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CLASS ndi.ontology.Uberon

  Location: +ndi/+ontology/@Uberon/Uberon.m

Superclasses

ndi.ontology

Properties

none

Methods

Method Description
Uberon Constructor for the Uberon ontology object.
clearCache Clears all persistent caches in the ndi.ontology class.
getOntologies Returns the ontology details list from JSON cache.
getOntologyNameFromPrefix Extracts prefix, maps to ontology name (case-insensitive).
getPrefixOntologyMappings Returns the prefix->ontology mappings from JSON cache.
lookup Look up a term in an ontology using a prefixed string.
lookupOBOFile Looks up a term in a parsed OBO file with caching.
lookupTermOrID Looks up a term in the Uberon ontology by ID or name.
performIriLookup PERFORMIRILOOKUP Fetches ontology term details from EBI OLS using its IRI.
preprocessLookupInput PREPROCESSLOOKUPINPUT Processes input for ontology lookup functions.
searchOLSAndPerformIRILookup SEARCHOLSANDPERFORMIRILOOKUP Searches OLS and looks up unique result by IRI.

Methods help

Uberon - Constructor for the Uberon ontology object.

Currently takes no arguments.

    Documentation for ndi.ontology.Uberon/Uberon
       doc ndi.ontology.Uberon

clearCache - Clears all persistent caches in the ndi.ontology class.

Help for ndi.ontology.Uberon.clearCache is inherited from superclass ndi.ontology

getOntologies - Returns the ontology details list from JSON cache.

Help for ndi.ontology.Uberon.getOntologies is inherited from superclass ndi.ontology

getOntologyNameFromPrefix - Extracts prefix, maps to ontology name (case-insensitive).

[...] = ndi.ontology.getOntologyNameFromPrefix(...)

Help for ndi.ontology.Uberon.getOntologyNameFromPrefix is inherited from superclass ndi.ontology

getPrefixOntologyMappings - Returns the prefix->ontology mappings from JSON cache.

Help for ndi.ontology.Uberon.getPrefixOntologyMappings is inherited from superclass ndi.ontology

lookup - Look up a term in an ontology using a prefixed string.

[ID, NAME, PREFIX, DEFINITION, SYNONYMS, SHORTNAME] = ndi.ontology.lookup(LOOKUPSTRING)

    Looks up a term using a prefixed string (e.g., 'CL:0000000', 'OM:metre').
    This function uses a persistent cache to store results. Subsequent lookups
    for the same string are returned instantly from memory.

    To clear the cache, call: ndi.ontology.lookup('clear');

Help for ndi.ontology.Uberon.lookup is inherited from superclass ndi.ontology

lookupOBOFile - Looks up a term in a parsed OBO file with caching.

No longer caches individual term lookups; this is handled by ndi.ontology.lookup.
    Still caches the parsed OBO file to avoid re-reading from disk.

Help for ndi.ontology.Uberon.lookupOBOFile is inherited from superclass ndi.ontology

lookupTermOrID - Looks up a term in the Uberon ontology by ID or name.

[ID, NAME, DEFINITION, SYNONYMS] = lookupTermOrID(OBJ, TERM_OR_ID_OR_NAME)

    Overrides the base class method to provide specific lookup functionality
    for the Uberon ontology using the EBI OLS API.

    The input TERM_OR_ID_OR_NAME is the part of the original lookup string
    after the 'UBERON:' prefix has been removed (e.g., '0000948' or 'heart').

    This method uses the static helper functions from the base class:
    ndi.ontology.ontology.preprocessLookupInput and
    ndi.ontology.ontology.searchOLSAndPerformIRILookup.

    See also: ndi.ontology.ontology.lookup (static dispatcher)

performIriLookup - PERFORMIRILOOKUP Fetches ontology term details from EBI OLS using its IRI.

No longer caches results directly; caching is handled by ndi.ontology.lookup.

Help for ndi.ontology.Uberon.performIriLookup is inherited from superclass ndi.ontology

preprocessLookupInput - PREPROCESSLOOKUPINPUT Processes input for ontology lookup functions.

Handles standard prefix/ID/name logic and OM-specific heuristic.
    [...] = ndi.ontology.preprocessLookupInput(...)

Help for ndi.ontology.Uberon.preprocessLookupInput is inherited from superclass ndi.ontology

searchOLSAndPerformIRILookup - SEARCHOLSANDPERFORMIRILOOKUP Searches OLS and looks up unique result by IRI.

Handles specific logic for non-exact label searches (needed for OM).
    [...] = ndi.ontology.searchOLSAndPerformIRILookup(...)

Help for ndi.ontology.Uberon.searchOLSAndPerformIRILookup is inherited from superclass ndi.ontology