All Classes

Class	Description
AllFieldsEquals	A deep equals that compares all fields of a Class, also ones that are not used by Object.equals(Object) (for example due to design-reasons, though validity for all fields still needs to be checked in unit-tests to assess everything functions as it should).
BiologicalEntity	Describes a biological entity (such as a Gene, Disease or Phenotype).
BiologicalEntityCollection<T1 extends BiologicalEntity,T2 extends BiologicalEntity,T3 extends BiologicalEntityCombination<T1,T2>>	A collection of 0 or more BiologicalEntityCombinations that have the same BiologicalEntityCollection and BiologicalEntityCollection class types.
BiologicalEntityCombination<T1 extends BiologicalEntity,T2 extends BiologicalEntity>	A combination of 2 BiologicalEntity subclass objects.
ChildrenRetriever
Disease	A disease.
DisgenetRdfDataRetriever	Retrieves data for further usage from the DisGeNET database.
Entity	Describes an entity.
EntityWithIntId
EnumTypeDefiner
Gene	A gene.
GeneDiseaseCollection	A collection of GeneDiseaseCombinations.
GeneDiseaseCollectionDeserializer
GeneDiseaseCollectionJsonSerialization
GeneDiseaseCollectionRetrievalRunner
GeneDiseaseCollectionSerializer	Serializers a GeneDiseaseCollection to json.
GeneDiseaseCombination	A combination of a Gene and a Disease.
GeneDiseaseCombinationType	Based on: http://semanticscience.org/ontology/sio.owl (which is licensed under http://creativecommons.org/licenses/by/4.0/) Please refer to http://www.disgenet.org/ds/DisGeNET/html/images/ontology.svg for the Ontology overview.
GenePrioritizer	Returns a Gene priority from a GeneDiseaseCollection.
GenesForPhenotypeRetriever	Retrieves all required information for further processing regarding the genes belonging to a given phenotype.
GeneSymbol
HighestSingleDisgenetScoreGenePrioritizer	A Gene priority for a GeneDiseaseCollection that is based on the highest GeneDiseaseCombination.getDisgenetScore() per Gene.
InvalidStringFormatException	Thrown to indicate that a method has been given a String that is formatted in an inappropriate/unexpected way.
MaxDistanceRetriever
ModelFilesReader	Creates an (Ontology) Model from RDF files.
ModelReader	Interface describing a Class that reads in a Model.
OntologyModelFilesReader	Generates an OntModel using OntModelSpec.OWL_MEM.
Phenotype	Defines a phenotype.
PhenotypeNetwork	A network of Phenotypes with a single source Phenotype from which the network is created.
PhenotypeNetworkCollection	A collection of PhenotypeNetworks.
PhenotypesRetrievalRunner	Class containing all required logic for retrieving related Phenotypes for the input Phenotypes.
PhenotypesRetriever	For one or more Phenotypes within an OntModel, retrieves other Phenotypes that are linked to it.
PhenotypesRetrieverFactory
Prioritizer<T1 extends BiologicalEntity,T2 extends BiologicalEntityCollection>	Returns a priority of T1 from T2.
PubmedEvidence
QueryRunner	Is able to run a SPARQL query on a Model.
QueryString	A String that can be used for SPARQL querying.
QueryStringGenerator	Generates SPARQL queries specific for the DisGeNET RDF dataset.
QueryStringPathRange	A String defining the path which should be used in the RDF graph.
ResourceUri	An Object that also contains a reference to the unique ID within an RDF database (and this reference is an URI).
Source	Describes the source (the database) for a specific piece of information.
Source.Level	The possible Source levels.
TripleStoreDbReader	Creates an (Ontology) Model from a TDB database.