public class ProteinTools extends Object
Constructor and Description |
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ProteinTools() |
Modifier and Type | Method and Description |
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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.
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static void |
createProteinOntologies(Set<String> ids,
String inputFolder,
String outputFolder,
String catalogXML)
Create protein ontologies from the qfo files.
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static org.semanticweb.owlapi.model.IRI |
createProteinOntologyIRI(String name)
Create an protein ontology IRI for the given subset name.
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static Map<String,String> |
getDefaultDbToTaxon()
Retrieve the default mapping from db name to the numeric part of the NCBI
taxon id.
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public static Map<String,String> getDefaultDbToTaxon()
public static void createProteinOntologies(Set<String> ids, String inputFolder, String outputFolder, String catalogXML) throws Exception
ids
- set of taxon idsinputFolder
- the folder for the input qfo seq xml fileoutputFolder
- folder for the owl filescatalogXML
- Exception
public static org.semanticweb.owlapi.model.IRI createProteinOntologyIRI(String name)
name
- subsetpublic 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
manager
- ontologyId
- ontology idfile
- qfo fileIOException
XMLStreamException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public static void createProteinClassesFromQuestForOrthologs(org.semanticweb.owlapi.model.OWLOntology ontology, InputStream inputStream, org.semanticweb.owlapi.model.OWLClass proRoot) throws XMLStreamException
InputStream
.
Expects to stream to be an seqXML from Quest for Orthologs.ontology
- inputStream
- proRoot
- XMLStreamException
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