Hourly export update

waldronlab · Jan 14, 2025 · af41cb8 · af41cb8
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diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2025-01-14_15:58_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
@@ -5108,6 +5108,8 @@ bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Ad
 bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-S)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN	NA	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia	k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium	k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella	k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella
 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_UP	NA	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella	k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus	k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella	k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium	k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia
 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_DOWN	NA	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia	k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium	k__Bacteria|k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium	k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella	k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella	k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas	k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella
+bsdb:1086/18/1_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_UP	NA	k__Bacteria|k__Bacillati|p__Bacillota	k__Bacteria|k__Pseudomonadati|p__Campylobacterota	k__Bacteria|k__Fusobacteriati|p__Fusobacteriota	k__Bacteria	k__Bacteria|k__Pseudomonadati|p__Pseudomonadota	k__Bacteria|k__Pseudomonadati|p__Spirochaetota
+bsdb:1086/18/2_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_DOWN	NA	k__Bacteria|k__Bacillati|p__Actinomycetota	k__Bacteria|k__Pseudomonadati|p__Bacteroidota
 bsdb:1087/1/4_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_UP	NA	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta	k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii
 bsdb:1087/1/5_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_DOWN	NA	k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis
 bsdb:1087/3/1_Treatment-refractory-schizophrenia:TRS:-individuals-with-treatment-resistant-schizophrenia-taking-clozapine_vs_AAP:-individuals-with-treatment-responsive-schizophrenia-taking-atypical-antipsychotics-(not-clozapine)_UP	NA	k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi	k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii	k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans

diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2025-01-14_15:58_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
@@ -5108,6 +5108,8 @@ bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Ad
 bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-S)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN	NA	1654	2801844	194	1016	2717	1716	848	133925	970	195950
 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_UP	NA	1283313	1380	1378	724	1164882	482	836	838	1301	29465	265975	508215
 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_DOWN	NA	1654	2801844	194	1016	2717	1716	1434006	848	32257	133925	970	195950
+bsdb:1086/18/1_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_UP	NA	1239	29547	32066	2	1224	203691
+bsdb:1086/18/2_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_DOWN	NA	201174	976
 bsdb:1087/1/4_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_UP	NA	169435	33035	84112	562	1335613	1096246
 bsdb:1087/1/5_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_DOWN	NA	1776391
 bsdb:1087/3/1_Treatment-refractory-schizophrenia:TRS:-individuals-with-treatment-resistant-schizophrenia-taking-clozapine_vs_AAP:-individuals-with-treatment-responsive-schizophrenia-taking-atypical-antipsychotics-(not-clozapine)_UP	NA	84112	1432052	1096246	1550024

diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt
@@ -1,4 +1,4 @@
-# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
+# BugSigDB 2025-01-14_15:58_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
@@ -5108,6 +5108,8 @@ bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Ad
 bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-S)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN	NA	Actinomyces	Arachnia	Campylobacter	Capnocytophaga	Cardiobacterium	Corynebacterium	Fusobacterium	Olsenella	Selenomonas	Tannerella
 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_UP	NA	Alloprevotella	Atopobium	Gemella	Haemophilus	Lachnoanaerobaculum	Neisseria	Porphyromonas	Prevotella	Streptococcus	Veillonella	Oribacterium	Rothia
 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_DOWN	NA	Actinomyces	Arachnia	Campylobacter	Capnocytophaga	Cardiobacterium	Corynebacterium	Fretibacterium	Fusobacterium	Kingella	Olsenella	Selenomonas	Tannerella
+bsdb:1086/18/1_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_UP	NA	Bacillota	Campylobacterota	Fusobacteriota	Bacteria	Pseudomonadota	Spirochaetota
+bsdb:1086/18/2_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_DOWN	NA	Actinomycetota	Bacteroidota
 bsdb:1087/1/4_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_UP	NA	Anaerotruncus colihominis	Blautia producta	Eggerthella lenta	Escherichia coli	Gordonibacter urolithinfaciens	Hungatella effluvii
 bsdb:1087/1/5_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_DOWN	NA	Romboutsia timonensis
 bsdb:1087/3/1_Treatment-refractory-schizophrenia:TRS:-individuals-with-treatment-resistant-schizophrenia-taking-clozapine_vs_AAP:-individuals-with-treatment-responsive-schizophrenia-taking-atypical-antipsychotics-(not-clozapine)_UP	NA	Eggerthella lenta	Eisenbergiella tayi	Hungatella effluvii	Ruthenibacterium lactatiformans

diff --git a/file_size.csv b/file_size.csv
@@ -2536,3 +2536,4 @@
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 "2025-01-14_13:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6670" "6670" "6670" "3012" "3012" "3012" "3012" "3012" "3012" "4497" "7770" "7375" "1368"
 "2025-01-14_14:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6671" "6671" "6671" "3012" "3012" "3012" "3012" "3012" "3012" "4498" "7771" "7375" "1368"
+"2025-01-14_15:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6673" "6673" "6673" "3012" "3012" "3012" "3012" "3012" "3012" "4498" "7772" "7377" "1368"