.

Eilbeck K., Lewis S., Mungall C.J., Yandell M., Stein
L., Durbin R., Ashburner M.
Genome Biology (2005) 6:R44


Sequence Ontology Annotation Guide.

Eilbeck K. and Lewis S.
Comparative and Functional Genomics (2004) 5:642-647