kilicogluh / lbd-covid Goto Github PK
View Code? Open in Web Editor NEWDrug repurposing for COVID-19 using literature-based discovery
Drug repurposing for COVID-19 using literature-based discovery
Hi, could you please provide the download link of your KG?
https://github.com/kilicogluh/lbd-covid/tree/master/preprocessing
For preprocessing, the given code asks you to run "run.sh", where two pearl scripts are called for before finding concept_degree i.e. count.pl and statistics.pl . In order to run the compute_score script, the script takes concept degree and stats as input to calculate the score. I was wondering if the scripts were missing or was not provided for other reasons. Also, it would be helpful if you could provide if there are any example files for extracted sub_rel_obj, stats, count, and concept degree from the dataset that you used.
Where can I find the statistic.pl and count.pl files?
In addition to filtering according to the GENERIC concepts table in SemMedDB43, we can further filter out concepts (arguments of semantic relations) that we believe are still too general. Below are two lists. They both have the same format. The counts(frequencies) correspond to the degrees of the nodes (sum of in+out degrees).
Please have a look at these files and suggest which concepts (arguments) we should eliminate by adding them to the GENERIC concepts list. Of course, all the semantic relations where they appear should be filtered out, too. @kilicogluh , @daltonsUMN , @akastrin @DimitarH @[email protected] @[email protected]
The files are TAB delimited with these fields:
Links to the files:
Ordered by descending semantic relation occurrence. download link
Ordered by descending semantic relation instance occurrence count. download link
Can a link be provided from where we can download this file?
Filter out non-informative concepts and semantic relations. Obviously, we are already having two filtering scripts (UNI-LJ and UMN). This issue is for the UNI-LJ group. At some stage, we will have to merge them together or select one of them.
The filtering script should be flexible with an external JSON file where the filtering constraints are specified and can be modified without changing the main filtering script.
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