display results $ mechanism of action

[dgcovell]

Thanks you for this service. From your tutorial I cannot display the example results. Error message yields

Firefox is already running, but is not responding. To use Firefox, you must first close the existing Firefox process, restart your device, or use a different profile.

Within R the command plot(1:10) generates a plot.

Restarted Firefox, with same message. Can you provide the steps for modifying my profile?

In addition, can you please provide the steps for listing the Mechanism of Action for compounds.

Thanks in advance,
David

[dgcovell]

Please indicate how I might rephrase my query in Markdown language.

[MohammedFCIS]

Hi @dgcovell,
For mechanism_of_action it can be found in pharmacology data.frame . You can obtain this data.frame with either of the following:

• Using dbdataset package that contains the latest parsed dvobject

library(dbdataset)
View(dbdataset::drugbank$drugs$pharmacology)

• Or by creating your own dvobject using dbparser as follow:

library(dbparser)
dvobj <- parseDrugBank(db_path = "C:/drugbank_all_full_database.xml.zip", drug_options = "pharmacology")
View(dvobj$drugs$pharmacology)

• The final data.frame is the same and should be similar to the following:

For the examples in https://docs.ropensci.org/dbparser/articles/dbparser.html#exploring-the-data, I tested them using the recent versions of used packages and they are running fine as expected. So may you please provide me with more details about what errors you are facing and how to reproduce them? thank you

[dgcovell]

Mohammed,

Thanks for your prompt response. Could you please include the steps for listing drug_options in the download?
Originally I used 'pharmacology' however I would like to download the contents listed under

https://docs.drugbank.com/xml/#targets-enzymes-carriers-transporters

I tried drug_options='targets' and 'transporters' without success.

Your help again?

Thanks,
David

[MohammedFCIS]

Hi David,

• There are multiple node options based on the type as follow (the help can be obtained by executing R command

?dbparser::parseDrugBank:

• 'targets' and 'transporters' options are part of cett_options as follow (the help can be obtained by executing R command

?dbparser::cett_nodes_options:

• That is made to make it easy to customize the parsing process, what you need can be obtained by executing the following:

dvobj <- parseDrugBank(db_path = "C:/drugbank_all_full_database.xml.zip", drug_options = "pharmacology", cett_options = c("enzymes", "transporters"))

• The output will be something similar to:

I hope that will help :)
Best regards,

[MohammedFCIS]

@dgcovell - I am assuming this issue is resolved. Please feel free to open new issue if help is needed. Thanks