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diff --git a/SUPPORT.html b/SUPPORT.html index 829c58d..2994ccc 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ diff --git a/articles/bugsigdbr.html b/articles/bugsigdbr.html index 80443f3..a49e835 100644 --- a/articles/bugsigdbr.html +++ b/articles/bugsigdbr.html @@ -33,7 +33,7 @@ @@ -74,7 +74,7 @@vignettes/bugsigdbr.Rmd
bugsigdbr.Rmd
bsdb <- importBugSigDB()
dim(bsdb)
-#> [1] 2270 48
+#> [1] 3518 50
colnames(bsdb)
-#> [1] "Study" "Study design"
-#> [3] "PMID" "DOI"
-#> [5] "URL" "Authors list"
-#> [7] "Title" "Journal"
-#> [9] "Year" "Experiment"
-#> [11] "Location of subjects" "Host species"
-#> [13] "Body site" "UBERON ID"
-#> [15] "Condition" "EFO ID"
-#> [17] "Group 0 name" "Group 1 name"
-#> [19] "Group 1 definition" "Group 0 sample size"
-#> [21] "Group 1 sample size" "Antibiotics exclusion"
-#> [23] "Sequencing type" "16S variable region"
-#> [25] "Sequencing platform" "Statistical test"
-#> [27] "Significance threshold" "MHT correction"
-#> [29] "LDA Score above" "Matched on"
-#> [31] "Confounders controlled for" "Pielou"
-#> [33] "Shannon" "Chao1"
-#> [35] "Simpson" "Inverse Simpson"
-#> [37] "Richness" "Signature page name"
-#> [39] "Source" "Curated date"
-#> [41] "Curator" "Revision editor"
-#> [43] "Description" "Abundance in Group 1"
-#> [45] "MetaPhlAn taxon names" "NCBI Taxonomy IDs"
-#> [47] "State" "Reviewer"Each row of the resulting data.frame corresponds to a
microbe signature from differential abundance analysis, i.e. a set of
microbes that has been found with increased or decreased abundance in
@@ -182,14 +183,14 @@
sigs <- getSignatures(bsdb)
length(sigs)
-#> [1] 2270
+#> [1] 3444
sigs[1:3]
-#> $`bsdb:1/1/1_adenoma:conventional-adenoma-cases_vs_controls_UP`
+#> $`bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP`
#> [1] "91061" "1236" "1654" "1716" "1301" "162289" "189330" "33024"
#> [9] "40544" "2037" "2049" "506" "186826" "1300" "31977" "91347"
#> [17] "1653" "57037" "1386" "186817"
#>
-#> $`bsdb:1/1/2_adenoma:conventional-adenoma-cases_vs_controls_DOWN`
+#> $`bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN`
#> [1] "100883" "1117"
#>
#> $`bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP`
@@ -199,40 +200,40 @@ Extracting microbe signatures
mp.sigs <- getSignatures(bsdb, tax.id.type = "metaphlan")
mp.sigs[1:3]
-#> $`bsdb:1/1/1_adenoma:conventional-adenoma-cases_vs_controls_UP`
-#> [1] "k__Bacteria|p__Firmicutes|c__Bacilli"
-#> [2] "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria"
-#> [3] "k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces"
-#> [4] "k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium"
-#> [5] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus"
-#> [6] "k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus"
-#> [7] "k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea"
-#> [8] "k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium"
-#> [9] "k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella"
-#> [10] "k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales"
-#> [11] "k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae"
-#> [12] "k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae"
-#> [13] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales"
-#> [14] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae"
-#> [15] "k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae"
-#> [16] "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales"
-#> [17] "k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae"
-#> [18] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae"
-#> [19] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus"
-#> [20] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae"
+#> $`bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP`
+#> [1] "k__Bacteria|p__Bacillota|c__Bacilli"
+#> [2] "k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria"
+#> [3] "k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces"
+#> [4] "k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium"
+#> [5] "k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus"
+#> [6] "k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus"
+#> [7] "k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea"
+#> [8] "k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium"
+#> [9] "k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella"
+#> [10] "k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales"
+#> [11] "k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae"
+#> [12] "k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae"
+#> [13] "k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales"
+#> [14] "k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae"
+#> [15] "k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae"
+#> [16] "k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales"
+#> [17] "k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae"
+#> [18] "k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae"
+#> [19] "k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus"
+#> [20] "k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae"
#>
-#> $`bsdb:1/1/2_adenoma:conventional-adenoma-cases_vs_controls_DOWN`
-#> [1] "k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus"
-#> [2] "k__Bacteria|p__Cyanobacteria"
+#> $`bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN`
+#> [1] "k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus"
+#> [2] "k__Bacteria|p__Cyanobacteriota"
#>
#> $`bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP`
-#> [1] "k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes"
-#> [2] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae"
+#> [1] "k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes"
+#> [2] "k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae"
… or using the taxonomic name only:
tn.sigs <- getSignatures(bsdb, tax.id.type = "taxname")
tn.sigs[1:3]
-#> $`bsdb:1/1/1_adenoma:conventional-adenoma-cases_vs_controls_UP`
+#> $`bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP`
#> [1] "Bacilli" "Gammaproteobacteria"
#> [3] "Actinomyces" "Corynebacterium"
#> [5] "Streptococcus" "Peptoniphilus"
@@ -244,8 +245,8 @@ Extracting microbe signatures#> [17] "Corynebacteriaceae" "Lacticaseibacillus zeae"
#> [19] "Bacillus" "Bacillaceae"
#>
-#> $`bsdb:1/1/2_adenoma:conventional-adenoma-cases_vs_controls_DOWN`
-#> [1] "Coprobacillus" "Cyanobacteria"
+#> $`bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN`
+#> [1] "Coprobacillus" "Cyanobacteriota"
#>
#> $`bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP`
#> [1] "Anaerostipes" "Lacticaseibacillus zeae"
Note that restricting signatures to microbes given at the genus level, will per default exclude microbes given at a more specific @@ -299,12 +300,12 @@
efo <- getOntology("efo")
#> Loading required namespace: ontologyIndex
-#> Using cached version from 2023-02-20 10:51:07
+#> Using cached version from 2024-02-07 15:01:07
efo
-#> Ontology with 34648 terms
+#> Ontology with 45748 terms
#>
#> format-version: 1.2
-#> data-version: http://www.ebi.ac.uk/efo/releases/v3.51.0/efo.owl
+#> data-version: http://www.ebi.ac.uk/efo/releases/v3.62.0/efo.owl
#> ontology: http://www.ebi.ac.uk/efo/efo.owl
#>
#> Properties:
@@ -384,10 +385,10 @@ Ontology
#> disease_has_feature - disease has feature
#> located_in - located_in
#> location_of - location_of
-#> ... 50 more
uberon <- getOntology("uberon")
-#> Using cached version from 2023-02-20 10:51:42
+#> Using cached version from 2024-02-07 15:01:36
uberon
#> Ontology with 14107 terms
#>
@@ -422,78 +423,82 @@ Ontology
more general ontology terms. This facilitates grouping of signatures
that semantically belong together.
More specifically, subsetting BugSigDB signatures by an EFO term then
-involves subsetting the Condition column to all descendants
-of that term in the EFO ontology and that are present in the
-Condition column. Here, we demonstrate the usage by
-subsetting to signatures associated with cancer.
+involves subsetting the Condition column to the term itself
+and all descendants of that term in the EFO ontology and that are
+present in the Condition column. Here, we demonstrate the
+usage by subsetting to signatures associated with cancer.
sdf <- subsetByOntology(bsdb,
column = "Condition",
term = "cancer",
ontology = efo)
dim(sdf)
-#> [1] 305 48
+#> [1] 311 50
table(sdf[,"Condition"])
#>
-#> acute myeloid leukemia
-#> 10
-#> breast cancer
-#> 4
-#> breast carcinoma
+#> Acute myeloid leukemia
+#> 13
+#> Breast cancer
+#> 16
+#> Breast carcinoma
#> 4
-#> cervical cancer
-#> 19
-#> cervical glandular intraepithelial neoplasia,cervical cancer
-#> 1
-#> colorectal cancer
-#> 50
-#> colorectal carcinoma
+#> Cervical cancer
+#> 18
+#> Cervical glandular intraepithelial neoplasia,Cervical cancer
#> 2
-#> digestive system cancer
+#> Colorectal adenocarcinoma
+#> 9
+#> Colorectal carcinoma
+#> 7
+#> Digestive system cancer
#> 2
-#> endometrial cancer
+#> Endometrial cancer
#> 4
-#> esophageal cancer
+#> Esophageal cancer
#> 10
-#> esophageal squamous cell carcinoma
+#> Esophageal squamous cell carcinoma
#> 4
-#> gastric adenocarcinoma
+#> Gastric adenocarcinoma
#> 6
-#> gastric cancer
-#> 61
-#> gastric carcinoma
+#> Gastric cancer
+#> 73
+#> Gastric carcinoma
#> 2
#> Genital neoplasm, female
#> 2
-#> head and neck carcinoma
+#> Head and neck carcinoma
#> 7
-#> hepatocellular carcinoma
-#> 4
+#> Head and neck squamous cell carcinoma
+#> 12
+#> Hepatocellular carcinoma
+#> 9
#> HER2 Positive Breast Carcinoma
#> 2
-#> human papilloma virus infection,cervical cancer
+#> Human papilloma virus infection,Cervical cancer
#> 2
-#> lung cancer
+#> Lung cancer
#> 23
-#> multiple myeloma
-#> 10
-#> non-small cell lung carcinoma,renal cell carcinoma
+#> Multiple myeloma
+#> 11
+#> Nasopharyngeal squamous cell carcinoma
+#> 4
+#> Non-small cell lung carcinoma,Renal cell carcinoma
#> 5
-#> oral squamous cell carcinoma
-#> 6
-#> ovarian cancer
+#> Oral squamous cell carcinoma
+#> 20
+#> Ovarian cancer
#> 4
-#> pancreatic carcinoma
-#> 17
-#> prostate cancer
-#> 6
-#> squamous cell carcinoma
-#> 36
-#> thyroid carcinoma
+#> Pancreatic carcinoma
+#> 14
+#> Prostate cancer
+#> 4
+#> Squamous cell carcinoma
+#> 20
+#> Thyroid carcinoma
#> 2
-And analogously, subsetting by an UBERON term will involves
-subsetting the Body site column to all descendants of that
-term in the UBERON ontology and that are present in the
+
And analogously, subsetting by an UBERON term involves subsetting the
+Body site column to the term itself and all descendants of
+that term in the UBERON ontology and that are present in the
Body site column. For example, we can use
subsetByOntology to subset to signatures for which
microbiome samples have been obtained from parts of the digestive
@@ -504,84 +509,138 @@
Ontology
term = "digestive system",
ontology = uberon)
dim(sdf)
-#> [1] 410 48
+#> [1] 625 50
table(sdf[,"Body site"])
#>
-#> bronchus,mouth
-#> 2
-#> buccal mucosa
-#> 6
-#> buccal mucosa,lower lip
-#> 8
-#> caecum
-#> 15
-#> colon
-#> 19
-#> colonic mucosa
-#> 2
-#> dental plaque
-#> 13
-#> digestive system,digestive tract,lower digestive tract
-#> 20
-#> feces,mouth
-#> 4
-#> feces,mucosa of small intestine
-#> 4
-#> feces,stomach,caecum,small intestine,colon
-#> 2
-#> gingiva
-#> 5
-#> hypopharynx
-#> 1
-#> ileum
-#> 2
-#> Major salivary gland
-#> 1
-#> mouth
-#> 57
-#> mouth,skin of cheek,tongue,gingiva,oropharynx
-#> 2
-#> mucosa of small intestine,feces
-#> 3
-#> mucosa of stomach
-#> 3
-#> nasopharynx
-#> 38
-#> nasopharynx,oropharynx
-#> 8
-#> nose,mouth
-#> 2
-#> oral gland
-#> 51
-#> oropharynx
-#> 24
-#> rectum
-#> 24
-#> saliva-secreting gland
-#> 2
-#> small intestine
-#> 10
-#> sputum,mouth
-#> 2
-#> stomach
-#> 41
-#> subgingival dental plaque
-#> 11
-#> tongue
-#> 28
sessionInfo()
-#> R version 4.2.1 (2022-06-23)
-#> Platform: x86_64-pc-linux-gnu (64-bit)
-#> Running under: Ubuntu 20.04.4 LTS
+#> R Under development (unstable) (2024-01-31 r85845)
+#> Platform: x86_64-pc-linux-gnu
+#> Running under: Ubuntu 22.04.3 LTS
#>
#> Matrix products: default
-#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
-#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
+#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
+#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
@@ -591,33 +650,34 @@ Session info#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
+#> time zone: UTC
+#> tzcode source: system (glibc)
+#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
-#> [1] bugsigdbr_1.5.8 BiocStyle_2.24.0
+#> [1] bugsigdbr_1.9.2 BiocStyle_2.31.0
#>
#> loaded via a namespace (and not attached):
-#> [1] Rcpp_1.0.10 pillar_1.8.1 dbplyr_2.3.0
-#> [4] bslib_0.4.2 compiler_4.2.1 BiocManager_1.30.19
-#> [7] jquerylib_0.1.4 tools_4.2.1 digest_0.6.31
-#> [10] bit_4.0.5 tibble_3.1.8 jsonlite_1.8.4
-#> [13] evaluate_0.20 memoise_2.0.1 BiocFileCache_2.4.0
-#> [16] RSQLite_2.2.20 lifecycle_1.0.3 pkgconfig_2.0.3
-#> [19] rlang_1.0.6 cli_3.6.0 DBI_1.1.3
-#> [22] filelock_1.0.2 curl_5.0.0 yaml_2.3.7
-#> [25] pkgdown_2.0.7.9000 xfun_0.37 fastmap_1.1.0
-#> [28] withr_2.5.0 httr_1.4.4 dplyr_1.1.0
-#> [31] stringr_1.5.0 knitr_1.42 rappdirs_0.3.3
-#> [34] generics_0.1.3 desc_1.4.2 fs_1.6.1
-#> [37] sass_0.4.5 vctrs_0.5.2 systemfonts_1.0.4
-#> [40] tidyselect_1.2.0 rprojroot_2.0.3 bit64_4.0.5
-#> [43] glue_1.6.2 R6_2.5.1 textshaping_0.3.6
-#> [46] ontologyIndex_2.10 fansi_1.0.4 rmarkdown_2.20
-#> [49] bookdown_0.32 purrr_1.0.1 blob_1.2.3
-#> [52] magrittr_2.0.3 htmltools_0.5.4 assertthat_0.2.1
-#> [55] ragg_1.2.5 utf8_1.2.3 stringi_1.7.12
-#> [58] cachem_1.0.6
Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Claire Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Isaac Hecht, Aarthi Ravikrishnan, Rafael Goncalves, Eric Franzosa, Karthik Raman, Vincent Carey, Jennifer B. Dowd, Heidi E. Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron (2022) BugSigDB: accelerating microbiome research through systematic comparison to published microbial signatures. medRxiv, doi: 10.1101/2022.10.24.22281483.
+Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Isaac Hecht, Aarthi Ravikrishnan, Rafael S. Goncalves, Eric Franzosa, Karthik Raman, Vincent Carey, Jennifer B. Dowd, Heidi E. Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron (2023) BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures Nature Biotechnology, doi: 10.1038/s41587-023-01872-y.
@Article{,
- title = {BugSigDB: accelerating microbiome research through systematic comparison to published microbial signatures},
- author = {Ludwig Geistlinger and Chloe Mirzayi and Fatima Zohra and Rimsha Azhar and Shaimaa Elsafoury and Claire Grieve and Jennifer Wokaty and Samuel David Gamboa-Tuz and Pratyay Sengupta and Isaac Hecht and Aarthi Ravikrishnan and Rafael Goncalves and Eric Franzosa and Karthik Raman and Vincent Carey and Jennifer Dowd and Heidi Jones and Sean Davis and Nicola Segata and Curtis Huttenhower and Levi Waldron},
- year = {2022},
- journal = {medRxiv},
- doi = {10.1101/2022.10.24.22281483},
+ title = {BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures},
+ author = {Ludwig Geistlinger and Chloe Mirzayi and Fatima Zohra and Rimsha Azhar and Shaimaa Elsafoury and Clare Grieve and Jennifer Wokaty and Samuel David Gamboa-Tuz and Pratyay Sengupta and Isaac Hecht and Aarthi Ravikrishnan and Rafael Goncalves and Eric Franzosa and Karthik Raman and Vincent Carey and Jennifer Dowd and Heidi Jones and Sean Davis and Nicola Segata and Curtis Huttenhower and Levi Waldron},
+ year = {2023},
+ journal = {Nature Biotechnology},
+ doi = {10.1038/s41587-023-01872-y},
}
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