nimare.annotate.cogat
.CogAtLemmatizer
- class CogAtLemmatizer(ontology_df=None)[source]
Bases:
object
Replace synonyms and abbreviations with Cognitive Atlas identifiers in text.
- Parameters
ontology_df (
pandas.DataFrame
, optional) – DataFrame with three columns (id, name, alias) and one row for each alias (e.g., synonym or abbreviation) for each term in the Cognitive Atlas. If None, loads ontology file from resources folder.- Variables
ontology_ (
pandas.DataFrame
) – Ontology in DataFrame form.regex_ (
dict
) – Dictionary linking aliases in ontology to regular expressions for lemmatization.
References
Poldrack, Russell A., et al. “The cognitive atlas: toward a knowledge foundation for cognitive neuroscience.” Frontiers in neuroinformatics 5 (2011): 17. https://doi.org/10.3389/fninf.2011.00017
See also
nimare.extract.download_cognitive_atlas
This function will be called automatically if
ontology_df
is not provided.