From 2cfaa70f34886c1e75cc0dd8b9adee495130fb5a Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Thu, 11 Apr 2024 14:35:32 +0200
Subject: [PATCH] Add chemical landscape configuration

---
 src/semra/landscape/chemical.py | 77 +++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 src/semra/landscape/chemical.py

diff --git a/src/semra/landscape/chemical.py b/src/semra/landscape/chemical.py
new file mode 100644
index 0000000..1102587
--- /dev/null
+++ b/src/semra/landscape/chemical.py
@@ -0,0 +1,77 @@
+"""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()