OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Table 2 Galaxy workflows for reproducing the use cases

Name	Galaxy workflow
Basic usage	http://biordf.org:8090/u/mikel-egana-aranguren/w/basic-usage-1
Ontology debugging andevaluation ^∗	http://biordf.org:8090/u/mikel-egana-aranguren/w/ontology-debugging-and-evaluation
Complex querying of GO	http://biordf.org:8090/u/mikel-egana-aranguren/w/complex-querying-of-go
Expansion of gene productannotations through GOstructure	http://biordf.org:8090/u/mikel-egana-aranguren/w/expansion-of-gene-product-annotations-through-go-structure
Selective extraction of modulesfrom GO for term enrichment	http://biordf.org:8090/u/mikel-egana-aranguren/w/selective-extraction-of-modules-from-go-for-term-enrichment
OWL TBox to ABoxtransformation for assistingSPARQL queries	http://biordf.org:8090/u/mikel-egana-aranguren/w/owl-tbox-to-abox-transformation-for-assisting-sparql-queries

The name of the use case (as per section name) is provided in the left column; the URL of the Galaxy workflow is provided in the right column. In order to execute a workflow, the datasets (ontologies, OPPL scripts, GAFs, etc.) must be taken from the history (http://biordf.org:8090/u/mikel-egana-aranguren/h/oppl-galaxy-use-cases-for-jbs) or the workflow can be reproduced manually with the same datasets, by uploading them. The workflow “Ontology debugging and evaluation” obtains the ontologies directly from NCBO services. For detailed instructions, see http://wilkinsonlab.info/OPPL-Galaxy. All the workflows can be reproduced in a local Galaxy installation; in order to do so, the workflows and datasets can be downloaded from http://biordf.org:8080/JBSusecases.tar.gz.

ISSN: 2041-1480