CTD (indra.sources.ctd
)¶
This module implements an API and processor to extract INDRA Statements from the Comparative Toxicogenomics Database (CTD), see http://ctdbase.org/. It currently extracts chemical-gene, gene-disease, and chemical-disease relationships. In particular, it extracts the curated (not inferred) and directional/causal relationships from these subsets.
CTD API (indra.sources.ctd.api
)¶
-
indra.sources.ctd.api.
process_dataframe
(df, subset)[source]¶ Process a subset of CTD from a DataFrame into INDRA Statements.
Parameters: - df (pandas.DataFrame) – A DataFrame of the given CTD subset.
- subset (str) – A CTD subset, one of chemical_gene, chemical_disease, gene_disease.
Returns: A CTDProcessor which contains INDRA Statements extracted from the given CTD subset as its statements attribute.
Return type: CTDProcessor
-
indra.sources.ctd.api.
process_from_web
(subset, url=None)[source]¶ Process a subset of CTD from the web into INDRA Statements.
Parameters: - subset (str) – A CTD subset, one of chemical_gene, chemical_disease, gene_disease.
- url (Optional[str]) – If not provided, the default CTD URL is used (beware, it usually gives permission denied). If provided, the given URL is used to access a tsv or tsv.gz file.
Returns: A CTDProcessor which contains INDRA Statements extracted from the given CTD subset as its statements attribute.
Return type: CTDProcessor
-
indra.sources.ctd.api.
process_tsv
(fname, subset)[source]¶ Process a subset of CTD from a tsv or tsv.gz file into INDRA Statements.
Parameters: - fname (str) – Path to a tsv or tsv.gz file of the given CTD subset.
- subset (str) – A CTD subset, one of chemical_gene, chemical_disease, gene_disease.
Returns: A CTDProcessor which contains INDRA Statements extracted from the given CTD subset as its statements attribute.
Return type: CTDProcessor