MIND Informatics develops and applies integrative computational methods in biomedical and brain research, working with leading clinicians and researchers to understand and cure neurological disorders.


Domeo is an extensible web application enabling users to visually and efficiently create and share ontology-based stand-off annotation on HTML or XML document targets. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control.

Related Publications

  • Ciccarese P, Soiland-Reyes S, Clark T. (In press) Web Annotation as a First-Class Object. IEEE Internet Computing.
  • Ciccarese P, Ocana M and Clark T (2012) Open semantic annotation of scientific publications using DOMEO. Journal of Biomedical Semantics 2012, 3(Suppl 1):S1 PMID.: 2254159
  • Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe J, Martone ME: A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database vol. 2012, March 2012. PMID: 22434839
  • Ciccarese P, Ocana M, Clark T. DOMEO: a web-based tool for semantic annotation of online documents. Bio-Ontologies 2011, July 15-16, Vienna Austria
  • Clark T, Ciccarese P, Attwood T, de Waard A and Pettifer S. A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications. Beyond the PDF, San Diego, 19-21 Jan 2011.