import CMap/LINCS data

[andrewsu]

CMap should provide gene expression measurements associated with chemical compounds. In theory, that data should be accessible via https://clue.io/cmap, but on first glance it is unclear how one can actually access these data (via either downloadable files or API). Needs someone to dig through the links (including the GEO records mentioned in https://clue.io/GEO-guide and this user guide).

Also, I believe CMap and LINCS are a partially overlapping set of data. Would also be good to import LINCS -- more info probably available at http://www.lincsproject.org/.

This ticket is partially motivated by a request from the alpha translator team, so they should be notified when we have more info...

[andrewsu]

on the cmap front, I was reminded on the KGS call this morning that cmap v2 is based on creating a 1000-gene "signature" (L1000), not transcriptome-wide measurement of gene expression. (There is some imputation that has been done for the genes that were not directly profiled, but not great I think...) however, cmap v1 was based on microarray data -- definitely older but it is roughly transcriptome wide. Can be downloaded here https://portals.broadinstitute.org/cmap/#. Someone will need to look into this to see if that data can be converted to links between drugs and downstream genes...

[andrewsu]

This article https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty763/5088320 and this tool http://amp.pharm.mssm.edu/DGB/ may be useful guides on how to process these data...