Hourly export update

waldronlab · Nov 16, 2024 · 9e8ab1a · 9e8ab1a
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diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-11-16_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-11-16_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
 bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP	NA	k__Bacteria|p__Bacillota|c__Bacilli	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus	k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea	k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium	k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae	k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae	k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae	k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus	k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae
 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN	NA	k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus	k__Bacteria|p__Cyanobacteriota
 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP	NA	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae
@@ -5949,7 +5949,7 @@ bsdb:1221/1/1_Clostridium-difficile-infection:Survived_vs_Before-Clostridioides-
 bsdb:1221/1/2_Clostridium-difficile-infection:Survived_vs_Before-Clostridioides-difficile-infection-(CDI)_DOWN	NA	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus canintestini	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron
 bsdb:1221/2/1_Clostridium-difficile-infection:Euthanized_vs_Before-Clostridioides-difficile-infection-(CDI)_UP	NA	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile	k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila
 bsdb:1221/2/2_Clostridium-difficile-infection:Euthanized_vs_Before-Clostridioides-difficile-infection-(CDI)_DOWN	NA	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis	k__Bacteria|k__Bacillati|p__Bacillota	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis
-bsdb:1222/1/1_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_UP	NA	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae	k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales	k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae	k__Bacteria|p__Synergistota	k__Bacteria|p__Synergistota|c__Synergistia	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria
+bsdb:1222/1/1_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_UP	NA	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota	k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae	k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales	k__Bacteria|p__Synergistota|c__Synergistia	k__Bacteria|p__Synergistota	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales
 bsdb:1222/1/2_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_DOWN	NA	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia	k__Bacteria|k__Bacillati|p__Bacillota	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira
 bsdb:1222/2/1_Cervical-cancer:HIV-Positive_vs_HIV-Negative_UP	NA	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales	k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales
 bsdb:1222/2/2_Cervical-cancer:HIV-Positive_vs_HIV-Negative_DOWN	NA	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor

diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-11-16_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-11-16_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
 bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP	NA	91061	1236	1654	1716	1301	162289	189330	33024	40544	2037	2049	506	186826	1300	31977	91347	1653	57037	1386	186817
 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN	NA	100883	1117
 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP	NA	207244	57037
@@ -5949,7 +5949,7 @@ bsdb:1221/1/1_Clostridium-difficile-infection:Survived_vs_Before-Clostridioides-
 bsdb:1221/1/2_Clostridium-difficile-infection:Survived_vs_Before-Clostridioides-difficile-infection-(CDI)_DOWN	NA	1633	328812	487175	508451	1350	564	317010	818
 bsdb:1221/2/1_Clostridium-difficile-infection:Euthanized_vs_Before-Clostridioides-difficile-infection-(CDI)_UP	NA	816	1496	239935
 bsdb:1221/2/2_Clostridium-difficile-infection:Euthanized_vs_Before-Clostridioides-difficile-infection-(CDI)_DOWN	NA	154288	487175	1239	1633	508451	1605
-bsdb:1222/1/1_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_UP	NA	128827	526525	526524	216572	649776	649777	508458	649775	1283313	196013	1224	119060	1236
+bsdb:1222/1/1_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_UP	NA	1283313	119060	196013	128827	526525	526524	1236	216572	1224	649777	649776	649775	508458	80840
 bsdb:1222/1/2_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_DOWN	NA	186801	1239	28050
 bsdb:1222/2/1_Cervical-cancer:HIV-Positive_vs_HIV-Negative_UP	NA	526524	526525	128827	1508657	91061	186826
 bsdb:1222/2/2_Cervical-cancer:HIV-Positive_vs_HIV-Negative_DOWN	NA	44259

diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-11-16_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-11-16_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
 bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP	NA	Bacilli	Gammaproteobacteria	Actinomyces	Corynebacterium	Streptococcus	Peptoniphilus	Dorea	Phascolarctobacterium	Sutterella	Actinomycetales	Actinomycetaceae	Alcaligenaceae	Lactobacillales	Streptococcaceae	Veillonellaceae	Enterobacterales	Corynebacteriaceae	Lacticaseibacillus zeae	Bacillus	Bacillaceae
 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN	NA	Coprobacillus	Cyanobacteriota
 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP	NA	Anaerostipes	Lacticaseibacillus zeae
@@ -5949,7 +5949,7 @@ bsdb:1221/1/1_Clostridium-difficile-infection:Survived_vs_Before-Clostridioides-
 bsdb:1221/1/2_Clostridium-difficile-infection:Survived_vs_Before-Clostridioides-difficile-infection-(CDI)_DOWN	NA	Limosilactobacillus vaginalis	Parabacteroides goldsteinii	Parasutterella excrementihominis	Lactobacillus taiwanensis	Enterococcus	Escherichia fergusonii	Enterococcus canintestini	Bacteroides thetaiotaomicron
 bsdb:1221/2/1_Clostridium-difficile-infection:Euthanized_vs_Before-Clostridioides-difficile-infection-(CDI)_UP	NA	Bacteroides	Clostridioides difficile	Akkermansia muciniphila
 bsdb:1221/2/2_Clostridium-difficile-infection:Euthanized_vs_Before-Clostridioides-difficile-infection-(CDI)_DOWN	NA	Turicibacter sanguinis	Parasutterella excrementihominis	Bacillota	Limosilactobacillus vaginalis	Lactobacillus taiwanensis	Ligilactobacillus animalis
-bsdb:1222/1/1_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_UP	NA	Erysipelotrichaceae	Erysipelotrichales	Erysipelotrichia	Oscillospiraceae	Synergistales	Synergistaceae	Synergistota	Synergistia	Alloprevotella	Caldimonas	Pseudomonadota	Burkholderiaceae	Gammaproteobacteria
+bsdb:1222/1/1_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_UP	NA	Alloprevotella	Burkholderiaceae	Caldimonas	Erysipelotrichaceae	Erysipelotrichales	Erysipelotrichia	Gammaproteobacteria	Oscillospiraceae	Pseudomonadota	Synergistaceae	Synergistales	Synergistia	Synergistota	Burkholderiales
 bsdb:1222/1/2_Cervical-cancer:Cervical-Cancer-patients_vs_Cervical-Dysplasia_DOWN	NA	Clostridia	Bacillota	Lachnospira
 bsdb:1222/2/1_Cervical-cancer:HIV-Positive_vs_HIV-Negative_UP	NA	Erysipelotrichia	Erysipelotrichales	Erysipelotrichaceae	Ruminiclostridium	Bacilli	Lactobacillales
 bsdb:1222/2/2_Cervical-cancer:HIV-Positive_vs_HIV-Negative_DOWN	NA	Filifactor

diff --git a/file_size.csv b/file_size.csv
@@ -1124,3 +1124,4 @@
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+"2024-11-16_17:58_UTC" "4447" "5308" "4378" "5227" "4447" "5308" "5964" "5964" "5964" "2597" "2597" "2558" "2558" "2597" "2597" "4101" "6996" "6697" "1322"