diff --git a/src/mondo_robot_template.py b/src/mondo_robot_template.py index cb321d4..245bf89 100644 --- a/src/mondo_robot_template.py +++ b/src/mondo_robot_template.py @@ -18,6 +18,11 @@ FTP_DIR = PROJECT_DIR / "ftp.ncbi.nlm.nih.gov" / "pub" / "medgen" INPUT_FILE = str(FTP_DIR / "MedGenIDMappings.txt") OUTPUT_FILE = str(PROJECT_DIR / "medgen-xrefs.robot.template.tsv") +ROBOT_ROW_MAP = { + 'mondo_id': 'ID', + 'xref_id': 'A oboInOwl:hasDbXref', + 'source_id': '>A oboInOwl:source' +} def _prefixed_id_rows_from_common_df(source_df: pd.DataFrame, mondo_col='mondo_id', xref_col='xref_id') -> List[Dict]: @@ -29,9 +34,10 @@ def _prefixed_id_rows_from_common_df(source_df: pd.DataFrame, mondo_col='mondo_i df = copy(source_df) df[xref_col] = df[xref_col].apply( lambda x: f'MEDGENCUI:{x}' if x.startswith('CN') # "CUI Novel" - else f'UMLS:{x}' if x.startswith('C') # CUI: will be created twice: one for MEDGENCUI, one for UMLS + else f'UMLS:{x}' if x.startswith('C') # CUI 1 of 2: UMLS else f'MEDGEN:{x}') # UID rows = df.to_dict('records') + # CUI 2 of 2: MEDGENCUI: rows2 = [{mondo_col: x[mondo_col], xref_col: x[xref_col].replace('UMLS', 'MEDGENCUI')} for x in rows if x[xref_col].startswith('UMLS')] return rows + rows2 @@ -50,13 +56,14 @@ def run(input_file: str = INPUT_FILE, output_file: str = OUTPUT_FILE): # - Done by proxy: UID <-> CUI <-> MONDO df_medgen_medgenuid = df[df['source'] == 'MedGen'][['source_id', 'xref_id']].rename( columns={'source_id': 'medgen_uid'}) - out_df_uid = pd.merge(df_medgen_mondo, df_medgen_medgenuid, on='xref_id')[['mondo_id', 'medgen_uid']]\ - .rename(columns={'medgen_uid': 'xref_id'}) + out_df_uid = pd.merge(df_medgen_mondo, df_medgen_medgenuid, on='xref_id').rename( + columns={'xref_id': 'source_id', 'medgen_uid': 'xref_id'})[['mondo_id', 'xref_id', 'source_id']] out_df_uid['xref_id'] = out_df_uid['xref_id'].apply(lambda x: f'MEDGEN:{x}') + out_df_uid['source_id'] = out_df_uid['source_id'].apply(lambda x: f'UMLS:{x}') # Save - out_df = pd.concat([out_df_cui_cn, out_df_uid]).sort_values(['xref_id', 'mondo_id']).drop_duplicates() - out_df = pd.concat([pd.DataFrame([{'mondo_id': 'ID', 'xref_id': 'A oboInOwl:hasDbXref'}]), out_df]) + out_df = pd.concat([out_df_cui_cn, out_df_uid]).sort_values(['xref_id', 'mondo_id']).drop_duplicates().fillna('') + out_df = pd.concat([pd.DataFrame([ROBOT_ROW_MAP]), out_df]) out_df.to_csv(output_file, index=False, sep='\t') def cli():