WIP #50

lotusnprod · May 13, 2024 · e0749b4 · e0749b4
1 parent 65657f9
commit e0749b4
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Showing 14 changed files with 178 additions and 2 deletions.
diff --git a/update/config.py b/update/config.py
@@ -137,6 +137,51 @@
             "output_file": "structures_ids_csd.csv",
         },
     ),
+    Task(
+        name="structures_ids_drugbank",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_drugbank.rq",
+            "output_file": "structures_ids_drugbank.csv",
+        },
+    ),
+    Task(
+        name="structures_ids_dsstox_compound",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_dsstox_compound.rq",
+            "output_file": "structures_ids_dsstox_compound.csv",
+        },
+    ),
+    Task(
+        name="structures_ids_dsstox_substance",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_dsstox_substance.rq",
+            "output_file": "structures_ids_dsstox_substance.csv",
+        },
+    ),
+    Task(
+        name="structures_ids_ec",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_ec.rq",
+            "output_file": "structures_ids_ec.csv",
+        },
+    ),
+    Task(
+        name="structures_ids_echa",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_echa.rq",
+            "output_file": "structures_ids_echa.csv",
+        },
+    ),
     Task(
         name="structures_ids_hmdb",
         f=download_query_as_csv.run,
@@ -164,6 +209,15 @@
             "output_file": "structures_ids_knapsack.csv",
         },
     ),
+    Task(
+        name="structures_ids_lipidmaps",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_lipidmaps.rq",
+            "output_file": "structures_ids_lipidmaps.csv",
+        },
+    ),
     Task(
         name="structures_ids_massbank",
         f=download_query_as_csv.run,
@@ -191,6 +245,15 @@
             "output_file": "structures_ids_npatlas.csv",
         },
     ),
+    Task(
+        name="structures_ids_nsc",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_nsc.rq",
+            "output_file": "structures_ids_nsc.csv",
+        },
+    ),
     Task(
         name="structures_ids_pdb_ligand",
         f=download_query_as_csv.run,
@@ -209,6 +272,15 @@
             "output_file": "structures_ids_pdb_structure.csv",
         },
     ),
+    Task(
+        name="structures_ids_probes_and_drugs",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_probes_and_drugs.rq",
+            "output_file": "structures_ids_probes_and_drugs.csv",
+        },
+    ),
     Task(
         name="structures_ids_pubchem",
         f=download_query_as_csv.run,
@@ -236,6 +308,33 @@
             "output_file": "structures_ids_surechembl.csv",
         },
     ),
+    Task(
+        name="structures_ids_swisslipids",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_swisslipids.rq",
+            "output_file": "structures_ids_swisslipids.csv",
+        },
+    ),
+    Task(
+        name="structures_ids_unichem",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_unichem.rq",
+            "output_file": "structures_ids_unichem.csv",
+        },
+    ),
+    Task(
+        name="structures_ids_unii",
+        f=download_query_as_csv.run,
+        group=DownloadGroup,
+        params={
+            "query_file": "update/queries/structures_ids_unii.rq",
+            "output_file": "structures_ids_unii.csv",
+        },
+    ),
     Task(
         name="structures_ids_zinc",
         f=download_query_as_csv.run,

diff --git a/update/queries/structures_ids_cas.rq b/update/queries/structures_ids_cas.rq
@@ -2,6 +2,6 @@ PREFIX hint: <http://www.bigdata.com/queryHints#>
 PREFIX wdt: <http://www.wikidata.org/prop/direct/>
 
 SELECT ?structure ?structure_id_cas WHERE {
-    ?structure wdt:P231 ?structure_id_cas. hint:Prior hint:rangeSafe TRUE. # int
+    ?structure wdt:P231 ?structure_id_cas. hint:Prior hint:rangeSafe TRUE. # str
 }
 # LIMIT 2000000
diff --git a/update/queries/structures_ids_drugbank.rq b/update/queries/structures_ids_drugbank.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_drugbank WHERE {
+    ?structure wdt:P715 ?structure_id_drugbank. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_dsstox_compound.rq b/update/queries/structures_ids_dsstox_compound.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_dsstox_compound WHERE {
+    ?structure wdt:P8494 ?structure_id_dsstox_compound. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_dsstox_substance.rq b/update/queries/structures_ids_dsstox_substance.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_dsstox_substance WHERE {
+    ?structure wdt:P231 ?structure_id_dsstox_substance. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_ec.rq b/update/queries/structures_ids_ec.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_ec WHERE {
+    ?structure wdt:P232 ?structure_id_ec. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_echa.rq b/update/queries/structures_ids_echa.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_echa WHERE {
+    ?structure wdt:P2566 ?structure_id_echa. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_lipidmaps.rq b/update/queries/structures_ids_lipidmaps.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_lipidmaps WHERE {
+    ?structure wdt:P2063 ?structure_id_lipidmaps. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_nsc.rq b/update/queries/structures_ids_nsc.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_nsc WHERE {
+    ?structure wdt:P2840 ?structure_id_nsc. hint:Prior hint:rangeSafe TRUE. # int
+}
diff --git a/update/queries/structures_ids_probes_and_drugs.rq b/update/queries/structures_ids_probes_and_drugs.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_probes_and_drugs WHERE {
+    ?structure wdt:P11199 ?structure_id_probes_and_drugs. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_swisslipids.rq b/update/queries/structures_ids_swisslipids.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_swisslipids WHERE {
+    ?structure wdt:P8691 ?structure_id_swisslipids. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/structures_ids_unichem.rq b/update/queries/structures_ids_unichem.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_unichem WHERE {
+    ?structure wdt:P11089 ?structure_id_unichem. hint:Prior hint:rangeSafe TRUE. # int
+}
diff --git a/update/queries/structures_ids_unii.rq b/update/queries/structures_ids_unii.rq
@@ -0,0 +1,6 @@
+PREFIX hint: <http://www.bigdata.com/queryHints#>
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+
+SELECT ?structure ?structure_id_unii WHERE {
+    ?structure wdt:P652 ?structure_id_unii. hint:Prior hint:rangeSafe TRUE. # str
+}
diff --git a/update/queries/urls_formatters.rq b/update/queries/urls_formatters.rq
@@ -6,17 +6,20 @@ SELECT * WHERE {
   # All properties we use with a formatter URL
   VALUES ?property {
     wd:P231   # STRUCTURE CAS
+    wd:P232   # STRUCTURE EC number
     wd:P233   # STRUCTURE SMILES (canonical)
     wd:P234   # STRUCTURE InChI
     wd:P235   # STRUCTURE InChIKey
     wd:P356   # REFERENCE DOI
     wd:P592   # STRUCTURE ChEMBL
     wd:P638   # STRUCTURE PDB structure
+    wd:P652   # STRUCTURE UNII
     wd:P661   # STRUCTURE ChemSpider
     wd:P662   # STRUCTURE PubChem CID
-    wd:P683   # STRUCTURE ChEBI
     wd:P665   # STRUCTURE KEGG
+    wd:P683   # STRUCTURE ChEBI
     wd:P685   # TAXON     NCBI
+    wd:P715   # STRUCTURE DrugBank
     wd:P815   # TAXON     ITIS
     wd:P830   # TAXON     EOL
     wd:P846   # TAXON     GBIF
@@ -25,9 +28,13 @@ SELECT * WHERE {
     wd:P961   # TAXON     IPNI
     wd:P2017  # STRUCTURE SMILES (isomeric)
     wd:P2057  # STRUCTURE HMDB
+    wd:P2063  # STRUCTURE LIPID MAPS
     wd:P2064  # STRUCTURE KNApSAcK
     wd:P2084  # STRUCTURE ZINC
+    wd:P2566  # STRUCTURE ECHA
+    wd:P2840  # STRUCTURE NSC
     wd:P2877  # STRUCTURE SureChEMBL
+    wd:P3117  # STRUCTURE DSSTox substance
     wd:P3151  # TAXON     iNat
     wd:P3636  # STRUCTURE PDB ligand
     wd:P4964  # STRUCTURE SPLASH
@@ -36,10 +43,14 @@ SELECT * WHERE {
     wd:P6689  # STRUCTURE MassBank
     wd:P7715  # TAXON     WFO
     wd:P7746  # STRUCTURE NPAtlas
+    wd:P8494  # STRUCTURE DSSTox compound
     wd:P8533  # STRUCTURE SMARTS
+    wd:P8691  # STRUCTURE SwissLipids
     wd:P9157  # TAXON     OTL
     wd:P9405  # STRUCTURE NMRShiftDB
     wd:P10718 # STRUCTURE CXSMILES
+    wd:P11089 # STRUCTURE UniChem
+    wd:P11199 # STRUCTURE Probes And Drugs
     wd:P11375 # STRUCTURE CSD
   }
   ?property wdt:P1630 ?formatter. hint:Prior hint:rangeSafe TRUE.