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Dataset for Vijay #777

Closed ReneRanzinger closed 9 months ago

ReneRanzinger commented 1 year ago
T1.2 Generate reference dataset
Due Date 12/31/2023
Task owner GW
Dependencies None
Description For all protein/glycan abstracts in GlyGen generate a table with the annotation
Deliverable CSV table with annotations 
PMID 
Disease ID 
Species ID
Tissue ID
Cell line ID

This table is for Vijay.

ReneRanzinger commented 1 year ago

Let @Shovan5795 know once you have a first version of this file. I can talk with Vijay and see if there are change requests.

kmartinez834 commented 10 months ago

@kmartinez834 Add datasets to target for this task...

kmartinez834 commented 10 months ago

@ReneRanzinger no need for meeting on Friday, I will provide info to Robel so he can generate these datasets.

kmartinez834 commented 9 months ago

@rykahsay the files to target are listed here: generated/misc/files_for_udel_dataset.csv

Do you have time to create the dataset for Vijay this week? If not, let me know and I will fit it into my schedule.

rykahsay commented 9 months ago

@kmartinez834

I have created a script for (you can modify it if it is missing something), and have an new file (files_for_udel_dataset.csv -- which has now three fields) that can work with the script. This new file is not fully populated -- you need to edit/fully populate it.

I have moved the file you created to files_for_udel_dataset.csv-backup

cd /software/glygen/
$ python3 make-udel-dataset.py
kmartinez834 commented 9 months ago

The curated and reference files for Tasks 1.1 and 1.2 are located in this Sharepoint folder: Literature Mining

Direct links to the file and README: literature_mining_t1.2.csv README.xlsx