napistu.ingestion.identifiers_etl
Functions
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Read SBO Ontology Read the Systems Biology Ontology (SBO) identifiers and reformat the obo results into a pd.DataFrame. |
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Read Yeast Identifiers Generate a pd.DataFrame which maps between yeast identifiers including common and systematic (OLN) names, as well as Swiss-Prot and SGD identifiers. |
- napistu.ingestion.identifiers_etl.read_sbo_ontology(url: str = 'https://raw.githubusercontent.com/EBI-BioModels/SBO/master/SBO_OBO.obo', verbose: bool = False) DataFrame
Read SBO Ontology Read the Systems Biology Ontology (SBO) identifiers and reformat the obo results into a pd.DataFrame.
- Params:
url (str): url to the obo specification file verbose (bool): throw warnings when attributes are overwritten
- Returns:
pd.DataFrame
- napistu.ingestion.identifiers_etl.read_yeast_identifiers(url: str = 'https://www.uniprot.org/docs/yeast.txt')
Read Yeast Identifiers Generate a pd.DataFrame which maps between yeast identifiers including common and systematic (OLN) names, as well as Swiss-Prot and SGD identifiers.
- Params:
url (str): url to the identifier file
- Returns:
pd.DataFrame with one row per gene