Explain your data by Concept Profile Analysis Web Services

Kristina Hettne,Barend Mons,Eelke Van Der Horst,Jan A Kors,Rajaram Kaliyaperumal,Eleni Mina,Mark Thompson,Erik Van Mulligen,Reinout Van Schouwen,Marco Roos

doi:10.12688/f1000research.4830.1

Kristina Hettne, Barend Mons + Show 8 more

Open Access

https://doi.org/10.12688/f1000research.4830.1

Copy DOI

Abstract

The Concept Profile Analysis technology (overlapping co-occurring concept sets based on knowledge contained in biomedical abstracts) has led to new biomedical discoveries, and users have been able to interact with concept profiles through the interactive tool “Anni” (http://biosemantics.org/anni). However, Anni provides no way for users to save their procedures, results, or related provenance. Here we present a new suite of Web Service operations that allows bioinformaticians to design and execute their own Concept Profile Analysis workflow, possibly as part of a larger bioinformatics analysis. The source code can be downloaded from ZENODO at http://www.dx.doi.org/10.5281/zenodo.10963.

Highlights

Concept Profile Analysis (CPA) has proven a powerful tool for interpreting and prioritizing results of bioinformatics analysis, and for linking data sets based on the best “educated guess” when precise links are not available
The CPA algorithms have for example been successfully applied to compare microarray studies[2], for predicting proteins putatively associated with muscular dystrophy pathways[3], and for associating chemical structures with gene expression data[4]
To match the list of genes with pathways, the user performs the operation “match concept sets” for the gene concept set with a predefined concept set of the category “Gene Ontology (GO) biological process”