MiriamLink (BioPAX Normalizer and MiriamLink 5.0.0-beta1 API)

java.lang.Object
- org.biopax.paxtools.normalizer.MiriamLink

```
public class MiriamLink
extends Object
```
Singleton local MIRIAM data resolver with all methods static.

Author:

rodche

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`BINDING` package name for jaxb to use
`static String`	`SCHEMA_LOCATION`
`static boolean`	`useObsoleteDatatypes`
`static boolean`	`useObsoleteResources`
`static String`	`XML_LOCATION` default web service URL to get the Miriam.xml db content; see also: http://www.ebi.ac.uk/miriam/main/export/.

Constructor Summary

Constructors
Modifier Constructor and Description

protected MiriamLink()
Default constructor: initialization of some parameters

Constructors
Modifier	Constructor and Description
`protected`	`MiriamLink()` Default constructor: initialization of some parameters

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static boolean`	`checkRegExp(String identifier, String datatype)` Checks if the identifier given follows the regular expression of its data type (also provided).
`static boolean`	`containsIdOrName(String searchKey)` Check whether Miriam contains a data type record with this name (any synonym) or identifier (case insensitive)
`static boolean`	`containsUri(String searchUri)` Check whether Miriam contains a data type record with this URI (case sensitive)
`static String`	`convertUrn(String urn)` Deprecated. this method applies `URLDecoder.decode(String)` to the last part of the URN, which may not always work as expected (test yours!)
`static String[]`	`getDataResources(String datatypeKey)` Retrieves home page URLs of a datatype.
`static net.biomodels.miriam.Miriam.Datatype`	`getDatatype(String datatypeKey)` Gets Miriam Datatype by its ID, Name, Synonym, or URI (URN/URL)
`static String`	`getDataTypeDef(String datatypeKey)` Retrieves the definition of a data type.
`static String`	`getDataTypePattern(String datatypeKey)` Retrieves the pattern (regular expression) used by the identifiers within a data type.
`static String[]`	`getDataTypesId()` Retrieves the internal identifier (stable and perennial) of all the data types (for example: "MIR:00000005").
`static String[]`	`getDataTypesName()` Retrieves the list of preferred names of all the data types available.
`static String`	`getDataTypeURI(String datatypeKey)` Retrieves the unique (official) URI of a data type (example: "urn:miriam:uniprot").
`static String[]`	`getDataTypeURIs(String datatypeKey)` Retrieves all the URIs of a data type, including all the deprecated ones (examples: "urn:miriam:uniprot", "http://www.uniprot.org/", "urn:lsid:uniprot.org:uniprot", ...).
`static String`	`getIdentifiersOrgURI(String name, String id)` Gets the Identifiers.org URI/URL of the entity (example: "http://identifiers.org/obo.go/GO:0045202").
`static String[]`	`getLocations(String datatypeKey, String entityId)` Retrieves the physical locationS (URLs) of web pageS providing knowledge about an entity.
`static String`	`getName(String datatypeKey)` Retrieves the preferred name of a data type.
`static String[]`	`getNames(String datatypeKey)` Retrieves all the synonyms (incl.
`static String`	`getOfficialDataTypeURI(net.biomodels.miriam.Miriam.Datatype datatype)` Retrieves the unique (official) URI of a data type (example: "http://identifiers.org/uniprot").
`static String`	`getOfficialDataTypeURI(String uri)` Deprecated. use getDataTypeURI instead
`static net.biomodels.miriam.Resource`	`getResource(String resourceId)` Retrieves the resource by id (for example: "MIR:00100008" (bind) ).
`static String`	`getResourceInstitution(String resourceId)` Retrieves the institution which manages a resource (example: "European Bioinformatics Institute").
`static String`	`getResourceLocation(String resourceId)` Retrieves the location (or country) of a resource (example: "United Kingdom").
`static String[]`	`getResourcesId()` Retrieves the internal identifier (stable and perennial) of all the resources (for example: "MIR:00100008" (bind) ).
`static String`	`getServicesVersion()` Retrieves the current version of MIRIAM Web Services.
`static String`	`getURI(String name, String id)` Retrieves the unique MIRIAM URI of a specific entity (example: "urn:miriam:obo.go:GO%3A0045202").
`static boolean`	`isDeprecated(String uri)` To know if a URI of a data type is deprecated.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - XML_LOCATION
```
public static final String XML_LOCATION
```
    default web service URL to get the Miriam.xml db content; see also: http://www.ebi.ac.uk/miriam/main/export/. Sometimes (e.g., 2016/01/07) the connection becomes EXTREMELY slow (1MB takes dozens minutes to download or stuck).
    
    See Also:
    
    Constant Field Values
  - BINDING
```
public static final String BINDING
```
    package name for jaxb to use
    
    See Also:
    
    Constant Field Values
  - SCHEMA_LOCATION
```
public static final String SCHEMA_LOCATION
```
    See Also:
    
    Constant Field Values
  - useObsoleteDatatypes
```
public static boolean useObsoleteDatatypes
```
  - useObsoleteResources
```
public static boolean useObsoleteResources
```
- Constructor Detail
  - MiriamLink
```
protected MiriamLink()
```
    Default constructor: initialization of some parameters
- Method Detail
  - getServicesVersion
```
public static String getServicesVersion()
```
    Retrieves the current version of MIRIAM Web Services.
    
    Returns:
    
    Current version of the Web Services
  - getDataTypeURI
```
public static String getDataTypeURI(String datatypeKey)
```
    Retrieves the unique (official) URI of a data type (example: "urn:miriam:uniprot").
    
    Parameters:
    
    datatypeKey - - ID, name, synonym, or (incl. deprecated) URI (URN or URL) of a data type (examples: "UniProt")
    
    Returns:
    
    unique URI of the data type
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getDataTypeURIs
```
public static String[] getDataTypeURIs(String datatypeKey)
```
    Retrieves all the URIs of a data type, including all the deprecated ones (examples: "urn:miriam:uniprot", "http://www.uniprot.org/", "urn:lsid:uniprot.org:uniprot", ...).
    
    Parameters:
    
    datatypeKey - name (or synonym), ID, or URI (URN or URL) of the data type (examples: "ChEBI", "UniProt")
    
    Returns:
    
    all the URIs of a data type (including the deprecated ones)
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getResourceLocation
```
public static String getResourceLocation(String resourceId)
```
    Retrieves the location (or country) of a resource (example: "United Kingdom").
    
    Parameters:
    
    resourceId - identifier of a resource (example: "MIR:00100009")
    
    Returns:
    
    the location (the country) where the resource is managed
  - getResourceInstitution
```
public static String getResourceInstitution(String resourceId)
```
    Retrieves the institution which manages a resource (example: "European Bioinformatics Institute").
    
    Parameters:
    
    resourceId - identifier of a resource (example: "MIR:00100009")
    
    Returns:
    
    the institution managing the resource
  - getURI
```
public static String getURI(String name,
                            String id)
```
    Retrieves the unique MIRIAM URI of a specific entity (example: "urn:miriam:obo.go:GO%3A0045202").
    
    Parameters:
    
    name - - name, URI/URL, or ID of a data type (examples: "ChEBI", "MIR:00000005")
    
    id - identifier of an entity within the data type (examples: "GO:0045202", "P62158")
    
    Returns:
    
    unique standard MIRIAM URI of a given entity
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getDataTypeDef
```
public static String getDataTypeDef(String datatypeKey)
```
    Retrieves the definition of a data type.
    
    Parameters:
    
    datatypeKey - - ID, name or URI (URN or URL) of a data type
    
    Returns:
    
    definition of the data type
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getLocations
```
public static String[] getLocations(String datatypeKey,
                                    String entityId)
```
    Retrieves the physical locationS (URLs) of web pageS providing knowledge about an entity.
    
    Parameters:
    
    datatypeKey - name (can be a synonym), ID, or URI of a data type (examples: "Gene Ontology", "UniProt")
    
    entityId - identifier of an entity within the given data type (examples: "GO:0045202", "P62158")
    
    Returns:
    
    physical locationS (URL templates) of web pageS providing knowledge about the given entity
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getDataResources
```
public static String[] getDataResources(String datatypeKey)
```
    Retrieves home page URLs of a datatype.
    
    Parameters:
    
    datatypeKey - - name (can be a synonym), ID, or URI (URL or URN) of a data type
    
    Returns:
    
    array of strings containing all the address of the main page of the resources of the data type
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - isDeprecated
```
public static boolean isDeprecated(String uri)
```
    To know if a URI of a data type is deprecated.
    
    Parameters:
    
    uri - (URN or URL) of a data type
    
    Returns:
    
    answer ("true" or "false") to the question: is this URI deprecated?
  - getDataTypePattern
```
public static String getDataTypePattern(String datatypeKey)
```
    Retrieves the pattern (regular expression) used by the identifiers within a data type.
    
    Parameters:
    
    datatypeKey - data type ID, name (or synonym), or URI (URL or URN)
    
    Returns:
    
    pattern of the data type
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getName
```
public static String getName(String datatypeKey)
```
    Retrieves the preferred name of a data type.
    
    Parameters:
    
    datatypeKey - URI (URL or URN), ID, or nickname of a data type
    
    Returns:
    
    the common name of the data type
    
    Throws:
    
    IllegalArgumentException - when not found
  - getNames
```
public static String[] getNames(String datatypeKey)
```
    Retrieves all the synonyms (incl. the preferred name) of a data type.
    
    Parameters:
    
    datatypeKey - ID, any name, or URI (URL or URN) of a data type
    
    Returns:
    
    all the data type's synonyms (incl. preferred name)
  - getDataTypesName
```
public static String[] getDataTypesName()
```
    Retrieves the list of preferred names of all the data types available.
    
    Returns:
    
    list of names of all the data types
  - getDataTypesId
```
public static String[] getDataTypesId()
```
    Retrieves the internal identifier (stable and perennial) of all the data types (for example: "MIR:00000005").
    
    Returns:
    
    list of the identifier of all the data types
  - getOfficialDataTypeURI
```
public static String getOfficialDataTypeURI(String uri)
```
    Deprecated. use getDataTypeURI instead
    
    Retrieves the official URI (it will always be URN) of a data type corresponding to the deprecated one.
    
    Parameters:
    
    uri - deprecated URI (URN or URL) of a data type
    
    Returns:
    
    the official URI of a data type corresponding to the deprecated one
  - checkRegExp
```
public static boolean checkRegExp(String identifier,
                                  String datatype)
```
    Checks if the identifier given follows the regular expression of its data type (also provided).
    
    Parameters:
    
    identifier - internal identifier used by the data type
    
    datatype - name, synonym or URI of a data type
    
    Returns:
    
    "true" if the identifier follows the regular expression, "false" otherwise
    
    Throws:
    
    IllegalArgumentException - when datatype not found
  - getOfficialDataTypeURI
```
public static String getOfficialDataTypeURI(net.biomodels.miriam.Miriam.Datatype datatype)
```
    Retrieves the unique (official) URI of a data type (example: "http://identifiers.org/uniprot").
    
    Parameters:
    
    datatype - net.biomodels.miriam.Miriam.Datatype
    
    Returns:
    
    URI
  - getDatatype
```
public static net.biomodels.miriam.Miriam.Datatype getDatatype(String datatypeKey)
```
    Gets Miriam Datatype by its ID, Name, Synonym, or URI (URN/URL)
    
    Parameters:
    
    datatypeKey - - a datatype ID, name, synonym, or URI
    
    Returns:
    
    MIRIAM Datatype bean
    
    Throws:
    
    IllegalArgumentException - when not found
  - getResourcesId
```
public static String[] getResourcesId()
```
    Retrieves the internal identifier (stable and perennial) of all the resources (for example: "MIR:00100008" (bind) ).
    
    Returns:
    
    list of the identifiers of all data types
  - getResource
```
public static net.biomodels.miriam.Resource getResource(String resourceId)
```
    Retrieves the resource by id (for example: "MIR:00100008" (bind) ).
    
    Parameters:
    
    resourceId - - resource identifier (similar to, but not a data type identifier!)
    
    Returns:
    
    MIRIAM Resource bean
  - containsIdOrName
```
public static boolean containsIdOrName(String searchKey)
```
    Check whether Miriam contains a data type record with this name (any synonym) or identifier (case insensitive)
    
    Parameters:
    
    searchKey - - ID, name, or synonym (case insensitive)
    
    Returns:
    
    true/false
  - containsUri
```
public static boolean containsUri(String searchUri)
```
    Check whether Miriam contains a data type record with this URI (case sensitive)
    
    Parameters:
    
    searchUri - - URI (case sensitive)
    
    Returns:
    
    true/false
  - convertUrn
```
public static String convertUrn(String urn)
```
    Deprecated. this method applies URLDecoder.decode(String) to the last part of the URN, which may not always work as expected (test yours!)
    
    Converts a MIRIAM URN into its equivalent Identifiers.org URL.
    
    Parameters:
    
    urn - - an existing Miriam URN, e.g., "urn:miriam:obo.go:GO%3A0045202"
    
    Returns:
    
    the Identifiers.org URL corresponding to the data URN, e.g., "http://identifiers.org/obo.go/GO:0045202"
    
    See Also:
    
    - use this to get the URN, - prefered URI
  - getIdentifiersOrgURI
```
public static String getIdentifiersOrgURI(String name,
                                          String id)
```
    Gets the Identifiers.org URI/URL of the entity (example: "http://identifiers.org/obo.go/GO:0045202").
    
    Parameters:
    
    name - - name, URI/URL, or ID of a data type (examples: "ChEBI", "MIR:00000005")
    
    id - identifier of an entity within the data type (examples: "GO:0045202", "P62158")
    
    Returns:
    
    Identifiers.org URL for the id
    
    Throws:
    
    IllegalArgumentException - when datatype not found

Class MiriamLink

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

XML_LOCATION

BINDING

SCHEMA_LOCATION

useObsoleteDatatypes

useObsoleteResources

Constructor Detail

MiriamLink

Method Detail

getServicesVersion

getDataTypeURI

getDataTypeURIs

getResourceLocation

getResourceInstitution

getURI

getDataTypeDef

getLocations

getDataResources

isDeprecated

getDataTypePattern

getName

getNames

getDataTypesName

getDataTypesId

getOfficialDataTypeURI

checkRegExp

getOfficialDataTypeURI

getDatatype

getResourcesId

getResource

containsIdOrName

containsUri

convertUrn

getIdentifiersOrgURI