Dataset Information

Thesaurus-based disambiguation of gene symbols.

ABSTRACT:

Background

Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.

Results

We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data. The thesaurus comprises the information from five human genetic databases and MeSH. The extent of the homonym problem for human gene symbols is shown to be substantial (33% of the genes in our combined thesaurus had one or more ambiguous symbols), not only because one symbol can refer to multiple genes, but also because a gene symbol can have many non-gene meanings. A test set of 52,529 Medline abstracts, containing 690 ambiguous human gene symbols taken from OMIM, was automatically generated. Overall accuracy of the disambiguation algorithm was up to 92.7% on the test set.

Conclusion

The ambiguity of human gene symbols is substantial, not only because one symbol may denote multiple genes but particularly because many symbols have other, non-gene meanings. The proposed disambiguation approach resolves most ambiguities in our test set with high accuracy, including the important gene/not a gene decisions. The algorithm is fast and scalable, enabling gene-symbol disambiguation in massive text mining applications.

SUBMITTER: Schijvenaars BJ

PROVIDER: S-EPMC1183190 | biostudies-literature | 2005 Jun

REPOSITORIES: biostudies-literature

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Publications

Thesaurus-based disambiguation of gene symbols.

Schijvenaars Bob J A BJ Mons Barend B Weeber Marc M Schuemie Martijn J MJ van Mulligen Erik M EM Wain Hester M HM Kors Jan A JA

BMC bioinformatics 20050616

<h4>Background</h4>Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.<h4>Results</h4>We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data. The thesaurus comprises the information from five human genetic databases and MeSH. The extent of the homonym problem for human gene symbols is shown to be s ...[more]

PMID: 15958172

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Project description:Numeracy is of critical importance for scholastic success and modern-day living, but the precise mechanisms that drive its development are poorly understood. Here we used novel experimental training methods to begin to investigate the role of symbols in the development of numeracy in preschool-aged children. We assigned pre-school children in the U.S. and Italy (N = 215; Mean age = 49.15 months) to play one of five versions of a computer-based numerical comparison game for two weeks. The different versions of the game were equated on basic features of gameplay and demands but systematically varied in numerical content. Critically, some versions included non-symbolic numerical comparisons only, while others combined non-symbolic numerical comparison with symbolic aids of various types. Before and after training we assessed four components of early numeracy: counting proficiency, non-symbolic numerical comparison, one-to-one correspondence, and arithmetic set transformation. We found that overall children showed improvement in most of these components after completing these short trainings. However, children trained on numerical comparisons with symbolic aids made larger gains on assessments of one-to-one correspondence and arithmetic transformation compared to children whose training involved non-symbolic numerical comparison only. Further exploratory analyses suggested that, although there were no major differences between children trained with verbal symbols (e.g., verbal counting) and non-verbal visuo-spatial symbols (i.e., abacus counting), the gains in one-to-one correspondence may have been driven by abacus training, while the gains in non-verbal arithmetic transformations may have been driven by verbal training. These results provide initial evidence that the introduction of symbols may contribute to the emergence of numeracy by enhancing the capacity for thinking about exact equality and the numerical effects of set transformations. More broadly, this study provides an empirical basis to motivate further focused study of the processes by which children's mastery of symbols influences children's developing mastery of numeracy.

Dataset Information

Thesaurus-based disambiguation of gene symbols.

Background

Results

Conclusion

Publications

Thesaurus-based disambiguation of gene symbols.

Similar Datasets

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