Merge pull request #2 from SuLab/main

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SuLab · Jul 14, 2021 · 30e2c4d · 30e2c4d
2 parents 03624b7 + 2c6f658
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diff --git a/indication_paths.json b/indication_paths.json
@@ -136374,7 +136374,7 @@
     ]
   },
   {
-    "comments": "The drug may also modulate other members of the Voltage-gated L-type calcium channel protein family (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1275868/) or T-type calcium channel protein family (https://en.wikipedia.org/wiki/Azelnidipine).",
+    "comment": "The drug may also modulate other members of the Voltage-gated L-type calcium channel protein family (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1275868/) or T-type calcium channel protein family (https://en.wikipedia.org/wiki/Azelnidipine).",
     "directed": true,
     "graph": {
       "_id": "DB09230_MESH_D006973_1",
@@ -137113,7 +137113,7 @@
     ]
   },
   {
-    "comment": "At higher doses, bisoprolol antagonizes the B2 adrenergic receptors, but is mainly selective for B1 receptors.",
+    "comment": "At higher doses, bisoprolol antagonizes the B2 receptors, but is mainly selective for B1 receptors.",
     "directed": true,
     "graph": {
       "_id": "DB00612_MESH_D006973_1",
@@ -137899,11 +137899,11 @@
     ]
   },
   {
-    "comment": "The drug needs to be converted to vidarabine phosphate first (monophosphate --> diphosphate --> triphosphate) to become active and exert its role as inhibitor (https://pubchem.ncbi.nlm.nih.gov/compound/21704#section=Mechanism-of-Action).",
+    "comment": "This disease is also known as Herpes simplex keratitis as per DrugCentral. The drug needs to be converted to Vidarabine Phosphate first (monophosphate --> diphosphate --> triphosphate) to become active and exert its role as inhibitor (https://pubchem.ncbi.nlm.nih.gov/compound/21704#section=Mechanism-of-Action).",
     "directed": true,
     "graph": {
       "_id": "DB00194_MESH_D016849_1",
-      "disease": "Herpes simplex keratitis",
+      "disease": "Keratitis, Herpetic",
       "disease_mesh": "MESH:D016849",
       "drug": "vidarabine",
       "drug_mesh": "MESH:D014740",
@@ -137996,7 +137996,7 @@
       {
         "id": "MESH:D016849",
         "label": "Disease",
-        "name": "Herpes simplex keratitis"
+        "name": "Keratitis, Herpetic"
       }
     ],
     "reference": [
@@ -138006,10 +138006,11 @@
     ]
   },
   {
+    "comment": "This disease is denoted as Herpes simplex dendritic keratitis in the original file as per DrugCentral. The drug needs to be converted to Vidarabine Phosphate first (monophosphate --> diphosphate --> triphosphate) to become active and exert its role as inhibitor (https://pubchem.ncbi.nlm.nih.gov/compound/21704#section=Mechanism-of-Action).",
     "directed": true,
     "graph": {
       "_id": "DB00194_MESH_D007635_1",
-      "disease": "Herpes simplex dendritic keratitis",
+      "disease": "Keratitis, Dendritic",
       "disease_mesh": "MESH:D007635",
       "drug": "vidarabine",
       "drug_mesh": "MESH:D014740",
@@ -138102,7 +138103,7 @@
       {
         "id": "MESH:D007635",
         "label": "Disease",
-        "name": "Herpes simplex dendritic keratitis"
+        "name": "Keratitis, Dendritic"
       }
     ],
     "reference": [
@@ -138112,7 +138113,7 @@
     ]
   },
   {
-    "comments": "This disease is denoted as Malignant neoplasm of liver in the original file as per DrugCentral.",
+    "comment": "This disease is denoted as Malignant neoplasm of liver in the original file as per DrugCentral.",
     "directed": true,
     "graph": {
       "_id": "DB00322_MESH_D008113_1",
@@ -138124,7 +138125,7 @@
     },
     "links": [
       {
-        "key": "produces",
+        "key": "has metabolite",
         "source": "MESH:D005467",
         "target": "CHEBI:46345"
       },
@@ -145278,7 +145279,7 @@
     ]
   },
   {
-    "comments": "Drospirenone seems to have much lower affinity to androgen receptor than to the progesterone counterpart (https://en.wikipedia.org/wiki/Drospirenone#Pharmacology).",
+    "comment": "Drospirenone seems to have much lower affinity to androgen receptor than to the progesterone counterpart (https://en.wikipedia.org/wiki/Drospirenone#Pharmacology).",
     "directed": true,
     "graph": {
       "_id": "DB01395_MESH_D000152_1",
@@ -145368,7 +145369,7 @@
     ]
   },
   {
-    "comments": "The use of progesterone, progestin and similar compounds may not be superior to placebo in reducing premenstrual symptoms judging from the results of the majority of controlled trials (https://pubmed.ncbi.nlm.nih.gov/7791258/). Also note that it is generally agreed that neither a deficiency nor excess in progesterone/progestin levels is etiologically relevant to the disorder (https://pubmed.ncbi.nlm.nih.gov/16650465/). It's largelly accepted that SSRIs as better treatment and should be the first attempt for treatment of premenstrual dysphoric disorder.",
+    "comment": "The use of progesterone, progestin and similar compounds may not be superior to placebo in reducing premenstrual symptoms judging from the results of the majority of controlled trials (https://pubmed.ncbi.nlm.nih.gov/7791258/). Also note that it is generally agreed that neither a deficiency nor excess in progesterone/progestin levels is etiologically relevant to the disorder (https://pubmed.ncbi.nlm.nih.gov/16650465/). It's largelly accepted that SSRIs as better treatment and should be the first attempt for treatment of premenstrual dysphoric disorder.",
     "directed": true,
     "graph": {
       "_id": "DB01395_MESH_D065446_1",
@@ -145392,7 +145393,7 @@
       {
         "key": "positively correlated with",
         "source": "UniProt:P08235",
-        "target": "MESH:D015222"
+        "target": "InterPro:IPR001696"
       },
       {
         "key": "regulates",
@@ -145406,7 +145407,7 @@
       },
       {
         "key": "regulates",
-        "source": "MESH:D015222",
+        "source": "InterPro:IPR001696",
         "target": "GO:0070294"
       },
       {
@@ -145453,9 +145454,9 @@
         "name": "Mineralocorticoid receptor"
       },
       {
-        "id": "MESH:D015222",
+        "id": "InterPro:IPR001696",
         "label": "GeneFamily",
-        "name": "Sodium Channels"
+        "name": "Voltage gated sodium channel, alpha subunit"
       },
       {
         "id": "GO:0005890",
@@ -145495,7 +145496,7 @@
     ]
   },
   {
-    "comments": "The disease is denoted Menopausal flushing in the original file. Note that a combination therapy of estradiol and drospirenone would be more effective at reducing the frequency of hot flushes and other menopausal symptoms, than a mono-therapy relying on progestin only. Also, since many progestogens have off-target effects including estrogenic effects, the improvement in hot flashes maybe due to the drug binding to estrogen receptors instead. Note the term Vasomotor System (https://en.wikipedia.org/wiki/Vasomotor_center) does not seem to be represented in other ontologies.",
+    "comment": "The disease is denoted Menopausal flushing in the original file. Note that a combination therapy of estradiol and drospirenone would be more effective at reducing the frequency of hot flushes and other menopausal symptoms, than a mono-therapy relying on progestin only. Also, since many progestogens have off-target effects including estrogenic effects, the improvement in hot flashes maybe due to the drug binding to estrogen receptors instead. Note the term Vasomotor System (https://en.wikipedia.org/wiki/Vasomotor_center) does not seem to be represented in other ontologies.",
     "directed": true,
     "graph": {
       "_id": "DB01395_MESH_D019584_1",
@@ -145588,7 +145589,7 @@
     ]
   },
   {
-    "comments": "Note that the combination therapy of estradiol and drospirenone would be more effective at treating atrophic vaginitis, than a mono-therapy relying on progestin only. Also, since many progestogens have off-target effects including estrogenic effects, the improvement in hot flashes maybe due to the drug binding to estrogen receptors instead.",
+    "comment": "Note that the combination therapy of estradiol and drospirenone would be more effective at treating atrophic vaginitis, than a mono-therapy relying on progestin only. Also, since many progestogens have off-target effects including estrogenic effects, the improvement in hot flashes maybe due to the drug binding to estrogen receptors instead.",
     "directed": true,
     "graph": {
       "_id": "DB01395_MESH_D059268_1",
@@ -146035,7 +146036,7 @@
     ]
   },
   {
-    "comments": "Etidronate is a weak inhibitor of proton transport in animal models (https://pubmed.ncbi.nlm.nih.gov/8889850/).",
+    "comment": "Etidronate is a weak inhibitor of proton transport in animal models (https://pubmed.ncbi.nlm.nih.gov/8889850/).",
     "directed": true,
     "graph": {
       "_id": "DB01077_MESH_D010001_1",
@@ -146534,7 +146535,7 @@
     ]
   },
   {
-    "comments": "Note that this drug is used as a support to the treatment of chronic alcoholism by producing an acute sensitivity to ethanol (as part of an avoidance therapy for alcohol abuse). It's been suggested that disulfiram itself is unlikely responsible for the enzyme inactivation in vivo; several active metabolites of the drug, especially diethylthiomethylcarbamate, inhibits the enzyme in vitro (https://pubchem.ncbi.nlm.nih.gov/compound/3117#section=Mechanism-of-Action).",
+    "comment": "Note that this drug is used as a support to the treatment of chronic alcoholism by producing an acute sensitivity to ethanol (as part of an avoidance therapy for alcohol abuse). It's been suggested that disulfiram itself is unlikely responsible for the enzyme inactivation in vivo; several active metabolites of the drug, especially diethylthiomethylcarbamate, inhibits the enzyme in vitro (https://pubchem.ncbi.nlm.nih.gov/compound/3117#section=Mechanism-of-Action).",
     "directed": true,
     "graph": {
       "_id": "DB00822_MESH_D000437_1",
@@ -146548,11 +146549,11 @@
       {
         "key": "negatively regulates",
         "source": "MESH:D004221",
-        "target": "Pfam:PF00171"
+        "target": "UniProt:P05091"
       },
       {
         "key": "positively regulates",
-        "source": "Pfam:PF00171",
+        "source": "UniProt:P05091",
         "target": "GO:0006069"
       },
       {
@@ -146586,17 +146587,17 @@
         "target": "HP:0002017"
       },
       {
-        "key": "correlated with",
+        "key": "negatively correlated with",
         "source": "HP:0001033",
         "target": "MESH:D000437"
       },
       {
-        "key": "correlated with",
+        "key": "negatively correlated with",
         "source": "HP:0002098",
         "target": "MESH:D000437"
       },
       {
-        "key": "correlated with",
+        "key": "negatively correlated with",
         "source": "HP:0002017",
         "target": "MESH:D000437"
       }
@@ -146609,9 +146610,9 @@
         "name": "disulfiram"
       },
       {
-        "id": "Pfam:PF00171",
-        "label": "GeneFamily",
-        "name": "Aldehyde dehydrogenase family"
+        "id": "UniProt:P05091",
+        "label": "Protein",
+        "name": "Aldehyde dehydrogenase, mitochondrial"
       },
       {
         "id": "CHEBI:15343",
@@ -146996,7 +146997,7 @@
     ]
   },
   {
-    "comments": "MESH:D003865 is denoted as Depressive Disorder, Major in the MESH website. Note that the drug may slighlty inhibit the reuptake of serotonin too.",
+    "comment": "MESH:D003865 is denoted as Depressive Disorder, Major in the MESH website. Note that the drug may slighlty inhibit the reuptake of serotonin too.",
     "directed": true,
     "graph": {
       "_id": "DB00234_MESH_D003865_1",
@@ -156562,7 +156563,7 @@
     ]
   },
   {
-    "comments": "MESH:D014987 is denoted as Xerostomia in MESH.",
+    "comment": "MESH:D014987 is denoted as Xerostomia in MESH.",
     "directed": true,
     "graph": {
       "_id": "DB01085_MESH_D014987_1",
@@ -157184,7 +157185,7 @@
     ]
   },
   {
-    "comments": "Drug has been withdrawn in Europe due to increased risk of abuse or addiction, intoxication and events related to psychomotor impairment (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1233/).",
+    "comment": "Drug has been withdrawn in Europe due to increased risk of abuse or addiction, intoxication and events related to psychomotor impairment (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1233/).",
     "directed": true,
     "graph": {
       "_id": "DB00395_MESH_D001416_1",
@@ -157269,7 +157270,7 @@
     ]
   },
   {
-    "comments": "Drug has been withdrawn in Europe due to increased risk of abuse or addiction, intoxication and events related to psychomotor impairment (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1233/).",
+    "comment": "Drug has been withdrawn in Europe due to increased risk of abuse or addiction, intoxication and events related to psychomotor impairment (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1233/).",
     "directed": true,
     "graph": {
       "_id": "DB00395_MESH_D009128_1",
@@ -157324,7 +157325,7 @@
     ]
   },
   {
-    "comments": "Drug has been withdrawn in Europe due to increased risk of abuse or addiction, intoxication and events related to psychomotor impairment (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1233/).",
+    "comment": "Drug has been withdrawn in Europe due to increased risk of abuse or addiction, intoxication and events related to psychomotor impairment (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1233/).",
     "directed": true,
     "graph": {
       "_id": "DB00004_MESH_D016410_1",
@@ -157962,7 +157963,7 @@
     ]
   },
   {
-    "comments": "The disease is known as Chagas Disease in MESH (MESH:D014355). The drug is metabolized by nitoreductases (https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/213464s000lbl.pdf) rather than nitoreductases being the target of this drug (https://go.drugbank.com/drugs/DB11820#BE0010011).",
+    "comment": "The disease is known as Chagas Disease in MESH (MESH:D014355). The drug is metabolized by nitoreductases (https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/213464s000lbl.pdf) rather than nitoreductases being the target of this drug (https://go.drugbank.com/drugs/DB11820#BE0010011).",
     "directed": true,
     "graph": {
       "_id": "DB11820_MESH_D014355_1",
@@ -157976,11 +157977,11 @@
       {
         "key": "produces",
         "source": "MESH:D009547",
-        "target": "CHEBI:26519"
+        "target": "CHEBI:26523"
       },
       {
         "key": "disrupts",
-        "source": "CHEBI:26519",
+        "source": "CHEBI:26523",
         "target": "CHEBI:16991"
       },
       {
@@ -158002,9 +158003,9 @@
         "name": "nifurtimox"
       },
       {
-        "id": "CHEBI:26519",
+        "id": "CHEBI:26523",
         "label": "ChemicalSubstance",
-        "name": "radical"
+        "name": "reactive oxygen species"
       },
       {
         "id": "CHEBI:16991",
@@ -158028,7 +158029,7 @@
     ]
   },
   {
-    "comments": "Withdrawn from the market in many countries. Never been marketed in the US.",
+    "comment": "Withdrawn from the market in many countries. Never been marketed in the US.",
     "directed": true,
     "graph": {
       "_id": "DB04830_MESH_D003924_1",
@@ -170408,7 +170409,7 @@
     ]
   },
   {
-    "comments": "Unlike other NSAIDs, it does not inhibit cyclooxygenase or lipooxygenase (https://en.wikipedia.org/wiki/Benzydamine#Pharmacology).",
+    "comment": "Unlike other NSAIDs, it does not inhibit cyclooxygenase or lipooxygenase (https://en.wikipedia.org/wiki/Benzydamine#Pharmacology).",
     "directed": true,
     "graph": {
       "_id": "DB09084_MESH_D010146_1",
@@ -171089,7 +171090,7 @@
     ]
   },
   {
-    "comments": "Dilators could open up airways and help to reduce cough (https://www.mayoclinic.org/diseases-conditions/chronic-cough/diagnosis-treatment/drc-20351580).",
+    "comment": "Dilators could open up airways and help to reduce cough (https://www.mayoclinic.org/diseases-conditions/chronic-cough/diagnosis-treatment/drc-20351580).",
     "directed": true,
     "graph": {
       "_id": "DB01240_MESH_D003371_1",
@@ -171602,7 +171603,7 @@
     ]
   },
   {
-    "comments": "Camphor is analgesic (https://www.genome.jp/dbget-bin/www_bget?cpd:C00808). The activation of members of the transient receptor ion channel protein family applications lead to desensitization, which in turn contributes to the analgesic effects of camphor after prolonged/repeated applications (https://pubmed.ncbi.nlm.nih.gov/33804078/).",
+    "comment": "Camphor is analgesic (https://www.genome.jp/dbget-bin/www_bget?cpd:C00808). The activation of members of the transient receptor ion channel protein family applications lead to desensitization, which in turn contributes to the analgesic effects of camphor after prolonged/repeated applications (https://pubmed.ncbi.nlm.nih.gov/33804078/).",
     "directed": true,
     "graph": {
       "_id": "DB01744_MESH_D001416_1",
@@ -171614,9 +171615,9 @@
     },
     "links": [
       {
-        "key": "increases activity of",
+        "key": "decreases activity of",
         "source": "MESH:D002164",
-        "target": "InterPro:IPR013555"
+        "target": "UniProt:O75762"
       },
       {
         "key": "negatively correlated with",
@@ -171625,7 +171626,7 @@
       },
       {
         "key": "regulates",
-        "source": "InterPro:IPR013555",
+        "source": "UniProt:O75762",
         "target": "GO:0050968"
       },
       {
@@ -171650,9 +171651,9 @@
         "name": "camphor"
       },
       {
-        "id": "InterPro:IPR013555",
-        "label": "GeneFamily",
-        "name": "Transient receptor ion channel domain"
+        "id": "UniProt:O75762",
+        "label": "Protein",
+        "name": "Transient receptor potential cation channel subfamily A member 1"
       },
       {
         "id": "GO:0050968",
@@ -171878,7 +171879,7 @@
     ]
   },
   {
-    "comments": "Cholestyramine is a bile acid sequestrant (https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http://purl.obolibrary.org/obo/NCIT_C98148) and its ultimate action is to lower serum concentration of lipids, namely cholesterol, phospholipids, triglycerides, and cholesterol esters.",
+    "comment": "Cholestyramine is a bile acid sequestrant (https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http://purl.obolibrary.org/obo/NCIT_C98148) and its ultimate action is to lower serum concentration of lipids, namely cholesterol, phospholipids, triglycerides, and cholesterol esters.",
     "directed": true,
     "graph": {
       "_id": "DB01432_MESH_D006949_1",
@@ -171933,7 +171934,7 @@
     ]
   },
   {
-    "comments": "Cholestyramine is a bile acid sequestrant (https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http://purl.obolibrary.org/obo/NCIT_C98148) and its ultimate action is to lower plasma cholesterol concentrations.",
+    "comment": "Cholestyramine is a bile acid sequestrant (https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http://purl.obolibrary.org/obo/NCIT_C98148) and its ultimate action is to lower plasma cholesterol concentrations.",
     "directed": true,
     "graph": {
       "_id": "DB01432_MESH_D006937_1",
@@ -171988,7 +171989,7 @@
     ]
   },
   {
-    "comments": "DrugBank and ChEMBL seem to disagree on the target of this drug (UniProt:P43088 in ChEMBL, UniProt:P34995 in DrugBank). Hence using a more generic term (IPR008365) to encompass both entries from those two databases.",
+    "comment": "DrugBank and ChEMBL seem to disagree on the target of this drug (UniProt:P43088 in ChEMBL, UniProt:P34995 in DrugBank). Hence using a more generic term (IPR008365) to encompass both entries from those two databases.",
     "directed": true,
     "graph": {
       "_id": "DB00429_MESH_D006473_1",