Natural language processing of gene descriptions for overrepresentation analysis with GeneTEA

Data and models supporting "Natural language processing of gene descriptions for overrepresentation analysis with GeneTEA" (Boyle et al. 2025)File descriptions:GeneTEA.pkl, GeneTEA-yeast.pkl, PharmaTEA.pkl - pickled GeneTEA modelsFig2b/d.csv: Top terms in Figure 2 b/d.gProfiler_hsapiens_7-16-2025_4-35-07 PM__intersections.csv: g:GOSt results for Fig2b, downloaded from the g:Profiler site.gProfiler_hsapiens_7-16-2025_4-41-03 PM__intersections.csv: g:GOSt results for Fig2d, downloaded from the g:Profiler site.enrichr_sets_03_01_2025.csv: Enrichr database downloaded 3/1/2025, used for Figure 3 and S1.gene sets for connexin.gmt: Enrichr gene sets containing the term "connexin", downloaded from the Enrichr site.false_discoveries.csv: Benchmarking results for false discovery control in Figures 4 and S1.EF_hand_example.csv: Top terms and MedCPT scores for EF-hand example in Figure 4.[Hallmark or Experimentally Derived Queries]_scores.csv: Benchmarking results for [Hallmark or Experimentally Derived Queries] across joined top terms in Figures 4 and S2. The "joined_ranking" column corresponds to the MedCPT Relevance score across the top terms and "num_high_redundancy" contains the number of redundant term pairs.[Hallmark or Experimentally Derived Queries]_indiv.csv: Benchmarking results for [Hallmark or Experimentally Derived Queries] for each top term in Figures 4 and S2. The "indiv_ranking" column corresponds to the MedCPT Relevance score for a single term.Fig4_left/right: Examples of top terms shown in what is now Figure 5.gProfiler_hsapiens_3-13-2025_9-14-59 AM__intersections.csv: g:GOSt results for Fig4_left, downloaded from the g:Profiler site.gProfiler_hsapiens_2-11-2025_10-18-19 AM__intersections.csv: g:GOSt results for Fig4_right, downloaded from the g:Profiler site.