Right now, Mondo mappings are MONDO ids to external. We would like to add external-external mappings to the Monarch mapping commons. Here is some code using semra that can roughly achieve this but may need tweaks.
import pandas as pd
from semra.api import infer_chains, infer_reversible
from semra.io import from_sssom_df, get_sssom_df
data = [
["UBERON:1", "skos:exactMatch", "FBbt:9"],
["UBERON:1", "skos:exactMatch", "WBbt:6"],
]
# replace the following with mondo mappings
df = pd.DataFrame(data=data, columns=["subject_id", "predicate_id", "object_id"])
mappings = from_sssom_df(df, mapping_set_name="test")
mappings = infer_reversible(mappings, progress=False)
mappings = infer_chains(mappings, progress=False)
df = get_sssom_df(mappings)
msdf = MappingSetDataFrame(df=df, converter=get_converter())
msdf.standardize_references()
msdf.clean_prefix_map()
Right now, Mondo mappings are MONDO ids to external. We would like to add external-external mappings to the Monarch mapping commons. Here is some code using semra that can roughly achieve this but may need tweaks.