Library of Network based Cellular Signatures (LINCS) and CMap and LINCS Unified Environment (CLUE)

[eKathleenCarter]

In an effort to remove Hetionet as a KP (#117) but preserve the data there within, this KP is recommended for addition.

LINCS (https://lincsproject.org) aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. Hetionet used this data set to inform its metaedges:
*Compound - down regulates - Gene (CdG)
*Gene -> regulates -> Gene (GrG) (unidirectional edges)
*Compound - up regulates - Gene (CuG)

LINCS L1000 Data sets can be downloaded here:
https://maayanlab.cloud/sigcom-lincs/#/Download

The main location of the data for the LINCS project is hosted by CLUE.
CLUE (https://clue.io/about) is a cloud-based software platform for the analysis of perturbational datasets. The CLUE platform provides integrated access to datasets, results from the processing and analysis of these data, and software tools that the community can leverage to advance their research.

CLUE also has several other data sets that could be of interest.
https://clue.io/data

The up to date LINCS data set can be found here:
https://clue.io/data/CMap2020#LINCS2020
CLUE hosts a python package to access data programmatically https://cmapbq.readthedocs.io/en/latest/

Hetionet's last import of the L1000 dataset was from 2016. The most up to date data on CLUE is from 2021. Their original work can be found here for comparison:
https://zenodo.org/records/47223