I'm seeking to obtain the complete list of all small-molecule perturbagens used in the LINCS L1000 drug perturbation dataset. I have reviewed available resources including the following:
LINCS Data Portal: http://lincsportal.ccs.miami.edu/dcic-portal/ Connectivity Map website: https://clue.io/ The main L1000 publication: https://www.sciencedirect.com/science/article/pii/S0092867417313090 LINCS Overview publication: https://www.sciencedirect.com/science/article/pii/S2405471217304908
While a number of interactive applications are available that allow the querying of the L1000 database to find the data present for one particular small-molecule perturbagen at a time, so far, I haven’t encountered a way to download the complete list of small-molecule perturbagen / drug names used in the L1000 dataset. To clarify, I don’t want all of the associated data, just the drug names. Is anyone aware of an efficient way that I can obtain this list of drug names, without having to work with the full, large, L1000 dataset via a database platform such as MongoDB?
Also, I’m curious about whether anyone can clarify this point: The Subramanian et al. (2017) L1000 publication, as well as the Connectivity Map website, report that 19,811 small-molecule perturbagens were used for the L1000 dataset, whereas the more recent LINCS Overview paper (2018) reports in Table 1 that there are 25,581 small-molecule perturbagens. Does anyone know the source of this discrepancy? Based on Table 1 in the Overview paper, I see that the most recent release of the L1000 data was in 2015, so I would think that the dataset hasn’t been updated between those two (2017 & 2018) publications; I’ll look forward to any clarifications available. Thanks!
