Curating indication group 98

[dede2021]

Curating, curating, curating...

[dede2021]

@TanskaAnnna will be checking group 98 curation which can be found here https://github.com/dede2021/DrugMechDB/blob/main/submission.yaml

This should be checked by @TanskaAnnna.

If all is well, I'll be opening a PR when the time is right.

[dede2021]

Issue #303 can be closed as we will be using the same issue when the group list was claimed (i.e. curating indication group issue).

[TanskaAnnna]

Hi @dede2021. For this batch I would like to suggest a few things: 1) For the graph Herpes labialis-valaciclovir: Is this disease caused by 2 viruses at the same time? If so then it's correct to have that represented in one graph. If this is either virus 1 or virus 2 - then there should be 2 graphs. 2) Urge incontinence of urine- solifenacin: have a look if all muscarinic acetylcholine receptors are involved in the urinary bladder smooth muscle contraction. 3) Human immunodeficiency virus infection-enfuvirtide you have 2 targets fot this bit of the graph:

• key: in taxon source: GO:0039663 target: GO:Q53I07 target: NCBITaxon:11676

The rest looks fine to me :)

[TanskaAnnna]

`- directed: true graph: disease: Human immunodeficiency virus infection disease_mesh: MESH:D015658 drug: enfuvirtide drug_mesh: MESH:C105196 drugbank: DB:DB00109 links:

• key: decreases activity of source: MESH:C105196 target: UniProt:Q53I07
• key: positively regulates source: UniProt:Q53I07 target: GO:0039663
• key: in taxon source: GO:0039663 target: GO:Q53I07 target: NCBITaxon:11676
• key: causes source: NCBITaxon:11676 target: MESH:D015658 multigraph: true nodes:
• id: MESH:C105196 label: Drug name: enfuvirtide
• id: UniProt:Q53I07 label: Protein name: Env polyprotein
• id: GO:0039663 label: BiologicalProcess name: membrane fusion involved in viral entry into host cell
• id: NCBITaxon:11676 label: OrganismTaxon name: Human immunodeficiency virus 1
• id: MESH:D015658 label: Disease name: Human immunodeficiency virus infection reference:
• https://go.drugbank.com/drugs/DB00109
• https://en.wikipedia.org/wiki/Enfuvirtide#Mechanism_of_action comment: Enfuvirtide is a type of HIV Fusion Inhibitors (MESH:D023581)
  • directed: true graph: disease: Gonorrhea disease_mesh: MESH:D006069 drug: enoxacin drug_mesh: MESH:D015365 drugbank: DB:DB00467 links:
• key: decreases activity of source: MESH:D015365 target: UniProt:P48374
• key: decreases activity of source: MESH:D015365 target: UniProt:Q5EP76
• key: decreases activity of source: MESH:D015365 target: UniProt:P48371
• key: decreases activity of source: MESH:D015365 target: UniProt:P22118
• key: positively regulates source: UniProt:P48374 target: GO:0006265
• key: positively regulates source: UniProt:Q5EP76 target: GO:0006265
• key: positively regulates source: UniProt:P48371 target: GO:0006265
• key: positively regulates source: UniProt:P22118 target: GO:0006265
• key: in taxon source: GO:0006265 target: NCBITaxon:485
• key: causes source: NCBITaxon:485 target: MESH:D006069 multigraph: true nodes:
• id: MESH:D015365 label: Drug name: enoxacin
• id: UniProt:P48374 label: Protein name: DNA topoisomerase 4 subunit A
• id: UniProt:Q5EP76 label: Protein name: DNA topoisomerase
• id: UniProt:P48371 label: Protein name: DNA gyrase subunit A
• id: UniProt:P22118 label: Protein name: DNA gyrase subunit B
• id: GO:0006265 label: BiologicalProcess name: DNA topological change
• id: NCBITaxon:485 label: OrganismTaxon name: Neisseria gonorrhoeae
• id: MESH:D006069 label: Disease name: Gonorrhea reference:
• https://go.drugbank.com/drugs/DB00467
• https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL826/ comment: Note that UniProt:Q5EP76 is not a reviewed UniProt annotation, rather unreviewed (protein inferred from homology).
  • directed: true graph: disease: Urinary tract infectious disease disease_mesh: MESH:D014552 drug: enoxacin drug_mesh: MESH:D015365 drugbank: DB:DB00467 links:
• key: decreases activity of source: MESH:D015365 target: UniProt:P48374
• key: decreases activity of source: MESH:D015365 target: UniProt:Q5EP76
• key: decreases activity of source: MESH:D015365 target: UniProt:P48371
• key: decreases activity of source: MESH:D015365 target: UniProt:P22118
• key: positively regulates source: UniProt:P48374 target: GO:0006265
• key: positively regulates source: UniProt:Q5EP76 target: GO:0006265
• key: positively regulates source: UniProt:P48371 target: GO:0006265
• key: positively regulates source: UniProt:P22118 target: GO:0006265
• key: in taxon source: GO:0006265 target: NCBITaxon:562
• key: causes source: NCBITaxon:562 target: MESH:D014552 multigraph: true nodes:
• id: MESH:D015365 label: Drug name: enoxacin
• id: UniProt:P48374 label: Protein name: DNA topoisomerase 4 subunit A
• id: UniProt:Q5EP76 label: Protein name: DNA topoisomerase
• id: UniProt:P48371 label: Protein name: DNA gyrase subunit A
• id: UniProt:P22118 label: Protein name: DNA gyrase subunit B
• id: GO:0006265 label: BiologicalProcess name: DNA topological change
• id: NCBITaxon:562 label: OrganismTaxon name: Escherichia coli
• id: MESH:D014552 label: Disease name: Urinary tract infectious disease reference:
• https://go.drugbank.com/drugs/DB00467
• https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL826/ comment: Note that UniProt:Q5EP76 is not a reviewed UniProt annotation, rather unreviewed (protein inferred from homology).
  • directed: true graph: disease: Postmenopausal osteoporosis disease_mesh: MESH:D015663 drug: raloxifene drug_mesh: MESH:D020849 drugbank: DB:DB00481 links:
• key: increases activity of source: MESH:D020849 target: UniProt:P03372
• key: increases activity of source: MESH:D020849 target: UniProt:Q92731
• key: positively regulates source: UniProt:P03372 target: GO:0006874
• key: positively correlated with source: GO:0006874 target: GO:0001503
• key: positively correlated with source: UniProt:Q92731 target: GO:0001503
• key: negatively correlated with source: GO:0001503 target: MESH:D015663 multigraph: true nodes:
• id: MESH:D020849 label: Drug name: raloxifene
• id: UniProt:P03372 label: Protein name: Estrogen receptor
• id: UniProt:Q92731 label: Protein name: Estrogen receptor beta
• id: GO:0001503 label: BiologicalProcess name: ossification
• id: GO:0006874 label: BiologicalProcess name: cellular calcium ion homeostasis
• id: MESH:D015663 label: Disease name: Postmenopausal osteoporosis reference:
• https://go.drugbank.com/drugs/DB00481
• https://en.wikipedia.org/wiki/Raloxifene#Pharmacodynamics
  • directed: true graph: disease: Genital herpes simplex disease_mesh: MESH:D006558 drug: valaciclovir drug_mesh: MESH:C084555 drugbank: DB:DB00577 links:
• key: has metabolite source: MESH:C084555 target: MESH:D000212
• key: negatively regulates source: MESH:D000212 target: Pfam:PF11590
• key: positively regulates source: Pfam:PF11590 target: GO:0039693
• key: in taxon source: GO:0039693 target: NCBITaxon:10310
• key: causes source: NCBITaxon:10310 target: MESH:D006558 multigraph: true nodes:
• id: MESH:C084555 label: Drug name: valaciclovir
• id: MESH:D000212 label: Drug name: Acyclovir alt-name:
  • Aciclovir
• id: Pfam:PF11590 label: GeneFamily name: DNA polymerase catalytic subunit Pol
• id: GO:0039693 label: BiologicalProcess name: viral DNA genome replication
• id: NCBITaxon:10310 label: OrganismTaxon name: Human alphaherpesvirus 2
• id: MESH:D006558 label: Disease name: Genital herpes simplex reference: https://go.drugbank.com/drugs/DB00577
  • directed: true graph: disease: Herpes zoster disease_mesh: MESH:D006562 drug: valaciclovir drug_mesh: MESH:C084555 drugbank: DB:DB00577 links:
• key: has metabolite source: MESH:C084555 target: MESH:D000212
• key: negatively regulates source: MESH:D000212 target: UniProt:P09252
• key: positively regulates source: UniProt:P09252 target: GO:0039693
• key: in taxon source: GO:0039693 target: NCBITaxon:10335
• key: causes source: NCBITaxon:10335 target: MESH:D006562 multigraph: true nodes:
• id: MESH:C084555 label: Drug name: valaciclovir
• id: MESH:D000212 label: Drug name: Acyclovir alt-name:
  • Aciclovir
• id: UniProt:P09252 label: Protein name: DNA polymerase catalytic subunit
• id: GO:0039693 label: BiologicalProcess name: viral DNA genome replication
• id: NCBITaxon:10335 label: OrganismTaxon name: Human alphaherpesvirus 3
• id: MESH:D006562 label: Disease name: Herpes zoster reference: https://go.drugbank.com/drugs/DB00577
  • directed: true graph: disease: Varicella disease_mesh: MESH:D002644 drug: valaciclovir drug_mesh: MESH:C084555 drugbank: DB:DB00577 links:
• key: has metabolite source: MESH:C084555 target: MESH:D000212
• key: negatively regulates source: MESH:D000212 target: UniProt:P09252
• key: positively regulates source: UniProt:P09252 target: GO:0039693
• key: in taxon source: GO:0039693 target: NCBITaxon:10335
• key: causes source: NCBITaxon:10335 target: MESH:D002644 multigraph: true nodes:
• id: MESH:C084555 label: Drug name: valaciclovir
• id: MESH:D000212 label: Drug name: Acyclovir alt-name:
  • Aciclovir
• id: UniProt:P09252 label: Protein name: DNA polymerase catalytic subunit
• id: GO:0039693 label: BiologicalProcess name: viral DNA genome replication
• id: NCBITaxon:10335 label: OrganismTaxon name: Human alphaherpesvirus 3
• id: MESH:D002644 label: Disease name: Varicella reference: https://go.drugbank.com/drugs/DB00577
  • directed: true graph: disease: Herpes labialis disease_mesh: MESH:D006560 drug: valaciclovir drug_mesh: MESH:C084555 drugbank: DB:DB00577 links:
• key: has metabolite source: MESH:C084555 target: MESH:D000212
• key: negatively regulates source: MESH:D000212 target: Pfam:PF11590
• key: positively regulates source: Pfam:PF11590 target: GO:0039693
• key: in taxon source: GO:0039693 target: NCBITaxon:10298
• key: in taxon source: GO:0039693 target: NCBITaxon:10310
• key: causes source: NCBITaxon:10310 target: MESH:D006560
• key: causes source: NCBITaxon:10298 target: MESH:D006560 multigraph: true nodes:
• id: MESH:C084555 label: Drug name: valaciclovir
• id: MESH:D000212 label: Drug name: Acyclovir alt-name:
  • Aciclovir
• id: Pfam:PF11590 label: GeneFamily name: DNA polymerase catalytic subunit Pol
• id: GO:0039693 label: BiologicalProcess name: viral DNA genome replication
• id: NCBITaxon:10298 label: OrganismTaxon name: Human alphaherpesvirus 1
• id: NCBITaxon:10310 label: OrganismTaxon name: Human alphaherpesvirus 2
• id: MESH:D006560 label: Disease name: Herpes labialis reference: https://go.drugbank.com/drugs/DB00577
  • directed: true graph: disease: Common cold disease_mesh: MESH:D003139 drug: hydrocodone drug_mesh: MESH:D006853 drugbank: DB:DB00956 links:
• key: positively regulates source: MESH:D006853 target: InterPro:IPR001418
• key: negatively regulates source: InterPro:IPR001418 target: GO:0019233
• key: negatively regulates source: InterPro:IPR001418 target: GO:0007600
• key: positively correlated with source: GO:0007600 target: MESH:D020078
• key: positively correlated with source: MESH:D020078 target: HP:0012735
• key: positively correlated with source: GO:0019233 target: HP:0012531
• key: manifestation of source: HP:0012735 target: MESH:D003139
• key: manifestation of source: HP:0012531 target: MESH:D003139 multigraph: true nodes:
• id: MESH:D006853 label: Drug name: hydrocodone
• id: InterPro:IPR001418 label: GeneFamily name: Opioid receptor
• id: GO:0019233 label: BiologicalProcess name: sensory perception of pain
• id: GO:0007600 label: BiologicalProcess name: sensory perception
• id: HP:0012735 label: PhenotypicFeature name: Cough
• id: MESH:D020078 label: PhenotypicFeature name: Neurogenic Inflammation
• id: HP:0012531 label: PhenotypicFeature name: Pain
• id: MESH:D003139 label: Disease name: Common cold reference:
• https://go.drugbank.com/drugs/DB00956
• https://en.wikipedia.org/wiki/Hydrocodone#Pharmacodynamics
  • directed: true graph: disease: Allergic rhinitis disease_mesh: MESH:D065631 drug: hydrocodone drug_mesh: MESH:D006853 drugbank: DB:DB00956 links:
• key: positively regulates source: MESH:D006853 target: InterPro:IPR001418
• key: negatively regulates source: InterPro:IPR001418 target: GO:0007600
• key: positively correlated with source: GO:0007600 target: MESH:D020078
• key: positively correlated with source: MESH:D020078 target: MESH:D065631 multigraph: true nodes:
• id: MESH:D006853 label: Drug name: hydrocodone
• id: InterPro:IPR001418 label: GeneFamily name: Opioid receptor
• id: GO:0007600 label: BiologicalProcess name: sensory perception
• id: MESH:D020078 label: PhenotypicFeature name: Neurogenic Inflammation
• id: MESH:D065631 label: Disease name: Allergic rhinitis reference:
• https://go.drugbank.com/drugs/DB00956
• https://en.wikipedia.org/wiki/Hydrocodone#Pharmacodynamics
  • directed: true graph: disease: Rhinitis disease_mesh: MESH:D012220 drug: hydrocodone drug_mesh: MESH:D006853 drugbank: DB:DB00956 links:
• key: positively regulates source: MESH:D006853 target: InterPro:IPR001418
• key: negatively regulates source: InterPro:IPR001418 target: GO:0007600
• key: positively correlated with source: GO:0007600 target: MESH:D020078
• key: positively correlated with source: MESH:D020078 target: MESH:D012220 multigraph: true nodes:
• id: MESH:D006853 label: Drug name: hydrocodone
• id: InterPro:IPR001418 label: GeneFamily name: Opioid receptor
• id: GO:0007600 label: BiologicalProcess name: sensory perception
• id: MESH:D020078 label: PhenotypicFeature name: Neurogenic Inflammation
• id: MESH:D012220 label: Disease name: Rhinitis reference:
• https://go.drugbank.com/drugs/DB00956
• https://en.wikipedia.org/wiki/Hydrocodone#Pharmacodynamics
  • directed: true graph: disease: Cough disease_mesh: MESH:D003371 drug: hydrocodone drug_mesh: MESH:D006853 drugbank: DB:DB00956 links:
• key: positively regulates source: MESH:D006853 target: InterPro:IPR001418
• key: negatively regulates source: InterPro:IPR001418 target: GO:0007600
• key: positively correlated with source: GO:0007600 target: MESH:D020078
• key: positively correlated with source: MESH:D020078 target: MESH:D003371 multigraph: true nodes:
• id: MESH:D006853 label: Drug name: hydrocodone
• id: InterPro:IPR001418 label: GeneFamily name: Opioid receptor
• id: GO:0007600 label: BiologicalProcess name: sensory perception
• id: MESH:D020078 label: PhenotypicFeature name: Neurogenic Inflammation
• id: MESH:D003371 label: Disease name: Cough reference:
• https://go.drugbank.com/drugs/DB00956
• https://en.wikipedia.org/wiki/Hydrocodone#Pharmacodynamics
  • directed: true graph: disease: Pain disease_mesh: MESH:D010146 drug: hydrocodone drug_mesh: MESH:D006853 drugbank: DB:DB00956 links:
• key: positively regulates source: MESH:D006853 target: InterPro:IPR001418
• key: negatively regulates source: InterPro:IPR001418 target: GO:0019233
• key: positively correlated with source: GO:0019233 target: MESH:D010146 multigraph: true nodes:
• id: MESH:D006853 label: Drug name: hydrocodone
• id: InterPro:IPR001418 label: GeneFamily name: Opioid receptor
• id: GO:0019233 label: BiologicalProcess name: sensory perception of pain
• id: MESH:D010146 label: Disease name: Pain reference:
• https://go.drugbank.com/drugs/DB00956
• https://en.wikipedia.org/wiki/Hydrocodone#Pharmacodynamics
  • directed: true graph: disease: Pain disease_mesh: MESH:D010146 drug: lornoxicam drug_mesh: MESH:C059451 drugbank: DB:DB06725 links:
• key: negatively regulates source: MESH:C059451 target: UniProt:P23219
• key: negatively regulates source: MESH:C059451 target: UniProt:P35354
• key: positively regulates source: UniProt:P23219 target: GO:0006954
• key: positively regulates source: UniProt:P35354 target: GO:0006954
• key: positively correlated with source: GO:0006954 target: MESH:D010146 multigraph: true nodes:
• id: MESH:C059451 label: Drug name: lornoxicam
• id: UniProt:P23219 label: Protein name: Prostaglandin G/H synthase 1
• id: UniProt:P35354 label: Protein name: Prostaglandin G/H synthase 2
• id: GO:0006954 label: BiologicalProcess name: inflammatory response
• id: MESH:D010146 label: Disease name: Pain reference: https://go.drugbank.com/drugs/DB06725
  • directed: true graph: disease: Falciparum malaria disease_mesh: MESH:D016778 drug: halofantrine drug_mesh: MESH:C023768 drugbank: DB:DB01218 links:
• key: molecularly interacts with source: MESH:C023768 target: CHEBI:15430
• key: disrupts source: CHEBI:15430 target: NCBITaxon:5833
• key: causes source: NCBITaxon:5833 target: MESH:D016778 multigraph: true nodes:
• id: MESH:C023768 label: Drug name: halofantrine
• id: CHEBI:15430 label: ChemicalSubstance name: protoporphyrin
• id: NCBITaxon:5833 label: OrganismTaxon name: Plasmodium falciparum
• id: MESH:D016778 label: Disease name: Falciparum malaria reference: https://go.drugbank.com/drugs/DB01218 comment: Mechanism of action is unknown (https://en.wikipedia.org/wiki/Halofantrine#Pharmacology). Halofantrine is never used to prevent malaria, rather for treatment only due to its toxicity.
  • directed: true graph: disease: Vivax malaria disease_mesh: MESH:D016780 drug: halofantrine drug_mesh: MESH:C023768 drugbank: DB:DB01218 links:
• key: molecularly interacts with source: MESH:C023768 target: CHEBI:15430
• key: disrupts source: CHEBI:15430 target: NCBITaxon:5855
• key: causes source: NCBITaxon:5855 target: MESH:D016780 multigraph: true nodes:
• id: MESH:C023768 label: Drug name: halofantrine
• id: CHEBI:15430 label: ChemicalSubstance name: protoporphyrin
• id: NCBITaxon:5855 label: OrganismTaxon name: Plasmodium vivax
• id: MESH:D016780 label: Disease name: Vivax malaria reference: https://go.drugbank.com/drugs/DB01218 comment: Mechanism of action is unknown (https://en.wikipedia.org/wiki/Halofantrine#Pharmacology). Halofantrine is never used to prevent malaria, rather for treatment only due to its toxicity.
  • directed: true graph: disease: Urge incontinence of urine disease_mesh: MESH:D053202 drug: solifenacin drug_mesh: MESH:D000069464 drugbank: DB:DB01591 links:
• key: negatively regulates source: MESH:D000069464 target: InterPro:IPR000995
• key: positively regulates source: InterPro:IPR000995 target: GO:0014832
• key: positively correlated with source: GO:0014832 target: GO:0060073
• key: positively correlated with source: GO:0060073 target: MESH:D053202 multigraph: true nodes:
• id: MESH:D000069464 label: Drug name: solifenacin
• id: InterPro:IPR000995 label: GeneFamily name: Muscarinic acetylcholine receptor family
• id: GO:0014832 label: BiologicalProcess name: urinary bladder smooth muscle contraction
• id: GO:0060073 label: BiologicalProcess name: micturition
• id: MESH:D053202 label: Disease name: Urge incontinence of urine reference: https://go.drugbank.com/drugs/DB01591
  • directed: true graph: disease: Hypertensive disorder disease_mesh: MESH:D006973 drug: hydralazine drug_mesh: MESH:D006830 drugbank: DB:DB01275 links:
• key: negatively regulates source: MESH:D006830 target: GO:0048763
• key: positively regulates source: GO:0048763 target: GO:0042310
• key: positively correlated with source: GO:0042310 target: HP:0032263
• key: manifestation of source: HP:0032263 target: MESH:D006973 multigraph: true nodes:
• id: MESH:D006830 label: Drug name: hydralazine
• id: GO:0048763 label: MolecularActivity name: calcium-induced calcium release activity
• id: GO:0042310 label: BiologicalProcess name: vasoconstriction
• id: HP:0032263 label: PhenotypicFeature name: Increased blood pressure
• id: MESH:D006973 label: Disease name: Hypertensive disorder reference: https://go.drugbank.com/drugs/DB01275
  • directed: true graph: disease: Ventricular fibrillation disease_mesh: MESH:D014693 drug: amiodarone drug_mesh: MESH:D000638 drugbank: DB:DB01118 links:
• key: negatively regulates source: MESH:D000638 target: InterPro:IPR003938
• key: regulates source: InterPro:IPR003938 target: GO:0086013
• key: affects risk for source: GO:0086013 target: HP:0011675
• key: superclass of source: HP:0011675 target: MESH:D014693 multigraph: true nodes:
• id: MESH:D000638 label: Drug name: amiodarone
• id: InterPro:IPR003938 label: GeneFamily name: Potassium channel, voltage-dependent, EAG/ELK/ERG
• id: GO:0086013 label: BiologicalProcess name: membrane repolarization during cardiac muscle cell action potential
• id: HP:0011675 label: PhenotypicFeature name: Arrhythmia
• id: MESH:D014693 label: Disease name: Ventricular fibrillation reference: https://go.drugbank.com/drugs/DB01118
  • directed: true graph: disease: Myasthenia gravis disease_mesh: MESH:D009157 drug: pyridostigmine drug_mesh: MESH:D011729 drugbank: DB:DB00545 links:
• key: negatively regulates source: MESH:D011729 target: UniProt:P22303
• key: positively regulates source: UniProt:P22303 target: GO:0001507
• key: affects risk for source: GO:0001507 target: HP:0011804
• key: manifestation of source: HP:0011804 target: MESH:D009157 multigraph: true nodes:
• id: MESH:D011729 label: Drug name: pyridostigmine
• id: UniProt:P22303 label: Protein name: Acetylcholinesterase
• id: GO:0001507 label: BiologicalProcess name: acetylcholine catabolic process in synaptic cleft
• id: HP:0011804 label: PhenotypicFeature name: Abnormal muscle physiology
• id: MESH:D009157 label: Disease name: Myasthenia gravis reference:
• https://go.drugbank.com/drugs/DB00545#BE0000426
• https://en.wikipedia.org/wiki/Pyridostigmine#Mechanism_of_action
• https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1115/`

This code has been added just for the tracking history, as the file from the submission file will be automatically erased at some point.

[dede2021]

I think the submission.yaml in my repo won't be reset to blank, just the one in the original repo.

[dede2021]

I think the submission.yaml in my repo won't be reset to blank, just the one in the original repo.

Or at least not before being merged.