This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

Marco Falda1*, Stefano Toppo1, Alessandro Pescarolo1, Enrico Lavezzo2, Barbara Di Camillo3, Andrea Facchinetti3, Elisa Cilia4, Riccardo Velasco4 and Paolo Fontana4

Author Affiliations

1 Department of Molecular Medicine, University of Padova, via U. Bassi 58/B, 35121, Padova, Italy

2 Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121, Padova, Italy

3 Department of Information Engineering, University of Padova, via Gradenigo 6, 35131, Padova, Italy

4 Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (Trento), Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S14  doi:10.1186/1471-2105-13-S4-S14

Published: 28 March 2012

Additional files

Additional file 1:

GOClass algorithm details. Details of the GOClass algorithm used to cluster the GO terms, and more general views of the results obtained by Argot2.

Format: PDF Size: 260KB Download file

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Open Data

Additional file 2:

Datasets statistics. Parameters used in the benchmarks and some statistics about the datasets.

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Open Data

Additional file 3:

Precision/Recall curves for the Eukaryota dataset. Precision/recall curves for Molecular Function (MF), Biological Process (BP) and Cellular Component (CC) calculated with methods m1 and m2 for Eukaryota test set.

Format: XLS Size: 382KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Precision/Recall curves for the Prokaryota dataset. Precision/recall curves for Molecular Function (MF), Biological Process (BP) and Cellular Component (CC) calculated with methods m1 and m2 for Prokaryota test set.

Format: XLS Size: 382KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Precision/Recall curves for the Yeast dataset. Precision/recall curves for Molecular Function (MF), Biological Process (BP) and Cellular Component (CC) calculated with methods m1 and m2 for Yeast test set.

Format: XLS Size: 377KB Download file

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Open Data

Additional file 6:

Precision/Recall curves for the Euk, Pro and Yeast datasets. Precision/recall curves for Molecular Function (MF) and Biological Process (BP) calculated with methods m1 and m2 for Euk, Pro and Yeast test sets.

Format: PDF Size: 1.1MB Download file

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Open Data

Additional file 7:

CAFA guidelines explanation. Document that explains m1 and m2 methods using a simple example.

Format: PDF Size: 850KB Download file

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Open Data