{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T12:58:59Z","timestamp":1776517139660,"version":"3.51.2"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,1,31]],"date-time":"2012-01-31T00:00:00Z","timestamp":1327968000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2012,1,31]],"date-time":"2012-01-31T00:00:00Z","timestamp":1327968000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/uberon.org\">http:\/\/uberon.org<\/jats:ext-link><\/jats:p>","DOI":"10.1186\/gb-2012-13-1-r5","type":"journal-article","created":{"date-parts":[[2012,1,31]],"date-time":"2012-01-31T14:45:18Z","timestamp":1328021118000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":665,"title":["Uberon, an integrative multi-species anatomy ontology"],"prefix":"10.1186","volume":"13","author":[{"given":"Christopher J","family":"Mungall","sequence":"first","affiliation":[]},{"given":"Carlo","family":"Torniai","sequence":"additional","affiliation":[]},{"given":"Georgios V","family":"Gkoutos","sequence":"additional","affiliation":[]},{"given":"Suzanna E","family":"Lewis","sequence":"additional","affiliation":[]},{"given":"Melissa A","family":"Haendel","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,1,31]]},"reference":[{"key":"2753_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.0021-8782.2005.00376.x","volume":"206","author":"JB Bard","year":"2005","unstructured":"Bard JB: Anatomics: the intersection of anatomy and bioinformatics. J Anat. 2005, 206: 1-16. 10.1111\/j.0021-8782.2005.00376.x.","journal-title":"J Anat"},{"key":"2753_CR2","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.jbi.2003.11.007","volume":"36","author":"C Rosse","year":"2003","unstructured":"Rosse C, Mejino JL: A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2003, 36: 478-500. 10.1016\/j.jbi.2003.11.007.","journal-title":"J Biomed Inform"},{"key":"2753_CR3","doi-asserted-by":"publisher","first-page":"D768","DOI":"10.1093\/nar\/gkm956","volume":"36","author":"J Sprague","year":"2008","unstructured":"Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M: The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 2008, 36: D768-772.","journal-title":"Nucleic Acids Res"},{"key":"2753_CR4","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/1471-213X-8-92","volume":"8","author":"E Segerdell","year":"2008","unstructured":"Segerdell E, Bowes JB, Pollet N, Vize PD: An ontology for Xenopus anatomy and development. BMC Dev Biol. 2008, 8: 92-10.1186\/1471-213X-8-92.","journal-title":"BMC Dev Biol"},{"key":"2753_CR5","doi-asserted-by":"publisher","first-page":"D484","DOI":"10.1093\/nar\/gkj068","volume":"34","author":"G Grumbling","year":"2006","unstructured":"Grumbling G, Strelets V: FlyBase: anatomical data, images and queries. Nucleic Acids Res. 2006, 34: D484-488. 10.1093\/nar\/gkj068.","journal-title":"Nucleic Acids Res"},{"key":"2753_CR6","doi-asserted-by":"publisher","first-page":"R29","DOI":"10.1186\/gb-2005-6-3-r29","volume":"6","author":"TF Hayamizu","year":"2005","unstructured":"Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M: The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 2005, 6: R29-10.1186\/gb-2005-6-3-r29.","journal-title":"Genome Biol"},{"key":"2753_CR7","unstructured":"Human developmental anatomy, abstract version, v2. [http:\/\/obofoundry.org\/cgi-bin\/detail.cgi?id=human-dev-anat-abstract2]"},{"key":"2753_CR8","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1385\/NI:1:4:309","volume":"1","author":"RA Baldock","year":"2003","unstructured":"Baldock RA, Bard JB, Burger A, Burton N, Christiansen J, Feng G, Hill B, Houghton D, Kaufman M, Rao J, Sharpe J, Ross A, Stevenson P, Venkataraman S, Waterhouse A, Yang Y, Davidson DR: EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics. 2003, 1: 309-325. 10.1385\/NI:1:4:309.","journal-title":"Neuroinformatics"},{"key":"2753_CR9","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/s12021-008-9032-z","volume":"6","author":"WJ Bug","year":"2008","unstructured":"Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME: The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics. 2008, 6: 175-194. 10.1007\/s12021-008-9032-z.","journal-title":"Neuroinformatics"},{"key":"2753_CR10","first-page":"414","volume-title":"Proc Annu Symp Comput Appl Med Care","author":"A Rector","year":"1993","unstructured":"Rector A, Nowlan W, Glowinski A: Goals for concept representation in the GALEN project. Proc Annu Symp Comput Appl Med Care. 1993, 414-418."},{"key":"2753_CR11","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.jbi.2009.01.003","volume":"42","author":"S de Coronado","year":"2009","unstructured":"de Coronado S, Wright LW, Fragoso G, Haber MW, Hahn-Dantona EA, Hartel FW, Quan SL, Safran T, Thomas N, Whiteman L: The NCI Thesaurus quality assurance life cycle. J Biomed Inform. 2009, 42: 530-539. 10.1016\/j.jbi.2009.01.003.","journal-title":"J Biomed Inform"},{"key":"2753_CR12","first-page":"822","volume":"129","author":"S Zhang","year":"2007","unstructured":"Zhang S, Bodenreider O: Lessons learned from cross-validating alignments between large anatomical ontologies. Stud Health Technol Inform. 2007, 129: 822-826.","journal-title":"Stud Health Technol Inform"},{"key":"2753_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4018\/jswis.2007040101","volume":"3","author":"S Zhang","year":"2007","unstructured":"Zhang S, Bodenreider O: Experience in aligning anatomical ontologies. Int J Semant Web Inf Syst. 2007, 3: 1-26.","journal-title":"Int J Semant Web Inf Syst"},{"key":"2753_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.artmed.2010.10.001","volume":"51","author":"RS Travillian","year":"2011","unstructured":"Travillian RS, Diatchka K, Judge TK, Wilamowska K, Shapiro LG: An ontology-based comparative anatomy information system. Artif Intell Med. 2011, 51: 1-15. 10.1016\/j.artmed.2010.10.001.","journal-title":"Artif Intell Med"},{"key":"2753_CR15","doi-asserted-by":"publisher","first-page":"R21","DOI":"10.1186\/gb-2005-6-2-r21","volume":"6","author":"J Bard","year":"2005","unstructured":"Bard J, Rhee SY, Ashburner M: An ontology for cell types. Genome Biol. 2005, 6: R21-10.1186\/gb-2005-6-2-r21.","journal-title":"Genome Biol"},{"key":"2753_CR16","doi-asserted-by":"publisher","first-page":"D440","DOI":"10.1093\/nar\/gkm883","volume":"36","author":"Consortium TGO","year":"2008","unstructured":"Consortium TGO: The Gene Ontology project in 2008. Nucleic Acids Res. 2008, 36: D440-444.","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 1","key":"2753_CR17","doi-asserted-by":"publisher","first-page":"S7","DOI":"10.1186\/2041-1480-1-S1-S7","volume":"1","author":"RR Brinkman","year":"2010","unstructured":"Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J, OBI consortium: Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010, 1 (Suppl 1): S7-","journal-title":"J Biomed Semantics"},{"key":"2753_CR18","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1007\/978-1-84628-885-2_16","volume":"6","author":"M Haendel","year":"2008","unstructured":"Haendel M, Neuhaus F, Osumi-Sutherland D: CARO-The Common Anatomy Reference Ontology. Anatomy Ontologies Bioinformatics Principles Practice. 2008, 6: 327-350. 10.1007\/978-1-84628-885-2_16.","journal-title":"Anatomy Ontologies Bioinformatics Principles Practice"},{"key":"2753_CR19","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/sysbio\/syq013","volume":"59","author":"WM Dahdul","year":"2010","unstructured":"Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM: The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol. 2010, 59: 369-383. 10.1093\/sysbio\/syq013.","journal-title":"Syst Biol"},{"key":"2753_CR20","first-page":"367","volume-title":"Pac Symp Biocomput","author":"AM Maglia","year":"2007","unstructured":"Maglia AM, Leopold JL, Pugener LA, Gauch S: An anatomical ontology for amphibians. Pac Symp Biocomput. 2007, 367-378."},{"key":"2753_CR21","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1104\/pp.106.092825","volume":"143","author":"K Ilic","year":"2007","unstructured":"Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY: The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. 2007, 143: 587-599.","journal-title":"Plant Physiol"},{"key":"2753_CR22","doi-asserted-by":"publisher","first-page":"D588","DOI":"10.1093\/nar\/gkn820","volume":"37","author":"A Chang","year":"2009","unstructured":"Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 2009, 37: D588-592. 10.1093\/nar\/gkn820.","journal-title":"Nucleic Acids Res"},{"key":"2753_CR23","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1093\/bioinformatics\/btq099","volume":"26","author":"J Malone","year":"2010","unstructured":"Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010, 26: 1112-1118. 10.1093\/bioinformatics\/btq099.","journal-title":"Bioinformatics"},{"key":"2753_CR24","unstructured":"Uberon September 2011 release. [http:\/\/purl.obolibrary.org\/obo\/uberon\/releases\/2011-09-25\/]"},{"key":"2753_CR25","volume-title":"OWLED","author":"M Horridge","year":"2006","unstructured":"Horridge M, Drummond N, Goodwin J, Rector A, Stevens R, Wan H: The Manchester OWL Syntax. OWLED. 2006, [http:\/\/www.webont.org\/owled\/2006\/acceptedLong\/submission_9.pdf]"},{"key":"2753_CR26","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2005-6-5-r46","volume":"6","author":"B Smith","year":"2005","unstructured":"Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C: Relations in biomedical ontologies. Genome Biol. 2005, 6: R46-10.1186\/gb-2005-6-5-r46.","journal-title":"Genome Biol"},{"key":"2753_CR27","unstructured":"Uberon main ontology files. http:\/\/purl.obolibrary.org\/obo\/uberon.obo\n                           http:\/\/purl.obolibrary.org\/obo\/uberon.owl,"},{"key":"2753_CR28","unstructured":"Uberon basic ontology files. http:\/\/purl.obolibrary.org\/obo\/uberon\/basic.obo\n                           http:\/\/purl.obolibrary.org\/obo\/uberon\/basic.owl,"},{"key":"2753_CR29","doi-asserted-by":"publisher","first-page":"R229","DOI":"10.1186\/gb-2007-8-10-r229","volume":"8","author":"A Kruger","year":"2007","unstructured":"Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W: Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome Biol. 2007, 8: R229-10.1186\/gb-2007-8-10-r229.","journal-title":"Genome Biol"},{"key":"2753_CR30","first-page":"178","volume-title":"Pac Symp Biocomput","author":"GV Gkoutos","year":"2004","unstructured":"Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building mouse phenotype ontologies. Pac Symp Biocomput. 2004, 178-189."},{"issue":"Suppl 9","key":"2753_CR31","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-8-S9-S1","volume":"8","author":"DA Natale","year":"2007","unstructured":"Natale DA, Arighi CN, Barker WC, Blake J, Chang T-C, Hu Z, Liu H, Smith B, Wu CH: Framework for a protein ontology. BMC Bioinformatics. 2007, 8 (Suppl 9): S1-10.1186\/1471-2105-8-S9-S1.","journal-title":"BMC Bioinformatics"},{"key":"2753_CR32","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkm791","volume":"36","author":"K Degtyarenko","year":"2008","unstructured":"Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M: ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008, 36: D344-350.","journal-title":"Nucleic Acids Res"},{"key":"2753_CR33","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1471-2105-12-6","volume":"12","author":"TF Meehan","year":"2011","unstructured":"Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD: Logical development of the cell ontology. BMC Bioinformatics. 2011, 12: 6-10.1186\/1471-2105-12-6.","journal-title":"BMC Bioinformatics"},{"key":"2753_CR34","unstructured":"Uberon merged ontology. http:\/\/purl.obolibrary.org\/obo\/uberon\/merged.owl\n                           http:\/\/purl.obolibrary.org\/obo\/uberon\/merged.obo,"},{"key":"2753_CR35","volume-title":"Transcriptional Control of Neural Crest Development","author":"BL Nelms","year":"2010","unstructured":"Nelms BL, Labosky PA: Transcriptional Control of Neural Crest Development. 2010, San Rafael, CA: Morgan and Claypool Life Sciences"},{"key":"2753_CR36","doi-asserted-by":"publisher","first-page":"e1001065","DOI":"10.1371\/journal.pcbi.1001065","volume":"7","author":"M Hawrylycz","year":"2011","unstructured":"Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larson SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J: Digital atlasing and standardization in the mouse brain. PLoS Comput Biol. 2011, 7: e1001065-10.1371\/journal.pcbi.1001065.","journal-title":"PLoS Comput Biol"},{"key":"2753_CR37","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1186\/1471-2105-11-530","volume":"11","author":"JI Deegan","year":"2010","unstructured":"Deegan JI, Dimmer EC, Mungall CJ: Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics. 2010, 11: 530-10.1186\/1471-2105-11-530.","journal-title":"BMC Bioinformatics"},{"key":"2753_CR38","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.jbi.2010.02.002","volume":"44","author":"CJ Mungall","year":"2011","unstructured":"Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J: Cross-product extensions of the Gene Ontology. J Biomed Inform. 2011, 44: 80-86. 10.1016\/j.jbi.2010.02.002.","journal-title":"J Biomed Inform"},{"key":"2753_CR39","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1145\/945645.945664","volume-title":"Proceedings of the 2nd International Conference on Knowledge Capture: October 23-25, 2003; Sanibel Island, FL, USA","author":"AL Rector","year":"2003","unstructured":"Rector AL: Modularisation of domain ontologies implemented in description logics and related formalisms including OWL. Proceedings of the 2nd International Conference on Knowledge Capture: October 23-25, 2003; Sanibel Island, FL, USA. 2003, New York, NY: ACM, 121-128."},{"key":"2753_CR40","unstructured":"Ontology Alignment Evaluation Initiative. [http:\/\/oaei.ontologymatching.org\/]"},{"key":"2753_CR41","volume-title":"Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY","author":"A Gro\u00df","year":"2011","unstructured":"Gro\u00df A, Hartung M, Kirsten T, Rahm E: Mapping Composition for Matching Large Life Science Ontologies. Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http:\/\/icbo.buffalo.edu\/ICBO-2011_Proceedings.pdf]"},{"key":"2753_CR42","doi-asserted-by":"publisher","first-page":"1766","DOI":"10.1093\/bioinformatics\/btq283","volume":"26","author":"G Parmentier","year":"2010","unstructured":"Parmentier G, Bastian FB, Robinson-Rechavi M: Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics. 2010, 26: 1766-1771. 10.1093\/bioinformatics\/btq283.","journal-title":"Bioinformatics"},{"key":"2753_CR43","volume-title":"Bioinformatics","author":"A Niknejad","year":"2012","unstructured":"Niknejad A, Comte A, Parmentier G, Roux J, Bastian FB, Robinson-Rechavi M: vHOG, a multi-species vertebrate ontology of homologous organs groups. Bioinformatics. 2012, [Epub ahead of print],"},{"key":"2753_CR44","volume-title":"Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY","author":"R Travillian","year":"2011","unstructured":"Travillian R, Malone J, Pang C, Hancock J, Holland PW, Schofield P, Parkinson H: The Vertebrate Bridging Ontology (VBO). Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http:\/\/icbo.buffalo.edu\/ICBO-2011_Proceedings.pdf]"},{"key":"2753_CR45","doi-asserted-by":"publisher","first-page":"e29","DOI":"10.1371\/journal.pgen.0040029","volume":"4","author":"DA Kleinjan","year":"2008","unstructured":"Kleinjan DA, Bancewicz RM, Gautier P, Dahm R, Schonthaler HB, Damante G, Seawright A, Hever AM, Yeyati PL, van Heyningen V, Coutinho P: Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. PLoS Genet. 2008, 4: e29-10.1371\/journal.pgen.0040029.","journal-title":"PLoS Genet"},{"key":"2753_CR46","unstructured":"Human PAX6. [http:\/\/www.abdn.ac.uk\/ims\/staff\/details.php?id=M.Collinson]"},{"key":"2753_CR47","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1534\/genetics.108.088591","volume":"179","author":"J Favor","year":"2008","unstructured":"Favor J, Gloeckner CJ, Neuhauser-Klaus A, Pretsch W, Sandulache R, Saule S, Zaus I: Relationship of Pax6 activity levels to the extent of eye development in the mouse, Mus musculus. Genetics. 2008, 179: 1345-1355. 10.1534\/genetics.108.088591.","journal-title":"Genetics"},{"key":"2753_CR48","doi-asserted-by":"publisher","first-page":"5162","DOI":"10.1073\/pnas.94.10.5162","volume":"94","author":"G Panganiban","year":"1997","unstructured":"Panganiban G, Irvine SM, Lowe C, Roehl H, Corley LS, Sherbon B, Grenier JK, Fallon JF, Kimble J, Walker M, Wray GA, Swalla BJ, Martindale MQ, Carroll SB: The origin and evolution of animal appendages. Proc Natl Acad Sci USA. 1997, 94: 5162-5166. 10.1073\/pnas.94.10.5162.","journal-title":"Proc Natl Acad Sci USA"},{"key":"2753_CR49","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1002\/bies.200900175","volume":"32","author":"RW Scotland","year":"2010","unstructured":"Scotland RW: Deep homology: a view from systematics. Bioessays. 2010, 32: 438-449. 10.1002\/bies.200900175.","journal-title":"Bioessays"},{"key":"2753_CR50","unstructured":"Skeletal Anatomy Jamboree. [https:\/\/www.nescent.org\/phenoscape\/Skeletal_Anatomy_Jamboree]"},{"key":"2753_CR51","unstructured":"Arthropod ontology. [http:\/\/code.google.com\/p\/arthropod-anatomy-ontology\/]"},{"key":"2753_CR52","volume-title":"Proceedings of the First International Conference on Biomedical Ontology: July 24-26, 2009; Buffalo, NY","author":"M Courtot","year":"2009","unstructured":"Courtot M, Gibson F, Lister A: MIREOT: the Minimum Information to Reference an External Ontology Term. Proceedings of the First International Conference on Biomedical Ontology: July 24-26, 2009; Buffalo, NY. 2009, [http:\/\/icbo.buffalo.edu\/2009\/Proceedings.pdf]"},{"key":"2753_CR53","volume-title":"Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY","author":"D Osumi-Sutherland","year":"2011","unstructured":"Osumi-Sutherland D: FUNCARO-a functional extension to CARO. Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http:\/\/icbo.buffalo.edu\/ICBO-2011_Proceedings.pdf]"},{"key":"2753_CR54","volume-title":"Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY","author":"D Osumi-Sutherland","year":"2011","unstructured":"Osumi-Sutherland D: CARO 2.0. Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http:\/\/icbo.buffalo.edu\/ICBO-2011_Proceedings.pdf]"},{"key":"2753_CR55","volume-title":"Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY","author":"C Torniai","year":"2011","unstructured":"Torniai C, Brush M, Vasilevsky N, Segerdell E, Wilson ML, Johnson T, Corday K, Shaffer C, Haendel M: Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned. Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http:\/\/icbo.buffalo.edu\/ICBO-2011_Proceedings.pdf]"},{"key":"2753_CR56","volume-title":"Nat Precedings","author":"E Segerdell","year":"2010","unstructured":"Segerdell E, Wilson ML, Bashor T, Bourges-Waldegg D, Corday K, Frost HR, Johnson T, Shaffer CJ, Stone L, Torniai C, Haendel MA: eagle-i: an ontology-driven framework for biomedical resource annotation and discovery. Nat Precedings. 2010, [http:\/\/precedings.nature.com\/documents\/5176\/version\/1\/files\/npre20105176-1.pdf]"},{"key":"2753_CR57","doi-asserted-by":"publisher","first-page":"R2","DOI":"10.1186\/gb-2010-11-1-r2","volume":"11","author":"CJ Mungall","year":"2010","unstructured":"Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M: Integrating phenotype ontologies across multiple species. Genome Biol. 2010, 11: R2-10.1186\/gb-2010-11-1-r2.","journal-title":"Genome Biol"},{"key":"2753_CR58","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1016\/j.ajhg.2008.09.017","volume":"83","author":"PN Robinson","year":"2008","unstructured":"Robinson PN, Kohler S, Bauer S, Seelow D, Horn D, Mundlos S: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet. 2008, 83: 610-615. 10.1016\/j.ajhg.2008.09.017.","journal-title":"Am J Hum Genet"},{"key":"2753_CR59","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1093\/bioinformatics\/btr058","volume":"27","author":"R Hoehndorf","year":"2011","unstructured":"Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV: A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics. 2011, 27: 1001-1008. 10.1093\/bioinformatics\/btr058.","journal-title":"Bioinformatics"},{"key":"2753_CR60","doi-asserted-by":"publisher","first-page":"3112","DOI":"10.1093\/bioinformatics\/btq578","volume":"26","author":"R Hoehndorf","year":"2010","unstructured":"Hoehndorf R, Oellrich A, Rebholz-Schuhmann D: Interoperability between phenotype and anatomy ontologies. Bioinformatics. 2010, 26: 3112-3118. 10.1093\/bioinformatics\/btq578.","journal-title":"Bioinformatics"},{"key":"2753_CR61","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/1471-2105-12-32","volume":"12","author":"G Schindelman","year":"2011","unstructured":"Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW: Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics. 2011, 12: 32-10.1186\/1471-2105-12-32.","journal-title":"BMC Bioinformatics"},{"key":"2753_CR62","doi-asserted-by":"publisher","first-page":"e1000247","DOI":"10.1371\/journal.pbio.1000247","volume":"7","author":"NL Washington","year":"2009","unstructured":"Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE: Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009, 7: e1000247-10.1371\/journal.pbio.1000247.","journal-title":"PLoS Biol"},{"key":"2753_CR63","volume-title":"BMC Bioinformatics","author":"SM Maynard","year":"2012","unstructured":"Maynard SM, Mungall CJ, Lewis SE, Imam F, Martone ME: A knowledge based approach to matching human neurodegenerative disease and animal models. BMC Bioinformatics. 2012,"},{"key":"2753_CR64","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.ydbio.2011.02.033","volume":"355","author":"H Hochheiser","year":"2011","unstructured":"Hochheiser H, Aronow BJ, Artinger K, Beaty TH, Brinkley JF, Chai Y, Clouthier D, Cunningham ML, Dixon M, Donahue LR, Fraser SE, Hallgrimsson B, Iwata J, Klein O, Marazita ML, Murray JC, Murray S, de Villena FP, Postlethwait J, Potter S, Shapiro L, Spritz R, Visel A, Weinberg SM, Trainor PA: The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol. 2011, 355: 175-182. 10.1016\/j.ydbio.2011.02.033.","journal-title":"Dev Biol"},{"key":"2753_CR65","unstructured":"FANTOM5. [http:\/\/fantom.gsc.riken.jp\/5\/]"},{"key":"2753_CR66","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25: 1251-1255. 10.1038\/nbt1346.","journal-title":"Nat Biotechnol"},{"key":"2753_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-642-02846-5_1","volume":"5649","author":"C Mungall","year":"2009","unstructured":"Mungall C: Experiences Using Logic Programming in Bioinformatics. Lecture Notes Comput Sci. 2009, 5649: 1-21. 10.1007\/978-3-642-02846-5_1.","journal-title":"Lecture Notes Comput Sci"},{"key":"2753_CR68","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1108\/eb046814","volume":"14","author":"MF Porter","year":"1980","unstructured":"Porter MF: An algorithm for suffix stripping. Program. 1980, 14: 130-137. 10.1108\/eb046814.","journal-title":"Program"},{"key":"2753_CR69","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1093\/bioinformatics\/btm112","volume":"23","author":"J Day-Richter","year":"2007","unstructured":"Day-Richter J, Harris MA, Haendel M, Lewis S: OBO-Edit-an ontology editor for biologists. Bioinformatics. 2007, 23: 2198-2200. 10.1093\/bioinformatics\/btm112.","journal-title":"Bioinformatics"},{"key":"2753_CR70","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1002\/cfg.435","volume":"5","author":"CJ Mungall","year":"2004","unstructured":"Mungall CJ: Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics. 2004, 5: 509-520. 10.1002\/cfg.435.","journal-title":"Comp Funct Genomics"},{"key":"2753_CR71","unstructured":"Uberon repository. [http:\/\/github.com\/cmungall\/uberon]"},{"key":"2753_CR72","unstructured":"Example of Uberon bridge file. [https:\/\/github.com\/cmungall\/uberon\/blob\/master\/mouse_anatomy_xp.obo]"},{"key":"2753_CR73","unstructured":"Example of Uberon bridge file referencing external ontologies. [https:\/\/github.com\/cmungall\/uberon\/blob\/master\/mouse_anatomy_xp_uberon.obo]"},{"key":"2753_CR74","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2004-6-1-r7","volume":"6","author":"CL Smith","year":"2005","unstructured":"Smith CL, Goldsmith CW, Eppig JT: The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2005, 6: R7-10.1186\/gb-2005-6-5-p7.","journal-title":"Genome Biol"},{"key":"2753_CR75","first-page":"154","volume-title":"J Web Semantics","author":"C Bizer","year":"2009","unstructured":"Bizer C, Lehmann J, Kobilarov G, Auer S, Becker C, Cyganiak R, Hellmann S: DBpedia-a crystallization point for the web of data. J Web Semantics. 2009, 154-165."},{"key":"2753_CR76","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2105-5-8","volume":"5","author":"EC Swart","year":"2004","unstructured":"Swart EC, Hide WA, Seoighe C: FRAGS: estimation of coding sequence substitution rates from fragmentary data. BMC Bioinformatics. 2004, 5: 8-10.1186\/1471-2105-5-8.","journal-title":"BMC Bioinformatics"},{"key":"2753_CR77","unstructured":"Mouse Anatomy Ontology tracker example. [https:\/\/sourceforge.net\/tracker\/?func=detail&aid=3291162&group_id=76834&atid=1205376]"},{"key":"2753_CR78","unstructured":"SNOMEDCT. [http:\/\/www.ihtsdo.org\/snomed-ct\/]"},{"key":"2753_CR79","unstructured":"OBO scripts. [http:\/\/github.com\/cmungall\/obo-scripts]"},{"key":"2753_CR80","doi-asserted-by":"publisher","first-page":"RESEARCH0088","DOI":"10.1186\/gb-2002-3-12-research0088","volume":"3","author":"P Tomancak","year":"2002","unstructured":"Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM: Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002, 3: RESEARCH0088-","journal-title":"Genome Biol"},{"key":"2753_CR81","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1007\/11814771_26","volume":"4130 LNAI","author":"D Tsarkov","year":"2006","unstructured":"Tsarkov D, Horrocks I: FaCT++ description logic reasoner: System description. Lecture Notes Comput Sci. 2006, 4130 LNAI: 292-297.","journal-title":"Lecture Notes Comput Sci"}],"container-title":["Genome Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/gb-2012-13-1-r5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/gb-2012-13-1-r5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/gb-2012-13-1-r5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T11:06:45Z","timestamp":1728385605000},"score":1,"resource":{"primary":{"URL":"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/gb-2012-13-1-r5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,31]]},"references-count":81,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2012,1]]}},"alternative-id":["2753"],"URL":"https:\/\/doi.org\/10.1186\/gb-2012-13-1-r5","relation":{},"ISSN":["1474-760X"],"issn-type":[{"value":"1474-760X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,1,31]]},"assertion":[{"value":"2 December 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 January 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 January 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"R5"}}