Metadata for all the OmniPath databases.

[ecarrenolozano]

Hi OmniPath team and community,

Context

As far as I understand, the OmniPath database is a collection of five (5) databases:

• network (interactions)
• enzyme-substrate interactions (enz_sub or ptms)
• protein complexes (complexes)
• molecular entity annotations (annotations)
• intercellular communication roles (intercell).

As a Python user, I am interested in using the OmniPath client to retrieve the information of each one. It means that for each database I am using the following commands:

• network (interactions)
  • omnipath.interactions.AllInteractions.get()
• enzyme-substrate interactions (enz_sub or ptms)
  • omnipath.requests.Enzsub.get()
• protein complexes (complexes)
  • omnipath.requests.Complexes.get()
• molecular entity annotations (annotations)
  • omnipath.requests.Annotations.get()
• intercellular communication roles (intercell).
  • omnipath.requests.Intercell.get()

Questions

1. Am I using the correct commands to download the complete dataset (rather than just subsets)?
2. Where can I find the metadata for each database to verify if the information I downloaded is accurate? For example: the number of tables, rows, columns, column names, and descriptions for each column
3. Additionally, I am experimenting with the pypath package to build data from the original resources. How can I verify that the data generated is identical to what is available on omnipathdb.org?

Thanks in advance