nimare.annotate.cogat
.extract_cogat
- extract_cogat(text_df, id_df=None, text_column='abstract')[source]
Extract Cognitive Atlas terms and count instances using regular expressions.
- Parameters
text_df ((D x 2)
pandas.DataFrame
) – Pandas dataframe with at least two columns: ‘id’ and the text. D = document.id_df ((T x 3)
pandas.DataFrame
) –Cognitive Atlas ontology dataframe with one row for each term and at least three columns:
"id"
: A unique identifier for each term."alias"
: A natural language expression for each term."name"
: The preferred name of each term. Currently unused.
text_column (
str
, optional) – Name of column in text_df that contains text. Default is ‘abstract’.
- Returns
counts_df ((D x T)
pandas.DataFrame
) – Term counts for documents in the corpus. One row for each document and one column for each term.rep_text_df ((D x 2)
pandas.DataFrame
) – An updated version of thetext_df
DataFrame with terms in the text column replaced with their CogAt IDs.
Notes
The Cognitive Atlas 1 is an ontology for describing cognitive neuroscience concepts and tasks.
References
- 1
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
id_df
is not provided.