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documentation
downloaded_abstracts
LICENSE.md
README.md
annotate_abstracts.py
annotated_abstracts.csv
download_articles.py
filter_idmapping.py
filter_out_genetukit_output.py
filtered_idmapping.csv
gtk_output.csv
map_geneid_to_uniprotid.py
map_to_dict.py
merged_file.csv
pmid_geneid_syn.csv
pubmed_result.txt
save.p

README.md

GeneTUKit-Pipeline

This pipeline annotates genes/proteins in a set of PubMed abstracts with GeneTUKit. It uses PubMedPortable to build a PostgreSQL database from PubMed XML files that can be downloaded from NCBI.