The language of gene ontology: a Zipf’s law analysis View Full Text


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Article Info

DATE

2012-06-07

AUTHORS

Leila Ranandeh Kalankesh, Robert Stevens, Andy Brass

ABSTRACT

BACKGROUND: Most major genome projects and sequence databases provide a GO annotation of their data, either automatically or through human annotators, creating a large corpus of data written in the language of GO. Texts written in natural language show a statistical power law behaviour, Zipf's law, the exponent of which can provide useful information on the nature of the language being used. We have therefore explored the hypothesis that collections of GO annotations will show similar statistical behaviours to natural language. RESULTS: Annotations from the Gene Ontology Annotation project were found to follow Zipf's law. Surprisingly, the measured power law exponents were consistently different between annotation captured using the three GO sub-ontologies in the corpora (function, process and component). On filtering the corpora using GO evidence codes we found that the value of the measured power law exponent responded in a predictable way as a function of the evidence codes used to support the annotation. CONCLUSIONS: Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that provide a signal which correlates with the nature of the evidence codes used to support the annotations, suggesting that the measured exponent might provide a signal regarding the information content of the annotation. More... »

PAGES

127-127

References to SciGraph publications

  • 2008-05-13. Use and misuse of the gene ontology annotations in NATURE REVIEWS GENETICS
  • 2000-05. Gene Ontology: tool for the unification of biology in NATURE GENETICS
  • 2005-03. The variation of Zipf’s law in human language in THE EUROPEAN PHYSICAL JOURNAL B
  • 2005-10-28. Zipf's law from a communicative phase transition in THE EUROPEAN PHYSICAL JOURNAL B
  • 2009. On Quality of Different Annotation Sources for Gene Expression Analysis in ARTIFICIAL INTELLIGENCE IN MEDICINE
  • 2008-10-27. Forty years of SNOMED: a literature review in BMC MEDICAL INFORMATICS AND DECISION MAKING
  • 2009. Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes in DATA INTEGRATION IN THE LIFE SCIENCES
  • 2008-01-11. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments in GENOME BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2105-13-127

    DOI

    http://dx.doi.org/10.1186/1471-2105-13-127

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1053278667

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22676436


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    192 School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    193 rdf:type schema:Organization
     




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