Search results for "distribution:ONTO-PERL perl"
ONTO-PERL - PERL modules for OBO-formatted ontologies
ONTO-PERL a collection of PERL modules for dealing with OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (to handle ontology elements such as a Term, a Relationship, a Synonym, and so forth), s...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::Def - A definition structure of a term. A term should have zero or one instance of this type per term description.
A OBO::Core::Def object encapsules a definition for a universal. There must be zero or one instance of this type per term description. An object of this type should have a quote enclosed definition text, and a OBO::Core::Dbxref set containing data ba...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Util::Set - An implementation of a set of scalars (sensu PERL).
A collection that contains no duplicate elements. More formally, sets contain no pair of elements $e1 and $e2 such that $e1->equals($e2). As implied by its name, this interface models the mathematical set abstraction....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Util::Map - An implementation of a map (key -> value).
An object that maps keys to values. A map cannot contain duplicate keys; each key can map to at most one value....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::XO::OBO_ID - A module for describing identifiers of any OBO ontology (e.g. XO). Its IDSpace and LocalID are stored.
The OBO::XO::OBO_ID class implements an identifier for any OBO ontology. A XO ID holds: IDSPACE, and a LOCALID in the following form: IDSPACE:LOCALID For instance: XO:1234567 Identifiers (IDs) in OBO should be strings consisting of an IDSpace concate...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::Term - A universal/term/class/concept in an ontology.
A Term in the ontology. c.f. OBO flat file specification. Recommended: http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::APO::APO_ID - A module for describing Application Ontology (APO) identifiers. Its idspace, subnamespace and localID are stored.
The OBO::APO::APO_ID class implements an Application Ontology identifier. A APO ID holds: IDSPACE, SUBNAMESPACE and a NUMBER in the following form: APO:[A-Z][a-z]?nnnnnnn For instance: APO:Pa1234567 The SUBNAMESPACE may be one of the following: C Cel...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::Dbxref - A database reference structure.
A dbxref object encapsules a reference for a universal....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::Synonym - A term synonym.
A synonym for a term held by the ontology. This synonym must have a type and a definition (OBO::Core::Def) describing the origins of the synonym, and may indicate a synonym category or scope information. The synonym scope may be one of four values: E...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::APO::GoaToRDF - A GOA associations to RDF converter.
Converts a GOA association file to a RDF graph. The RDF graph is very simple, containing a node for each line from the association file (called GOA_ASSOC_n), and several triples for the fields (e.g. obj_symb). GOA associations files can be obtained f...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Util::TermSet - A Set implementation.
A set (OBO::Util::ObjectSet) of terms (OBO::Core::Term)....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::IDspace - A mapping between a "local" ID space and a "global" ID space.
An IDSpace is a mapping between a "local" ID space and a "global" ID space. This object captures: a local idspace, a URI, quote-enclosed description (optional). Example: GO urn:lsid:bioontology.org:GO: "gene ontology terms"...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::XO::OBO_ID_Set - An implementation of a set of OBO::XO::OBO_ID objects.
The OBO::XO::OBO_ID_Set class implements a set of identifiers for any OBO ontology....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::Instance - An instance in an ontology.
A Instance in the ontology. c.f. OBO flat file specification....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Core::Ontology - An ontology of terms/concepts/universals, instances/individuals and relationships/properties.
This module supports the manipulation of OBO-formatted ontologies, such as the Gene Ontology (http://www.geneontology.org/) or the Cell Cycle Ontology (http://www.cellcycleontology.org). For a longer list of OBO-formatted ontologies, look at http://w...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::APO::NCBIToRDF - A NCBI taxonomy dump to RDF converter.
Converts NCBI taxonomy dump files (names and nodes) to a RDF graph. NCBI taxonomy dump files files can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/ The method 'work' gets the nodes file, the names file, and file handler for the RDF graph....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Util::Ontolome - A set of ontologies. This module supports the management of a set of ontologies.
An Ontolome is a collection of ontologies that contains no duplicate ontology elements. More formally, an Ontolome contains no pair of ontologies $e1 and $e2 such that $e1->equals($e2). As implied by its name, this package models the set of ontologie...
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::APO::APO_ID_Set - An implementation of a set of OBO::APO::APO_ID objects.
The OBO::APO::APO_ID_Set class implements a Cell-Cycle Ontology identifiers set....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Util::ObjectSet - An implementation of a set of OBO ontology objects.
The OBO::Util::ObjectSet class implements a set of ontology objects such as Terms, Relationships, etc....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC
OBO::Util::DbxrefSet - A Dbxref set implementation.
A set (OBO::Util::ObjectSet) of dbxref (OBO::Core::Dbxref) elements....
EASR/ONTO-PERL-1.45 - 30 Oct 2015 16:04:26 UTC