Uses of Package
org.biojava.ontology
Packages that use org.biojava.ontology
Package
Description
Support for reading and writing GFF3.
Classes and interfaces for defining biological sequences and informatics
objects.
General purpose Sequence storage in a relational database.
Standard in-memory implementations of
Sequence
and
Feature
.
A general-purpose API for ontologies.
Tools for loading and saving ontologies.
Rich implementations of Sequences, Locations and Features.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Classes in org.biojava.ontology used by org.biojava.bio.program.gff3
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Classes in org.biojava.ontology used by org.biojava.bio.seqClassDescriptionThrown to indicate that an ontology term is not acceptable or appropriate in a given contextA term in an ontology.
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Classes in org.biojava.ontology used by org.biojava.bio.seq.db.biosql
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Classes in org.biojava.ontology used by org.biojava.bio.seq.impl
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Classes in org.biojava.ontology used by org.biojava.ontologyClassDescriptionAbstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.Thrown to indicate that a term or triple can't be added to an ontology because it is already present.An ontology.Thrown to indicate an error in an Ontology objectA factory for Ontology instances.This is an interface for optimizing ontology operators.A term in an ontology which identifies another ontology.A term in another ontology.A term in an ontology.Simple in-memory implementation of an ontology term.A triple in an ontology.
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Classes in org.biojava.ontology used by org.biojava.ontology.ioClassDescriptionAn ontology.Thrown to indicate an error in an Ontology objectA factory for Ontology instances.
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Classes in org.biojava.ontology used by org.biojava.ontology.obo
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Classes in org.biojava.ontology used by org.biojavax.bio.seqClassDescriptionThrown to indicate that an ontology term is not acceptable or appropriate in a given contextA term in an ontology.
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Classes in org.biojava.ontology used by org.biojavax.ontologyClassDescriptionThrown to indicate that a term or triple can't be added to an ontology because it is already present.An ontology.This is an interface for optimizing ontology operators.A term in an ontology.A triple in an ontology.