Package org.bridgedb

Class DataSource

java.lang.Object

org.bridgedb.DataSource

public final class DataSource
extends Object

Contains information about a certain DataSource. This includes:

• Its full name ("Ensembl")
• Its system code ("En")
• Its main url ("http://www.ensembl.org")
• Id-specific url's ("http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=" + id)

The DataSource class uses the extensible enum pattern. You cannot instantiate DataSources directly, instead you have to use one of the constants from the org.bridgedb.bio module such as BioDataSource.ENSEMBL, or the getBySystemcode or "getByFullname" methods. These methods return a predefined DataSource object if it exists. If a predefined DataSource for a requested SystemCode doesn't exists, a new one springs to life automatically. This can be used when the user requests new, unknown data sources. If you call getBySystemCode twice with the same argument, it is guaranteed that you get the same return object. However, there is no way to combine a new DataSource with a new FullName unless you use the "register" method.

This way any number of pre-defined DataSources can be used, but plugins can define new ones and you can handle unknown data sources in the same way as predefined ones.

Definitions for common DataSources can be found in org.bridgedb.bio.BioDataSource.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DataSource.Builder	Uses builder pattern to set optional attributes for a DataSource.

Field Summary

Fields

Modifier and Type	Field	Description
static String	UNKOWN

Method Summary

Modifier and Type	Method	Description
static boolean	fullNameExists(String fullName)	Check if a DataSoucre with this sfullName has been registered
String	getAlternative()	Retrieves any saved alternative name.
static DataSource	getByAlias(String alias)
static DataSource	getByCompactIdentifierPrefix(String prefix)
static DataSource	getByIdentiferOrgBase(String base)	Since version 2.0 this method will return null if no DataSource is known
static DataSource	getByMiriamBase(String base)	Since version 2.0 this method will return null if no DataSource is known
String	getCompactIdentifier(String id)	Creates a compact identifier.
String	getCompactIdentifierPrefix()	Returns the compact identifier prefix (previously known as MIRIAM base.
static Set<DataSource>	getDataSources()	get all registered datasoures as a set.
String	getDescription()	Retrieves any saved description.
Xref	getExample()
static DataSource	getExistingByFullName(String fullName)	returns pre-existing DataSource object
static DataSource	getExistingBySystemCode(String systemCode)
static Set<DataSource>	getFilteredSet(Boolean primary, Boolean metabolite, Object o)	returns a filtered subset of available datasources.
String	getFullName()	returns full name of DataSource e.g.
static List<String>	getFullNames()	Get a list of all non-null full names.
String	getIdentifiersOrgUri(String id)
String	getKnownUrl(String id)	Turn id into url pointing to info page on the web, e.g.
String	getMainUrl()	Return the main Url for this datasource, that can be used to refer to the datasource in general.
String	getMiriamURN(String id)	Creates a global identifier.
Object	getOrganism()
String	getSystemCode()	returns GenMAPP SystemCode, e.g.
String	getType()
boolean	isDeprecated()	A DataSource is deprecated if it is replaced by another data source which should be used instead.
DataSource	isDeprecatedBy()	Returns the DataSource that should be used instead if this DataSource is deprecated.
boolean	isMetabolite()
boolean	isPrimary()
static DataSource.Builder	register(String sysCode, String fullName)	Register a new DataSource with (optional) detailed information.
void	registerAlias(String alias)
static boolean	systemCodeExists(String systemCode)	Check if a DataSoucre with this systemCode has been registered
String	toString()	The string representation of a DataSource is equal to it's full name.
boolean	urlPatternKnown()	Check if a Url pattern is know for this DataSource.

Methods inherited from class java.lang.Object

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

Field Detail

UNKOWN

public static final String UNKOWN

See Also:

Constant Field Values

Method Detail

getKnownUrl

public String getKnownUrl(String id)

Turn id into url pointing to info page on the web, e.g. "http://www.ensembl.org/get?id=ENSG..." Since version 2 this will return null if no pattern has been set.

Parameters:

id - identifier to use in url

Returns:

Url

urlPatternKnown

public boolean urlPatternKnown()

Check if a Url pattern is know for this DataSource.

Returns:

True if and only if a Url pattern is known/ has been registered

getFullName

public String getFullName()

returns full name of DataSource e.g. "Ensembl". May return null if only the system code is known. Also used as identifier in GPML

Returns:

full name of DataSource

getSystemCode

public String getSystemCode()

returns GenMAPP SystemCode, e.g. "En". May return null, if only the full name is known. Also used as identifier in

1. Gdb databases,
2. Gex databases.
3. Imported data
4. the Mapp format.

We should try not to use the system code anywhere outside these 4 uses.

Returns:

systemcode, a short unique code.

getMainUrl

public String getMainUrl()

Return the main Url for this datasource, that can be used to refer to the datasource in general. (e.g. http://www.ensembl.org/) May return null in case the main url is unknown.

Returns:

main url

getType

public String getType()

Returns:

type of entity that this DataSource describes, for example "metabolite", "gene", "protein", "interaction" or "probe"

getMiriamURN

public String getMiriamURN(String id)

Creates a global identifier. It uses the MIRIAM data type list to create a MIRIAM URI like "urn:miriam:uniprot:P12345", or if this DataSource is not included in the MIRIAM data types list, a bridgedb URI.

Parameters:

id - Id to generate URN from.

Returns:

the URN.

Since:

Version 2.0.0

getCompactIdentifier

public String getCompactIdentifier(String id)

Creates a compact identifier. It uses the MIRIAM data type list to create a compact identifier like "uniprot:P12345".

Parameters:

id - identifier to generate compact identifier from.

Returns:

the compact identifier.

Since:

Version 3.0.0

getIdentifiersOrgUri

public String getIdentifiersOrgUri(String id)

getAlternative

public String getAlternative()

Retrieves any saved alternative name.

Returns:

Saved alternative name or null if none is known

Since:

version 2.0.0

getDescription

public String getDescription()

Retrieves any saved description.

Returns:

Saved description or null if none is known

Since:

version 2.0.0

register

public static DataSource.Builder register(String sysCode,
                                          String fullName)

Register a new DataSource with (optional) detailed information. This can be used by other modules to define new DataSources. Note: Since version 2 this method is stricter. It will no longer allow an existing dataSource to have either its full name of sysCode changed.

Parameters:

sysCode - short unique code between 1-4 letters, originally used by GenMAPP

fullName - full name used in GPML.

Returns:

Builder that can be used for adding detailed information.

registerAlias

public void registerAlias(String alias)

getExistingBySystemCode

public static DataSource getExistingBySystemCode(String systemCode)

Parameters:

systemCode - short unique code to query for

Returns:

pre-existing DataSource object by system code if it exists

Throws:

IllegalArgumentException - if no DataSource is known with this systemCode

systemCodeExists

public static boolean systemCodeExists(String systemCode)

Check if a DataSoucre with this systemCode has been registered

Parameters:

systemCode - to check

Returns:

True if and only if a DataSource has been registered with this systemCode.

getExistingByFullName

public static DataSource getExistingByFullName(String fullName)

returns pre-existing DataSource object

Parameters:

fullName - full name to query for

Returns:

DataSource

Throws:

IllegalArgumentException - if no DataSource is known with this systemCode

fullNameExists

public static boolean fullNameExists(String fullName)

Check if a DataSoucre with this sfullName has been registered

Parameters:

fullName - to check

Returns:

True if and only if a DataSource has been registered with this systemCode.

getByAlias

public static DataSource getByAlias(String alias)

getDataSources

public static Set<DataSource> getDataSources()

get all registered datasoures as a set.

Returns:

set of all registered DataSources

getFilteredSet

public static Set<DataSource> getFilteredSet(Boolean primary,
                                             Boolean metabolite,
                                             Object o)

returns a filtered subset of available datasources.

Parameters:

primary - Filter for specified primary-ness. If null, don't filter on primary-ness.

metabolite - Filter for specified metabolite-ness. If null, don't filter on metabolite-ness.

o - Filter for specified organism. If null, don't filter on organism.

Returns:

filtered set.

getFullNames

public static List<String> getFullNames()

Get a list of all non-null full names.

Warning: the ordering of this list is undefined. Two subsequent calls may give different results.

Returns:

List of full names

toString

public String toString()

The string representation of a DataSource is equal to it's full name. (e.g. "Ensembl")

Overrides:

toString in class Object

Returns:

String representation

getExample

public Xref getExample()

Returns:

example Xref, mostly for testing purposes

isPrimary

public boolean isPrimary()

Returns:

if this is a primary DataSource or not. Primary DataSources are preferred when annotating models. A DataSource is primary if it is not of type probe, so that means e.g. Affymetrix or Agilent probes are not primary. All gene, protein and metabolite identifiers are primary.

isDeprecated

public boolean isDeprecated()

A DataSource is deprecated if it is replaced by another data source which should be used instead. Even if this DataSource is deprecated, it does not imply it says what it is deprecated by.

Returns:

true if this DataSource is deprecated

isDeprecatedBy

public DataSource isDeprecatedBy()

Returns the DataSource that should be used instead if this DataSource is deprecated. This method may return null even if this DataSource is deprecated.

Returns:

if defined, the DataSource that should be used instead of this one

isMetabolite

public boolean isMetabolite()

Returns:

if this DataSource describes metabolites or not.

getOrganism

public Object getOrganism()

Returns:

Organism that this DataSource describes, or null if multiple / not applicable.

getByCompactIdentifierPrefix

public static DataSource getByCompactIdentifierPrefix(String prefix)

getByMiriamBase

public static DataSource getByMiriamBase(String base)

Since version 2.0 this method will return null if no DataSource is known

Parameters:

base - the base urn, which must start with "urn:miriam:". It it isn't, null is returned.

getByIdentiferOrgBase

public static DataSource getByIdentiferOrgBase(String base)

Since version 2.0 this method will return null if no DataSource is known

Parameters:

base - the base urn, which must start with "http://identifiers.org/". It it isn't, null is returned.

getCompactIdentifierPrefix

public String getCompactIdentifierPrefix()

Returns the compact identifier prefix (previously known as MIRIAM base.