The following research articles provide excellent, concrete examples of ontological engineering in biological knowledge domains directly relevant to Mouse BIRN research efforts. They each focus on a different aspect of how extended semantic formalisms can be used to represent complex and highly integrative scientific knowledge relevant to the biological questions being addressed by various Mouse BIRN projects. If one disregards for the present the issue of whether such complexity is achievable and/or useful at this stage in the evolution of Mouse BIRN, these papers prime value is in their cogent, logical deconstruction of biological examples where onto-centric data management & access methods can provide significant added value.
| Authors |
YoP |
Title |
Citation |
| Aitken S. |
2005 |
Formalizing concepts of species, sex and developmental stage in anatomical ontologies. |
Bioinformatics. Jun 1, v21, n11, p2773-9. Epub 2005 Mar 29 |
| Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector and Cornelius Rosse |
2005 |
Relations in Biomedical Ontologies (Method). |
Genome Biology, 6:R46, April 2005 (doi:10.1186/gb-2005-6-5-r46). |
| Jonathan Bard |
2005 |
Anatomics - The intersection of anatomy and bioinformatics. |
J Anat., v206, n1, p1-16, Jan. 2005. |
| Nicki Tiffin, Janet F. Kelso, Alan R. Powell, Hong Pan, Vladimir B. Bajic and Winston A. Hide |
2005 |
Integration of text- and data-mining using ontologies successfully selects disease gene candidates. |
Nucleic Acids Research, v33, n5, p1544-1552. |
| Gangemi A, Catenacci C, Battaglia M. |
2004 |
Inflammation ontology design pattern: an exercise in building a core biomedical ontology with descriptions and situations. |
Stud Health Technol Inform., v102, p64-80. |
| Natalya F. Noy, Daniel L. Rubin, and Mark A. Musen. |
2004 |
Making Biomedical Ontologies and Ontological Repositories Work. |
IEEE Intelligent Sys., Nov/Dec 2004, p78. |
| Songmao Zhang, Peter Mork, Olivier Bodenreider. |
2004 |
Lessons Learned from Aligning two Representations of Anatomy. |
Proceedings of the KR 2004 Workshop on Formal Biomedical Knowledge Representation. |
| Amarnath Gupta, Bertram Ludascher, Jeffrey S. Grethe, Maryann E. Martone. |
2003 |
Towards a formalization of disease-specific ontologies for neuroinformatics. |
Neural Networks, v16, p1277-1292. |
| P.K. Tulipano, W.S. Millar, and J.J. Cimino. |
2003 |
Linking Molecular Imaging Technology to the Gene Ontology (GO). |
Pacific Symposium on Biocomputing v8, p613-623. |
| C.J. Wroe, R. Stevens, C. A. Goble. |
2003 |
A Methodology to Migrate The Gene Ontology To A Description Logic Environment Using DAML+OIL. |
Pacific Symposium on Biocomputing 8:624-635. |
| B. Smith, J. Williams and S. Schulze-Kremer. |
2003 |
The Ontology of the Gene Ontology. |
Proceedings of the Annual Symposium of the American Medical Informatics Association, Washington DC, November 2003, 609–613. |
| David P. Hill, Judith A. Blake, Joel E. Richardson, and Martin Ringwald. |
2002 |
Extension and Integration of the Gene Ontology(GO): Combining GO Vocabularies With External Vocabularies. |
Genome Research, v12, p1982-1991. |
| Robert E. Marc and Bryan W. Jones.
RobertMarcJN2002.pdf |
2002 |
Molecular Phenotyping of Retinal Ganglion Cells. |
Journal of Neuroscience 22(2):413-427 |
| Robert Stevens, Chris Wroe, Sean Bechhofer, Phillip Lord, Alan Rector and Carole Goble. |
2002 |
Building ontologies in DAML + OIL. |
Comp Funct Genom, v4, p133–141. |
RobertMarcJN2002.pdf