Index (BioPAX Normalizer and MiriamLink 5.0.1 API)

A B C G I M N O P S U V X

A

autoName(Provenance) - Static method in class org.biopax.paxtools.normalizer.Normalizer: Auto-generates standard and other names for the datasource from either its ID (if URN) or one of its existing names (preferably - standard name)

B

BINDING - Static variable in class org.biopax.paxtools.normalizer.MiriamLink: package name for jaxb to use

C

checkRegExp(String, String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Checks if the identifier given follows the regular expression of its data type (also provided).
containsIdOrName(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Check whether Miriam contains a data type record with this name (any synonym) or identifier (case insensitive)
containsUri(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Check whether Miriam contains a data type record with this URI (case sensitive)
convertToLevel3(String) - Static method in class org.biopax.paxtools.normalizer.Normalizer: Converts BioPAX L1 or L2 RDF/XML string data to BioPAX L3 string.
convertUrn(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Deprecated.
this method applies URLDecoder.decode(String) to the last part of the URN, which may not always work as expected (test yours!)

G

getDataResources(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves home page URLs of a datatype.
getDatatype(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Gets Miriam Datatype by its ID, Name, Synonym, or URI (URN/URL)
getDataTypeDef(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the definition of a data type.
getDataTypePattern(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the pattern (regular expression) used by the identifiers within a data type.
getDataTypesId() - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the internal identifier (stable and perennial) of all the data types (for example: "MIR:00000005").
getDataTypesName() - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the list of preferred names of all the data types available.
getDataTypeURI(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the unique (official) URI of a data type (example: "urn:miriam:uniprot").
getDataTypeURIs(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: 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", ...).
getDescription() - Method in class org.biopax.paxtools.normalizer.Normalizer: Description of the model to normalize.
getIdentifiersOrgURI(String, String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Gets the Identifiers.org URI/URL of the entity (example: "http://identifiers.org/obo.go/GO:0045202").
getLocations(String, String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the physical locationS (URLs) of web pageS providing knowledge about an entity.
getName(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the preferred name of a data type.
getNames(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves all the synonyms (incl.
getOfficialDataTypeURI(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Deprecated.
use getDataTypeURI instead
getOfficialDataTypeURI(Miriam.Datatype) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the unique (official) URI of a data type (example: "http://identifiers.org/uniprot").
getResource(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the resource by id (for example: "MIR:00100008" (bind) ).
getResourceInstitution(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the institution which manages a resource (example: "European Bioinformatics Institute").
getResourceLocation(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the location (or country) of a resource (example: "United Kingdom").
getResourcesId() - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the internal identifier (stable and perennial) of all the resources (for example: "MIR:00100008" (bind) ).
getServicesVersion() - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the current version of MIRIAM Web Services.
getURI(String, String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: Retrieves the unique MIRIAM URI of a specific entity (example: "urn:miriam:obo.go:GO%3A0045202").
getXmlBase() - Method in class org.biopax.paxtools.normalizer.Normalizer

I

isDeprecated(String) - Static method in class org.biopax.paxtools.normalizer.MiriamLink: To know if a URI of a data type is deprecated.
isFixDisplayName() - Method in class org.biopax.paxtools.normalizer.Normalizer

M

MiriamLink - Class in org.biopax.paxtools.normalizer: Singleton local MIRIAM data resolver with all methods static.
MiriamLink() - Constructor for class org.biopax.paxtools.normalizer.MiriamLink: Default constructor: initialization of some parameters

N

normalize(String) - Method in class org.biopax.paxtools.normalizer.Normalizer: Deprecated.
this method will fail if the data exceeds ~1Gb (max UTF8 java String length)
normalize(Model) - Method in class org.biopax.paxtools.normalizer.Normalizer: BioPAX normalization (modifies the original Model)
Normalizer - Class in org.biopax.paxtools.normalizer: BioPAX (Level 3) Normalizer, an advanced BioPAX utility to help pathway data integrating and linking.
Normalizer() - Constructor for class org.biopax.paxtools.normalizer.Normalizer: Constructor

O

org.biopax.paxtools.normalizer - package org.biopax.paxtools.normalizer

P

PROPERTY_NORMALIZER_URI_STRATEGY - Static variable in class org.biopax.paxtools.normalizer.Normalizer

S

SCHEMA_LOCATION - Static variable in class org.biopax.paxtools.normalizer.MiriamLink
setDescription(String) - Method in class org.biopax.paxtools.normalizer.Normalizer
setFixDisplayName(boolean) - Method in class org.biopax.paxtools.normalizer.Normalizer
setXmlBase(String) - Method in class org.biopax.paxtools.normalizer.Normalizer

U

uri(String, String, String, Class<? extends BioPAXElement>) - Static method in class org.biopax.paxtools.normalizer.Normalizer: Consistently generates a new BioPAX element URI using given URI namespace (xml:base), BioPAX class, and two different identifiers (at least one is required).
useObsoleteDatatypes - Static variable in class org.biopax.paxtools.normalizer.MiriamLink
useObsoleteResources - Static variable in class org.biopax.paxtools.normalizer.MiriamLink

V

VALUE_NORMALIZER_URI_STRATEGY_MD5 - Static variable in class org.biopax.paxtools.normalizer.Normalizer
VALUE_NORMALIZER_URI_STRATEGY_SIMPLE - Static variable in class org.biopax.paxtools.normalizer.Normalizer

X

XML_LOCATION - Static variable in class org.biopax.paxtools.normalizer.MiriamLink: default web service URL to get the Miriam.xml db content; see also: http://www.ebi.ac.uk/miriam/main/export/.

A B C G I M N O P S U V X