owltools.gaf.bioentities
Class ProteinTools

java.lang.Object
  extended by owltools.gaf.bioentities.ProteinTools

public class ProteinTools
extends Object


Constructor Summary
ProteinTools()
           
 
Method Summary
static void createProteinClassesFromQuestForOrthologs(org.semanticweb.owlapi.model.OWLOntology ontology, InputStream inputStream, org.semanticweb.owlapi.model.OWLClass proRoot)
          Add a named class for each protein extracted from the InputStream.
static org.semanticweb.owlapi.model.OWLOntology createProteinLabelOntology(org.semanticweb.owlapi.model.OWLOntologyManager manager, org.semanticweb.owlapi.model.IRI ontologyId, File file)
          Create a new ontology (with the given ID) for all proteins in the given Quest for Orthlogs seq XML file.
static void createProteinOntologies(Set<String> ids, String inputFolder, String outputFolder, String catalogXML)
          Create protein ontologies from the qfo files.
static org.semanticweb.owlapi.model.IRI createProteinOntologyIRI(String name)
          Create an protein ontology IRI for the given subset name.
static Map<String,String> getDefaultDbToTaxon()
          Retrieve the default mapping from db name to the numeric part of the NCBI taxon id.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProteinTools

public ProteinTools()
Method Detail

getDefaultDbToTaxon

public static Map<String,String> getDefaultDbToTaxon()
Retrieve the default mapping from db name to the numeric part of the NCBI taxon id.

Returns:
map

createProteinOntologies

public static void createProteinOntologies(Set<String> ids,
                                           String inputFolder,
                                           String outputFolder,
                                           String catalogXML)
                                    throws Exception
Create protein ontologies from the qfo files.

Parameters:
ids - set of taxon ids
inputFolder - the folder for the input qfo seq xml file
outputFolder - folder for the owl files
catalogXML -
Throws:
Exception

createProteinOntologyIRI

public static org.semanticweb.owlapi.model.IRI createProteinOntologyIRI(String name)
Create an protein ontology IRI for the given subset name.

Parameters:
name - subset
Returns:
IRI

createProteinLabelOntology

public static org.semanticweb.owlapi.model.OWLOntology createProteinLabelOntology(org.semanticweb.owlapi.model.OWLOntologyManager manager,
                                                                                  org.semanticweb.owlapi.model.IRI ontologyId,
                                                                                  File file)
                                                                           throws IOException,
                                                                                  XMLStreamException,
                                                                                  org.semanticweb.owlapi.model.OWLOntologyCreationException
Create a new ontology (with the given ID) for all proteins in the given Quest for Orthlogs seq XML file. It will create a named class for each protein.

Parameters:
manager -
ontologyId - ontology id
file - qfo file
Returns:
ontology
Throws:
IOException
XMLStreamException
org.semanticweb.owlapi.model.OWLOntologyCreationException

createProteinClassesFromQuestForOrthologs

public static void createProteinClassesFromQuestForOrthologs(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             InputStream inputStream,
                                                             org.semanticweb.owlapi.model.OWLClass proRoot)
                                                      throws XMLStreamException
Add a named class for each protein extracted from the InputStream. Expects to stream to be an seqXML from Quest for Orthologs.

Parameters:
ontology -
inputStream -
proRoot -
Throws:
XMLStreamException


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