Lincs #267
Lincs #267
Conversation
|
How did you obtain the LINCS files that are parsed here? I believe all of the LINCS data is dependent on cell line in which gene expression is measured, so I'm a little worried about saying a compound positively/negatively regulating some gene without providing the cell contexts in which it was measured. |
|
The code looks great at a glance. I would probably delete some of the template comments, and it's also 2024 now ;) But lets address JMs question before I start testing. Maybe we can use the anatomical context qualifier? The biolink docs actually mention a "experimental_context_qualifier" that has HeLa cells as the example, but I don't think that's actually in the model. I'm not sure if there is one for cell types otherwise. |
fixing several bugs and broken variable names - fixing source data download location - source data delimiter is comma not tab - cleaning up properties (they need to be a dictionary, but node props were unnecessary anyway) simplifying/fixing qualifier handling - using predicates like RO:0002212 includes directionality and will normalize to qualified version, old implementation didn't work anyway, so this is better
|
We decided that addressing JM's concern was not possible with the source data provided, not going to include cell line information for now. The parser turned out to have several issues but I refactored it. |
Data stored on renci nfs. File path specified in parser.
Need review before completion of PR since no test ran for the new LICNS parser.