Uses of Package
org.molgenis.vibe.core.formats

Packages that use org.molgenis.vibe.core.formats

Package	Description
org.molgenis.vibe.core
org.molgenis.vibe.core.formats
org.molgenis.vibe.core.ontology_processing
org.molgenis.vibe.core.query_output_digestion.prioritization
org.molgenis.vibe.core.query_output_digestion.prioritization.gene
org.molgenis.vibe.core.tdb_processing
org.molgenis.vibe.core.tdb_processing.query_string_creation

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core

Class	Description
GeneDiseaseCollection	A collection of GeneDiseaseCombinations.
Phenotype	Defines a phenotype.
PhenotypeNetworkCollection	A collection of PhenotypeNetworks.

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core.formats

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	A collection of 0 or more BiologicalEntityCombinations that have the same BiologicalEntityCollection and BiologicalEntityCollection class types.
BiologicalEntityCombination	A combination of 2 BiologicalEntity subclass objects.
Disease	A disease.
Entity	Describes an entity.
EntityWithIntId
EnumTypeDefiner
Gene	A gene.
GeneDiseaseCollection	A collection of GeneDiseaseCombinations.
GeneDiseaseCollectionJsonSerialization
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.
GeneSymbol
Phenotype	Defines a phenotype.
PhenotypeNetwork	A network of Phenotypes with a single source Phenotype from which the network is created.
PubmedEvidence
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.

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core.ontology_processing

Class	Description
EnumTypeDefiner
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.

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core.query_output_digestion.prioritization

Class	Description
BiologicalEntity	Describes a biological entity (such as a Gene, Disease or Phenotype).
BiologicalEntityCollection	A collection of 0 or more BiologicalEntityCombinations that have the same BiologicalEntityCollection and BiologicalEntityCollection class types.

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core.query_output_digestion.prioritization.gene

Class	Description
Gene	A gene.
GeneDiseaseCollection	A collection of GeneDiseaseCombinations.

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core.tdb_processing

Class	Description
GeneDiseaseCollection	A collection of GeneDiseaseCombinations.
Phenotype	Defines a phenotype.
Source	Describes the source (the database) for a specific piece of information.

Classes in org.molgenis.vibe.core.formats used by org.molgenis.vibe.core.tdb_processing.query_string_creation

Class	Description
Phenotype	Defines a phenotype.