Package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg

Class IdentifiersOrg

java.lang.Object

de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg

All Implemented Interfaces:

Registry

public class IdentifiersOrg
extends Object
implements Registry

The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry. MIRIAM is a standard for annotating computational models in biology with machine-readable information.

This class provides static methods and utilities to handle, validate, and correct resource URLs based on the MIRIAM standards. It ensures that identifiers and URLs conform to recognized formats and corrects common errors in identifiers from various biological databases. The class also initializes necessary resources and configurations at the start through a static block.

Constructor Summary

Constructors

Constructor	Description
IdentifiersOrg()

Method Summary

Modifier and Type	Method	Description
static IdentifiersOrgURI	fixIdentifiersOrgUri(IdentifiersOrgURI uri)
String	getNamespaceForPrefix(String prefix)
String	getPatternByNamespaceName(String namespaceName)
String	getPrefixByNamespaceName(String namespaceName)
boolean	isValid(String url)
Optional<RegistryURI>	resolveBackwards(String url)	Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
boolean	validRegistryUrlPrefix(RegistryURI uri)	Existing models on BiGG and Biomodels use some namespaces that were removed from identifiers.org.

Methods inherited from class java.lang.Object

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

Constructor Details

IdentifiersOrg

public IdentifiersOrg()

Method Details

getNamespaceForPrefix

public String getNamespaceForPrefix(String prefix)

Specified by:

getNamespaceForPrefix in interface Registry

getPrefixByNamespaceName

public String getPrefixByNamespaceName(String namespaceName)

Specified by:

getPrefixByNamespaceName in interface Registry

getPatternByNamespaceName

public String getPatternByNamespaceName(String namespaceName)

Specified by:

getPatternByNamespaceName in interface Registry

resolveBackwards

public Optional<RegistryURI> resolveBackwards(String url)

Checks and processes a given resource URL to ensure it conforms to expected formats and corrections. This method handles specific cases such as URLs containing "omim", "ncbigi", and "reactome". It also processes general identifiers.org URLs and other alternative formats.

Specified by:

resolveBackwards in interface Registry

Parameters:

url - The URL to be checked and potentially modified.

Returns:

An Optional containing the processed URL if valid, or empty if the URL should be skipped.

validRegistryUrlPrefix

public boolean validRegistryUrlPrefix(RegistryURI uri)

Existing models on BiGG and Biomodels use some namespaces that were removed from identifiers.org. While for some namespaces updated mappings were available (see fixIdentifiersOrgUri(de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI)), this checks for those that could not be migrated.

Specified by:

validRegistryUrlPrefix in interface Registry

isValid

public boolean isValid(String url)

Specified by:

isValid in interface Registry

fixIdentifiersOrgUri

public static IdentifiersOrgURI fixIdentifiersOrgUri(IdentifiersOrgURI uri)