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Table 1 OPPL-Galaxy distribution and related Galaxy tools

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

 

OPPL-Galaxy bundle

OPPL

Executes OPPL scripts

OWL Query

Perform DL (Description Logics) queries against OWL ontologies, returning a list of namedentities that satisfy the query

OPPL Query

Perform OPPL queries, thus, queries that mix MOS with variables

Inference

Add the inferred axioms to the input ontology as asserted axioms, generating a new ontologythat includes all the axioms

Merge

Resolves the import axioms and adds the imported ontology to the input ontology file

 

NCBO-Galaxy bundle

The NCBO-Galaxy bundle includes modules for retrieving ontologies, extracting subtrees from ontologies,

 

search for terms in ontologies, annotate texts against ontologies, etc. using NCBO Web services. See [38] for details

 
 

SPARQL-Galaxy bundle

SPARQL-Galaxy includes a tool for performing SPARQL queries on an OWL (RDF/XML) ontology;

 

it can be downloaded from the Galaxy Tool Shed (http://toolshed.g2.bx.psu.edu), under ‘Ontology manipulation’.

 
 

Galaxy-OBO

Galaxy-OBO [39] is a fork of Galaxy that includes wrappers for common tools like GO::TermFinder [40]

 
  1. This table provides a detailed list of the OPPL-Galaxy tools and other tools that are executed in the workflows of the use cases.