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:
'ID<tab>LABEL<tab>Synonyms<tab><Other_Common_Name'
and then 1 entry per anatomical node.
This function also takes name/value pairs that modify the behavior.
Parameter (default) | Description
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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'])|