Working with Dataframes

Filtering

In the following examples, we’ll use a dataframe representing semantic mappings between disease ontologies in the SSSOM format:

subject_id	predicate_id	object_id	mapping_justification
DOID:0080795	skos:exactMatch	EFO:0003029	semapv:ManualMappingCuration
DOID:0080795	skos:exactMatch	mesh:D015471	semapv:ManualMappingCuration
DOID:0080799	skos:exactMatch	EFO:1000527	semapv:ManualMappingCuration
DOID:0080808	skos:exactMatch	mesh:D000069295	semapv:ManualMappingCuration

To get the set of unique prefixes appearing in a column, use curies.dataframe.get_df_unique_prefixes():

from curies.dataframe import get_df_unique_prefixes

df = ...
prefixes = get_df_unique_prefixes(df, column="object_id")
assert prefixes == {"EFO", "mesh"}

To filter to objects that use EFO, use curies.dataframe.filter_df_by_prefixes():

from curies.dataframe import filter_df_by_prefixes

df = ...
df = filter_df_by_prefixes(df, column="object_id", prefixes=["efo"])

subject_id	predicate_id	object_id	mapping_justification
DOID:0080795	skos:exactMatch	EFO:0003029	semapv:ManualMappingCuration
DOID:0080799	skos:exactMatch	EFO:1000527	semapv:ManualMappingCuration

To filter to rows that have the subject DOID:0080795, use curies.dataframe.filter_df_by_curies():

from curies.dataframe import filter_df_by_curies

df = ...
df = filter_df_by_curies(df, column="subjects_id", curies=["DOID:0080795"])

subject_id	predicate_id	object_id	mapping_justification
DOID:0080795	skos:exactMatch	EFO:0003029	semapv:ManualMappingCuration
DOID:0080795	skos:exactMatch	mesh:D015471	semapv:ManualMappingCuration