Hourly export update

waldronlab · Oct 22, 2024 · d0acc4b · d0acc4b
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diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-10-22_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-10-22_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
@@ -5402,7 +5402,7 @@ bsdb:1114/2/1_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Health
 bsdb:1114/2/2_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_DOWN	NA	k__Bacteria|p__Actinomycetota	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales
 bsdb:1115/1/1_Ischemic-stroke:Patients-with-stroke-associated-pneumonia-(SAP)_vs_Patients-without-stroke-associated-pneumonia-(non-SAP)_UP	NA	k__Bacteria|p__Bacillota|c__Bacilli	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales	k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium	k__Bacteria|s__uncultured bacterium	s__uncultured organism
 bsdb:1115/1/2_Ischemic-stroke:Patients-with-stroke-associated-pneumonia-(SAP)_vs_Patients-without-stroke-associated-pneumonia-(non-SAP)_DOWN	NA	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales	k__Bacteria|p__Bacteroidota	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter	k__Bacteria|p__Bacillota|c__Negativicutes	k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales	k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium L2-12	s__uncultured organism
-bsdb:1115/2/1_Ischemic-stroke:Patients-with-stroke-associated-Pnuemonia(SAP)_vs_Patients-without-stroke-associated-Pnuemonia(non-SAP)_UP	NA	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae
+bsdb:1115/2/1_Ischemic-stroke:Patients-with-stroke-associated-Pnuemonia(SAP)_vs_Patients-without-stroke-associated-Pnuemonia(non-SAP)_UP	NA	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus	k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter
 bsdb:1117/1/1_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_UP	NA	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae	k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales	k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga	k__Bacteria|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae	k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae	k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Xanthobacter	k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia
 bsdb:1117/1/2_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_DOWN	NA	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus	k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae	k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium	k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter	k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles
 bsdb:1118/1/1_HIV-infection:Immunological-Responder-(IR)-HIV-infected-individual_vs_Healthy-HIV-negative-individual_UP	NA	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.	k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium	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__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus	k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus	k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus

diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-10-22_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-10-22_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
@@ -5402,7 +5402,7 @@ bsdb:1114/2/1_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Health
 bsdb:1114/2/2_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_DOWN	NA	201174	102106	189330	31957	1743	22	267890	292632	2049	135622
 bsdb:1115/1/1_Ischemic-stroke:Patients-with-stroke-associated-pneumonia-(SAP)_vs_Patients-without-stroke-associated-pneumonia-(non-SAP)_UP	NA	91061	830	1502	1653	1716	186826	1522	297314	77133	155900
 bsdb:1115/1/2_Ischemic-stroke:Patients-with-stroke-associated-pneumonia-(SAP)_vs_Patients-without-stroke-associated-pneumonia-(non-SAP)_DOWN	NA	171549	976	580596	1407607	909932	909929	995019	136624	155900
-bsdb:1115/2/1_Ischemic-stroke:Patients-with-stroke-associated-Pnuemonia(SAP)_vs_Patients-without-stroke-associated-Pnuemonia(non-SAP)_UP	NA	816	580596	574697	33042	1407607	186803
+bsdb:1115/2/1_Ischemic-stroke:Patients-with-stroke-associated-Pnuemonia(SAP)_vs_Patients-without-stroke-associated-Pnuemonia(non-SAP)_UP	NA	816	580596	574697	33042	1407607
 bsdb:1117/1/1_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_UP	NA	1654	2049	2037	978	89373	335928	1903411	279	2985502
 bsdb:1117/1/2_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_DOWN	NA	186827	1375	506	212791	543	186802	216851	963	216572	497	93681
 bsdb:1118/1/1_HIV-infection:Immunological-Responder-(IR)-HIV-infected-individual_vs_Healthy-HIV-negative-individual_UP	NA	46123	547	1940338	848	1506553	186803	906	1827	1301	29465	33038

diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2024-10-22_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2024-10-22_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
@@ -5402,7 +5402,7 @@ bsdb:1114/2/1_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Health
 bsdb:1114/2/2_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_DOWN	NA	Actinomycetota	Collinsella	Dorea	Propionibacteriaceae	Propionibacterium	Shewanella	Shewanellaceae	Subdoligranulum	Actinomycetaceae	Alteromonadales
 bsdb:1115/1/1_Ischemic-stroke:Patients-with-stroke-associated-pneumonia-(SAP)_vs_Patients-without-stroke-associated-pneumonia-(non-SAP)_UP	NA	Bacilli	Butyrivibrio	Clostridium perfringens	Corynebacteriaceae	Corynebacterium	Lactobacillales	[Clostridium] innocuum	uncultured Lachnospiraceae bacterium	uncultured bacterium	uncultured organism
 bsdb:1115/1/2_Ischemic-stroke:Patients-with-stroke-associated-pneumonia-(SAP)_vs_Patients-without-stroke-associated-pneumonia-(non-SAP)_DOWN	NA	Bacteroidales	Bacteroidota	Butyricicoccus	Fusicatenibacter	Negativicutes	Selenomonadales	Sutterellaceae	butyrate-producing bacterium L2-12	uncultured organism
-bsdb:1115/2/1_Ischemic-stroke:Patients-with-stroke-associated-Pnuemonia(SAP)_vs_Patients-without-stroke-associated-Pnuemonia(non-SAP)_UP	NA	Bacteroides	Butyricicoccus	Butyricimonas	Coprococcus	Fusicatenibacter	Lachnospiraceae
+bsdb:1115/2/1_Ischemic-stroke:Patients-with-stroke-associated-Pnuemonia(SAP)_vs_Patients-without-stroke-associated-Pnuemonia(non-SAP)_UP	NA	Bacteroides	Butyricicoccus	Butyricimonas	Coprococcus	Fusicatenibacter
 bsdb:1117/1/1_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_UP	NA	Actinomyces	Actinomycetaceae	Actinomycetales	Cytophaga	Cytophagaceae	Xanthobacteraceae	Yersiniaceae	Xanthobacter	Serratia
 bsdb:1117/1/2_Gestational-diabetes:Gestational-diabetes-mellitus-(GDM)_vs_Healthy-controls_DOWN	NA	Aerococcaceae	Aerococcus	Alcaligenaceae	Enhydrobacter	Enterobacteriaceae	Eubacteriales	Faecalibacterium	Herbaspirillum	Oscillospiraceae	Psychrobacter	Roseateles
 bsdb:1118/1/1_HIV-infection:Immunological-Responder-(IR)-HIV-infected-individual_vs_Healthy-HIV-negative-individual_UP	NA	Abiotrophia	Enterobacter	Escherichia/Shigella sp.	Fusobacterium	Lachnoclostridium	Lachnospiraceae	Megasphaera	Rhodococcus	Streptococcus	Veillonella	Mediterraneibacter gnavus

diff --git a/file_size.csv b/file_size.csv
@@ -525,3 +525,4 @@
 "2024-10-22_14:58_UTC" "4100" "4913" "4100" "4913" "4100" "4913" "5565" "5565" "5565" "2335" "2335" "2335" "2335" "2335" "2335" "3748" "6666" "6028" "1360"
 "2024-10-22_15:58_UTC" "4104" "4917" "4104" "4917" "4104" "4917" "5567" "5567" "5567" "2337" "2337" "2337" "2337" "2337" "2337" "3747" "6665" "6026" "1359"
 "2024-10-22_16:58_UTC" "4106" "4919" "4106" "4919" "4106" "4919" "5567" "5567" "5567" "2337" "2337" "2337" "2337" "2337" "2337" "3745" "6662" "6027" "1360"
+"2024-10-22_17:58_UTC" "4106" "4919" "4106" "4919" "4106" "4919" "5567" "5567" "5567" "2337" "2337" "2337" "2337" "2337" "2337" "3745" "6662" "6028" "1360"