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

Description

static final String

BINDING

package name for jaxb to use

static boolean

useObsoleteDatatypes

static boolean

useObsoleteResources
Constructor Summary

Constructors

Modifier

Constructor

Description

protected

MiriamLink()

Default constructor: initialization of some parameters
Method Summary

Modifier and Type

Method

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(String uri)

Deprecated.
use getDataTypeURI instead

static String

getOfficialDataTypeURI(net.biomodels.miriam.Miriam.Datatype datatype)

Retrieves the unique (official) URI of a data type (example: "http://identifiers.org/uniprot").

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 Details
- BINDING
  
  public static final String BINDING
  
  package name for jaxb to use
  See Also:
  
  Constant Field Values
- useObsoleteDatatypes
  
  public static boolean useObsoleteDatatypes
- useObsoleteResources
  
  public static boolean useObsoleteResources
Constructor Details
- MiriamLink
  
  protected MiriamLink()
  
  Default constructor: initialization of some parameters
Method Details
- 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 Details

BINDING

useObsoleteDatatypes

useObsoleteResources

Constructor Details

MiriamLink

Method Details

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