Author image Erick Antezana
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Changes for version 1.23

Documentation

PERL modules for CCO and OBO ontologies
Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
Collects the child terms (list of term IDs and their names) from a given term (existing ID) in the given OBO ontology.
Collects the descendent terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
Find all the obsolete terms in a given ontology.
Collects the parent terms (list of term IDs and their names) from a given term (existing ID) in the given OBO ontology.
Find all the relationship types in a given ontology.
Find all the root terms in a given ontology.
Extracts a subontology (in OBO format) of a given ontology having as root the given term ID.
Find all the synonyms of a given term name in an ontology.
Find all the terms in a given ontology.
Find all the terms in a given ontology that have a given string in their names.
Gene Ontology (in OBO) to OWL translator.
Generates a simple RDF graph from a given GOA file.
Converts an ontology into another one which could be integrated into CCO.
OBO to OWL translator.
OBO to RDF translator.
OBOF into RDF translator. The resulting file has (full) transitive closure.
OBO to XML translator (CCO scheme).
This script trims a given branch of an OBO ontology.
Obsolete terms vs their definitions.
Obsolete terms vs their names.
OWL to OBO translator (oboinowl mapping).
Gets the term IDs and term defintions of a given ontology.
Gets the term IDs and term names of a given ontology.
Gets the term IDs and its namespaces in a given ontology.

Modules

A module for describing Cell Cycle Ontology (CCO) identifiers. Its namespace, subnamespace and number are stored.
An implementation of a set of OBO::CCO::CCO_ID objects.
A map between CCO IDs and term names.
A GOA association record.
A GoaAssociationSet implementation
A GOA associations to OBO translator.
A GOA associations to RDF converter.
An IntAct to OBO parser/filter.
An interaction from IntAct
An IntAct to OBO parser/filter manager.
An interactor from IntAct
A NCBI taxonomy to OBO translator.
A NCBI taxonomy dump to RDF converter.
A new IntAct to OBO parser/filter.
An orthoMCL data to OBO translator
A UniProt to OBO translator.
An IntAct XML parser
A database reference structure.
A definition structure of the current term. A term must have zero or one instance of this type per term description.
A mapping between a "local" ID space and a "global" ID space.
An ontology holding terms and their relationships.
A relationship between two terms or two relationships within an ontology.
A type of relationship type in an ontology.
A term synonym.
A synonym type definition. It should contain a synonym type name, a space, a quote enclosed description, and an optional scope specifier.
A universal/term/class/concept in an ontology.
An OBO (Open Biomedical Ontologies) file parser.
An OWL parser (oboInOwl mapping).
A Dbxref set implementation.
A Set implementation of object IDs.
An implementation of a set of ontology objects.
A set of ontologies.
A Set implementation.
A Set implementation of Synonyms.
A Set implementation of Synonym Types.
A Set implementation.