My NCBISign In
Relations in biomedical ontologies
Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse
Genome Biol. 2005; 6(5): R46. Published online 2005 April 28. doi: 10.1186/gb-2005-6-5-r46
PMCID:
PMC1175958
Abstract Full Text PDF–359K

Is Cited by the Following 127 Articles in this Archive:

Improving integrative searching of systems chemical biology data using semantic annotation
Bin Chen, Ying Ding, David J Wild
J Cheminform. 2012; 4: 6. Published online 2012 March 8. doi: 10.1186/1758-2946-4-6
PMCID:
PMC3320537
Abstract Full Text PDF–503K
Uberon, an integrative multi-species anatomy ontology
Christopher J Mungall, Carlo Torniai, Georgios V Gkoutos, Suzanna E Lewis, Melissa A Haendel
Genome Biol. 2012; 13(1): R5. Published online 2012 January 31. doi: 10.1186/gb-2012-13-1-r5
PMCID:
PMC3334586
Abstract Full Text PDF–1.1M Supplementary Material
Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities
Lars Vogt, Peter Grobe, Björn Quast, Thomas Bartolomaeus
PLoS One. 2012; 7(1): e30004. Published online 2012 January 9. doi: 10.1371/journal.pone.0030004
PMCID:
PMC3253816
Abstract Full Text PDF–1.4M Supplementary Material
A unified framework for managing provenance information in translational research
Satya S Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P Sheth
BMC Bioinformatics. 2011; 12: 461. Published online 2011 November 29. doi: 10.1186/1471-2105-12-461
PMCID:
PMC3298549
Abstract Full Text PDF–4.4M
Unintended consequences of existential quantifications in biomedical ontologies
Martin Boeker, Ilinca Tudose, Janna Hastings, Daniel Schober, Stefan Schulz
BMC Bioinformatics. 2011; 12: 456. Published online 2011 November 24. doi: 10.1186/1471-2105-12-456
PMCID:
PMC3280341
Abstract Full Text PDF–501K Supplementary Material
Disease Ontology: a backbone for disease semantic integration
Lynn Marie Schriml, Cesar Arze, Suvarna Nadendla, Yu-Wei Wayne Chang, Mark Mazaitis, Victor Felix, Gang Feng, Warren Alden Kibbe
Nucleic Acids Res. 2012 January; 40(D1): D940–D946. Published online 2011 November 12. doi: 10.1093/nar/gkr972
PMCID:
PMC3245088
Abstract Full Text PDF–1.9M
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology
Yu Lin, Zuoshuang Xiang, Yongqun He
J Biomed Semantics. 2011; 2: 9. Published online 2011 October 31. doi: 10.1186/2041-1480-2-9
PMCID:
PMC3217896
Abstract Full Text PDF–2.4M Supplementary Material
Controlled vocabularies and semantics in systems biology
Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère
Mol Syst Biol. 2011; 7: 543. Published online 2011 October 25. doi: 10.1038/msb.2011.77
PMCID:
PMC3261705
Abstract Full Text PDF–1.4M
The representation of protein complexes in the Protein Ontology (PRO)
Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu
BMC Bioinformatics. 2011; 12: 371. Published online 2011 September 19. doi: 10.1186/1471-2105-12-371
PMCID:
PMC3189193
Abstract Full Text PDF–1.1M
The Challenges of Defining Oral Cancer: Analysis of an Ontological Approach
Jose Luis Tapia, Louis J. Goldberg
Head Neck Pathol. 2011 December; 5(4): 376–384. Published online 2011 September 14. doi: 10.1007/s12105-011-0300-0
PMCID:
PMC3210219
Free in PMC on 2012/09/14
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution
Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm
J Biomed Semantics. 2011; 2: 6. Published online 2011 September 13. doi: 10.1186/2041-1480-2-6
PMCID:
PMC3198872
Abstract Full Text PDF–4.3M
The Cognitive Atlas: Toward a Knowledge Foundation for Cognitive Neuroscience
Russell A. Poldrack, Aniket Kittur, Donald Kalar, Eric Miller, Christian Seppa, Yolanda Gil, D. Stott Parker, Fred W. Sabb, Robert M. Bilder
Front Neuroinform. 2011; 5: 17. Published online 2011 September 6. doi: 10.3389/fninf.2011.00017
PMCID:
PMC3167196
Abstract Full Text PDF–2.0M
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions
Bernard de Bono, Robert Hoehndorf , Sarala Wimalaratne, George Gkoutos, Pierre Grenon
BMC Res Notes. 2011; 4: 313. Published online 2011 August 30. doi: 10.1186/1756-0500-4-313
PMCID:
PMC3192696
Abstract Full Text PDF–2.9M
Integrating systems biology models and biomedical ontologies
Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook, Georgios V Gkoutos
BMC Syst Biol. 2011; 5: 124. Published online 2011 August 11. doi: 10.1186/1752-0509-5-124
PMCID:
PMC3170340
Abstract Full Text PDF–984K
Grains, components and mixtures in biomedical ontologies
Ludger Jansen, Stefan Schulz
J Biomed Semantics. 2011; 2(Suppl 4): S2. Published online 2011 August 9. doi: 10.1186/2041-1480-2-S4-S2
PMCID:
PMC3194169
Abstract Full Text PDF–279K Supplementary Material
Representing dispositions
Johannes Röhl, Ludger Jansen
J Biomed Semantics. 2011; 2(Suppl 4): S4. Published online 2011 August 9. doi: 10.1186/2041-1480-2-S4-S4
PMCID:
PMC3194171
Abstract Full Text PDF–478K
How the gene ontology evolves
Sabina Leonelli, Alexander D Diehl, Karen R Christie, Midori A Harris, Jane Lomax
BMC Bioinformatics. 2011; 12: 325. Published online 2011 August 5. doi: 10.1186/1471-2105-12-325
PMCID:
PMC3166943
Abstract Full Text PDF–1.4M
Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning
Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos
PLoS One. 2011; 6(7): e22006. Published online 2011 July 18. doi: 10.1371/journal.pone.0022006
PMCID:
PMC3138764
Abstract Full Text PDF–387K
The GUDMAP database – an online resource for genitourinary research
Simon D. Harding, Chris Armit, Jane Armstrong, Jane Brennan, Ying Cheng, Bernard Haggarty, Derek Houghton, Sue Lloyd-MacGilp, Xingjun Pi, Yogmatee Roochun, Mehran Sharghi, Christopher Tindal, Andrew P. McMahon, Brian Gottesman, Melissa H. Little, Kylie Georgas, Bruce J. Aronow, S. Steven Potter, Eric W. Brunskill, E. Michelle Southard-Smith, Cathy Mendelsohn, Richard A. Baldock, Jamie A. Davies, Duncan Davidson
Development. 2011 July 1; 138(13): 2845–2853. doi: 10.1242/dev.063594
PMCID:
PMC3188593
Free in PMC on 2012/07/01
Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases
Filipe Santana, Daniel Schober, Zulma Medeiros, Fred Freitas, Stefan Schulz
Bioinformatics. 2011 July 1; 27(13): i349–i356. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr226
PMCID:
PMC3117366
Abstract Full Text
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
Joanne S Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine K Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, Scott M Marshall, James P McCusker, Deborah L McGuinness, Chimezie Ogbuji, Elgar Pichler, Robert L Powers, Eric Prud’hommeaux, Matthias Samwald, Lynn Schriml, Peter J Tonellato, Patricia L Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier
J Biomed Semantics. 2011; 2(Suppl 2): S1. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S1
PMCID:
PMC3102889
Abstract Full Text PDF–1002K Supplementary Material
Integration and publication of heterogeneous text-mined relationships on the Semantic Web
Adrien Coulet, Yael Garten, Michel Dumontier, Russ B Altman, Mark A Musen, Nigam H Shah
J Biomed Semantics. 2011; 2(Suppl 2): S10. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S10
PMCID:
PMC3102890
Abstract Full Text PDF–1.2M Supplementary Material
An open annotation ontology for science on web 3.0
Paolo Ciccarese, Marco Ocana, Leyla Jael Garcia Castro, Sudeshna Das, Tim Clark
J Biomed Semantics. 2011; 2(Suppl 2): S4. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S4
PMCID:
PMC3102893
Abstract Full Text PDF–1.0M
Automating generation of textual class definitions from OWL to English
Robert Stevens, James Malone, Sandra Williams, Richard Power, Allan Third
J Biomed Semantics. 2011; 2(Suppl 2): S5. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S5
PMCID:
PMC3102894
Abstract Full Text PDF–1.2M
Scalable representations of diseases in biomedical ontologies
Stefan Schulz, Kent Spackman, Andrew James, Cristian Cocos, Martin Boeker
J Biomed Semantics. 2011; 2(Suppl 2): S6. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S6
PMCID:
PMC3102895
Abstract Full Text PDF–329K
Developing a kidney and urinary pathway knowledge base
Simon Jupp, Julie Klein, Joost Schanstra, Robert Stevens
J Biomed Semantics. 2011; 2(Suppl 2): S7. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S7
PMCID:
PMC3102896
Abstract Full Text PDF–718K
Representation of research hypotheses
Larisa N Soldatova, Andrey Rzhetsky
J Biomed Semantics. 2011; 2(Suppl 2): S9. Published online 2011 May 17. doi: 10.1186/2041-1480-2-S2-S9
PMCID:
PMC3102898
Abstract Full Text PDF–1.1M
TparvaDB: a database to support Theileria parva vaccine development
Paul Visendi, Wanjiku Ng'ang'a, Wallace Bulimo, Richard Bishop, James Ochanda, Etienne P. de Villiers
Database (Oxford) 2011; 2011: bar015. Published online 2011 May 4. doi: 10.1093/database/bar015
PMCID:
PMC3092609
Abstract Full Text PDF–824K
Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology
Lars Vogt, Peter Grobe, Björn Quast, Thomas Bartolomaeus
PLoS One. 2011; 6(4): e18794. Published online 2011 April 21. doi: 10.1371/journal.pone.0018794
PMCID:
PMC3080885
Abstract Full Text PDF–707K
The Representation of Heart Development in the Gene Ontology
Varsha K. Khodiyar, David P. Hill, Doug Howe, Tanya Z. Berardini, Susan Tweedie, Philippa J. Talmud, Ross Breckenridge, Shoumo Bhattarcharya, Paul Riley, Peter Scambler, Ruth C. Lovering
Dev Biol. Author manuscript; available in PMC 2012 June 1.
Published in final edited form as: Dev Biol. 2011 June 1; 354(1): 9–17. Published online 2011 March 17. doi: 10.1016/j.ydbio.2011.03.011
PMCID:
PMC3302178
Free in PMC on 2012/06/01
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