Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[PA166122732] Bad GPML for Succinylcholine Pathway, Pharmacokinetics/Pharmacodynamics #95

Closed
pharmgen opened this issue Mar 30, 2018 · 0 comments
Labels
Milestone

Comments

@pharmgen
Copy link
Collaborator

pharmgen commented Mar 30, 2018

Latest GPML for pathwayPA166122732 is obsolete.
Use this instead: PA166122732-new.gpml

Note that even the updated GPML has errors that must be fixed:

  • 'neuromuscular block' [id:c60cf]: Missing PharmGKB Accession ID.
  • 'neuromuscular block' [id:c60cf]: BlackBox should be converted to Phenotype or Process.
  • 'nicotinic acetylcholine receptor' [id:c8e75]: Evidence should only be provided on interactions.
  • 'sodium' [id:c6f32]: Extracellular nodes should not have cell specified.
  • 'potassium' [id:ca76b]: Extracellular nodes should not have cell specified.
  • 'dihydropyridine receptor' [id:a7f75]: Evidence should only be provided on interactions.
  • 'calcium' [id:d5f6c]: Cellular location is 'Intracellular' but it's in a Info Label.
  • 'SERCA' [id:a1c5c]: Missing cellular location.
  • 'muscle paralysis' [id:b3e52]: Missing PharmGKB Accession ID.
  • 'muscle paralysis' [id:b3e52]: BlackBox should be converted to Phenotype or Process.
  • Transport line [id:e9d1f] (from 'calcium' [id:a9deb] to 'SERCA' [id:a1c5c]): Transport does not have same entity on both ends.
  • Transport line [id:e9d1f] (from 'calcium' [id:a9deb] to 'SERCA' [id:a1c5c]): Missing evidence.
  • Transport line [id:id380412c9] (from 'RYR1' [id:ca004] to 'calcium' [id:a9deb]): Transport does not have same entity on both ends.
  • Info Line line [id:idb25d2bd3] (from 'nicotinic acetylcholine receptor' [id:c8e75] to 'neuromuscular block' [id:c60cf]): Info labels lines are no longer allowed.
  • Info Line line [id:idc22d419d] (from 'muscle paralysis' [id:b3e52] to 'SERCA' [id:a1c5c]): Info labels lines are no longer allowed.
  • Info Line line [id:idf4c53f1] (from 'calcium' [id:a9deb] to 'muscle contraction' [id:e03b2]): Info labels lines are no longer allowed.
  • Transport line [id:a7b4a] (from 'sodium' [id:c6f32] to 'nicotinic acetylcholine receptor' [id:c8e75]): Transport does not have same entity on both ends.
  • Transport line [id:a7b4a] (from 'sodium' [id:c6f32] to 'nicotinic acetylcholine receptor' [id:c8e75]): Missing evidence.
  • Conversion line [id:e92b4] (from 'succinylcholine' [id:a21b4] to 'succinylmonocholine' [id:a27c3]): Missing evidence.
  • Conversion line [id:ab18d] (from 'succinylmonocholine' [id:a27c3] to 'succinic acid' [id:a4c77]): Missing evidence.
  • Transport line [id:d5a0b] (from 'nicotinic acetylcholine receptor' [id:c8e75] to 'sodium' [id:b5671]): Transport does not have same entity on both ends.
  • Transport line [id:d5a0b] (from 'nicotinic acetylcholine receptor' [id:c8e75] to 'sodium' [id:b5671]): Missing evidence.
  • Transport line [id:e39d3] (from 'nicotinic acetylcholine receptor' [id:c8e75] to 'potassium' [id:ca76b]): Transport does not have same entity on both ends.
  • Transport line [id:e39d3] (from 'nicotinic acetylcholine receptor' [id:c8e75] to 'potassium' [id:ca76b]): Missing evidence.
  • Transport line [id:ab670] (from 'potassium' [id:a3638] to 'nicotinic acetylcholine receptor' [id:c8e75]): Transport does not have same entity on both ends.
  • Transport line [id:ab670] (from 'potassium' [id:a3638] to 'nicotinic acetylcholine receptor' [id:c8e75]): Missing evidence.
  • Activation line [id:c8139] (from 'sodium' [id:b5671] to 'membrane depolarization' [id:b30b8]): Missing evidence.
  • Activation line [id:c4e8c] (from 'potassium' [id:a3638] to 'membrane depolarization' [id:b30b8]): Missing evidence.
  • Conversion line [id:d512e] (from 'succinylmonocholine' [id:a27c3] to 'choline' [id:cb32d]): Missing evidence.
  • Transport line [id:b568b] (from 'calcium' [id:d5f6c] to 'RYR1' [id:ca004]): Transport does not have same entity on both ends.
  • Transport line [id:b568b] (from 'calcium' [id:d5f6c] to 'RYR1' [id:ca004]): Missing evidence.
  • Transport line [id:cf7ab] (from 'SERCA' [id:a1c5c] to 'calcium' [id:d5f6c]): Transport does not have same entity on both ends.
  • 'neuromuscular block' [id:c60cf]: Not linked to anything.
  • 'muscle paralysis' [id:b3e52]: Not linked to anything.
  • 'muscle contraction' [id:e03b2]: Not linked to anything.
@pharmgen pharmgen added this to the Update GPML milestone Mar 30, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

2 participants