The Drosophila anatomy ontology

Journal of Biomedical Semantics

David Osumi-Sutherland¹  Gary Grumbling²  Simon Reeve¹  Marta Costa¹ 

[1] FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK;FlyBase, Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN, 47405-7005, USA

关键词: Description logic;    FlyBase;    Gene Ontology;    OBO;    OWL;    Ontology;    Anatomy;    Drosophila;   

Others  :  806584
DOI  :  10.1186/2041-1480-4-32

 received in 2013-07-01, accepted in 2013-10-11,  发布年份 2013

【 摘 要 】

Background

Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmatically accessible forms. They are also frequently used to group annotations in biologically meaningful ways. Accurate annotation requires clear textual definitions for terms, ideally accompanied by images. Accurate grouping and fruitful programmatic usage requires high-quality formal definitions that can be used to automate classification and check for errors. The Drosophila anatomy ontology (DAO) consists of over 8000 classes with broad coverage of Drosophila anatomy. It has been used extensively for annotation by a range of resources, but until recently it was poorly formalised and had few textual definitions.

Results

We have transformed the DAO into an ontology rich in formal and textual definitions in which the majority of classifications are automated and extensive error checking ensures quality. Here we present an overview of the content of the DAO, the patterns used in its formalisation, and the various uses it has been put to.

Conclusions

As a result of the work described here, the DAO provides a high-quality, queryable reference for the wild-type anatomy of Drosophila melanogaster and a set of terms to annotate data related to that anatomy. Extensive, well referenced textual definitions make it both a reliable and useful reference and ensure accurate use in annotation. Wide use of formal axioms allows a large proportion of classification to be automated and the use of consistency checking to eliminate errors. This increased formalisation has resulted in significant improvements to the completeness and accuracy of classification. The broad use of both formal and informal definitions make further development of the ontology sustainable and scalable. The patterns of formalisation used in the DAO are likely to be useful to developers of other anatomy ontologies.

【 授权许可】

   
2013 Costa et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]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(Database issue):D768-D772.
• [2]Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE, Airey MT, Anagnostopoulos A, Babiuk R, Baldarelli RM, Beal JS, Bello SM, Butler NE, Campbell J, Corbani LE, Dene H, Drabkin HR, Forthofer KL, Giannatto SL, Knowlton M, Lewis JR, McAndrews M, McClatchy S, Miers DS, Ni L, Onda H, Ormsby JE, Recla JM, Reed DJ, Richards-Smith B, Shaw DR, et al.: The mouse genome database: genotypes, phenotypes, and models of human disease. Nucleic Acids Res 2013, 41(Database issue):D885-D891.
• [3]Grumbling G, Strelets V: FlyBase: anatomical data, images and queries. Nucleic Acids Res 2006, 34(Database issue):D484-D488.
• [4]Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM: Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res 2010, 38(Database issue):D433-D436.
• [5]Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD: The Virtual Fly Brain browser and query interface. Bioinformatics 2012, 28(3):411-415.
• [6]Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD: A strategy for building neuroanatomy ontologies. Bioinformatics 2012, 28(9):1262-1269.
• [7]OWL 2 Web Ontology Language Primer (Second Edition) - W3C Recommendation 11 December 2012 [http://www.w3.org/TR/owl2-primer/ webcite]
• [8]OWL 2 EL profile - W3C Recommendation 11 December 2012 [http://www.w3.org/TR/owl2-profiles/#OWL_2_EL webcite]
• [9]Kazakov Y, Krötzsch M, Simančík F: ELK reasoner: Architecture and evaluation. (From Proceedings of the 1st International OWL Reasoner Evaluation Workshop). CEUR Workshop Proc 2012, 858:10.
• [10]Golbreich C, Horrocks I: The OBO to OWL mapping, GO in OWL 1.1! (From Proc. of the third OWL Experiences and directions workshop). CEUR Workshop Proc 2007, 258:1-9.
• [11]Mungall C, Ruttenberg R, Horrocks I, Osumi-Sutherland D, Antezana E, Balhoff J, Courtot M, Dietze H, Day-Richter J, Horridge H, Ireland A, Lewis S, Manzoor S, Hamid Tirmizi S: OBO Flat File Format 1.4 Syntax and Semantics. [http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html webcite]
• [12]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.
• [13]Deegan nee Clark JI, Dimmer EC, Mungall CJ: Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics 2010, 11:530. BioMed Central Full Text
• [14]Gkoutos GV, Hoehndorf R: Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. J Biomed Semantics 2012, 3(Suppl 2):S6. BioMed Central Full Text
• [15]Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN: Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc 2009, 2009:7069-7072.
• [16]Gkoutos GV, Green EC, Mallon AM, Blake A, Greenaway S, Hancock JM, Davidson D: Ontologies for the description of mouse phenotypes. Comp Funct Genomics 2004, 5(6–7):545-551.
• [17]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. BioMed Central Full Text
• [18]Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA: Uberon, an integrative multi-species anatomy ontology. Genome Biol 2012, 13:R5. BioMed Central Full Text
• [19]Rector AL: Modularisation of domain ontologies implemented in description logics and related formalisms including OWL. In Proceedings of the 2nd International Conference on Knowledge Capture. New York: ACM; 2003:121-128. [http://doi.acm.org/10.1145/945645.945664 webcite]
• [20]Crossley AC: The morphology and development of the Drosophila muscular system. In The Genetics and Biology of Drosophila, Volume 2d. Edited by Ashburner M, Wright TRF. London: Academic Press; 1980:499-560.
• [21]Bate M: The mesoderm and its derivatives. In The development of Drosophila melanogaster. In The development of Drosophila melanogaster, Volume 2. Edited by Bate M, Martinez Arias A. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 1993:1013-1090.
• [22]Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JL, Mungall CJ, Smith B: CARO–the common anatomy reference ontology. (in Anatomy Ontologies for Bioinformatics). Comput Biol 2008, 6:327-349. Edited by Burger A, Davidson D, Baldock, R. Springer
• [23]Chiang AS, Lin CY, Chuang CC, Chang HM, Hsieh CH, Yeh CW, Shih CT, Wu JJ, Wang GT, Chen YC, Wu CC, Chen GY, Ching YT, Lee PC, Lin CY, Lin HH, Wu CC, Hsu HW, Huang YA, Chen JY, Chiang HJ, Lu CF, Ni RF, Yeh CY, Hwang JK: Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr Biol 2011, 21:1-11.
• [24]Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS: REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res 2011, 39(Database issue):D118-D123.
• [25]Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R: Populous: a tool for building OWL ontologies from templates. BMC Bioinformatics 2012, 13(Suppl 1):S5.
• [26]Egaña M, Rector A, Stevens R, Antezana E: Applying ontology design patterns in bio-ontologies. LNCS 2008, 5268:7-16.
• [27]Guarino N, Welty C: Evaluating ontological decisions with OntoClean. Commun ACM 2002, 45(2):61-65.