全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
PLOS ONE  2012 

A Unified Anatomy Ontology of the Vertebrate Skeletal System

DOI: 10.1371/journal.pone.0051070

Full-Text   Cite this paper   Add to My Lib

Abstract:

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

References

[1]  Hall BK (2005) TRIBUTE: In Goethe's Wake: Marvalee Wake's conceptual contributions to the development and evolution of a science of morphology. Zoology 108: 269–275.
[2]  Wilson JA (2006) Anatomical nomenclature of fossil vertebrates: standardized terms or 'lingua franca'? Journal of Vertebrate Paleontology 26: 511–518.
[3]  Dettai A, Bailly N, Vignes-Lebbe R, Lecointre G (2004) Metacanthomorpha: Essay on a phylogeny-oriented database for morphology – the acanthomorph (Teleostei) example. Systematic Biology 53: 822–834.
[4]  Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, et al. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution 22: 345–350.
[5]  Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, et al. (2007) Connecting evolutionary morphology to genomics using ontologies: A case study from Cypriniformes including zebrafish. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 308B: 655–668.
[6]  Parr CS, Guralnick R, Cellinese N, Page RD (2012) Evolutionary informatics: unifying knowledge about the diversity of life. Trends in Ecology & Evolution 27: 94–103.
[7]  Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, et al. (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biology 7: 1–20.
[8]  Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, et al. (2010) Integrating phenotype ontologies across multiple species. Genome Biology 11: R2.
[9]  Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, et al. (2011) Cross-product extensions of the Gene Ontology. Journal of Biomedical Informatics 44: 80–86.
[10]  Scott-Savage P, Hall BK (1979) The timing of the onset of osteogenesis in the tibia of the embryonic chick. Journal of Morphology 162: 453–464.
[11]  Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, et al. (2011) ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Research 39: D822–829.
[12]  Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS ONE 5: e10708.
[13]  Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, et al. (2010) The Teleost Anatomy Ontology: Anatomical representation for the genomics age. Systematic Biology 59: 369–383.
[14]  Yoder MJ, Miko I, Seltmann KC, Bertone MA, Deans AR (2010) A gross anatomy ontology for Hymenoptera. PLoS ONE 5: e15991.
[15]  Deans AR, Yoder MJ, Balhoff JP (2012) Time to change how we describe biodiversity. Trends in Ecology & Evolution 27: 78–84.
[16]  Maglia AM, Leopold JL, Pugener LA, Gauch S (2007) An anatomical ontology of amphibians. Proc of the Pacific Symposium on Biocomputing 12: 367–378.
[17]  Haendel MA, Neuhaus F, Osumi-Sutherland DS, Mabee PM, Mejino JLV, et al.. (2008) CARO – The Common Anatomy Reference Ontology. Anatomy Ontologies for Bioinformatics: Principles and Practice: 327–349.
[18]  Goujet D, Young GC (1995) Interrelationships of placoderms revisited. Geobios, Mem Spec 19: 89–95.
[19]  Workshop version of VSAO. Available: https://phenoscape.svn.sourceforge.net/s?vnroot/phenoscape/trunk/vocab/VSAO-works?hop.obo. Accessed 2012 Nov 6.
[20]  VSAO version 2012–11–06. Available: http://purl.obolibrary.org/obo/vsao/2012?-11-06/vsao.obo (OBO), http://purl.obolibrary.org/obo/vsao/2012?-11-06/vsao.owl (OWL). Accessed 2012 Nov 6.
[21]  VSAO at BioPortal. Available: http://bioportal.bioontology.org/ontolog?ies/1555. Accessed 2012 Nov 6.
[22]  VSAO at Ontobee. Available: http://www.ontobee.org/browser/index.php??o=VSAO. Accessed 2012 Nov 6.
[23]  VSAO deposited in the Dryad repository. Available: http://dx.doi.org/10.5061/dryad.6bt92. Accessed 2012 Nov 6.
[24]  GO Reference Collection. Available: http://www.geneontology.org/cgi-bin/refe?rences.cgi - GO_REF:0000034. Accessed 2012 Nov 6.
[25]  Bard J, Rhee SY, Ashburner M (2005) An ontology for cell types. Genome Biology 6: R21.
[26]  Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, et al. (2011) Logical development of the cell ontology. BMC Bioinformatics 12: 6.
[27]  Blake JA, Harris MA (2008) The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Current Protocols in Bioinformatics 23: 7.2.1–7.2.9.
[28]  Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA (2012) Uberon, an integrative multi-species anatomy ontology. Genome Biology 13: R5.
[29]  Smith B, Ceusters W, Klagges B, K?hler J, Kumar A, et al. (2005) Relations in biomedical ontologies. Genome Biology 6: R46–R46.15.
[30]  Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D (2004) Using ontologies to describe mouse phenotypes. Genome Biology 6: R8.
[31]  Burger A, Davidson D, Baldock R, editors (2008) Anatomy Ontologies for Bioinformatics: Principles and Practice: Springer. 372 p.
[32]  TAO at BioPortal. Available: http://bioportal.bioontology.org/ontolog?ies/1110. Accessed 2012 Nov 6.
[33]  TAO at Ontobee. Available: http://www.ontobee.org/browser/index.php??o=TAO. Accessed 2012 Nov 6.
[34]  TAO version 2012–08–10 at SourceForge. Available: http://purl.obolibrary.org/obo/tao/2012-?08-10/tao.obo (OBO), http://purl.obolibrary.org/obo/tao/2012-?08-10/tao.owl (OWL). Accessed 2012 Nov 6.
[35]  Segerdell E, Bowes JB, Pollet N, Vize PD (2008) An ontology for Xenopus anatomy and development. BMC Developmental Biology 8: 92.
[36]  Courtot M, Gibson F, Lister AL, Malone J, Schober D, et al. (2011) MIREOT: The minimum information to reference an external ontology term. Applied Ontology 6: 23–33.
[37]  Niknejad A, Comte A, Parmentier G, Roux J, Bastian FB, et al. (2012) vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinformatics 28: 1017–1020.
[38]  Rosse C, Mejino JL Jr (2003) A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics 36: 478–500.
[39]  Smith MM, Hall BK (1990) Development and evolutionary origins of vertebrate skeletogenic and odontogenic tissues. Biological Reviews 65: 277–373.
[40]  Hall BK, Witten PE (2007) Plasticity of and transitions between skeletal tissues in vertebrate evolution and development. In: Anderson JS, Sues H-D, editors. Major Transitions in Vertebrate Evolution. Bloomington: Indiana University Press. 13–56.
[41]  Janvier P (2011) Comparative anatomy: all vertebrates do have vertebrae. Current Biology 21: R661–663.
[42]  Patterson C (1977) Cartilage bones, dermal bones and membrane bones, or the exoskeleton versus the endoskeleton. In: Andrews SM, R. S Miles and A. D Walker, editor. Problems in Vertebrate Evolution. London: Academic Press. 77–121.
[43]  Hall BK (2005) Consideration of the neural crest and its skeletal derivatives in the context of novelty/innovation. Journal of Experimental Zoology Part B, Molecular and Developmental Evolution 304: 548–557.
[44]  Arratia G, Schultz H-P, Casciotta J (2001) Vertebral column and associated elements in dipnoans and comparison with other fishes: Development and homology. Journal of Morphology 250: 101–172.
[45]  Burke AC (1991) Proximal elements in the vertebrate limb; evolutionary and developmental origin of the pectoral girdle. In: Hinchliffe JR, Hurle J, Summerbell D, editors. Developmental patterning of the vertebrate limb. London: Plenum Press.
[46]  Rieppel O, Reisz RR (1999) The origin and early evolution of turtles. Annual Review of Ecology and Systematics 30: 1–22.
[47]  Vickaryous MK, Olson W (2007) Sesamoids and Ossicles in the Appendicular Skeleton. In: Hall BK, editor. Fins into Limbs: Evolution, Development and Transformation. Chicago: University of Chicago Press. 323–341.
[48]  Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M (2005) The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biology 6: R29.
[49]  Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, et al. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Research 36: D768–772.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133