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Add chemical landscape analysis #18

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Add chemical landscape analysis #18

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77 changes: 77 additions & 0 deletions src/semra/landscape/chemical.py
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"""A configuration for assembling mappings for chemical terms."""

import click
import pystow

from semra.pipeline import Configuration, Input, Mutation

MODULE = pystow.module("semra", "case-studies", "chemical")
PRIORITY = [
"chebi",
"pubchem.compound",
"drugbank",
"drugcentral",
"slm",
"chembl.compound",
]

CONFIGURATION = Configuration(
name="Chemical Landscape Analysis",
description="Analyze the landscape of chemicals.",
inputs=[
Input(prefix="wikidata", source="custom", extras=dict(prop="P665"), confidence=0.99),
Input(source="gilda"),
Input(source="biomappings"),
Input(prefix="chebi", source="bioontologies", confidence=0.99),
Input(prefix="slm", source="pyobo", confidence=0.99),
# Input(prefix="drugbank", source="pyobo", confidence=0.99),
#
Input(prefix="chebi", source="wikidata", confidence=0.99),
Input(prefix="mesh", source="wikidata", confidence=0.99),
Input(prefix="inchikey", source="wikidata", confidence=0.99),
Input(prefix="inchi", source="wikidata", confidence=0.99),
Input(prefix="smiles", source="wikidata", confidence=0.99),
Input(prefix="cas", source="wikidata", confidence=0.99),
Input(prefix="chemspider", source="wikidata", confidence=0.99),
Input(prefix="pubchem.compound", source="wikidata", confidence=0.99),
Input(prefix="gmelin", source="wikidata", confidence=0.99),
Input(prefix="chembl.compound", source="wikidata", confidence=0.99),
Input(prefix="unichem", source="wikidata", confidence=0.99),
Input(prefix="drugbank", source="wikidata", confidence=0.99),
Input(prefix="unii", source="wikidata", confidence=0.99),
Input(prefix="knapsack", source="wikidata", confidence=0.99),
Input(prefix="hmdb", source="wikidata", confidence=0.99),
Input(prefix="drugcentral", source="wikidata", confidence=0.99),
Input(prefix="rxnorm", source="wikidata", confidence=0.99),
Input(prefix="iuphar.ligand", source="wikidata", confidence=0.99),
Input(prefix="umbbd.compound", source="wikidata", confidence=0.99),
Input(prefix="zinc", source="wikidata", confidence=0.99),
Input(prefix="lipidmaps", source="wikidata", confidence=0.99),
Input(prefix="slm", source="wikidata", confidence=0.99),
],
add_labels=True,
priority=PRIORITY,
remove_imprecise=False,
mutations=[
Mutation(source="chebi", confidence=0.95),
],
raw_pickle_path=MODULE.join(name="raw.pkl"),
raw_sssom_path=MODULE.join(name="raw.sssom.tsv"),
# raw_neo4j_path=MODULE.join("neo4j_raw"),
processed_pickle_path=MODULE.join(name="processed.pkl"),
processed_sssom_path=MODULE.join(name="processed.sssom.tsv"),
processed_neo4j_path=MODULE.join("neo4j"),
processed_neo4j_name="semra-chemical",
priority_pickle_path=MODULE.join(name="priority.pkl"),
priority_sssom_path=MODULE.join(name="priority.sssom.tsv"),
)


@click.command()
def main():
"""Get the chemical landscape."""
CONFIGURATION.get_mappings(refresh_raw=True, refresh_processed=True)


if __name__ == "__main__":
main()
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