owltools.ncbi

Class NCBI2OWL

java.lang.Object

owltools.ncbi.OWLConverter

owltools.ncbi.NCBIConverter

owltools.ncbi.NCBI2OWL

public class NCBI2OWL
extends NCBIConverter

Provides static methods for converting NCBI Taxonomy data files into OWL format.

The National Center for Biotechnology Information provides a Taxonomy Database with a large number of terms for classifying organisms. This tool converts that data to a Web Ontology Language (OWL) representation.

The latest NCBI Taxonomy data can be downloaded from ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat (file size is more than 200MB). The data format is line-based. Blocks are separated by "//", and each line within the block provides the pair of a field name and a field value separated by a colon. See the src/test/resources/sample.dat file for an example.

This tool uses OWLAPI to create and manipulate the ontology, and depends on OBOFormat for the IRIs and labels of several annotation properties.

Author:

James A. Overton

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.log4j.Logger	logger Create a logger.
protected static String	usage Command line usage information.

Fields inherited from class owltools.ncbi.OWLConverter

format, IAO, NCBI, OBO, OIO

Constructor Summary

Constructors

Constructor and Description
NCBI2OWL()

Method Summary

Methods

Modifier and Type	Method and Description
static void	checkAxioms(String inputPath, String outputPath) Load an ontology from a file and then print a list of its axioms.
static org.semanticweb.owlapi.model.OWLOntology	convertToOWL(String inputPath, Map<String,String> uniqueNames) Read a data file and create an OWL representation.
static org.semanticweb.owlapi.model.OWLOntology	convertToOWL(String inputPath, String outputPath, InputStream mergeInfo, InputStream citationInfo, Map<String,String> uniqueNames) Read a data file, create an OWL representation, and save an OWL file.
static org.semanticweb.owlapi.model.OWLOntology	convertToOWL(String inputPath, String outputPath, Map<String,String> uniqueNames) Read a data file, create an OWL representation, and save an OWL file.
static void	error(String msg)
protected static org.semanticweb.owlapi.model.OWLClass	handleLine(org.semanticweb.owlapi.model.OWLOntology ontology, Map<String,List<org.semanticweb.owlapi.model.OWLClass>> labels, org.semanticweb.owlapi.model.OWLClass taxon, String line, int lineNumber) Handle one line of the data file.
static void	main(String[] args) Handle command-line arguments when this class is used in an executable Jar file.
static String[]	parseLine(String line, int lineNumber) Parse a line of the data file into a pair of strings: the field name and the field value.
static void	printAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, String outputPath) Print string representations of all the axioms in an ontology, one axiom statement per line.

Methods inherited from class owltools.ncbi.NCBIConverter

assertSubClass, checkTaxon, createNCBIIRI, createNCBIIRI, createTaxon, getTaxonID

Methods inherited from class owltools.ncbi.OWLConverter

annotate, annotate, annotate, annotate, annotate, annotate, assertSubAnnotationProperty, assertSubClass, createAnnotationProperty, createAnnotationProperty, createAnnotationProperty, declare, getFirstLiteral, getFirstLiteral, getFirstLiteral, initializeFormat, reformatName, synonym, synonym, updateAnnotation

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Create a logger.

usage

protected static String usage

Command line usage information.

Constructor Detail

NCBI2OWL

public NCBI2OWL()

Method Detail

main

public static void main(String[] args)

Handle command-line arguments when this class is used in an executable Jar file. See usage.

Parameters:

args - one or more strings to provide options and paths

error

public static void error(String msg)

convertToOWL

public static org.semanticweb.owlapi.model.OWLOntology convertToOWL(String inputPath,
                                                    Map<String,String> uniqueNames)
                                                             throws IOException,
                                                                    org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                                                    org.semanticweb.owlapi.model.OWLOntologyStorageException

Read a data file and create an OWL representation.

Parameters:

inputPath - the path to the input data file (e.g. taxonomy.dat)

uniqueNames -

Returns:

OWL ontology

Throws:

IOException - if the paths do not resolve

org.semanticweb.owlapi.model.OWLOntologyCreationException - if OWLAPI fails to create an empty ontology

org.semanticweb.owlapi.model.OWLOntologyStorageException - if OWLAPI can't save the file

convertToOWL

public static org.semanticweb.owlapi.model.OWLOntology convertToOWL(String inputPath,
                                                    String outputPath,
                                                    Map<String,String> uniqueNames)
                                                             throws IOException,
                                                                    org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                                                    org.semanticweb.owlapi.model.OWLOntologyStorageException

Read a data file, create an OWL representation, and save an OWL file.

Parameters:

inputPath - the path to the input data file (e.g. taxonomy.dat)

outputPath - the path to the output OWL file (e.g. ncbi_taxonomy.owl).

uniqueNames -

Returns:

OWL ontology

Throws:

IOException - if the paths do not resolve

org.semanticweb.owlapi.model.OWLOntologyCreationException - if OWLAPI fails to create an empty ontology

org.semanticweb.owlapi.model.OWLOntologyStorageException - if OWLAPI can't save the file

convertToOWL

public static org.semanticweb.owlapi.model.OWLOntology convertToOWL(String inputPath,
                                                    String outputPath,
                                                    InputStream mergeInfo,
                                                    InputStream citationInfo,
                                                    Map<String,String> uniqueNames)
                                                             throws IOException,
                                                                    org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                                                    org.semanticweb.owlapi.model.OWLOntologyStorageException

Read a data file, create an OWL representation, and save an OWL file. Create alternate identifiers from the merge.dmp file information

Parameters:

inputPath - the path to the input data file (e.g. taxonomy.dat)

outputPath - the path to the output OWL file (e.g. ncbi_taxonomy.owl).

mergeInfo - the input stream of the merged information

citationInfo - the input stream of the citation information

uniqueNames -

Returns:

OWL ontology

Throws:

IOException - if the paths do not resolve

org.semanticweb.owlapi.model.OWLOntologyCreationException - if OWLAPI fails to create an empty ontology

org.semanticweb.owlapi.model.OWLOntologyStorageException - if OWLAPI can't save the file

handleLine

protected static org.semanticweb.owlapi.model.OWLClass handleLine(org.semanticweb.owlapi.model.OWLOntology ontology,
                                               Map<String,List<org.semanticweb.owlapi.model.OWLClass>> labels,
                                               org.semanticweb.owlapi.model.OWLClass taxon,
                                               String line,
                                               int lineNumber)

Handle one line of the data file. There are several cases:

1. separator (//): return null
2. ID: create a new taxon (OWLClass)
4. PARENT ID: add the parent as the superclass of this taxon
5. RANK: add a rank annotation to the right IRI
6. GC ID: add a DbXref
7. MGC ID: do nothing (TODO)
8. INCLUDE: do nothing (TODO)
9. Synonyms: add a synonym annotation

Parameters:

ontology - the current ontology

labels - a list to check that labels are unique

taxon - the current class or null

line - the line to handle

lineNumber - for logging purposes

Returns:

null or the taxon for the next line

parseLine

public static String[] parseLine(String line,
                 int lineNumber)

Parse a line of the data file into a pair of strings: the field name and the field value. Lines are expected to be in two parts, separated by a colon. Leading and trailing whitespace is trimmed.

Parameters:

line - the line to be parsed

lineNumber - used for logging purposes

Returns:

either null or the pair of the field name (lower case) and field value

checkAxioms

public static void checkAxioms(String inputPath,
               String outputPath)
                        throws IOException,
                               org.semanticweb.owlapi.model.OWLOntologyCreationException

Load an ontology from a file and then print a list of its axioms.

Parameters:

inputPath - the path for the input ontology file

outputPath - the path for the output file

Throws:

IOException - if it cannot write to the outputPath

org.semanticweb.owlapi.model.OWLOntologyCreationException - if OWLAPI can't read the ontology file

printAxioms

public static void printAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
               String outputPath)
                        throws IOException

Print string representations of all the axioms in an ontology, one axiom statement per line. Sorted lists of axioms can be used to compare ontologies.

Parameters:

ontology - the ontology to print

outputPath - the path for the output file

Throws:

IOException - if it cannot write to the outputPath