Journal Article

Application and evaluation of automated semantic annotation of gene expression experiments

Leon French, Suzanne Lane, Tamryn Law, Lydia Xu and Paul Pavlidis

in Bioinformatics

Volume 25, issue 12, pages 1543-1549
Published in print June 2009 | ISSN: 1367-4803
Published online April 2009 | e-ISSN: 1460-2059 | DOI:

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Motivation: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets.

Results: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma.

Availability: The source code, documentation and Supplementary Materials are available at The results of the manual evaluations are provided as Supplementary Material. Both manual and predicted annotations can be viewed and searched via the Gemma website at The complete set of predicted annotations is available as a machine readable resource description framework graph.


Journal Article.  5433 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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