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The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data
Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald
Genome Biol. 2005; 6(3): R29. Published online 2005 February 15. doi: 10.1186/gb-2005-6-3-r29
PMCID:
PMC1088948
Abstract Full Text PDF–447K

Is Cited by the Following 35 Articles in this Archive:

Towards valid and reusable reference alignments — ten basic quality checks for ontology alignments and their application to three different reference data sets
Elena Beisswanger, Udo Hahn
J Biomed Semantics. 2012; 3(Suppl 1): S4. Published online 2012 April 24. doi: 10.1186/2041-1480-3-S1-S4
PMCID:
PMC3337267
Abstract Full Text PDF–602K
The mouse–human anatomy ontology mapping project
Terry F. Hayamizu, Sherri de Coronado, Gilberto Fragoso, Nicholas Sioutos, James A. Kadin, Martin Ringwald
Database (Oxford) 2012; 2012: bar066. Published online 2012 February 13. doi: 10.1093/database/bar066
PMCID:
PMC3308156
Abstract Full Text PDF–712K
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
PhenomeNET: a whole-phenome approach to disease gene discovery
Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos
Nucleic Acids Res. 2011 October; 39(18): e119. Published online 2011 July 6. doi: 10.1093/nar/gkr538
PMCID:
PMC3185433
Abstract Full Text PDF–1.6M
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
A common layer of interoperability for biomedical ontologies based on OWL EL
Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala Wimalaratne, Dietrich Rebholz-Schuhmann, Paul Schofield, Georgios V. Gkoutos
Bioinformatics. 2011 April 1; 27(7): 1001–1008. Published online 2011 February 21. doi: 10.1093/bioinformatics/btr058
PMCID:
PMC3065691
Abstract Full Text PDF–126K
An ontology-based comparative anatomy information system
Ravensara S. Travillian, Kremena Diatchka, Tejinder K. Judge, Katarzyna Wilamowska, Linda G. Shapiro
Artif Intell Med. Author manuscript; available in PMC 2012 January 1.
Published in final edited form as: Artif Intell Med. 2011 January; 51(1): 1–15. Published online 2010 December 10. doi: 10.1016/j.artmed.2010.10.001
PMCID:
PMC3055271
Abstract Full Text PDF–1.7M
Identifying Granularity Differences between Large Biomedical Ontologies through Rules
Pengfei Sun, Songmao Zhang
AMIA Annu Symp Proc. 2010; 2010: 927–931. Published online 2010 November 13.
PMCID:
PMC3041335
Abstract Full Text PDF–274K
The mouse Gene Expression Database (GXD): 2011 update
Jacqueline H. Finger, Constance M. Smith, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald
Nucleic Acids Res. 2011 January; 39(Database issue): D835–D841. Published online 2010 November 8. doi: 10.1093/nar/gkq1132
PMCID:
PMC3013713
Abstract Full Text PDF–8.6M
Pathbase and the MPATH ontology: Community Resources for Mouse Histopathology
Paul N. Schofield, Michael Gruenberge, John P. Sundberg
Vet Pathol. Author manuscript; available in PMC 2011 November 1.
Published in final edited form as: Vet Pathol. 2010 November; 47(6): 1016–1020. Published online 2010 June 29. doi: 10.1177/0300985810374845
PMCID:
PMC3038412
Abstract Full Text PDF–84K
Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology
David P. Hill, Tanya Z. Berardini, Douglas G. Howe, Kimberly M. Van Auken
Mol Reprod Dev. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Mol Reprod Dev. 2010 April; 77(4): 314–329. doi: 10.1002/mrd.21130
PMCID:
PMC2830379
Abstract Full Text PDF–837K
Applying the functional abnormality ontology pattern to anatomical functions
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso
J Biomed Semantics. 2010; 1: 4. Published online 2010 March 31. doi: 10.1186/2041-1480-1-4
PMCID:
PMC2895731
Abstract Full Text PDF–592K
Integrating phenotype ontologies across multiple species
Christopher J Mungall, Georgios V Gkoutos, Cynthia L Smith, Melissa A Haendel, Suzanna E Lewis, Michael Ashburner
Genome Biol. 2010; 11(1): R2. Published online 2010 January 8. doi: 10.1186/gb-2010-11-1-r2
PMCID:
PMC2847714
Abstract Full Text PDF–842K
More than a decade of developmental gene expression atlases: where are we now?
Bouke A. de Boer, Jan M. Ruijter, Frans P. J. M. Voorbraak, Antoon F. M. Moorman
Nucleic Acids Res. 2009 December; 37(22): 7349–7359. Published online 2009 December. doi: 10.1093/nar/gkp819
Correction in:
Nucleic Acids Res. 2010 May; 38(9): 3147.
PMCID:
PMC2794177
Abstract Full Text PDF–1.4M Correction
A Data Capture Tool for Mouse Pathology Phenotyping
Beth A. Sundberg, Paul N. Schofield, Michael Gruenberger, John P. Sundberg
Vet Pathol. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: Vet Pathol. 2009 November; 46(6): 1230–1240. Published online 2009 July 15. doi: 10.1354/vp.09-VP-0002-S-FL
PMCID:
PMC2879151
Abstract Full Text PDF–2.2M
aGEM: an integrative system for analyzing spatial-temporal gene-expression information
Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, José María Carazo
Bioinformatics. 2009 October 1; 25(19): 2566–2572. Published online 2009 July 9. doi: 10.1093/bioinformatics/btp422
PMCID:
PMC2752607
Abstract Full Text PDF–266K Supplementary Material
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data
Tim Beck, Hugh Morgan, Andrew Blake, Sara Wells, John M Hancock, Ann-Marie Mallon
BMC Bioinformatics. 2009; 10(Suppl 5): S2. Published online 2009 May 6. doi: 10.1186/1471-2105-10-S5-S2
PMCID:
PMC2679402
Abstract Full Text PDF–486K
PhenoGO: an integrated resource for the multiscale mining of clinical and biological data
Lee T Sam, Eneida A Mendonça, Jianrong Li, Judith Blake, Carol Friedman, Yves A Lussier
BMC Bioinformatics. 2009; 10(Suppl 2): S8. Published online 2009 February 5. doi: 10.1186/1471-2105-10-S2-S8
PMCID:
PMC2646241
Abstract Full Text PDF–1.6M
Muscle Research and Gene Ontology: New standards for improved data integration
Erika Feltrin, Stefano Campanaro, Alexander D Diehl, Elisabeth Ehler, Georgine Faulkner, Jennifer Fordham, Chiara Gardin, Midori Harris, David Hill, Ralph Knoell, Paolo Laveder, Lorenza Mittempergher, Alessandra Nori, Carlo Reggiani, Vincenzo Sorrentino, Pompeo Volpe, Ivano Zara, Giorgio Valle, Jennifer Deegan née Clark
BMC Med Genomics. 2009; 2: 6. Published online 2009 January 29. doi: 10.1186/1755-8794-2-6
PMCID:
PMC2657163
Abstract Full Text PDF–490K
The Mouse Genome Database genotypes::phenotypes
Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, the Mouse Genome Database Group
Nucleic Acids Res. 2009 January; 37(Database issue): D712–D719. Published online 2009 January. doi: 10.1093/nar/gkn886
PMCID:
PMC2686566
Abstract Full Text PDF–7.7M
The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis
Cynthia L. Smith, Janan T. Eppig
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2010 January 4.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2009; 1(3): 390–399. doi: 10.1002/wsbm.44
PMCID:
PMC2801442
Abstract Full Text PDF–1.4M
Integrating Mouse Anatomy and Pathology Ontologies into a Phenotyping Database: Tools for Data Capture and Training
John P. Sundberg, Beth A. Sundberg, Paul Schofield
Mamm Genome. Author manuscript; available in PMC 2010 March 24.
Published in final edited form as: Mamm Genome. 2008 June; 19(6): 413–419. Published online 2008 September 17. doi: 10.1007/s00335-008-9123-z
PMCID:
PMC2844541
Abstract Full Text PDF–968K
Gene Ontology annotations: what they mean and where they come from
David P Hill, Barry Smith, Monica S McAndrews-Hill, Judith A Blake
BMC Bioinformatics. 2008; 9(Suppl 5): S2. Published online 2008 April 29. doi: 10.1186/1471-2105-9-S5-S2
PMCID:
PMC2367625
Abstract Full Text PDF–372K
The Mouse Tumor Biology database
Debra M. Krupke, Dale A. Begley, John P. Sundberg, Carol J. Bult, Janan T. Eppig
Nat Rev Cancer. Author manuscript; available in PMC 2009 June 1.
Published in final edited form as: Nat Rev Cancer. 2008 June; 8(6): 459–465. Published online 2008 April 24. doi: 10.1038/nrc2390
PMCID:
PMC2574871
Abstract Full Text PDF–1.3M
Simplified ontologies allowing comparison of developmental mammalian gene expression
Adele Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide
Genome Biol. 2007; 8(10): R229. Published online 2007 October 25. doi: 10.1186/gb-2007-8-10-r229
PMCID:
PMC2246303
Abstract Full Text PDF–596K Supplementary Material
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies
Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre
BMC Bioinformatics. 2007; 8: 377. Published online 2007 October 9. doi: 10.1186/1471-2105-8-377
PMCID:
PMC2180186
Abstract Full Text PDF–537K
Celsius: a community resource for Affymetrix microarray data
Allen Day, Marc RJ Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson
Genome Biol. 2007; 8(6): R112. Published online 2007 June 14. doi: 10.1186/gb-2007-8-6-r112
PMCID:
PMC2394754
Abstract Full Text PDF–583K Supplementary Material
MPHASYS: a mouse phenotype analysis system
R Brent Calder, Rudolf B Beems, Harry van Steeg, I Saira Mian, Paul HM Lohman, Jan Vijg
BMC Bioinformatics. 2007; 8: 183. Published online 2007 June 6. doi: 10.1186/1471-2105-8-183
PMCID:
PMC1899519
Abstract Full Text PDF–874K
The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant
Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. McCouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee
Plant Physiol. 2007 February; 143(2): 587–599. doi: 10.1104/pp.106.092825
PMCID:
PMC1803752
Abstract Full Text PDF–1.2M Supplementary Material
Experience in Aligning Anatomical Ontologies
Songmao Zhang, Olivier Bodenreider
Int J Semant Web Inf Syst. Author manuscript; available in PMC 2008 October 29.
Published in final edited form as: Int J Semant Web Inf Syst. 2007; 3(2): 1–26.
PMCID:
PMC2575410
Abstract Full Text PDF–814K
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