Quick Start¶

Python library¶

Parse an SSSOM TSV file¶

import sssom

# Parse a local file
msdf = sssom.parse_tsv("my_mappings.sssom.tsv")

# Parse from a URL
url = "https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_eye_impc.sssom.tsv"
msdf = sssom.parse_tsv(url)

The returned MappingSetDataFrame object contains:

msdf.df -- a pandas DataFrame with the mapping rows
msdf.converter -- a curies.Converter for prefix handling
msdf.metadata -- a dictionary of mapping set metadata

Write to different formats¶

# Write back to TSV
sssom.write_tsv(msdf, "output.sssom.tsv")

# Convert to other formats
sssom.write_json(msdf, "output.json")
sssom.write_owl(msdf, "output.owl")
sssom.write_rdf(msdf, "output.ttl")

Warning

The export formats (JSON, RDF) are not yet finalised. Expect changes in future releases.

Inspect mappings¶

import sssom

msdf = sssom.parse_tsv("my_mappings.sssom.tsv")

# Access the DataFrame
print(f"Number of mappings: {len(msdf.df)}")
print(msdf.df.head())

# Access metadata
print(msdf.metadata)

Compare two mapping sets¶

import sssom

msdf1 = sssom.parse_tsv("set1.sssom.tsv")
msdf2 = sssom.parse_tsv("set2.sssom.tsv")

diff = sssom.compare_dataframes(msdf1.df, msdf2.df)
print(f"Common mappings: {len(diff.common_tuples)}")
print(f"Unique to set1: {len(diff.unique_tuples1)}")
print(f"Unique to set2: {len(diff.unique_tuples2)}")

Filter redundant mappings¶

import sssom

msdf = sssom.parse_tsv("my_mappings.sssom.tsv")
filtered_df = sssom.filter_redundant_rows(msdf.df)
print(f"Before: {len(msdf.df)} rows, After: {len(filtered_df)} rows")

Command line¶

Parse and convert¶

# Parse an SSSOM file (validates and pretty-prints)
sssom parse my_mappings.sssom.tsv

# Convert TSV to OWL
sssom convert my_mappings.sssom.tsv -o output.owl -O owl

# Convert TSV to RDF (Turtle)
sssom convert my_mappings.sssom.tsv -o output.ttl -O rdf

Compare mapping sets¶

sssom diff set1.sssom.tsv set2.sssom.tsv -o diff.sssom.tsv

Validate¶

sssom validate my_mappings.sssom.tsv

Merge multiple files¶

sssom merge set1.sssom.tsv set2.sssom.tsv -o merged.sssom.tsv

Query with SQL¶

sssom dosql -Q "SELECT * FROM df1 WHERE confidence > 0.5 ORDER BY confidence" my_mappings.sssom.tsv

Filter mappings¶

sssom filter --subject_id HP:% --object_id MP:% my_mappings.sssom.tsv

For the full list of CLI commands, see the CLI Reference.