Package de.uni_mannheim.informatik.dws.melt.matching_data

Class TrackRepository.Largebio

java.lang.Object

de.uni_mannheim.informatik.dws.melt.matching_data.TrackRepository.Largebio

Enclosing class:

TrackRepository

public static class TrackRepository.Largebio
extends Object

Large Biomedical Ontologies. This track consists of finding alignments between the Foundational Model of Anatomy (FMA), SNOMED CT, and the National Cancer Institute Thesaurus (NCI). These ontologies are semantically rich and contain tens of thousands of classes. UMLS Metathesaurus has been selected as the basis for the track reference alignments.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	TrackRepository.Largebio.V2015	2015 version of Large Biomedical Ontologies.
static class	TrackRepository.Largebio.V2016	2016 version of Large Biomedical Ontologies - these are also used for 2017 and 2018.

Constructor Summary

Constructors

Constructor	Description
Largebio()

Method Summary

Modifier and Type	Method	Description
static String	getArgumentForUnlimitEntityExpansion()	Returns the program argument which sets jdk.xml.entityExpansionLimit to zero because large bio needs it for parsing at least in jena.
static void	unlimitEntityExpansion()	Sets the system property of jdk.xml.entityExpansionLimit to zero because large bio needs it for parsing at least in jena.

Methods inherited from class java.lang.Object

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

Constructor Details

Largebio

public Largebio()

Method Details

unlimitEntityExpansion

public static void unlimitEntityExpansion()

Sets the system property of jdk.xml.entityExpansionLimit to zero because large bio needs it for parsing at least in jena. This modifies the current JVM. Call this function before parsing large bio ontologies and especially when getting the error: JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; this is the limit imposed by the JDK. or JAXP00010001: Der Parser hat mehr als 64000 Entityerweiterungen in diesem Dokument gefunden. Dies ist der von JDK vorgeschriebene Grenzwert.

getArgumentForUnlimitEntityExpansion

public static String getArgumentForUnlimitEntityExpansion()

Returns the program argument which sets jdk.xml.entityExpansionLimit to zero because large bio needs it for parsing at least in jena. This will not modify the current JVM but return the argument needed for executing another executable.

Returns:

the argument which should be used.

See Also:

• unlimitEntityExpansion()