Hourly export update

waldronlab · Oct 21, 2024 · 7a76538 · 7a76538
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diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-10-21_04:58_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
@@ -5370,7 +5370,7 @@ bsdb:1106/5/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-non
 bsdb:1106/5/3_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_DOWN	NA	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus	k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus	k__Bacteria|p__Pseudomonadota	k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae
 bsdb:1106/6/1_Breastfeeding-duration:Non-Exclusive-Breastfeeding-(Non-EBF)_vs_Exclusive-BreastFeeding-(EBF)_UP	NA	k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium	k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera	k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella
 bsdb:1106/7/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_UP	NA	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae	k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales	k__Bacteria|p__Bacteroidota|c__Bacteroidia
-bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae	k__Bacteria|p__Bacillota	k__Bacteria|p__Bacillota|c__Clostridia	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae
+bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia
 bsdb:1108/1/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN	NA	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae
 bsdb:1108/2/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae
 bsdb:1108/2/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN	NA	k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium

diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-10-21_04:58_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
@@ -5370,7 +5370,7 @@ bsdb:1106/5/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-non
 bsdb:1106/5/3_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_DOWN	NA	244127	33024	583	1224	1279	543
 bsdb:1106/6/1_Breastfeeding-duration:Non-Exclusive-Breastfeeding-(Non-EBF)_vs_Exclusive-BreastFeeding-(EBF)_UP	NA	904	816	1485	33042	1730	906	29465
 bsdb:1106/7/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_UP	NA	816	1485	1730	186803	906	31979	186802	200643
-bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	102106	84108	84999	1268	1239	186801	3085636	186803
+bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	102106	84999	1268	84108
 bsdb:1108/1/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN	NA	1485	31979
 bsdb:1108/2/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	1843491
 bsdb:1108/2/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN	NA	1501226	1485

diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-10-21_04:58_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
@@ -5370,7 +5370,7 @@ bsdb:1106/5/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-non
 bsdb:1106/5/3_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_DOWN	NA	Anaerotruncus	Phascolarctobacterium	Proteus	Pseudomonadota	Staphylococcus	Enterobacteriaceae
 bsdb:1106/6/1_Breastfeeding-duration:Non-Exclusive-Breastfeeding-(Non-EBF)_vs_Exclusive-BreastFeeding-(EBF)_UP	NA	Acidaminococcus	Bacteroides	Clostridium	Coprococcus	Eubacterium	Megasphaera	Veillonella
 bsdb:1106/7/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_UP	NA	Bacteroides	Clostridium	Eubacterium	Lachnospiraceae	Megasphaera	Clostridiaceae	Eubacteriales	Bacteroidia
-bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	Collinsella	Slackia	Coriobacteriales	Micrococcaceae	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae
+bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	Collinsella	Coriobacteriales	Micrococcaceae	Slackia
 bsdb:1108/1/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN	NA	Clostridium	Clostridiaceae
 bsdb:1108/2/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP	NA	Selenomonadaceae
 bsdb:1108/2/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN	NA	Romboutsia	Clostridium

diff --git a/file_size.csv b/file_size.csv
@@ -488,3 +488,4 @@
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 "2024-10-21_03:07_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357"
 "2024-10-21_03:58_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357"
+"2024-10-21_04:58_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357"