Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development - PubMed (original) (raw)

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

Jennifer I Deegan née Clark et al. BMC Bioinformatics. 2010.

Abstract

Background: The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation.

Results: We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology.

Conclusions: Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group\_id=36855.

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Figures

Figure 1

Figure 1

Lactation. The GO class 'lactation' is restricted for use with gene products from species of the taxonomic grouping Mammalia. The class inherits this restriction from the superclass 'mammary gland development'. In this figure, the GO classes are shown in blue, and the taxonomic classes are shown in yellow. The relationship types are labeled in the diagram.

Figure 2

Figure 2

C4 photosynthesis. The GO class 'C4 photosynthesis' is restricted for use with gene products from species of the taxonomic grouping Viridiplantae. This is a narrower taxonomic group than that to which the GO superclass 'photosynthesis' is restricted. The GO class 'photosynthesis' is restricted for use with gene products from any sub-type of the Viridiplantae, Euglenozoa, Archaea or Bacteria. The relationship between 'photosynthesis' and these four taxonomic groups is shown by the relationship only_ in_ taxon from 'photosynthesis' to the union term 'Viridiplantae or Euglenozoa or Archaea or Bacteria', and by the relationships between this union term and the four individual taxonomic groups. These latter relationships are shown as union_ of relationships (marked 'un'). In this figure, the GO classes are shown in blue, and the taxonomic classes are shown in yellow. The relationship types are labeled in the diagram.

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References

    1. The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9. doi: 10.1038/75556. - DOI - PMC - PubMed
    1. Clark JI, Brooksbank C, Lomax J. It's all GO for plant scientists. Plant Physiol. 2005;138(3):1268–79. doi: 10.1104/pp.104.058529. - DOI - PMC - PubMed
    1. Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Overduin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E. Ensembl. Nucleic Acids Res. 2007;35:D610–D617. doi: 10.1093/nar/gkl996. - DOI - PMC - PubMed
    1. Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol. 2009;5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. - DOI - PMC - PubMed
    1. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro. Bioinformatics. 2009;37:D211–D215. - PMC - PubMed

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