tlambert03
adding multiple EC/QY/spectra per protein
As some proteins are characterised by multiple labs, multiple EC/QY values/spectra exist in the literature, yet this cannot be captured on FPbase at the moment (except perhaps through the excerpt function). It would be really great if it would be possible to do this, perhaps even by connecting each value to a specific publication and/or experimental condition, to allow users to be aware if there are large discrepancies in the literature.
At the same time, for certain use cases it would be useful to keep an element of simplicity in the database by flagging one of these sets of values as the 'default' value - perhaps the original dataset.
in strong agreement here! As discussed offline, this has long been considered a high value feature, but will require somewhat deeper changes to the database schema. Very important though, and thanks for opening an issue to track the progress
Is there a possible solution in the meantime, such as a field for comments on those key attributes? It might be 'nicer' than adding an extract from a paper every time, particularly when quoting from a paper is not necessarily applicable.
eg1. "Original paper (citation 1) measures QY at 0.24 but two subsequent papers measure ~0.7 (citation 2, citation 3)." eg2. "ex_max and em_max obtained from spectra in Smith et al 2016, Figure 6."
Related question: would such comment-type information available to those who grab FP info via the API?
Is there a possible solution in the meantime, such as a field for comments on those key attributes? Related question: would such comment-type information available to those who grab FP info via the API?
all of this represents work: work on the database schema to introduce new fields, work on the front end templates to use the new data, work on the API backend to add the data, etc... I'm not sure that all of that is significantly less work than doing it the right way, and even if it is less work, I'd rather put that (limited) time into doing it the right way.
I am very sorry about this inconveniences, believe me, it's been with me a while and I agree it's a huge problem. But I have a lot of stuff on my plate in addition to being the sole maintainer of FPbase, and it's going to have to wait unless someone else can dig into the code and add it themselves. Feel free to direct people to this issue and say "unfortunately, Talley is a bum and hasn't done this yet" :joy:
In the meantime, I would absolutely welcome you to maintain a list of those conflicting notes here in this issue (or anywhere) and we'll have them easily accessible once the site is ready for them
No problem, I just thought it would be significantly less work! I am keeping a list of conflicts, not to worry.