MouseBIRN.BioOntologyBibliography (r1.1 vs. r1.11)
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 <<O>>  Difference Topic BioOntologyBibliography (r1.11 - 28 Jan 2006 - MouseBIRN)

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Bio-Ontology References

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Genome Research, v12, p1982-1991.
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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.
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Studies in Health Technology and Informatics IOS Press
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META FILEATTACHMENT RobertMarcJN2002?.pdf attr="" comment="Superb paper on an objective multivariate method to classify cells" date="1138413834" path="RobertMarcJN2002.pdf" size="1841475" user="mouseBIRN" version="1.1"

 <<O>>  Difference Topic BioOntologyBibliography (r1.10 - 18 Nov 2005 - MouseBIRN)

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Bio-Ontology References

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Pacific Symposium on Biocomputing 8:624-635.
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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.

 <<O>>  Difference Topic BioOntologyBibliography (r1.9 - 09 Nov 2005 - MouseBIRN)

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Bio-Ontology References

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Bioinformatics. Jun 1, v21, n11, p2773-9. Epub 2005 Mar 29
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Barry Smith, Werner Ceusters, Bert Klagges, Jacob Kφhler, 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.

 <<O>>  Difference Topic BioOntologyBibliography (r1.8 - 23 Jun 2005 - MouseBIRN)

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Journals In Which One Typical Will Find Research Articles on Semantic Biomedical Ontologies

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Journals In Which One Typical Will Find Research Articles on Biomedical Ontologies and Onto-centric Data Mining



 <<O>>  Difference Topic BioOntologyBibliography (r1.7 - 10 Jun 2005 - MouseBIRN)

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Bio-Ontology References

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Jonathan Bard 2005 Anatomics - The intersection of anatomy and bioinformatics.
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Nucleic Acids Research, v33, n5, p1544-1552.
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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

 <<O>>  Difference Topic BioOntologyBibliography (r1.6 - 06 Jun 2005 - MouseBIRN)

META TOPICPARENT MouseBIRNOntologyRelatedResources

Bio-Ontology References

Onto-centric Views of Biological Knowledge: some useful examples

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.
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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
Jonathan Bard 2005 Anatomics - The intersection of anatomy and bioinformatics. Nucleic Acids Research, v33, n5, p1544-1552.
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.
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 Stevens, Chris Wroe, Sean Bechhofer, Phillip Lord, Alan Rector and Carole Goble. 2002 Building ontologies in DAML + OIL. Comp Funct Genom, v4, p133–141.

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Journals In Which One Typical Will Find Research Articles on Semantic Biomedical Ontologies

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 <<O>>  Difference Topic BioOntologyBibliography (r1.5 - 06 Jun 2005 - MouseBIRN)

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Bio-Ontology References

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 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.

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  • Jonathan Bard. (2005) Anatomics: the intersection of anatomy and bioinformatics. J. Anatomy, v206, p1-16.
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  • 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
  • Jonathan Bard. (2005) Anatomics: the intersection of anatomy and bioinformatics. J. Anatomy, v206, p1-16.
  • 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.

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  • 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.
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    Artificial Intelligence in Medicine
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    Elsevier
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    Elsevier, Inc.

    Bioinformatics Oxford University Press
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    BMC Bioinformatics BioMed Central

    Comparative and Functional Genomics John Wiley & Sons
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    Genome Biology BioMed Central

    Genome Research Cold Spring Harbor Press
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    Bioinformation Systems e.V
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    Journal of Biomedical Informatics Elsevier, Inc.

    Neuroinformatics Humana Press
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    Nucleic Acids Researc
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    Nucleic Acids Research

    Oxford University Press
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    Studies in Health Technology and Informatics IOS Press


     <<O>>  Difference Topic BioOntologyBibliography (r1.4 - 06 Jun 2005 - MouseBIRN)

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    Bio-Ontology References

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    Journals In Which One Typical Will Find Research Articles on Semantic Bio-ontologies

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    Journals In Which One Typical Will Find Research Articles on Semantic Biomedical Ontologies


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    Journal Title Publisher
    Artificial Intelligence in Medicine Elsevier
    Bioinformatics Oxford University Press
    Comparative and Functional Genomics John Wiley & Sons
    Genome Research Cold Spring Harbor Press
    IEEE Intelligent Systems IEEE Computer Society
    In Silico Biology (ISB) Bioinformation Systems e.V
    Neuroinformatics Humana Press
    Nucleic Acids Researc Oxford University Press


     <<O>>  Difference Topic BioOntologyBibliography (r1.3 - 06 Jun 2005 - MouseBIRN)

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    Bio-Ontology References

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  • 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.
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    Tools For Curation, Searching & Data Mining with Semantic Bio-ontologies

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    Bibliography of Tools For Curation, Searching & Data Mining with Semantic Bio-ontologies

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    Journals In Which One Typical Will Find Research Articles on Semantic Bio-ontologies


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     <<O>>  Difference Topic BioOntologyBibliography (r1.2 - 06 Jun 2005 - MouseBIRN)

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    Onto-centric Views of Biological Knowledge: some useful examples

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    Onto-centric Views of Biological Knowledge: some useful examples


    		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.
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  • 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 Stevens, Chris Wroe, Sean Bechhofer, Phillip Lord, Alan Rector and Carole Goble. (2002) Building ontologies in DAML + OIL. Comp Funct Genom, v4, p133–141.
  • 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.
  • Jonathan Bard. (2005) Anatomics: the intersection of anatomy and bioinformatics. J. Anatomy, v206, p1-16.
  • Natalya F. Noy, Daniel L. Rubin, and Mark A. Musen (2000) Making Biomedical Ontologies and Ontological Repositories Work.IEEE Intelligent Sys., Nov/Dec 2004, p78.
    • >
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  • Jonathan Bard. (2005) Anatomics: the intersection of anatomy and bioinformatics. J. Anatomy, v206, p1-16.
  • 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.
  • 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 Stevens, Chris Wroe, Sean Bechhofer, Phillip Lord, Alan Rector and Carole Goble. (2002) Building ontologies in DAML + OIL. Comp Funct Genom, v4, p133–141.

    • Tools For Curation, Searching & Data Mining with Semantic Bio-ontologies

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     <<O>>  Difference Topic BioOntologyBibliography (r1.1 - 04 Jun 2005 - MouseBIRN)
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    META TOPICPARENT MouseBIRNOntologyRelatedResources

    Bio-Ontology References

    Onto-centric Views of Biological Knowledge: some useful examples

    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.
    • 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 Stevens, Chris Wroe, Sean Bechhofer, Phillip Lord, Alan Rector and Carole Goble. (2002) Building ontologies in DAML + OIL. Comp Funct Genom, v4, p133–141.
    • 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.
    • Jonathan Bard. (2005) Anatomics: the intersection of anatomy and bioinformatics. J. Anatomy, v206, p1-16.
    • Natalya F. Noy, Daniel L. Rubin, and Mark A. Musen (2000) Making Biomedical Ontologies and Ontological Repositories Work.IEEE Intelligent Sys., Nov/Dec 2004, p78.

    Topic: BioOntologyBibliography . { View | Diffs | r1.11 | > | r1.10 | > | r1.9 | More }

    Revision r1.1 - 04 Jun 2005 - 11:50 - MouseBIRN
    Revision r1.11 - 28 Jan 2006 - 02:04 - MouseBIRN