CLASS ndi.ontology.PATO

  Location: +ndi/+ontology/PATO.m

Superclasses

ndi.ontology

Properties

none

Methods

Method	Description
PATO	Constructor for the PATO ontology object.
clearCache	Clears cached ontology list JSON data and NDIC data.
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.
lookupTermOrID	Looks up a term in the PATO ontology.
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

PATO - Constructor for the PATO ontology object.

Implicitly calls the superclass constructor ndi.ontology().

    Documentation for ndi.ontology.PATO/PATO
       doc ndi.ontology.PATO

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clearCache - Clears cached ontology list JSON data and NDIC data.

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

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getOntologies - Returns the ontology details list from JSON cache.

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

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

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

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

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

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

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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').
    It identifies the ontology from the prefix using the mappings in
    'ontology_list.json', instantiates the specific ndi.ontology.ONTOLOGYNAME
    class (e.g., ndi.ontology.CL), and calls its lookupTermOrID instance method,
    passing the remainder of the string (after the prefix).

    Outputs:
      ID           - The canonical identifier for the term.
      NAME         - The primary name or label for the term.
      PREFIX       - The ontology prefix used in the lookup.
      DEFINITION   - A textual definition, if available.
      SYNONYMS     - A cell array of synonyms, if available.
      SHORTNAME    - The short name for the term.

    Examples:
        % Lookup neuron in Cell Ontology by ID
        [id, name, prefix] = ndi.ontology.lookup('CL:0000540');
        % Expected: id='CL:0000540', name='neuron', prefix='CL'

        % Lookup ethanol in ChEBI by ID
        [id, name, prefix] = ndi.ontology.lookup('CHEBI:16236');
        % Expected: id='CHEBI:16236', name='ethanol', prefix='CHEBI'

        % Lookup Heart in NCI Metathesaurus by CUI
        [id, name, prefix, def] = ndi.ontology.lookup('NCIm:C0018787');
        % Expected: id='C0018787', name='Heart', prefix='NCIm', def contains definition

        % Lookup Aspirin in PubChem by name
        [id, name, prefix] = ndi.ontology.lookup('PubChem:Aspirin');
        % Expected: id='2244', name='aspirin', prefix='PubChem'

        % Lookup Homo sapiens using alternative taxonomy prefix
        [id, name, prefix] = ndi.ontology.lookup('taxonomy:9606');
        % Expected: id='9606', name='Homo sapiens', prefix='taxonomy'

        % Example of a failed lookup (non-existent term)
        try
            ndi.ontology.lookup('CL:NoSuchTerm');
        catch ME
            disp(ME.identifier); % e.g., 'ndi:ontology:lookup_CL:NotFound' or similar
            disp(ME.message);
        end

    See also: ndi.ontology.PATO.lookupTermOrID (instance method to be overridden)

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

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

[ID, NAME, DEFINITION, SYNONYMS] = ndi.ontology.lookupOBOFile(...
        OBOFILEPATH, ONTOLOGYPREFIX, TERM_TO_LOOKUP_FRAGMENT)

    Parses an OBO file (if not already cached) and searches for a term.
    TERM_TO_LOOKUP_FRAGMENT is the part of the term after the prefix
    (e.g., '0000001' or 'some term name').

    The function caches the parsed OBO data to speed up subsequent lookups
    for the same file within a MATLAB session. Call ndi.ontology.clearCache()
    or 'clear functions' to clear this cache.

    Outputs:
        ID         - The full term ID (e.g., 'EMPTY:0000001').
        NAME       - The term's primary name.
        DEFINITION - The term's definition.
        SYNONYMS   - A cell array of synonym strings (currently basic,
                     not parsing synonym types).

    Throws:
        ndi:ontology:lookupOBOFile:FileNotFound
        ndi:ontology:lookupOBOFile:ParsingError
        ndi:ontology:lookupOBOFile:InvalidInput
        ndi:ontology:lookupOBOFile:TermNotFound

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

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lookupTermOrID - Looks up a term in the PATO ontology.

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

    Overrides the base class method to provide specific lookup functionality
    for the PATO ontology using the EBI OLS API via static helper methods
    from the ndi.ontology base class.

    The input TERM_OR_ID_OR_NAME is the part of the original lookup string
    after the 'PATO:' prefix has been removed (e.g., '0000001' for an ID,
    or 'color' for a name/label search).

    Example Usage (after being called by ndi.ontology.lookup):
    [id, name, ~, def] = ndi.ontology.lookup('PATO:0000012'); % quality
    [id, name, ~, def] = ndi.ontology.lookup('PATO:color');   % color

    See also: ndi.ontology.lookup (static dispatcher),
              ndi.ontology.preprocessLookupInput (static helper),
              ndi.ontology.searchOLSAndPerformIRILookup (static helper)

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

Used by OLS-based lookup implementations (CL, OM, CHEBI, UBERON).
    [...] = ndi.ontology.performIriLookup(...)

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

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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.PATO.preprocessLookupInput is inherited from superclass ndi.ontology

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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.PATO.searchOLSAndPerformIRILookup is inherited from superclass ndi.ontology

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