Comments (3)
A note from ropen sci
I think the "Exploring the data" section is a little too heavy for README. This kind of contents is great in the getting started vignette but is not that useful in README as it is basically demonstrating dplyr and ggplot.
from dbparser.
- I think it would help unfamiliar users to add another sentence in the introduction explaining what DrugBank is. It would also be helpful to include a note about the need to make an account and request access to the data.
- Suggest removing commented code
- It seems like you made some changes recently that are resulting in errors in the README, so I suggest combing through it to make sure it's working as expected. Below are a couple things I've noticed.
- parse_drug_targets_actions() no longer works (it's now parse_drug_targ_actions()). Side note: I agree with @haozhu233 it would be nice to shorten some of the function names if possible.
xml_db_name is not an argument in open_db() - As expected parse_drug(save_table = TRUE) (and all parse functions) throws an error when there is no database to save to. However, the error only happens after parsing the data for about a minute, so it would be nice to throw an early informative error to the user.
- Make sure all relevant libraries are called for the plots (ggplot2, dplyr)
- The package description in R help can use a bit of clarification. I'd suggest emphasizing the drug bank parser over the database functionality.
from dbparser.
Enhance db connection section as note below
Database
This may be due to inexperience on my part, but I was confused about how to save the database using the driver and server argument. I would have liked to be able to save it to a SQLite or other local database using DBI::dbConnect. Is it possible to make these functions more generalizable? Or at minimum, add more description of what type of databases the package supports?
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Related Issues (20)
- download sfd and drugs 3d structure
- Fix pkgdown configuration for reference HOT 11
- extract drug's corresponding target actions info HOT 1
- Call for co-maintainers :-) HOT 1
- Remove saving CSV options
- Created DrugBank Parser that returns dvobject
- Release dbparser 2.0.0
- Build package documentation failed
- CRAN build has errors on some platforms
- 'references_options' and 'cett_options' should be allowed to NULL in parseDrugBank function
- 'experimental_properties' and 'external_identifiers' data.frames are switched with each others
- Release dbparser 2.0.1
- CRAN note HOT 1
- Error upon loading Full Database (XML) HOT 1
- Drug-target gene, drug-drug indication mapping HOT 8
- Release dbparser 2.0.2
- Drug Targets has two "drugbank_id" columns
- Reactions tibble no info on enzymes that catalyze the reaction HOT 4
- Release dbparser 2.0.3
- Complete tutorial HOT 1
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