search

lanagarmire / lilikoi2

GNU General Public License v3.0
2 stars 4 forks source link

updateDB() does not exist #3

Open kohlkopf opened 3 years ago

kohlkopf commented 3 years ago

This function does not exist, though you published article introducing the software claims it does. This was in response to a reviewer's concern that the database included with the package would fall out of currency.

The function lilikoi.updateDB() method allows users to call to pull the latest curated databases from Lilikoi’s github repository. ((AlAkwaa et al, 2018)

Reviewer's comments

Lilikoi embeds 18000 metabolites from several sources. What is the update strategy ? Will it be updated on a defined e.g. quarterly schedule? Is there a description how the user can update the database?

Lilikoi provides a default database, it also allows updated database if the user prefers. We added a lilikoi.updateDB method, with which users can call to pull the latest curated databases from Lilikoi’s github repository. We plan to update the database periodically (eg. semi-annually).

lanagarmire commented 2 years ago

This updateDB() function is from lilikoi v1 (the paper you attached) The updateDB() function is deprecated from lilikoi v2.