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GOAssay: from Gene Ontology to Assays IDentifiers – Towards Automatic Functional Annotation of PubChem BioAssays

Rajarshi Guha¹, Julien Gobeill² & Patrick Ruch³

Correspondence: (Login to view email address)

1. University of Indiana
2. HEG/University of Applied Sciences and Swiss-Prot/Swiss Institute of Bioinformatics
3. HEG/University of Applied Sciences

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Document Type:

Poster

Date:

Received 24 April 2009 20:48 UTC; Posted 28 April 2009

Subjects:

Chemistry, Genetics & Genomics, Bioinformatics

Tags:

• text mining
• semantic enrichment
• gene ontology
• chemo-informatics
• GO
• PubChem
• biocuration
• curation

Abstract:

OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat).

METHODS and MATERIALS: The assays are processed to filter out non functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a GOA-learned association model.

RESULTS: The GO descriptors are regarded as irrelevant for only 18% of the assays.

CONCLUSION: Semantic enrichment of PubChem assays with functional genomics categories seems effective at least to navigate PubChem assays.

AVAILABILITIES: the database is hosted by the University of Indiana at http://goassay.rguha.net/index.html the GO categorizer interface and service is available at the University of Geneva http://eagl.unige.ch/EAGLi/.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Guha, Rajarshi, Gobeill, Julien, and Ruch, Patrick. GOAssay: from Gene Ontology to Assays IDentifiers – Towards Automatic Functional Annotation of PubChem BioAssays. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3176.1> (2009)

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