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ndi.database.fun.createNIFbrainareas

NDI_CREATENIFBRAINAREAS - create a list of allowable brain areas from the NIF-Ontology

BA = ndi.database.fun.createNIFbrainareas(...)

Creates a list of 'controlled' brain area labels and the corresponding nodes in the NIF-Ontology.

Traces all areas that make up a part of the UBERON node 'nervous system', excluding those in the first level of depth (which are all relatively vague descriptors). This is then written to a file 'NIFBrainAreaControlledVocabulary.tsv' with a string id that describes the NIF-Ontology node ID and a string lbl that describes the NIF-Ontology label:

Header row: 'IDLABELSynonyms<Other_Common_Name' and then 1 entry per anatomical node.

This function also takes name/value pairs that modify the behavior. Parameter (default) | Description


root ('UBERON:'... | Root node for establishing the controlled vocabulary. '0001016') | (Default is 'nervous system' in Uberon ontology.) depth (1000) | How deep past "nervous system" to look depth_exclude (1) | The depths to exclude from the list exclude_ontologies ({...| Ontologies to exclude 'CL'}) | outname (... | Output filen name of the file written to disk ['NIFBrainAreaContr'... | 'olledVocabulary.tsv'])|