Template revisions

[colleenXu]

Addresses biothings/biothings_explorer#461 (comment)

Specifically:

• make the directionality of m4-Chem-Gene-DoP.json more specific ➡️ replace with 3 templates
  • two have more specific directionality with qualifiers
  • one uses different gene-disease predicates (not causal)
• simplify templates now that qualifier expansion is supported

Other edits:

• renamed template files (trying to make a more-consistent format)
• add templates that we may want in the future (not added because of the effort involved in reviewing them and because they would tentatively be put later-in-execution compared to the current templates)

[colleenXu]

Testing the new "treats" templates

More-rare conditions

Results reviewed and found known treatments

• timothy syndrome (MONDO:0010979)
  • Beta-blockers (-lol): Propranolol, Carvedilol, Atenolol, Bisoprolol, Metoprolol, Nebivolol
  • potentially calcium-channel blockers: some -dipines like Nifedipine and Amlodipine, Diltiazem, gabapentin, magnesium (a few different forms)
• Familial dysautonomia (MONDO:0009131)
  • Brochodilators: Epinephrine, Theophylline, Salbutamol
  • stuff for autonomic symptoms like diazepam
  • stuff for orthostatic hypotension like Fludrocortisone
• Nephrotic syndrome (MONDO:0005377)
  • Diuretics like Furosemide
  • Hypolipidaemic drugs like statins (-statin), fibrates (-fibrate), niacin / Nicotinic acid, and Ezetimibe
  • Thrombophilia treatments like heparin
  • Antibiotics (-mycin, -micin, -floxacin, etc)
  • ACE inhibitors (-pril): Captopril, Enalapril, Ramipril, Lisinopril, Perindopril, Benazepril
  • Corticosteroids: Prednisone, Prednisolone, Methylprednisolone, dexamethasone,
  • Immunosuppressants: Cyclophosphamide.
  • Relapse treatments: Mechlorethamine (nitrogen mustard based), cyclosporin, Levamisole.

Table of tested diseases

All hit the cap of 500 total results

DiseaseOrPheno Name	ID	Time	# templates used
Nephrotic syndrome	MONDO:0005377	37 s	3
Noonan syndrome	MONDO:0018997	37 s	3
Huntington's disease	MONDO:0007739	56 s	3
Timothy syndrome	MONDO:0010979	1 min 40 s	4
alpha thalassemia	MONDO:0011399	1 min 41 s	4
Lesch-Nyhan syndrome	MONDO:0010298	1 min 51 s	4
Familial dysautonomia	MONDO:0009131	2 min 48 s	4
Schimke immuno-osseous dysplasia	MONDO:0009458	2 min 50 s	4
Zellweger syndrome	MONDO:0019609	4 min 20 s	4
neurofibromatosis	MONDO:0008078	5 min 13 s (will be cut off)	4
dermatomyositis	MONDO:0016367	5 min 14 s (will be cut off)	4
Fabry disease	MONDO:0010526	5 min 54 s (will be cut off)	4

Other conditions

Table of tested diseases

DiseaseOrPheno Name	ID	Time	# templates used
type 1 diabetes mellitus	MONDO:0005147	17 s	1
hypertension	HP:0000822	20 s	1
headache	HP:0002315	21 s	1
Alzheimer disease	MONDO:0004975	25 s	1
cirrhosis	MONDO:0005155	26 s	1
influenza	MONDO:0005812	29 s	3
diarrhea	HP:0002014	30 s	1
type 2 diabetes mellitus	MONDO:0005148	30 s	1
hepatitis	MONDO:0002251	30 s	1
colon cancer	HP:0003003	32 s	1
Autism	HP:0000717	32 s	2
Abnormal blood glucose concentration	HP:0011015	33 s	1
Acanthosis nigricans	MONDO:0007035	34 s	4
ovarian cancer	MONDO:0008170	35 s	1
copd	MONDO:0005002	40 s	1
Autism	MONDO:0005260	58 s	2
diabetes mellitus	MONDO:0005015	1 min 2 s	1
Ketoacidosis	HP:0001993	1 min 10 s	4
hepatitis D	MONDO:0005789	2 min 16 s	5
Hypercholesterolemia	HP:0003124	5 min 12 s (will be cut off)	5

[colleenXu]

Updated testing of "chem - affects - gene" templates

increases

starting w/ chem

Chem Name	Chem ID	Time	# templates used	# results (when not 500)
Maltodextrin	PUBCHEM.COMPOUND:79025	22 s	5	3
metformin	PUBCHEM.COMPOUND:4091	27 s	1
Testosterone	PUBCHEM.COMPOUND:6013	30 s	1
Magnesium	PUBCHEM.COMPOUND:5462224	39 s	5	359
Valproic acid	PUBCHEM.COMPOUND:3121	51 s	1
Estrogens	UMLS:C0014939	56 s	1
sumatriptan	PUBCHEM.COMPOUND:5358	1 min 34 s	2
Magnesium ion	PUBCHEM.COMPOUND:888	1 min 41 s	2
Dextroamphetamine	PUBCHEM.COMPOUND:5826	2 min 4 s	2
Gabapentin	PUBCHEM.COMPOUND:3446	3 min 2 s	2
Amitriptyline	PUBCHEM.COMPOUND:2160	4 min 14 s	2
Ethinylestradiol	PUBCHEM.COMPOUND:5991	4 min 23 s	2

Others in the old list had 0 results, would be cut off at 5 min, or appeared that it would be cut off at 5 min.

starting w/ gene

Gene Name	Gene ID	Time	# templates used	# results (when not 500)
XIST	NCBIGene:7503	21 s	5	1
MALAT1	NCBIGene:378938	24 s	5	7
TP53	NCBIGene:7157	33 s	1
CYP27B1 (a P450)	NCBIGene:1594	36 s	2
DYRK1A	NCBIGene:1859	37 s	2
PCSK1N	NCBIGene:27344	42 s	5	61
MEF2C	NCBIGene:4208	49 s	2
ADNP	NCBIGene:23394	50 s	4
TTR	NCBIGene:7276	1 min 12 s	2
MAPK8IP3	NCBIGene:23162	1 min 18 s	5	376
GAPDH	NCBIGene:2597	4 min 48 s	2
MMP9	NCBIGene:4318	4 min 54 s	2

Others in the old list had 0 results, would be cut off at 5 min, or appeared that it would be cut off at 5 min.

decreases

starting w/ chem

Chem Name	Chem ID	Time	# templates used	# results (when not 500)
metformin	PUBCHEM.COMPOUND:4091	20 s	1
Maltodextrin	PUBCHEM.COMPOUND:79025	21 s	5	2
Atorvastatin	PUBCHEM.COMPOUND:60823	22 s	1
Magnesium	PUBCHEM.COMPOUND:5462224	37 s	5	353
Valproic acid	PUBCHEM.COMPOUND:3121	40 s	1
Testosterone	PUBCHEM.COMPOUND:6013	1 min 12 s	1
Estrogens	UMLS:C0014939	1 min 16	1
sumatriptan	PUBCHEM.COMPOUND:5358	1 min 32 s	2
Magnesium ion	PUBCHEM.COMPOUND:888	1 min 46 s	2
Dextroamphetamine	PUBCHEM.COMPOUND:5826	2 min 13 s	2
Gabapentin	PUBCHEM.COMPOUND:3446	2 min 59 s	2

Others in the old list had 0 results, would be cut off at 5 min, or appeared that it would be cut off at 5 min.

starting w/ gene

Gene Name	Gene ID	Time	# templates used	# results (when not 500)
MALAT1	NCBIGene:378938	22 s	5	7
MMP9	NCBIGene:4318	24 s	1
XIST	NCBIGene:7503	25 s	5	1
TP53	NCBIGene:7157	27 s	1
PCSK1N	NCBIGene:27344	32 s	5	212
ADNP	NCBIGene:23394	34 s	3
MAPK8IP3	NCBIGene:23162	57 s	4
DYRK1A	NCBIGene:1859	1 min 2 s	3
MEF2C	NCBIGene:4208	1 min 12 s	2
TTR	NCBIGene:7276	1 min 49 s	2
CYP27B1 (a P450)	NCBIGene:1594	2 min 2 s	2

Others in the old list had 0 results, would be cut off at 5 min, or appeared that it would be cut off at 5 min.