Accessing and Manipulating the Database

These actions are performed with the mongolite package, along with helper functions in this package, sensorOverlord.

Accessing DB entries

I find it easiest to turn the database entries into a dataframe before using them in R.

Note: The database is a mongo database–so, it’s stored in JSON format. This wasn’t a design choice–mongodb just had a free server hosting platform that was really easy to use to store small amounts of data. If this database grows, it may need to be migrated to a tabular SQL format.

To access entries, use sensorOverlord::getDb()$find():

data.frame(sensorOverlord::getDb()$find())

Or, functions from data.table are a bit faster:

data.table::data.table(sensorOverlord::getDb()$find())

Adding a new DB entry

First, import a local file with your spectra. For example:

deGFP1 <- data.table::fread("/home/julian/2019_Sensor_Overlord_Local/Spectra_and_info/Sensors_Main/pH_Sensors/deGFP1/Hanson2002/deGFP1.csv")

Then, extract the columns with the wavelengths and expression values of Rdeprot/Rprot, Rox/Rred, etc.

In the following methods, “values_min”/other references to ‘min’ refer to the ligand-bound state (e.g. reduced or protenated) and the “values_max”/other references to ‘max’ refer to the ligand-unbound state (e.g. oxidized or deprotenated). This is just an artifact of depreciated terminology.

lambda_max <- deGFP1$V1
values_max <- deGFP1$V2
lambda_min <- deGFP1$V3
values_min <- deGFP1$V4

Now, you can use the sensorOverlord::formatSpectraData function to format the data into a list for submission to the database:

submission <- formatSpectraData(name = "deGFP1", type = "pH", readout = "emission ratiometric", lambda_max = lambda_max, values_max = values_max, lambda_min = lambda_min, values_min = values_min, sensor_midpoint = 8.02,
lambda1_recommended = 515, lambda2_recommended = 460)

Then, when you’re ready to submit your entry, you can use sensorOverlord::getDb() and $insert to add your new submission:

getDb()$insert(submission)

Removing a DB entry

If you made a mistake in your entry, you may want to remove it. Assuming that your sensor name is unique:

getDb()$remove('{"sensor_name" : "deGFP1"}')

In the future, it would be better if this database had unique IDs, in case you accidentally added a sensor with the same name as an existing one. I can do that–it just takes a little bit of effort. If you’re reading this and using SensorOverlord, please shoot me an email (julianst [at] mit [dot] edu) and I can spend some time to make this db more rigorous.

Modifying an entry

While updating this package recently, I noticed that I should add recommended \(\lambda_1\) and \(\lambda_2\) values to each sensor, based on the values we chose for the manuscript. So, I needed to modify entries with those values. To do that, you can use the $update method in a database. For example, here’s the format to add a new “lambda1_recommended” value to roGFP1 in the database:

sensorOverlord::getDb()$update('{"sensor_name": "roGFP1"}', '{"$set":{"lambda1_recommended": 410}}')